diff --git a/pf_test_assets_030424.tsv b/pf_test_assets_030424.tsv new file mode 100644 index 0000000..98f001f --- /dev/null +++ b/pf_test_assets_030424.tsv @@ -0,0 +1,390 @@ +id Relationship Settings InputName (user choice) InputID, node normalized OutputID OutputName Expected Result / Suggested Comparator Translator GitHubIssue Method of Generation Level of Validation Test Author, Owner, Watch List Test GithubIssue Overly Generic In First 50 In Acceptance Persona/Use Case TBD: Data modeling: Disease-modifying, specific to treating symptoms/sequale, general Semantic Severity Well Known Person who cares about this, know about this issue type Blocklist (here or separate tabs) Causes not treats ? issue labels Notes +Asset:1 Treats Inferred Aceruloplasminemia MONDO:0011426 DRUGBANK:DB01592 Iron (PUBCHEM) 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/506 Sandrine Muller clinical Yes causes not treats; TMKP The CQS is returning iron for MONDO:0011426 (https://monarchinitiative.org/MONDO:0011426) . I (Kara) would have classified this as 3_BadButForgiveable, and I see that it is classified as such in row 18. +Asset:10 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:5352425 lead 4_NeverShow Jennifer Hadlock look-up +Asset:100 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C5387588 Covid-19 vaccines 4_NeverShow Sandrine Muller +Asset:101 Treats Inferred Multiple Sclerosis MONDO:0005301 CHEMBL:2109042 Influenza vaccines 4_NeverShow Sandrine Muller +Asset:102 Treats Inferred Multiple Sclerosis MONDO:0005301 Vaccines, peptide 4_NeverShow Sandrine Muller +Asset:103 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0699680 Metric 4_NeverShow Sandrine Muller block-list +Asset:104 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0243192 Agonists 4_NeverShow Sandrine Muller block-list +Asset:105 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C1611640 Therapeutic agent 4_NeverShow Sandrine Muller block-list +Asset:106 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0302837 Vitamin supplementation 4_NeverShow Sandrine Muller block-list +Asset:107 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0003209 Anti-inflammatory agents 4_NeverShow Sandrine Muller block-list +Asset:108 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000276 Adjuvants, immunologic 4_NeverShow Sandrine Muller block-list +Asset:109 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000906 Antibodies 4_NeverShow Sandrine Muller block-list +Asset:11 Treats Inferred Castleman Disease MONDO:0015564 PUBCHEM.COMPOUND:5284616 sirolimus 1_TopAnswer Jennifer Hadlock look-up +Asset:110 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0040616 Anti-anxiety agents 4_NeverShow Sandrine Muller block-list +Asset:111 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000911 Antibodies, monoclonal 4_NeverShow Sandrine Muller block-list +Asset:112 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0005522 Biological products 4_NeverShow Sandrine Muller block-list +Asset:113 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0242912 Neuroprotective agents 4_NeverShow Sandrine Muller block-list +Asset:114 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0003232 Antibiotics 4_NeverShow Sandrine Muller block-list +Asset:115 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C1874451 basis 4_NeverShow Sandrine Muller block-list +Asset:116 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0242896 Anticholinergic agents 2_Acceptable Jennifer Hadlock Treats symptoms or sequelae +Asset:117 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000700 Analgesics 4_NeverShow Sandrine Muller block-list +Asset:118 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:23931 Mercury 4_NeverShow Sandrine Muller block-list +Asset:119 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D005227 Fatty acids 4_NeverShow Sandrine Muller block-list +Asset:12 Treats Inferred Castleman Disease MONDO:0015564 UNII:4F4X42SYQ6 rituximab 1_TopAnswer Jennifer Hadlock look-up +Asset:120 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D010936 Plant extracts 4_NeverShow Sandrine Muller block-list +Asset:121 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D004365 Drugs, chinese herbal 4_NeverShow Sandrine Muller block-list +Asset:122 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller block-list +Asset:123 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller block-list +Asset:124 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D011972 Receptor, insulin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/613 Sandrine Muller +Asset:125 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D001323 Autoantibodies 4_NeverShow Sandrine Muller +Asset:126 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 PUBCHEM.COMPOUND:53462828 Thyroid hormones 4_NeverShow Sandrine Muller +Asset:127 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D004798 Enzymes 4_NeverShow Sandrine Muller +Asset:128 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D017526 Receptor, IGF Type 1 4_NeverShow Sandrine Muller +Asset:129 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D003165 Complement system proteins 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/615 Sandrine Muller +Asset:13 Treats Inferred Castleman Disease MONDO:0015564 UNII:9013DUQ28K anakinra 1_TopAnswer Jennifer Hadlock look-up +Asset:130 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 PUBCHEM.COMPOUND:6623 bisphenol A 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/444 Sandrine Muller +Asset:131 Treats Inferred Hereditary Sensory And Autonomic Neuropathy Type MONDO:0015364 MESH:D016756 Immunoglobulins, intravenous 4_NeverShow Sandrine Muller +Asset:132 Treats Inferred Hereditary Sensory And Autonomic Neuropathy Type MONDO:0015364 PUBCHEM.COMPOUND:84098 Isoxaflutole 4_NeverShow Sandrine Muller +Asset:133 Treats Inferred Hereditary sensory and autonomic neuropathy type 4 MONDO:0009746 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/404 Sandrine Muller +Asset:134 Treats Inferred Hereditary sensory and autonomic neuropathy type 4 MONDO:0009746 UNII:E211KPY694 Botulinum toxin type a 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/405 Sandrine Muller +Asset:135 decreases activity or abundance of Inferred DDX3Y NCBI Gene:8653 UMLS:C0311474 dna double stranded 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/384 Sandrine Muller +Asset:136 decreases activity or abundance of Inferred DDX3Y NCBI Gene:8653 UMLS:C1328819 Small molecule 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/384 Sandrine Muller +Asset:137 Treats Inferred Hereditary sensory and autonomic neuropathy type 4 MONDO:0009746 PUBCHEM.COMPOUND:4096 Methamidophos 4_NeverShow Sandrine Muller +Asset:138 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:3562 Halothane 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:139 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:3763 isoflurane 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:14 Treats Inferred Castleman Disease MONDO:0015564 CHEMBL.COMPOUND:1201562 interferon-beta 1a 1_TopAnswer Jennifer Hadlock look-up +Asset:140 Treats Inferred scotoma MONDO:0004758 PUBCHEM.COMPOUND:5865 Prednisone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:141 Treats Inferred scotoma MONDO:0004758 PUBCHEM.COMPOUND:5665 vigabatrin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:142 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sandrine Muller +Asset:143 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller +Asset:144 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 MESH:D000779 Anesthetics, local 4_NeverShow Sandrine Muller +Asset:145 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:1727 4-aminopyridine 4_NeverShow Sandrine Muller +Asset:146 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C0002932 Anesthetics 4_NeverShow Sandrine Muller +Asset:147 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C0003232 Antibiotics 4_NeverShow Sandrine Muller +Asset:148 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C1874451 basis 4_NeverShow Sandrine Muller +Asset:149 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:33250 Atom 4_NeverShow Sandrine Muller +Asset:15 Treats Inferred Aceruloplasminemia MONDO:0011426 PUBCHEM.COMPOUND:4356 iron 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/506 Jennifer Hadlock https://github.com/NCATSTranslator/Tests/issues/8 look-up +Asset:150 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D002467 Cell nucleus 4_NeverShow Sandrine Muller +Asset:151 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D012492 salts 4_NeverShow Sandrine Muller +Asset:152 Treats Inferred Fatal familial insomnia MONDO:0010808 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller Y +Asset:153 Treats Inferred Fatal familial insomnia MONDO:0010808 PUBCHEM.COMPOUND:962 Hydrogen(.) 4_NeverShow Sandrine Muller Y +Asset:154 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D004583 Electrons 4_NeverShow Sandrine Muller +Asset:155 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D000838 Anions 4_NeverShow Sandrine Muller +Asset:156 Treats Inferred Fatal familial insomnia MONDO:0010808 PUBCHEM.COMPOUND:977 Oxygen 4_NeverShow Sandrine Muller +Asset:157 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D002412 Cations 4_NeverShow Sandrine Muller +Asset:158 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:24471 Halogen molecular entity 4_NeverShow Sandrine Muller +Asset:159 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:51143 Nitrogen molecular entity 4_NeverShow Sandrine Muller +Asset:16 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:50453 desferrioxamine 1_TopAnswer Jennifer Hadlock look-up +Asset:160 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D000438 Alcohols 4_NeverShow Sandrine Muller +Asset:161 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:25367 Molecule 4_NeverShow Sandrine Muller +Asset:162 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:24868 Organic salt 4_NeverShow Sandrine Muller +Asset:163 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D009930 Organic chemicals 4_NeverShow Sandrine Muller +Asset:164 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:36094 Organic chloride salt 4_NeverShow Sandrine Muller +Asset:165 Treats Inferred Fatal familial insomnia MONDO:0010808 UMLS:C0030054 Oxygen 4_NeverShow Sandrine Muller +Asset:166 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D000700 Analgesics 4_NeverShow Sandrine Muller +Asset:167 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:134179 Volatile organic compound 4_NeverShow Sandrine Muller +Asset:168 Treats Inferred Cerebral palsy MONDO:0006497 UMLS:C0003232 Antibiotics 4_NeverShow Sierra Moxon +Asset:169 Treats Inferred Cerebral palsy MONDO:0006497 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sierra Moxon +Asset:17 Treats Inferred Aceruloplasminemia MONDO:0011426 DRUGBANK:DB01592 Iron (PUBCHEM) 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/506 Sandrine Muller mechanistic Change management causes not treats; TMKP See comment from Kara in X2. +Asset:170 Treats Inferred Cerebral palsy MONDO:0006497 PUBCHEM.COMPOUND:3672 Ibuprofen 3_BadButForgivable Sierra Moxon +Asset:171 Treats Inferred Cerebral palsy MONDO:0006497 PUBCHEM.COMPOUND:2284 Baclofen 2_Acceptable Sierra Moxon +Asset:172 Treats Inferred Cerebral palsy MONDO:0006497 CHEBML:CHEMBL1201569 Botulinum toxin type b 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:173 Treats Inferred Cerebral palsy MONDO:0006497 PUBCHEM.COMPOUND:2554 Carbamazepine 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:174 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:6057 Tyrosine 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:175 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:460612 Melphalan 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:176 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:15625 2,3,7,8-tetrachlorodibenzo-p-dioxin 4_NeverShow Sierra Moxon +Asset:177 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:5426 Thalidimide 2_Acceptable Sierra Moxon +Asset:178 Treats Inferred ADHD MONDO:0007743 PUBCHEM.COMPOUND:446220 Cocaine 4_NeverShow Sierra Moxon +Asset:179 Treats Inferred ADHD MONDO:0007743 PUBCHEM.COMPOUND:4158 Methylphenidate 2_Acceptable Sierra Moxon +Asset:18 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D009930 Organic Chemicals 4_NeverShow Sandrine Muller all block-list +Asset:180 Treats Inferred Gout MONDO:0005393 UNNI:R581OT55EA Pegloticase 2_Acceptable Sierra Moxon +Asset:181 Treats Inferred Gout MONDO:0005393 PUBCHEM.COMPOUND:5865 Prednisone 2_Acceptable Sierra Moxon +Asset:182 Treats Inferred Hereditary Sensory And Autonomic Neuropathy MONDO:0015364 MONDO:0016028 Erythromelalgia 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/632 Sandrine Muller +Asset:183 Treats Inferred Hereditary Sensory And Autonomic Neuropathy MONDO:0015364 MONDO:0009131 Riley-day Syndrome 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/633 Sandrine Muller +Asset:184 Treats Inferred Diabetes Mellitus MONDO:0005015 UMLS:C0013227 Pharmaceutical preparations 5_OverlyGeneric Sandrine Muller +Asset:185 Treats Inferred Diabetes Mellitus MONDO:0005015 PUBCHEM.COMPOUND:4091 Metformin 1_TopAnswer Sandrine Muller +Asset:186 Treats Inferred Diabetes Mellitus MONDO:0005015 UNII:1Y17CTI5SR Insulin human 1_TopAnswer Sandrine Muller +Asset:187 Treats Inferred Diabetes Mellitus MONDO:0005015 PUBCHEM.COMPOUND:16137271 Insulin detremir 1_TopAnswer Sandrine Muller +Asset:188 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C3536832 Air 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman CP SMuRF +Asset:189 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C3536832 Air 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman Molecular focus +Asset:19 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:23367 molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:190 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C3536832 Air 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman CP SMuRF +Asset:191 Treats Inferred Cerebral Palsy MONDO:0006497 NCIT:C38065 Hyperbaric oxygen therapy 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:192 Treats Inferred Cerebral Palsy MONDO:0006497 MESH:D000336 Aerosols 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:193 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C0013227 Pharmaceutical Preparations 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:194 Treats Inferred Cerebral Palsy MONDO:0006497 NCIT:C38065 Hyperbaric oxygen therapy 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:195 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:702 Ethanol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/638 Sandrine Muller clinical +Asset:196 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:702 Ethanol 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/638 Sandrine Muller mechanistic +Asset:197 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:3346 Fenthion 4_NeverShow Sandrine Muller block-list +Asset:198 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:84098 Isoxaflutole 4_NeverShow Sandrine Muller block-list +Asset:199 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:6758 Rotenone 4_NeverShow Sandrine Muller block-list +Asset:2 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33247 organic group 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/572 Sandrine Muller all block-list category too generic +Asset:20 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:25367 molecule 4_NeverShow Sandrine Muller all block-list +Asset:200 Treats Inferred alcoholic hepatitis MONDO:0001505 UNII:59NEE7PCAB Lindane 4_NeverShow Sandrine Muller block-list +Asset:201 Treats Inferred alcoholic hepatitis MONDO:0001505 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sandrine Muller block-list +Asset:202 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:1983 Acetaminophen 3_BadButForgivable Sandrine Muller block-list +Asset:203 Treats Inferred alcoholic hepatitis MONDO:0001505 MESH:D037742 Nanotubes, carbon 4_NeverShow Sandrine Muller block-list +Asset:204 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:6623 Bisphenol a 4_NeverShow Sandrine Muller block-list +Asset:205 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller +Asset:206 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:3826 Ketorolac 4_NeverShow Sandrine Muller +Asset:207 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:439501 Ouabain 4_NeverShow Sandrine Muller +Asset:208 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:712 Formaldehyde 4_NeverShow Sandrine Muller +Asset:209 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:446220 Cocaine 4_NeverShow Sandrine Muller +Asset:21 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:25806 oxygen molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:210 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:323 Coumarin 4_NeverShow Sandrine Muller +Asset:211 Treats Inferred alcoholic hepatitis MONDO:0001505 CHEMBL:2109152 Mineral oil 4_NeverShow Sandrine Muller +Asset:212 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:10836 Methamphetamine 4_NeverShow Sandrine Muller +Asset:213 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:6741 Methylprednisolone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:214 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:5865 Prednisone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:215 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:5754 Hydrocortisone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:216 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:5743 Dexamethasone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:217 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:31307 Triamcinolone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:218 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D014028 Tobacco smoke pollution 4_NeverShow Sandrine Muller +Asset:219 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D002772 Cholera Toxin 4_NeverShow Sandrine Muller +Asset:22 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:36357 polyatomic entity 4_NeverShow Sandrine Muller all block-list +Asset:220 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D037342 Pertussis toxin 4_NeverShow Sandrine Muller +Asset:221 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:11302220 Cocain-chlorhydrat 4_NeverShow Sandrine Muller +Asset:222 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D002412 Cations 4_NeverShow Sandrine Muller +Asset:223 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:443495 Sodium arsenite 4_NeverShow Sandrine Muller +Asset:224 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D000838 Anions 4_NeverShow Sandrine Muller +Asset:225 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:23973 Cadmium 4_NeverShow Sandrine Muller +Asset:226 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND: Azoles 3_BadButForgivable Sandrine Muller +Asset:227 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:23424 Cyanides 3_BadButForgivable Sandrine Muller +Asset:228 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND: Imidazoles 3_BadButForgivable Sandrine Muller +Asset:229 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D007287 Inorganic chemicals 4_NeverShow Sandrine Muller +Asset:23 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33582 carbon group molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:230 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:24431 Chemical entity 4_NeverShow Sandrine Muller +Asset:231 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:23367 Molecular entity 4_NeverShow Sandrine Muller +Asset:232 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:51143 Nitrogen molecular entity 4_NeverShow Sandrine Muller +Asset:233 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:50860 Organic molecular entity 4_NeverShow Sandrine Muller +Asset:234 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:33582 Carbon group molecular entity 4_NeverShow Sandrine Muller +Asset:235 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D002467 Cell nucleus 4_NeverShow Sandrine Muller +Asset:236 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:36587 Organic oxo compound 4_NeverShow Sandrine Muller +Asset:237 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:33250 Atom 4_NeverShow Sandrine Muller +Asset:238 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND: Ions 4_NeverShow Sandrine Muller +Asset:239 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:24433 Group 4_NeverShow Sandrine Muller +Asset:24 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D007287 inorganic chemicals 4_NeverShow Sandrine Muller all block-list +Asset:240 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:446220 Cocaine 4_NeverShow Sandrine Muller +Asset:241 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:784 Hydrogen peroxide 3_BadButForgivable Sandrine Muller +Asset:242 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 UMLS:C1306770 Nitrogen 99.9 % 4_NeverShow Sandrine Muller +Asset:243 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:25806 Oxygen molecular entity 4_NeverShow Sandrine Muller +Asset:244 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D006219 Halogens 4_NeverShow Sandrine Muller +Asset:245 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:36586 Carbonyl compound 4_NeverShow Sandrine Muller +Asset:246 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 UMLS:C1337101 Nitrogen 99.7 % 4_NeverShow Sandrine Muller +Asset:247 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:36830 Monoanion 4_NeverShow Sandrine Muller +Asset:248 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:33832 Organic cyclic compound 4_NeverShow Sandrine Muller +Asset:249 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:24532 Organic heterocyclic compound 4_NeverShow Sandrine Muller +Asset:25 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33285 heteroorganic entity 4_NeverShow Sandrine Muller all block-list +Asset:250 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:784 Hydrogen peroxide 4_NeverShow Sandrine Muller +Asset:251 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D037742 Nanotubes, carbon 4_NeverShow Sandrine Muller +Asset:252 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:15938 Paraquat dichloride 4_NeverShow Sandrine Muller +Asset:253 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:443495 Sodium arsenite 4_NeverShow Sandrine Muller +Asset:254 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:2912 Cypermethrin 4_NeverShow Sandrine Muller +Asset:255 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D054328 Proton pump inhibitors 4_NeverShow Sandrine Muller +Asset:256 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 UMLS:C0699680 Metric (substance) 4_NeverShow Sandrine Muller +Asset:257 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D014028 Tobacco smoke pollution 4_NeverShow Sandrine Muller +Asset:258 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 UMLS:C3166216 Prescribed medications 4_NeverShow Sandrine Muller +Asset:259 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D001786 Blood glucose 4_NeverShow Sandrine Muller +Asset:26 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33579 main group molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:260 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:433294 Lithium Chloride 4_NeverShow Sandrine Muller +Asset:261 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 UMLS:C0003289 Antidepressive agents 4_NeverShow Sandrine Muller +Asset:262 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 DRUGBANK:DB05404 AZD 3355 1_TopAnswer Sandrine Muller +Asset:263 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:174 1,2-ethanediol 4_NeverShow Sandrine Muller +Asset:264 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:56842000 Talcid 1_TopAnswer Sandrine Muller +Asset:265 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:311 Citric acid 4_NeverShow Sandrine Muller The CQS is returning citric acid for MONDO:0007186 (https://monarchinitiative.org/MONDO:0007186). I (Kara) would have classified this as 3_BadButForgiveable. +Asset:266 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller +Asset:267 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:176 Acetic acid 4_NeverShow Sandrine Muller +Asset:268 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller +Asset:269 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND: Oxygen 4_NeverShow Sandrine Muller +Asset:27 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:37577 heteroatomic molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:270 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:23982 Gadolinium 4_NeverShow Sandrine Muller +Asset:271 Treats Inferred Cowden Disease MONDO:0016063 MESH:D007477 Ions 4_NeverShow Sandrine Muller +Asset:272 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:190217 Oxide 4_NeverShow Sandrine Muller +Asset:273 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller +Asset:274 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller +Asset:275 Treats Inferred Cowden Disease MONDO:0016063 MESH:D002412 Cations 4_NeverShow Sandrine Muller +Asset:276 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Electrons 4_NeverShow Sandrine Muller +Asset:277 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Formaldehyde 4_NeverShow Sandrine Muller +Asset:278 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Organic anion 4_NeverShow Sandrine Muller +Asset:279 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Acyl group 4_NeverShow Sandrine Muller +Asset:28 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33595 cyclic compound 4_NeverShow Sandrine Muller all block-list +Asset:280 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:25585 Nonmetal atom 4_NeverShow Sandrine Muller +Asset:281 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33677 F-block molecular entity 4_NeverShow Sandrine Muller +Asset:282 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33497 Transition element molecular entity 4_NeverShow Sandrine Muller +Asset:283 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:27081 Transition element atom 4_NeverShow Sandrine Muller +Asset:284 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33562 F-block element atom 4_NeverShow Sandrine Muller +Asset:285 Treats Inferred Cowden Disease MONDO:0016063 MESH:D000071940 Nucleons 4_NeverShow Sandrine Muller +Asset:286 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:36963 Organooxygen compound 4_NeverShow Sandrine Muller +Asset:287 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33695 Information biomacromolecule 4_NeverShow Sandrine Muller +Asset:288 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:24532 Organic heterocyclic compound 4_NeverShow Sandrine Muller +Asset:289 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33434 Elemental halogen 4_NeverShow Sandrine Muller +Asset:29 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D006571 heterocyclic compounds 4_NeverShow Sandrine Muller all block-list +Asset:290 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:24867 Monoatomic ion 4_NeverShow Sandrine Muller +Asset:291 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33432 Monoatomic chlorine 4_NeverShow Sandrine Muller +Asset:292 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33433 Monoatomic halogen 4_NeverShow Sandrine Muller +Asset:293 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33674 S-block molecular entity 4_NeverShow Sandrine Muller +Asset:294 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33431 Elemental chlorine 4_NeverShow Sandrine Muller +Asset:295 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:50047 Organic amino compound 4_NeverShow Sandrine Muller +Asset:296 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:37578 Halide 4_NeverShow Sandrine Muller +Asset:297 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:23991 Xenon 4_NeverShow Sandrine Muller +Asset:298 Treats Inferred Cowden Disease MONDO:0016063 MESH:D061065 Polyketides 4_NeverShow Sandrine Muller +Asset:299 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33710 Alpha-amino-acid residue 4_NeverShow Sandrine Muller +Asset:3 Treats Inferred NARP Syndrome MONDO:0010794 DRUGBANK:DB00313 Valproic Acid 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/147 Sandrine Muller clinical Yes contraindications +Asset:30 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:24836 inorganic oxide 4_NeverShow Sandrine Muller all block-list +Asset:300 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:79389 Monovalent inorganic anion 4_NeverShow Sandrine Muller +Asset:301 Treats Inferred Cowden Disease MONDO:0016063 MESH:D000470 Alkaloids 4_NeverShow Sandrine Muller +Asset:302 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:16042 Halide anion 4_NeverShow Sandrine Muller +Asset:303 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:2972 deferipone 1_TopAnswer Jennifer Hadlock look-up +Asset:304 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:49005 deferasirox 1_TopAnswer Jennifer Hadlock look-up +Asset:305 Treats Inferred Aceruloplasminemia MONDO:0011426 PUBCHEM.COMPOUND:2973 Deferoxamine 1_TopAnswer +Asset:306 Treats Inferred Castleman Disease MONDO:0015564 CHEMBL.COMPOUND:1201563 interferon-beta 1b 1_TopAnswer Jennifer Hadlock +Asset:307 increases activity or abundance of Inferred Beta 2 adrenergic (ADRB2) NCBIGene:154 PUBCHEM.COMPOUND:2083 Albuterol 1_TopAnswer Chris Bizon +Asset:308 increases activity or abundance of Inferred Beta 2 adrenergic (ADRB2) NCBIGene:154 PUBCHEM.COMPOUND:4946 Propranalol 4_NeverShow +Asset:309 Treats Inferred Neutropenia MONDO:0001475 PUBCHEM.COMPOUND:77910626 Pegfilgrastim 1_TopAnswer +Asset:31 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:24431 chemical entity 4_NeverShow Sandrine Muller all block-list +Asset:310 decreases abundance of Inferred Pseudoephedrine PUBCHEM.COMPOUND:7028 NCBIGene:3558 Interleukin-2 2_Acceptable +Asset:311 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:5362124 Benazapril 1_TopAnswer +Asset:312 decreases activity or abundance of Inferred MYC proto-oncogene, bHLH transcription factor NCBIGene:7553 MONDO:0004992 cancer 4_NeverShow +Asset:313 increases activity or abundance of Inferred CFTR (human) NCBIGene:1080 PUBCHEM.COMPOUND:16220172 Ivacaftor 2_Acceptable Sarah Stemann +Asset:314 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:5452 Thioridazine 2_Acceptable +Asset:315 Treats Inferred Asthma MONDO:0004979 PUBCHEM.COMPOUND:5311101 Fluticasone 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:316 Treats Inferred Asthma MONDO:0004979 UMLS:C2194286 Albuterol (salbutamol) 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:317 Treats Inferred Asthma MONDO:0004979 PUBCHEM.COMPOUND:4946 Propranolol 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:318 Treats Inferred Cystic fibrosis MONDO:0009061 PUBCHEM.COMPOUND:16220172 Ivacaftor 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:319 Treats Inferred Cystic fibrosis MONDO:0009061 UMLS:C3489797 AZD9668 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:32 Treats Inferred Lactose intolerance MONDO:0100345 CHEMBL.COMPOUND:2108505 Lactase 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/427 Sandrine Muller look-up yes reasoning;opposite of what I asked for; data error +Asset:320 Treats Inferred Cystic fibrosis MONDO:0009061 PUBCHEM.COMPOUND:55283 Itraconazole 4_NeverShow Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:321 Treats Inferred Idiopathic bronchiectasis MONDO:0018956 PUBCHEM.COMPOUND:447043 Azithromycin 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:322 Treats Inferred Idiopathic bronchiectasis MONDO:0018956 PUBCHEM.COMPOUND:12560 Erythromycin 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:323 Treats Inferred Idiopathic bronchiectasis MONDO:0018956 PUBCHEM.COMPOUND:4946 Propranolol 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:324 Treats Inferred Idiopathic pulmonary fibrosis MONDO:0008345 PUBCHEM.COMPOUND:40632 Pirfenidone 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:325 Treats Inferred Idiopathic pulmonary fibrosis MONDO:0008345 PUBCHEM.COMPOUND:11671467 Fostamatinib 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:326 Treats Inferred Idiopathic pulmonary fibrosis MONDO:0008345 PUBCHEM.COMPOUND:90420193 GLPG1690 (Ziritaxestat) 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:327 Treats Inferred Lymphangioleiomyomatosis MONDO:0011705 PUBCHEM.COMPOUND:5284616 Sirolimus 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:328 Treats Inferred Lymphangioleiomyomatosis MONDO:0011705 PUBCHEM.COMPOUND:11520894 Ridaforolimus 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:329 Treats Inferred Lymphangioleiomyomatosis MONDO:0011705 UMLS:C0116660 ESTROSTEP Fe (Norethindrone Acetate and Ethinyl Estradiol) 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:33 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:6134 beta-Lactose 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/427 Sandrine Muller clinical reasoning;opposite of what I asked for; data error +Asset:330 Treats Inferred Primary ciliary dyskinesia MONDO:0016575 PUBCHEM.COMPOUND:9934746 Ensifentrine 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:331 Treats Inferred Primary ciliary dyskinesia MONDO:0016575 PUBCHEM.COMPOUND:447043 Azithromycin 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:332 Treats Inferred Primary ciliary dyskinesia MONDO:0016575 PUBCHEM.COMPOUND:5360696 Dextromethorphan 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:333 decreases activity or abundance of Inferred Docetaxel PUBCHEM.COMPOUND:148124 NCBIGene:596 BCL2 2_Acceptable Sarah Stemann +Asset:334 Treats Inferred Eosinophilic Esophagitis MONDO:0005361 PUBCHEM.COMPOUND:223365910 DUPILUMAB 1_TopAnswer Sarah Stemann +Asset:335 decreases activity or abundance of Inferred BRAF (human) NCBIGene:673 PUBCHEM.COMPOUND:44462760 dabrafenib 2_Acceptable Sarah Stemann +Asset:336 decreases activity or abundance of Inferred PDE5A (human) NCBIGene:8654 PUBCHEM.COMPOUND:135398744 Sildenafil 1_TopAnswer Sarah Stemann (StatPearl) +Asset:337 decreases activity or abundance of Inferred MGAM (human) NCBIGene:8972 PUBCHEM.COMPOUND:41774 Acarbose 1_TopAnswer Sarah Stemann (DrugBank > Target) +Asset:338 decreases activity or abundance of Inferred SLC5A2 (human) NCBIGene:6524 PUBCHEM.COMPOUND:24812758 Canagliflozin 1_TopAnswer Sarah Stemann (StatPearl SGTL2 > SLC5A) +Asset:339 decreases activity or abundance of Inferred Eliglustat PUBCHEM.COMPOUND:23652731 NCBI:2629 GBA1 2_Acceptable Sarah Stemann (DrugBank) +Asset:34 Treats Inferred Lactose intolerance MONDO:0100345 MESH:D010936 Plant extracts 4_NeverShow Sandrine Muller all +Asset:340 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:23725625 olaparib 1_TopAnswer +Asset:341 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:11960529 veliparib 1_TopAnswer +Asset:342 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:24958200 niraparib 1_TopAnswer +Asset:343 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:44093 rucaparib 1_TopAnswer +Asset:344 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:135565082 talazoparib 1_TopAnswer +Asset:345 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:135565981 PARP inhibitor 2x-121 1_TopAnswer +Asset:346 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:16760621 PARP inhibitor VIII, PJ34 1_TopAnswer +Asset:347 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:712 formaldehyde 3_BadButForgivable +Asset:348 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:637511 Cinnamaldehyde 3_BadButForgivable +Asset:349 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:14423521 Ursolic aldehyde 3_BadButForgivable +Asset:35 Treats Inferred Lactose intolerance MONDO:0100345 MESH:D028321 Plant preparations 4_NeverShow Sandrine Muller all +Asset:350 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:5702198 Cisplatin 2_Acceptable +Asset:351 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:426756 Carboplatin 2_Acceptable +Asset:352 decreases activity or abundance of Inferred BRCA2 NCBIGene:675 PUBCHEM.COMPOUND:2733526 Tamoxifen 1_TopAnswer +Asset:353 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:44093 Captopril 1_TopAnswer +Asset:354 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:5388962 Enalapril 1_TopAnswer +Asset:355 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:55891 Fosinopril 1_TopAnswer +Asset:356 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:5362119 Lisinopril 1_TopAnswer +Asset:357 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:5362129 Ramipril 1_TopAnswer +Asset:358 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:107807 Perindopril 1_TopAnswer +Asset:359 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:54892 Quinapril 1_TopAnswer +Asset:36 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:6134 alpha-Lactose 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/427 Sandrine Muller clinical reasoning;opposite of what I asked for; data error +Asset:360 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:5484727 Trandolapril 1_TopAnswer +Asset:361 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:91270 Moexipril 1_TopAnswer +Asset:362 decreases activity or abundance of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:37056 ACE inhibitors 1_TopAnswer +Asset:37 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:5280793 Ergocalciferol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:38 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:4030 Mebendazole 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:39 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:2406 Bithionol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:4 Treats Inferred NARP Syndrome MONDO:0010794 MESH:D001463 Barbiturates 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/147 Sandrine Muller clinical Yes contraindications +Asset:40 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:5430 Thiabendazole 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:41 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:26879 Levamisole 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:42 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:4096 Methamidophos 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:43 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:516893 Potassium bicarbonate 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:44 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:5564 Triclosan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:45 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:445643 Tacrolimus 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:46 Treats Inferred Autism MONDO:0005260 PUBCHEM.COMPOUND:3121 Valproic acid 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/577 Sandrine Muller +Asset:47 Treats Inferred Autism MONDO:0005260 MESH:D010575 Pesticides 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/575 Sandrine Muller +Asset:48 Treats Inferred Premature Menopause MONDO:0001119 UMLS:C1874451 Basis 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/567 Sandrine Muller block-list +Asset:49 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 PUBCHEM.COMPOUND:4158 methylphenidate 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/562 Sandrine Muller +Asset:5 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:12358480 Hexadrin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/490 Sandrine Muller clinical chemical roles +Asset:50 Treats Inferred Allergic Asthma MONDO:0004784 MESH:D052638 particulate matter 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/561 Sandrine Muller +Asset:51 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:774 Histamine 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/488 Sandrine Muller +Asset:52 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:4030 Mebendazole 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller Yes +Asset:53 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:708857 Pyrantel 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller Yes +Asset:54 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:5430 Thiabendazole 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller Yes +Asset:55 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:3037 Dichlorophen 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller +Asset:56 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D002467 cell nucleus 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/597 Sandrine Muller block-list +Asset:57 Treats Inferred Alzheimer Disease MONDO:0004975 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sandrine Muller block-list +Asset:58 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 PUBCHEM.COMPOUND:24847884 Omniscan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/546 Sandrine Muller block-list +Asset:59 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 UNII:1BJ477IO2L Gadobutrol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/546 Sandrine Muller block-list +Asset:6 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:2478 Busulfan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/490 Sandrine Muller clinical chemical roles +Asset:60 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 PUBCHEM.COMPOUND:73415823 Gadopentetate dimeglumine 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/546 Sandrine Muller block-list +Asset:61 Treats Inferred Diabetes Milletus MONDO:0005015 Sandrine Muller +Asset:62 Treats Inferred Aceruloplasminemia MONDO:0011426 PUBCHEM.COMPOUND:6758 Rotenone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/505 Sandrine Muller clinical +Asset:63 Treats Inferred Gaucher Disease type1 MONDO:0009265 PUBCHEM.COMPOUND:23652731 Eliglustat 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller clinical +Asset:64 Treats Inferred Gaucher Disease type1 MONDO:0009265 UNII:Q6U6J48BWY Imiglucerase 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:65 Treats Inferred Gaucher Disease type1 MONDO:0009265 UNII:0R4NLX88O4 Taliglucerase alfa 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:66 Treats Inferred Gaucher Disease type1 MONDO:0009265 CHEMBL.COMPOUND:CHEMBL1201865 Velaglucerase-alfa 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:67 Treats Inferred Gaucher Disease type1 MONDO:0009265 PUBCHEM.COMPOUND:51634 Miglustat 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:68 Treats Inferred Obstructive Sleep Apnea MONDO:0007147 MESH:D053260 Soot 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller clinical +Asset:69 Treats Inferred Obstructive Sleep Apnea MONDO:0007147 MESH:D053260 Soot 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller mechanistic +Asset:7 Treats Inferred Castleman Disease MONDO:0015564 MESH:D001335 Vehicle Emissions 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/480 Sandrine Muller clinical block-list chemical roles +Asset:70 Treats Inferred Niemann-Pick type C MONDO:0018982 PUBCHEM.COMPOUND:51634 Miglustat 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:71 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 PUBCHEM.COMPOUND:446157 Rosuvastatin 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller This may be a feature issue for UI - and separate case: expected answer is that you can't choose those option for may treats. Second is do we restrict this from being enter at the API level? If not, is this a high pri test case? +Asset:72 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 PUBCHEM.COMPOUND:9853053 Lomitapide 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:73 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 UNII:9GJ8S4GU0M Mipomersen 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:74 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 UNII:LKC0U3A8NJ Evolocumab 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:75 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 PUBCHEM.COMPOUND:446157 Rosuvastatin 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:76 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:216416 Lasofoxifene 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/489 Sandrine Muller +Asset:77 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:2478 Busulfan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/608 Sandrine Muller +Asset:78 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:5757 estradiol 1_TopAnswer Sandrine Muller +Asset:79 Treats Inferred Premature Menopause MONDO:0001119 MESH:D011372 progestin 1_TopAnswer Sandrine Muller +Asset:8 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:107970 fingolimod 1_TopAnswer Jennifer Hadlock look-up +Asset:80 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:5291 Imatinib 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/486 Sandrine Muller +Asset:81 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:216239 Sorafenib 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/486 Sandrine Muller +Asset:82 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:1140 Toluene 4_NeverShow Sandrine Muller block-list +Asset:83 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:84098 Isoxaflutole 4_NeverShow Sandrine Muller block-list +Asset:84 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:3036 Clofenotane 4_NeverShow Sandrine Muller block-list +Asset:85 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:3672 ibuprofen 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:86 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 NCIT:C163032 botulinum toxin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:87 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 dinoprostone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:88 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 calcitriol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:89 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:5280793 ergocalciferol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:9 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000069442 natalizumab 1_TopAnswer Jennifer Hadlock look-up +Asset:90 Treats Inferred Heart Disorder MONDO:0005267 fibrinogen 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/477 Sandrine Muller +Asset:91 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:1727 4-Aminopyridine 4_NeverShow Sandrine Muller block-list +Asset:92 Treats Inferred familial pityriasis rubra pilaris MONDO:0008251 retinol 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/473 Sandrine Muller +Asset:93 Treats Inferred Rabies MONDO:0019173 Methionine 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/463 Sandrine Muller +Asset:94 Treats Inferred Rabies MONDO:0019173 Cefaclor 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/463 Sandrine Muller +Asset:95 Treats Inferred familial pityriasis rubra pilaris MONDO:0008251 MESH:D000438 Alcohols 4_NeverShow Sandrine Muller block-list +Asset:96 Treats Inferred Xeroderma Pigmentosum MONDO:0019600 cadmium 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/465 Sandrine Muller block-list +Asset:97 Treats Inferred Xeroderma Pigmentosum MONDO:0019600 mercury 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/465 Sandrine Muller block-list +Asset:98 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D014612 vaccines 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/431 Sandrine Muller block-list +Asset:99 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 alendronic acid 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/428 Sandrine Muller +Asset:363 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:3386 Fluoxetine 1_TopAnswer +Asset:364 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:43815 Paroxetine 1_TopAnswer +Asset:365 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:441074 Quinidine 1_TopAnswer +Asset:366 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:60835 Duloxetine 1_TopAnswer +Asset:367 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:3031065 Bupropion 1_TopAnswer +Asset:368 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:156419 Cinacalcet 1_TopAnswer +Asset:369 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:3100 Diphenhydramine 1_TopAnswer +Asset:370 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:2157 Amiodarone 1_TopAnswer +Asset:371 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:135398735 Rifampicin 4_NeverShow +Asset:372 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:2554 Carbamazepine 4_NeverShow +Asset:373 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:4763 Phenobarbital 4_NeverShow +Asset:374 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:1775 Phenytoin 4_NeverShow +Asset:375 decreases activity or abundance of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:3663 St. John's Wort (Hypericum perforatum) 4_NeverShow +Asset:376 decreases activity or abundance of Inferred DDX3Y NCBI Gene:8653 PUBCHEM.COMPOUND:31703 Doxorubicin 2_Acceptable +Asset:377 decreases activity or abundance of Inferred DDX3Y NCBI Gene:8653 PUBCHEM.COMPOUND:46184988 RK-33 2_Acceptable +Asset:378 decreases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:4946 propranolol 1_TopAnswer +Asset:379 decreases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:4171 metoprolol 1_TopAnswer +Asset:380 decreases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:2585 carvedilol 1_TopAnswer +Asset:381 decreases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:2249 atenolol 1_TopAnswer +Asset:382 decreases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:18026 Butaxamine 2_Acceptable rated lower because PubChem reports its an Irritant +Asset:383 decreases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:3682 ICI-118,551 1_TopAnswer +Asset:384 decreases activity or abundance of Inferred ADRB2 NCBIGene:154 PharmGKBID:PA2024 Beta-Blockers (Inhibitors) 1_TopAnswer +Asset:385 increases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:2083 albuterol, 1_TopAnswer +Asset:386 increases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:5582 salmeterol 1_TopAnswer +Asset:387 increases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:3410 formoterol 1_TopAnswer +Asset:388 increases activity or abundance of Inferred ADRB2 NCBIGene:154 PUBCHEM.COMPOUND:5403 terbutaline 1_TopAnswer +Asset:389 increases activity or abundance of Inferred ADRB2 NCBIGene:154 PharmGKBID:PA166165410 Beta-2 Agonists (Activators) 1_TopAnswer \ No newline at end of file diff --git a/pf_test_assets_2024_02_02.tsv b/pf_test_assets_2024_02_02.tsv new file mode 100644 index 0000000..621b3b3 --- /dev/null +++ b/pf_test_assets_2024_02_02.tsv @@ -0,0 +1,334 @@ +id Relationship Settings InputName (user choice) InputID, node normalized OutputID OutputName Expected Result / Suggested Comparator Translator GitHubIssue Method of Generation Level of Validation Test Author, Owner, Watch List Test GithubIssue Overly Generic In First 50 In Acceptance Persona/Use Case TBD: Data modeling: Disease-modifying, specific to treating symptoms/sequale, general Semantic Severity Well Known Person who cares about this, know about this issue type Blocklist (here or separate tabs) Causes not treats ? issue labels Notes +Asset:48 Treats Inferred Premature Menopause MONDO:0001119 UMLS:C1874451 Basis 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/567 Sandrine Muller block-list +Asset:5 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:12358480 Hexadrin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/490 Sandrine Muller clinical chemical roles +Asset:6 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:2478 Busulfan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/490 Sandrine Muller clinical chemical roles +Asset:76 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:216416 Lasofoxifene 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/489 Sandrine Muller +Asset:77 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:2478 Busulfan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/608 Sandrine Muller +Asset:78 Treats Inferred Premature Menopause MONDO:0001119 PUBCHEM.COMPOUND:5757 estradiol 1_TopAnswer Sandrine Muller +Asset:79 Treats Inferred Premature Menopause MONDO:0001119 MESH:D011372 progestin 1_TopAnswer Sandrine Muller +Asset:195 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:702 Ethanol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/638 Sandrine Muller clinical +Asset:196 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:702 Ethanol 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/638 Sandrine Muller mechanistic +Asset:197 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:3346 Fenthion 4_NeverShow Sandrine Muller block-list +Asset:198 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:84098 Isoxaflutole 4_NeverShow Sandrine Muller block-list +Asset:199 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:6758 Rotenone 4_NeverShow Sandrine Muller block-list +Asset:200 Treats Inferred alcoholic hepatitis MONDO:0001505 UNII:59NEE7PCAB Lindane 4_NeverShow Sandrine Muller block-list +Asset:201 Treats Inferred alcoholic hepatitis MONDO:0001505 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sandrine Muller block-list +Asset:202 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:1983 Acetaminophen 3_BadButForgivable Sandrine Muller block-list +Asset:203 Treats Inferred alcoholic hepatitis MONDO:0001505 MESH:D037742 Nanotubes, carbon 4_NeverShow Sandrine Muller block-list +Asset:204 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:6623 Bisphenol a 4_NeverShow Sandrine Muller block-list +Asset:205 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller +Asset:206 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:3826 Ketorolac 4_NeverShow Sandrine Muller +Asset:207 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:439501 Ouabain 4_NeverShow Sandrine Muller +Asset:208 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:712 Formaldehyde 4_NeverShow Sandrine Muller +Asset:209 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:446220 Cocaine 4_NeverShow Sandrine Muller +Asset:210 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:323 Coumarin 4_NeverShow Sandrine Muller +Asset:211 Treats Inferred alcoholic hepatitis MONDO:0001505 CHEMBL:2109152 Mineral oil 4_NeverShow Sandrine Muller +Asset:212 Treats Inferred alcoholic hepatitis MONDO:0001505 PUBCHEM.COMPOUND:10836 Methamphetamine 4_NeverShow Sandrine Muller +Asset:140 Treats Inferred scotoma MONDO:0004758 PUBCHEM.COMPOUND:5865 Prednisone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:141 Treats Inferred scotoma MONDO:0004758 PUBCHEM.COMPOUND:5665 vigabatrin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:50 Treats Inferred Allergic Asthma MONDO:0004784 MESH:D052638 particulate matter 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/561 Sandrine Muller +Asset:57 Treats Inferred Alzheimer Disease MONDO:0004975 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sandrine Muller block-list +Asset:184 Treats Inferred Diabetes Mellitus MONDO:0005015 UMLS:C0013227 Pharmaceutical preparations 5_OverlyGeneric Sandrine Muller +Asset:185 Treats Inferred Diabetes Mellitus MONDO:0005015 PUBCHEM.COMPOUND:4091 Metformin 1_TopAnswer Sandrine Muller +Asset:186 Treats Inferred Diabetes Mellitus MONDO:0005015 UNII:1Y17CTI5SR Insulin human 1_TopAnswer Sandrine Muller +Asset:187 Treats Inferred Diabetes Mellitus MONDO:0005015 PUBCHEM.COMPOUND:16137271 Insulin detremir 1_TopAnswer Sandrine Muller +Asset:61 Treats Inferred Diabetes Milletus MONDO:0005015 Sandrine Muller +Asset:46 Treats Inferred Autism MONDO:0005260 PUBCHEM.COMPOUND:3121 Valproic acid 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/577 Sandrine Muller +Asset:47 Treats Inferred Autism MONDO:0005260 MESH:D010575 Pesticides 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/575 Sandrine Muller +Asset:90 Treats Inferred Heart Disorder MONDO:0005267 fibrinogen 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/477 Sandrine Muller +Asset:10 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:5352425 lead 4_NeverShow Jennifer Hadlock look-up +Asset:100 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C5387588 Covid-19 vaccines 4_NeverShow Sandrine Muller +Asset:101 Treats Inferred Multiple Sclerosis MONDO:0005301 CHEMBL:2109042 Influenza vaccines 4_NeverShow Sandrine Muller +Asset:102 Treats Inferred Multiple Sclerosis MONDO:0005301 Vaccines, peptide 4_NeverShow Sandrine Muller +Asset:103 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0699680 Metric 4_NeverShow Sandrine Muller block-list +Asset:104 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0243192 Agonists 4_NeverShow Sandrine Muller block-list +Asset:105 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C1611640 Therapeutic agent 4_NeverShow Sandrine Muller block-list +Asset:106 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0302837 Vitamin supplementation 4_NeverShow Sandrine Muller block-list +Asset:107 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0003209 Anti-inflammatory agents 4_NeverShow Sandrine Muller block-list +Asset:108 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000276 Adjuvants, immunologic 4_NeverShow Sandrine Muller block-list +Asset:109 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000906 Antibodies 4_NeverShow Sandrine Muller block-list +Asset:110 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0040616 Anti-anxiety agents 4_NeverShow Sandrine Muller block-list +Asset:111 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000911 Antibodies, monoclonal 4_NeverShow Sandrine Muller block-list +Asset:112 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0005522 Biological products 4_NeverShow Sandrine Muller block-list +Asset:113 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0242912 Neuroprotective agents 4_NeverShow Sandrine Muller block-list +Asset:114 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0003232 Antibiotics 4_NeverShow Sandrine Muller block-list +Asset:115 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C1874451 basis 4_NeverShow Sandrine Muller block-list +Asset:116 Treats Inferred Multiple Sclerosis MONDO:0005301 UMLS:C0242896 Anticholinergic agents 2_Acceptable Jennifer Hadlock Treats symptoms or sequelae +Asset:117 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000700 Analgesics 4_NeverShow Sandrine Muller block-list +Asset:118 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:23931 Mercury 4_NeverShow Sandrine Muller block-list +Asset:119 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D005227 Fatty acids 4_NeverShow Sandrine Muller block-list +Asset:120 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D010936 Plant extracts 4_NeverShow Sandrine Muller block-list +Asset:121 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D004365 Drugs, chinese herbal 4_NeverShow Sandrine Muller block-list +Asset:122 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller block-list +Asset:123 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller block-list +Asset:8 Treats Inferred Multiple Sclerosis MONDO:0005301 PUBCHEM.COMPOUND:107970 fingolimod 1_TopAnswer Jennifer Hadlock look-up +Asset:9 Treats Inferred Multiple Sclerosis MONDO:0005301 MESH:D000069442 natalizumab 1_TopAnswer Jennifer Hadlock look-up +Asset:98 Treats Inferred multiple sclerosis MONDO:0005301 MESH:D014612 vaccines 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/431 Sandrine Muller block-list +Asset:180 Treats Inferred Gout MONDO:0005393 UNNI:R581OT55EA Pegloticase 2_Acceptable Sierra Moxon +Asset:181 Treats Inferred Gout MONDO:0005393 PUBCHEM.COMPOUND:5865 Prednisone 2_Acceptable Sierra Moxon +Asset:52 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:4030 Mebendazole 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller Yes +Asset:53 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:708857 Pyrantel 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller Yes +Asset:54 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:5430 Thiabendazole 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller Yes +Asset:55 Treats Inferred Hookworm Infectious Disease MONDO:0005799 PUBCHEM.COMPOUND:3037 Dichlorophen 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/483 Sandrine Muller +Asset:168 Treats Inferred Cerebral palsy MONDO:0006497 UMLS:C0003232 Antibiotics 4_NeverShow Sierra Moxon +Asset:169 Treats Inferred Cerebral palsy MONDO:0006497 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sierra Moxon +Asset:170 Treats Inferred Cerebral palsy MONDO:0006497 PUBCHEM.COMPOUND:3672 Ibuprofen 3_BadButForgivable Sierra Moxon +Asset:171 Treats Inferred Cerebral palsy MONDO:0006497 PUBCHEM.COMPOUND:2284 Baclofen 2_Acceptable Sierra Moxon +Asset:172 Treats Inferred Cerebral palsy MONDO:0006497 CHEBML:CHEMBL1201569 Botulinum toxin type b 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:173 Treats Inferred Cerebral palsy MONDO:0006497 PUBCHEM.COMPOUND:2554 Carbamazepine 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:188 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C3536832 Air 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman CP SMuRF +Asset:189 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C3536832 Air 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman Molecular focus +Asset:190 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C3536832 Air 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman CP SMuRF +Asset:191 Treats Inferred Cerebral Palsy MONDO:0006497 NCIT:C38065 Hyperbaric oxygen therapy 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:192 Treats Inferred Cerebral Palsy MONDO:0006497 MESH:D000336 Aerosols 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:193 Treats Inferred Cerebral Palsy MONDO:0006497 UMLS:C0013227 Pharmaceutical Preparations 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:194 Treats Inferred Cerebral Palsy MONDO:0006497 NCIT:C38065 Hyperbaric oxygen therapy 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/624 Gwênlyn Glusman +Asset:68 Treats Inferred Obstructive Sleep Apnea MONDO:0007147 MESH:D053260 Soot 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller clinical +Asset:69 Treats Inferred Obstructive Sleep Apnea MONDO:0007147 MESH:D053260 Soot 2_Acceptable https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller mechanistic +Asset:178 Treats Inferred ADHD MONDO:0007743 PUBCHEM.COMPOUND:446220 Cocaine 4_NeverShow Sierra Moxon +Asset:179 Treats Inferred ADHD MONDO:0007743 PUBCHEM.COMPOUND:4158 Methylphenidate 2_Acceptable Sierra Moxon +Asset:92 Treats Inferred familial pityriasis rubra pilaris MONDO:0008251 retinol 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/473 Sandrine Muller +Asset:95 Treats Inferred familial pityriasis rubra pilaris MONDO:0008251 MESH:D000438 Alcohols 4_NeverShow Sandrine Muller block-list +Asset:63 Treats Inferred Gaucher Disease type1 MONDO:0009265 PUBCHEM.COMPOUND:23652731 Eliglustat 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller clinical +Asset:64 Treats Inferred Gaucher Disease type1 MONDO:0009265 UNII:Q6U6J48BWY Imiglucerase 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:65 Treats Inferred Gaucher Disease type1 MONDO:0009265 UNII:0R4NLX88O4 Taliglucerase alfa 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:66 Treats Inferred Gaucher Disease type1 MONDO:0009265 CHEMBL.COMPOUND:CHEMBL1201865 Velaglucerase-alfa 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:67 Treats Inferred Gaucher Disease type1 MONDO:0009265 PUBCHEM.COMPOUND:51634 Miglustat 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:133 Treats Inferred Hereditary sensory and autonomic neuropathy type 4 MONDO:0009746 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/404 Sandrine Muller +Asset:134 Treats Inferred Hereditary sensory and autonomic neuropathy type 4 MONDO:0009746 UNII:E211KPY694 Botulinum toxin type a 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/405 Sandrine Muller +Asset:137 Treats Inferred Hereditary sensory and autonomic neuropathy type 4 MONDO:0009746 PUBCHEM.COMPOUND:4096 Methamidophos 4_NeverShow Sandrine Muller +Asset:3 Treats Inferred NARP Syndrome MONDO:0010794 DRUGBANK:DB00313 Valproic Acid 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/147 Sandrine Muller clinical Yes contraindications +Asset:4 Treats Inferred NARP Syndrome MONDO:0010794 MESH:D001463 Barbiturates 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/147 Sandrine Muller clinical Yes contraindications +Asset:149 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:33250 Atom 4_NeverShow Sandrine Muller +Asset:150 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D002467 Cell nucleus 4_NeverShow Sandrine Muller +Asset:151 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D012492 salts 4_NeverShow Sandrine Muller +Asset:152 Treats Inferred Fatal familial insomnia MONDO:0010808 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller Y +Asset:153 Treats Inferred Fatal familial insomnia MONDO:0010808 PUBCHEM.COMPOUND:962 Hydrogen(.) 4_NeverShow Sandrine Muller Y +Asset:154 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D004583 Electrons 4_NeverShow Sandrine Muller +Asset:155 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D000838 Anions 4_NeverShow Sandrine Muller +Asset:156 Treats Inferred Fatal familial insomnia MONDO:0010808 PUBCHEM.COMPOUND:977 Oxygen 4_NeverShow Sandrine Muller +Asset:157 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D002412 Cations 4_NeverShow Sandrine Muller +Asset:158 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:24471 Halogen molecular entity 4_NeverShow Sandrine Muller +Asset:159 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:51143 Nitrogen molecular entity 4_NeverShow Sandrine Muller +Asset:160 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D000438 Alcohols 4_NeverShow Sandrine Muller +Asset:161 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:25367 Molecule 4_NeverShow Sandrine Muller +Asset:162 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:24868 Organic salt 4_NeverShow Sandrine Muller +Asset:163 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D009930 Organic chemicals 4_NeverShow Sandrine Muller +Asset:164 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:36094 Organic chloride salt 4_NeverShow Sandrine Muller +Asset:165 Treats Inferred Fatal familial insomnia MONDO:0010808 UMLS:C0030054 Oxygen 4_NeverShow Sandrine Muller +Asset:166 Treats Inferred Fatal familial insomnia MONDO:0010808 MESH:D000700 Analgesics 4_NeverShow Sandrine Muller +Asset:167 Treats Inferred Fatal familial insomnia MONDO:0010808 CHEBI:134179 Volatile organic compound 4_NeverShow Sandrine Muller +Asset:1 Treats Inferred Aceruloplasminemia MONDO:0011426 DRUGBANK:DB01592 Iron (PUBCHEM) 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/506 Sandrine Muller clinical Yes causes not treats; TMKP The CQS is returning iron for MONDO:0011426 (https://monarchinitiative.org/MONDO:0011426) . I (Kara) would have classified this as 3_BadButForgiveable, and I see that it is classified as such in row 18. +Asset:15 Treats Inferred Aceruloplasminemia MONDO:0011426 PUBCHEM.COMPOUND:4356 iron 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/506 Jennifer Hadlock https://github.com/NCATSTranslator/Tests/issues/8 look-up +Asset:16 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:50453 desferrioxamine 1_TopAnswer Jennifer Hadlock look-up +Asset:17 Treats Inferred Aceruloplasminemia MONDO:0011426 DRUGBANK:DB01592 Iron (PUBCHEM) 3_BadButForgivable https://github.com/NCATSTranslator/Feedback/issues/506 Sandrine Muller mechanistic Change management causes not treats; TMKP See comment from Kara in X2. +Asset:18 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D009930 Organic Chemicals 4_NeverShow Sandrine Muller all block-list +Asset:19 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:23367 molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:2 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33247 organic group 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/572 Sandrine Muller all block-list category too generic +Asset:20 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:25367 molecule 4_NeverShow Sandrine Muller all block-list +Asset:21 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:25806 oxygen molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:22 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:36357 polyatomic entity 4_NeverShow Sandrine Muller all block-list +Asset:23 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33582 carbon group molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:24 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D007287 inorganic chemicals 4_NeverShow Sandrine Muller all block-list +Asset:25 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33285 heteroorganic entity 4_NeverShow Sandrine Muller all block-list +Asset:26 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33579 main group molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:27 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:37577 heteroatomic molecular entity 4_NeverShow Sandrine Muller all block-list +Asset:28 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:33595 cyclic compound 4_NeverShow Sandrine Muller all block-list +Asset:29 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D006571 heterocyclic compounds 4_NeverShow Sandrine Muller all block-list +Asset:30 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:24836 inorganic oxide 4_NeverShow Sandrine Muller all block-list +Asset:31 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:24431 chemical entity 4_NeverShow Sandrine Muller all block-list +Asset:56 Treats Inferred Aceruloplasminemia MONDO:0011426 MESH:D002467 cell nucleus 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/597 Sandrine Muller block-list +Asset:62 Treats Inferred Aceruloplasminemia MONDO:0011426 PUBCHEM.COMPOUND:6758 Rotenone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/505 Sandrine Muller clinical +Asset:131 Treats Inferred Hereditary Sensory And Autonomic Neuropathy Type MONDO:0015364 MESH:D016756 Immunoglobulins, intravenous 4_NeverShow Sandrine Muller +Asset:132 Treats Inferred Hereditary Sensory And Autonomic Neuropathy Type MONDO:0015364 PUBCHEM.COMPOUND:84098 Isoxaflutole 4_NeverShow Sandrine Muller +Asset:182 Treats Inferred Hereditary Sensory And Autonomic Neuropathy MONDO:0015364 MONDO:0016028 Erythromelalgia 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/632 Sandrine Muller +Asset:183 Treats Inferred Hereditary Sensory And Autonomic Neuropathy MONDO:0015364 MONDO:0009131 Riley-day Syndrome 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/633 Sandrine Muller +Asset:11 Treats Inferred Multiple Sclerosis MONDO:0015564 PUBCHEM.COMPOUND:5284616 sirolimus 1_TopAnswer Jennifer Hadlock look-up +Asset:12 Treats Inferred Multiple Sclerosis MONDO:0015564 UNII:4F4X42SYQ6 rituximab 1_TopAnswer Jennifer Hadlock look-up +Asset:13 Treats Inferred Multiple Sclerosis MONDO:0015564 UNII:9013DUQ28K anakinra 1_TopAnswer Jennifer Hadlock look-up +Asset:14 Treats Inferred Multiple Sclerosis MONDO:0015564 CHEMBL.COMPOUND:1201562 interferon-beta 1a 1_TopAnswer Jennifer Hadlock look-up +Asset:306 Treats Inferred Multiple Sclerosis MONDO:0015564 CHEMBL.COMPOUND:1201563 interferon-beta 1b 1_TopAnswer Jennifer Hadlock +Asset:7 Treats Inferred Multiple Sclerosis MONDO:0015564 MESH:D001335 Vehicle Emissions 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/480 Sandrine Muller clinical block-list chemical roles +Asset:49 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 PUBCHEM.COMPOUND:4158 methylphenidate 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/562 Sandrine Muller +Asset:58 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 PUBCHEM.COMPOUND:24847884 Omniscan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/546 Sandrine Muller block-list +Asset:59 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 UNII:1BJ477IO2L Gadobutrol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/546 Sandrine Muller block-list +Asset:60 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 PUBCHEM.COMPOUND:73415823 Gadopentetate dimeglumine 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/546 Sandrine Muller block-list +Asset:99 Treats Inferred Ehlers-Danlos Syndrome MONDO:0017314 alendronic acid 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/428 Sandrine Muller +Asset:71 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 PUBCHEM.COMPOUND:446157 Rosuvastatin 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller This may be a feature issue for UI - and separate case: expected answer is that you can't choose those option for may treats. Second is do we restrict this from being enter at the API level? If not, is this a high pri test case? +Asset:72 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 PUBCHEM.COMPOUND:9853053 Lomitapide 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:73 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 UNII:9GJ8S4GU0M Mipomersen 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:74 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 UNII:LKC0U3A8NJ Evolocumab 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:75 Treats Inferred Homozygous Familial Hypercholesterolemia MONDO:0018328 PUBCHEM.COMPOUND:446157 Rosuvastatin 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:138 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:3562 Halothane 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:139 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:3763 isoflurane 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/362 Sandrine Muller +Asset:142 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C0013227 Pharmaceutical preparations 4_NeverShow Sandrine Muller +Asset:143 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller +Asset:144 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 MESH:D000779 Anesthetics, local 4_NeverShow Sandrine Muller +Asset:145 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 PUBCHEM.COMPOUND:1727 4-aminopyridine 4_NeverShow Sandrine Muller +Asset:146 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C0002932 Anesthetics 4_NeverShow Sandrine Muller +Asset:147 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C0003232 Antibiotics 4_NeverShow Sandrine Muller +Asset:148 Treats Inferred Malignant Hyperthermia Of Anesthesia MONDO:0018493 UMLS:C1874451 basis 4_NeverShow Sandrine Muller +Asset:124 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D011972 Receptor, insulin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/613 Sandrine Muller +Asset:125 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D001323 Autoantibodies 4_NeverShow Sandrine Muller +Asset:126 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 PUBCHEM.COMPOUND:53462828 Thyroid hormones 4_NeverShow Sandrine Muller +Asset:127 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D004798 Enzymes 4_NeverShow Sandrine Muller +Asset:128 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D017526 Receptor, IGF Type 1 4_NeverShow Sandrine Muller +Asset:129 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 MESH:D003165 Complement system proteins 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/615 Sandrine Muller +Asset:130 Treats Inferred Maturity-onset Diabetes Of The Young MONDO:0018911 PUBCHEM.COMPOUND:6623 bisphenol A 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/444 Sandrine Muller +Asset:174 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:6057 Tyrosine 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:175 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:460612 Melphalan 2_Acceptable Sierra Moxon these should be "studied to treat" +Asset:176 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:15625 2,3,7,8-tetrachlorodibenzo-p-dioxin 4_NeverShow Sierra Moxon +Asset:177 Treats Inferred Nemaline myopathy MONDO:0018958 PUBCHEM.COMPOUND:5426 Thalidimide 2_Acceptable Sierra Moxon +Asset:70 Treats Inferred Niemann-Pick type C MONDO:0018982 PUBCHEM.COMPOUND:51634 Miglustat 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/494 Sandrine Muller +Asset:93 Treats Inferred Rabies MONDO:0019173 Methionine 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/463 Sandrine Muller +Asset:94 Treats Inferred Rabies MONDO:0019173 Cefaclor 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/463 Sandrine Muller +Asset:96 Treats Inferred Xeroderma Pigmentosum MONDO:0019600 cadmium 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/465 Sandrine Muller block-list +Asset:97 Treats Inferred Xeroderma Pigmentosum MONDO:0019600 mercury 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/465 Sandrine Muller block-list +Asset:51 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:774 Histamine 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/488 Sandrine Muller +Asset:85 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:3672 ibuprofen 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:86 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 NCIT:C163032 botulinum toxin 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:87 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 dinoprostone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:88 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 calcitriol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:89 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:5280793 ergocalciferol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/479 Sandrine Muller +Asset:91 Treats Inferred Aggressive Systemic Mastocytosis MONDO:0020333 PUBCHEM.COMPOUND:1727 4-Aminopyridine 4_NeverShow Sandrine Muller block-list +Asset:80 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:5291 Imatinib 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/486 Sandrine Muller +Asset:81 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:216239 Sorafenib 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/486 Sandrine Muller +Asset:82 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:1140 Toluene 4_NeverShow Sandrine Muller block-list +Asset:83 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:84098 Isoxaflutole 4_NeverShow Sandrine Muller block-list +Asset:84 Treats Inferred Exfoliative Dermatitis MONDO:0043233 PUBCHEM.COMPOUND:3036 Clofenotane 4_NeverShow Sandrine Muller block-list +Asset:32 Treats Inferred Lactose intolerance MONDO:0100345 CHEMBL.COMPOUND:2108505 Lactase 1_TopAnswer https://github.com/NCATSTranslator/Feedback/issues/427 Sandrine Muller look-up yes reasoning;opposite of what I asked for; data error +Asset:33 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:6134 beta-Lactose 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/427 Sandrine Muller clinical reasoning;opposite of what I asked for; data error +Asset:34 Treats Inferred Lactose intolerance MONDO:0100345 MESH:D010936 Plant extracts 4_NeverShow Sandrine Muller all +Asset:35 Treats Inferred Lactose intolerance MONDO:0100345 MESH:D028321 Plant preparations 4_NeverShow Sandrine Muller all +Asset:36 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:6134 alpha-Lactose 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/427 Sandrine Muller clinical reasoning;opposite of what I asked for; data error +Asset:37 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:5280793 Ergocalciferol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:38 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:4030 Mebendazole 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:39 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:2406 Bithionol 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:40 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:5430 Thiabendazole 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:41 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:26879 Levamisole 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:42 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:4096 Methamidophos 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:43 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:516893 Potassium bicarbonate 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:44 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:5564 Triclosan 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:45 Treats Inferred Lactose intolerance MONDO:0100345 PUBCHEM.COMPOUND:445643 Tacrolimus 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/601 Sandrine Muller clinical chemical roles;opposite of what I asked for;reasoning +Asset:135 downregulate Inferred DDX3Y NCBI Gene:8653 UMLS:C0311474 dna double stranded 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/384 Sandrine Muller +Asset:136 downregulate Inferred DDX3Y NCBI Gene:8653 UMLS:C1328819 Small molecule 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/384 Sandrine Muller +Asset:213 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:6741 Methylprednisolone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:214 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:5865 Prednisone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:215 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:5754 Hydrocortisone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:216 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:5743 Dexamethasone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:217 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:31307 Triamcinolone 4_NeverShow https://github.com/NCATSTranslator/Feedback/issues/636 Sandrine Muller +Asset:218 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D014028 Tobacco smoke pollution 4_NeverShow Sandrine Muller +Asset:219 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D002772 Cholera Toxin 4_NeverShow Sandrine Muller +Asset:220 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D037342 Pertussis toxin 4_NeverShow Sandrine Muller +Asset:221 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:11302220 Cocain-chlorhydrat 4_NeverShow Sandrine Muller +Asset:222 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D002412 Cations 4_NeverShow Sandrine Muller +Asset:223 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:443495 Sodium arsenite 4_NeverShow Sandrine Muller +Asset:224 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 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Nitrogen molecular entity 4_NeverShow Sandrine Muller +Asset:233 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:50860 Organic molecular entity 4_NeverShow Sandrine Muller +Asset:234 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:33582 Carbon group molecular entity 4_NeverShow Sandrine Muller +Asset:235 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D002467 Cell nucleus 4_NeverShow Sandrine Muller +Asset:236 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:36587 Organic oxo compound 4_NeverShow Sandrine Muller +Asset:237 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:33250 Atom 4_NeverShow Sandrine Muller +Asset:238 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND: Ions 4_NeverShow Sandrine Muller +Asset:239 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:24433 Group 4_NeverShow Sandrine Muller +Asset:240 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:446220 Cocaine 4_NeverShow Sandrine Muller +Asset:241 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 PUBCHEM.COMPOUND:784 Hydrogen peroxide 3_BadButForgivable Sandrine Muller +Asset:242 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 UMLS:C1306770 Nitrogen 99.9 % 4_NeverShow Sandrine Muller +Asset:243 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:25806 Oxygen molecular entity 4_NeverShow Sandrine Muller +Asset:244 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 MESH:D006219 Halogens 4_NeverShow Sandrine Muller +Asset:245 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:36586 Carbonyl compound 4_NeverShow Sandrine Muller +Asset:246 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 UMLS:C1337101 Nitrogen 99.7 % 4_NeverShow Sandrine Muller +Asset:247 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:36830 Monoanion 4_NeverShow Sandrine Muller +Asset:248 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:33832 Organic cyclic compound 4_NeverShow Sandrine Muller +Asset:249 Treats Inferred Peptic Ulcer Perforation MONDO:0004260 CHEBI:24532 Organic heterocyclic compound 4_NeverShow Sandrine Muller +Asset:250 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:784 Hydrogen peroxide 4_NeverShow Sandrine Muller +Asset:251 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D037742 Nanotubes, carbon 4_NeverShow Sandrine Muller +Asset:252 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:15938 Paraquat dichloride 4_NeverShow Sandrine Muller +Asset:253 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:443495 Sodium arsenite 4_NeverShow Sandrine Muller +Asset:254 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:2912 Cypermethrin 4_NeverShow Sandrine Muller +Asset:255 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D054328 Proton pump inhibitors 4_NeverShow Sandrine Muller +Asset:256 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 UMLS:C0699680 Metric (substance) 4_NeverShow Sandrine Muller +Asset:257 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D014028 Tobacco smoke pollution 4_NeverShow Sandrine Muller +Asset:258 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 UMLS:C3166216 Prescribed medications 4_NeverShow Sandrine Muller +Asset:259 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 MESH:D001786 Blood glucose 4_NeverShow Sandrine Muller +Asset:260 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:433294 Lithium Chloride 4_NeverShow Sandrine Muller +Asset:261 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 UMLS:C0003289 Antidepressive agents 4_NeverShow Sandrine Muller +Asset:262 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 DRUGBANK:DB05404 AZD 3355 1_TopAnswer Sandrine Muller +Asset:263 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:174 1,2-ethanediol 4_NeverShow Sandrine Muller +Asset:264 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:56842000 Talcid 1_TopAnswer Sandrine Muller +Asset:265 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:311 Citric acid 4_NeverShow Sandrine Muller The CQS is returning citric acid for MONDO:0007186 (https://monarchinitiative.org/MONDO:0007186). I (Kara) would have classified this as 3_BadButForgiveable. +Asset:266 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller +Asset:267 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:176 Acetic acid 4_NeverShow Sandrine Muller +Asset:268 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller +Asset:269 Treats Inferred Gastroesophageal Reflux Disease MONDO:0007186 PUBCHEM.COMPOUND: Oxygen 4_NeverShow Sandrine Muller +Asset:270 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:23982 Gadolinium 4_NeverShow Sandrine Muller +Asset:271 Treats Inferred Cowden Disease MONDO:0016063 MESH:D007477 Ions 4_NeverShow Sandrine Muller +Asset:272 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:190217 Oxide 4_NeverShow Sandrine Muller +Asset:273 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:5462310 Carbon 4_NeverShow Sandrine Muller +Asset:274 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:962 Water 4_NeverShow Sandrine Muller +Asset:275 Treats Inferred Cowden Disease MONDO:0016063 MESH:D002412 Cations 4_NeverShow Sandrine Muller +Asset:276 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Electrons 4_NeverShow Sandrine Muller +Asset:277 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Formaldehyde 4_NeverShow Sandrine Muller +Asset:278 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Organic anion 4_NeverShow Sandrine Muller +Asset:279 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND: Acyl group 4_NeverShow Sandrine Muller +Asset:280 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:25585 Nonmetal atom 4_NeverShow Sandrine Muller +Asset:281 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33677 F-block molecular entity 4_NeverShow Sandrine Muller +Asset:282 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33497 Transition element molecular entity 4_NeverShow Sandrine Muller +Asset:283 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:27081 Transition element atom 4_NeverShow Sandrine Muller +Asset:284 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33562 F-block element atom 4_NeverShow Sandrine Muller +Asset:285 Treats Inferred Cowden Disease MONDO:0016063 MESH:D000071940 Nucleons 4_NeverShow Sandrine Muller +Asset:286 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:36963 Organooxygen compound 4_NeverShow Sandrine Muller +Asset:287 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33695 Information biomacromolecule 4_NeverShow Sandrine Muller +Asset:288 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:24532 Organic heterocyclic compound 4_NeverShow Sandrine Muller +Asset:289 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33434 Elemental halogen 4_NeverShow Sandrine Muller +Asset:290 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:24867 Monoatomic ion 4_NeverShow Sandrine Muller +Asset:291 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33432 Monoatomic chlorine 4_NeverShow Sandrine Muller +Asset:292 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33433 Monoatomic halogen 4_NeverShow Sandrine Muller +Asset:293 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33674 S-block molecular entity 4_NeverShow Sandrine Muller +Asset:294 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33431 Elemental chlorine 4_NeverShow Sandrine Muller +Asset:295 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:50047 Organic amino compound 4_NeverShow Sandrine Muller +Asset:296 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:37578 Halide 4_NeverShow Sandrine Muller +Asset:297 Treats Inferred Cowden Disease MONDO:0016063 PUBCHEM.COMPOUND:23991 Xenon 4_NeverShow Sandrine Muller +Asset:298 Treats Inferred Cowden Disease MONDO:0016063 MESH:D061065 Polyketides 4_NeverShow Sandrine Muller +Asset:299 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:33710 Alpha-amino-acid residue 4_NeverShow Sandrine Muller +Asset:300 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:79389 Monovalent inorganic anion 4_NeverShow Sandrine Muller +Asset:301 Treats Inferred Cowden Disease MONDO:0016063 MESH:D000470 Alkaloids 4_NeverShow Sandrine Muller +Asset:302 Treats Inferred Cowden Disease MONDO:0016063 CHEBI:16042 Halide anion 4_NeverShow Sandrine Muller +Asset:303 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:2972 deferipone 1_TopAnswer Jennifer Hadlock look-up +Asset:304 Treats Inferred Aceruloplasminemia MONDO:0011426 CHEBI:49005 deferasirox 1_TopAnswer Jennifer Hadlock look-up +Asset:305 Treats Inferred Aceruloplasminemia MONDO:0011426 PUBCHEM.COMPOUND:2973 Deferoxamine 1_TopAnswer +Asset:307 Increases abundance or activity of Inferred Beta 2 adrenergic (ADRB2) NCBIGene:154 PUBCHEM.COMPOUND:2083 Albuterol 1_TopAnswer Chris Bizon +Asset:308 Increases abundance or activity of Inferred Beta 2 adrenergic (ADRB2) NCBIGene:154 PUBCHEM.COMPOUND:4946 Propranalol 4_NeverShow +Asset:309 Treats Inferred Neutropenia MONDO:0001475 PUBCHEM.COMPOUND:77910626 Pegfilgrastim 1_TopAnswer +Asset:310 Decreases abundance of Inferred Pseudoephedrine PUBCHEM.COMPOUND:7028 NCBIGene:3558 Interleukin-2 2_Acceptable +Asset:311 Decreases abundance or activity of Inferred ACE NCBIGene:1636 PUBCHEM.COMPOUND:5362124 Benazapril 1_TopAnswer +Asset:312 is down-regulated in Inferred MYC proto-oncogene, bHLH transcription factor NCBIGene:7553 MONDO:0004992 cancer 4_NeverShow +Asset:313 Increases abundance or activity of Inferred CFTR (human) NCBIGene:1080 PUBCHEM.COMPOUND:16220172 Ivacaftor 2_Acceptable Sarah Stemann +Asset:314 Decreases abundance or activity of Inferred CYP2D6 NCBIGene:1565 PUBCHEM.COMPOUND:5452 Thioridazine 2_Acceptable +Asset:315 Treats Inferred Asthma MONDO:0004979 PUBCHEM.COMPOUND:5311101 Fluticasone 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:316 Treats Inferred Asthma MONDO:0004979 UMLS:C2194286 Albuterol (salbutamol) 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:317 Treats Inferred Asthma MONDO:0004979 PUBCHEM.COMPOUND:4946 Propranolol 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:318 Treats Inferred Cystic fibrosis MONDO:0009061 PUBCHEM.COMPOUND:16220172 Ivacaftor 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:319 Treats Inferred Cystic fibrosis MONDO:0009061 UMLS:C3489797 AZD9668 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:320 Treats Inferred Cystic fibrosis MONDO:0009061 PUBCHEM.COMPOUND:55283 Itraconazole 4_NeverShow Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:321 Treats Inferred Idiopathic bronchiectasis MONDO:0018956 PUBCHEM.COMPOUND:447043 Azithromycin 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:322 Treats Inferred Idiopathic bronchiectasis MONDO:0018956 PUBCHEM.COMPOUND:12560 Erythromycin 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:323 Treats Inferred Idiopathic bronchiectasis MONDO:0018956 PUBCHEM.COMPOUND:4946 Propranolol 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:324 Treats Inferred Idiopathic pulmonary fibrosis MONDO:0008345 PUBCHEM.COMPOUND:40632 Pirfenidone 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:325 Treats Inferred Idiopathic pulmonary fibrosis MONDO:0008345 PUBCHEM.COMPOUND:11671467 Fostamatinib 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:326 Treats Inferred Idiopathic pulmonary fibrosis MONDO:0008345 PUBCHEM.COMPOUND:90420193 GLPG1690 (Ziritaxestat) 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:327 Treats Inferred Lymphangioleiomyomatosis MONDO:0011705 PUBCHEM.COMPOUND:5284616 Sirolimus 1_TopAnswer Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:328 Treats Inferred Lymphangioleiomyomatosis MONDO:0011705 PUBCHEM.COMPOUND:11520894 Ridaforolimus 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:329 Treats Inferred Lymphangioleiomyomatosis MONDO:0011705 UMLS:C0116660 ESTROSTEP Fe (Norethindrone Acetate and Ethinyl Estradiol) 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:330 Treats Inferred Primary ciliary dyskinesia MONDO:0016575 PUBCHEM.COMPOUND:9934746 Ensifentrine 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:331 Treats Inferred Primary ciliary dyskinesia MONDO:0016575 PUBCHEM.COMPOUND:447043 Azithromycin 2_Acceptable Automated, LLM SMuRF, SME Kara Fecho LLM-generated/SMurF-SME-validated +Asset:332 Treats Inferred Primary ciliary dyskinesia MONDO:0016575 PUBCHEM.COMPOUND:5360696 Dextromethorphan 4_NeverShow Automated, LLM SMuRF Kara Fecho LLM-generated/SMurF-validated +Asset:333 Decreases abundance or activity of Inferred Docetaxel PUBCHEM.COMPOUND:148124 NCBIGene:596 BCL2 2_Acceptable Sarah Stemann \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index cbb24c1..6e4d034 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. [[package]] name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" +category = "main" optional = false python-versions = "*" files = [ @@ -14,6 +15,7 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -27,12 +29,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -51,6 +54,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" +category = "dev" optional = false python-versions = ">=3.6.0" files = [ @@ -69,6 +73,7 @@ lxml = ["lxml"] name = "bioregistry" version = "0.10.86" description = "Integrated registry of biological databases and nomenclatures" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -95,10 +100,28 @@ health = ["click-default-group", "jinja2", "pandas", "pyyaml", "tabulate"] tests = ["coverage", "httpx", "more-itertools", "pytest"] web = ["bootstrap-flask (<=2.0.0)", "curies[fastapi]", "fastapi", "flask (<2.2.4)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint", "rdflib-jsonld", "uvicorn", "werkzeug (<2.3.0)"] +[[package]] +name = "bmt" +version = "1.2.1" +description = "Biolink Model Toolkit: A Python API for working with the Biolink Model" +category = "main" +optional = false +python-versions = ">=3.9,<4.0" +files = [ + {file = "bmt-1.2.1-py3-none-any.whl", hash = "sha256:5dda82c872ca4ee615e22a2dcd3b647491149ad8f92aaa3f04a69e5832542771"}, + {file = "bmt-1.2.1.tar.gz", hash = "sha256:9a0100458bc9d8045a9f268ee919819a254c84c36820f82703c92738cd294ae8"}, +] + +[package.dependencies] +deprecation = ">=2.1.0,<3.0.0" +linkml-runtime = ">=1.6.3,<2.0.0" +stringcase = ">=1.2.0,<2.0.0" + [[package]] name = "cachetools" version = "5.3.2" description = "Extensible memoizing collections and decorators" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -110,6 +133,7 @@ files = [ name = "certifi" version = "2023.11.17" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -121,6 +145,7 @@ files = [ name = "cfgraph" version = "0.2.1" description = "rdflib collections flattening graph" +category = "main" optional = false python-versions = "*" files = [ @@ -134,6 +159,7 @@ rdflib = ">=0.4.2" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -145,6 +171,7 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -244,6 +271,7 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -258,6 +286,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -269,6 +298,7 @@ files = [ name = "curies" version = "0.7.4" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -293,6 +323,7 @@ tests = ["coverage", "pytest"] name = "daff" version = "1.3.46" description = "Diff and patch tables" +category = "dev" optional = false python-versions = "*" files = [ @@ -303,6 +334,7 @@ files = [ name = "deprecated" version = "1.2.14" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -316,10 +348,26 @@ wrapt = ">=1.10,<2" [package.extras] dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"] +[[package]] +name = "deprecation" +version = "2.1.0" +description = "A library to handle automated deprecations" +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "deprecation-2.1.0-py2.py3-none-any.whl", hash = "sha256:a10811591210e1fb0e768a8c25517cabeabcba6f0bf96564f8ff45189f90b14a"}, + {file = "deprecation-2.1.0.tar.gz", hash = "sha256:72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff"}, +] + +[package.dependencies] +packaging = "*" + [[package]] name = "distlib" version = "0.3.7" description = "Distribution utilities" +category = "main" optional = false python-versions = "*" files = [ @@ -331,6 +379,7 @@ files = [ name = "editorconfig" version = "0.12.3" description = "EditorConfig File Locator and Interpreter for Python" +category = "dev" optional = false python-versions = "*" files = [ @@ -342,6 +391,7 @@ files = [ name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -353,6 +403,7 @@ files = [ name = "exceptiongroup" version = "1.2.0" description = "Backport of PEP 654 (exception groups)" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -367,6 +418,7 @@ test = ["pytest (>=6)"] name = "filelock" version = "3.13.1" description = "A platform independent file lock." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -383,6 +435,7 @@ typing = ["typing-extensions (>=4.8)"] name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" +category = "main" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -394,6 +447,7 @@ files = [ name = "ghp-import" version = "2.1.0" description = "Copy your docs directly to the gh-pages branch." +category = "dev" optional = false python-versions = "*" files = [ @@ -411,6 +465,7 @@ dev = ["flake8", "markdown", "twine", "wheel"] name = "google" version = "3.0.0" description = "Python bindings to the Google search engine." +category = "dev" optional = false python-versions = "*" files = [ @@ -425,6 +480,7 @@ beautifulsoup4 = "*" name = "google-api-core" version = "2.14.0" description = "Google API client core library" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -447,6 +503,7 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] name = "google-api-python-client" version = "2.108.0" description = "Google API Client Library for Python" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -455,7 +512,7 @@ files = [ ] [package.dependencies] -google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0.dev0" +google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0.dev0" google-auth = ">=1.19.0,<3.0.0.dev0" google-auth-httplib2 = ">=0.1.0" httplib2 = ">=0.15.0,<1.dev0" @@ -465,6 +522,7 @@ uritemplate = ">=3.0.1,<5" name = "google-auth" version = "2.23.4" description = "Google Authentication Library" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -488,6 +546,7 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"] name = "google-auth-httplib2" version = "0.1.1" description = "Google Authentication Library: httplib2 transport" +category = "dev" optional = false python-versions = "*" files = [ @@ -503,6 +562,7 @@ httplib2 = ">=0.19.0" name = "google-auth-oauthlib" version = "1.1.0" description = "Google Authentication Library" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -521,6 +581,7 @@ tool = ["click (>=6.0.0)"] name = "googleapis-common-protos" version = "1.61.0" description = "Common protobufs used in Google APIs" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -538,6 +599,7 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"] name = "graphviz" version = "0.20.1" description = "Simple Python interface for Graphviz" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -554,6 +616,7 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>= name = "greenlet" version = "3.0.1" description = "Lightweight in-process concurrent programming" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -624,6 +687,7 @@ test = ["objgraph", "psutil"] name = "gspread" version = "5.12.0" description = "Google Spreadsheets Python API" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -639,6 +703,7 @@ google-auth-oauthlib = ">=0.4.1" name = "gspread-formatting" version = "1.1.2" description = "Complete Google Sheets formatting support for gspread worksheets" +category = "dev" optional = false python-versions = "*" files = [ @@ -653,6 +718,7 @@ gspread = ">=3.0.0" name = "hbreader" version = "0.9.1" description = "Honey Badger reader - a generic file/url/string open and read tool" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -664,6 +730,7 @@ files = [ name = "httplib2" version = "0.22.0" description = "A comprehensive HTTP client library." +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -678,6 +745,7 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0 name = "idna" version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -689,6 +757,7 @@ files = [ name = "importlib-metadata" version = "6.8.0" description = "Read metadata from Python packages" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -708,6 +777,7 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -719,6 +789,7 @@ files = [ name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" +category = "main" optional = false python-versions = "*" files = [ @@ -733,6 +804,7 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -747,6 +819,7 @@ arrow = ">=0.15.0" name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -764,6 +837,7 @@ i18n = ["Babel (>=2.7)"] name = "jsbeautifier" version = "1.14.11" description = "JavaScript unobfuscator and beautifier." +category = "dev" optional = false python-versions = "*" files = [ @@ -778,6 +852,7 @@ six = ">=1.13.0" name = "json-flattener" version = "0.1.9" description = "Python library for denormalizing nested dicts or json objects to tables and back" +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -793,6 +868,7 @@ pyyaml = "*" name = "jsonasobj" version = "1.3.1" description = "JSON as python objects" +category = "main" optional = false python-versions = "*" files = [ @@ -804,6 +880,7 @@ files = [ name = "jsonasobj2" version = "1.0.4" description = "JSON as python objects - version 2" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -818,6 +895,7 @@ hbreader = "*" name = "jsonpatch" version = "1.33" description = "Apply JSON-Patches (RFC 6902)" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -832,6 +910,7 @@ jsonpointer = ">=1.9" name = "jsonpath-ng" version = "1.6.0" description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming." +category = "main" optional = false python-versions = "*" files = [ @@ -846,6 +925,7 @@ ply = "*" name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -857,6 +937,7 @@ files = [ name = "jsonschema" version = "4.20.0" description = "An implementation of JSON Schema validation for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -886,6 +967,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.11.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -900,6 +982,7 @@ referencing = ">=0.31.0" name = "linkml" version = "1.6.3" description = "Linked Open Data Modeling Language" +category = "main" optional = false python-versions = ">=3.8.1,<4.0.0" files = [ @@ -937,6 +1020,7 @@ watchdog = ">=0.9.0" name = "linkml-dataops" version = "0.1.0" description = "LinkML Data Operations API" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -953,13 +1037,14 @@ linkml-runtime = ">=1.1.6" [[package]] name = "linkml-runtime" -version = "1.6.2" +version = "1.7.2" description = "Runtime environment for LinkML, the Linked open data modeling language" +category = "main" optional = false -python-versions = ">=3.7.6,<4.0.0" +python-versions = ">=3.8,<4.0" files = [ - {file = "linkml_runtime-1.6.2-py3-none-any.whl", hash = "sha256:d9a915faf0ee8c8749f42d38394a06d37f016e155e077ff9cb5c5a21f24e19d6"}, - {file = "linkml_runtime-1.6.2.tar.gz", hash = "sha256:bcbeff96d24433276755db85375e3dff0c9af0fd04f8a05f7ccd8a669a9e9877"}, + {file = "linkml_runtime-1.7.2-py3-none-any.whl", hash = "sha256:45087530e6c89ec426be0e07a2b936f1b8f72f95caa9e8be347aeb934bf96e57"}, + {file = "linkml_runtime-1.7.2.tar.gz", hash = "sha256:216f5b6511ae1b11a5ba1a69f19fb729c06bc5bdbf7232ffd3149b2e03e1604c"}, ] [package.dependencies] @@ -981,6 +1066,7 @@ requests = "*" name = "markdown" version = "3.5.1" description = "Python implementation of John Gruber's Markdown." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -999,6 +1085,7 @@ testing = ["coverage", "pyyaml"] name = "markupsafe" version = "2.1.3" description = "Safely add untrusted strings to HTML/XML markup." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1058,6 +1145,7 @@ files = [ name = "mergedeep" version = "1.3.4" description = "A deep merge function for 🐍." +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1069,6 +1157,7 @@ files = [ name = "mkdocs" version = "1.5.3" description = "Project documentation with Markdown." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1100,6 +1189,7 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp name = "mkdocs-material" version = "8.5.11" description = "Documentation that simply works" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1120,6 +1210,7 @@ requests = ">=2.26" name = "mkdocs-material-extensions" version = "1.3.1" description = "Extension pack for Python Markdown and MkDocs Material." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1131,6 +1222,7 @@ files = [ name = "mkdocs-mermaid2-plugin" version = "0.6.0" description = "A MkDocs plugin for including mermaid graphs in markdown sources" +category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1152,6 +1244,7 @@ setuptools = ">=18.5" name = "more-click" version = "0.1.2" description = "More click." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1169,6 +1262,7 @@ tests = ["coverage", "pytest"] name = "numpy" version = "1.26.2" description = "Fundamental package for array computing in Python" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -1214,6 +1308,7 @@ files = [ name = "oauthlib" version = "3.2.2" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1230,6 +1325,7 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"] name = "ontodev-cogs" version = "0.3.3" description = "COGS Operates Google Sheets" +category = "dev" optional = false python-versions = ">=3.6, <4" files = [ @@ -1251,6 +1347,7 @@ termcolor = "*" name = "openpyxl" version = "3.1.2" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1265,6 +1362,7 @@ et-xmlfile = "*" name = "packaging" version = "23.2" description = "Core utilities for Python packages" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1276,6 +1374,7 @@ files = [ name = "pandas" version = "2.1.3" description = "Powerful data structures for data analysis, time series, and statistics" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -1344,6 +1443,7 @@ xml = ["lxml (>=4.8.0)"] name = "parse" version = "1.19.1" description = "parse() is the opposite of format()" +category = "main" optional = false python-versions = "*" files = [ @@ -1355,6 +1455,7 @@ files = [ name = "pathspec" version = "0.11.2" description = "Utility library for gitignore style pattern matching of file paths." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1366,6 +1467,7 @@ files = [ name = "platformdirs" version = "4.0.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1381,6 +1483,7 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co name = "pluggy" version = "1.3.0" description = "plugin and hook calling mechanisms for python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1396,6 +1499,7 @@ testing = ["pytest", "pytest-benchmark"] name = "ply" version = "3.11" description = "Python Lex & Yacc" +category = "main" optional = false python-versions = "*" files = [ @@ -1407,6 +1511,7 @@ files = [ name = "prefixcommons" version = "0.1.12" description = "A python API for working with ID prefixes" +category = "main" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -1424,6 +1529,7 @@ requests = ">=2.28.1,<3.0.0" name = "prefixmaps" version = "0.1.7" description = "A python library for retrieving semantic prefix maps" +category = "main" optional = false python-versions = ">=3.8.0,<4.0.0" files = [ @@ -1446,6 +1552,7 @@ refresh = ["bioregistry[refresh] (>=0.10.0,<0.11.0)", "rdflib[refresh] (>=6.2.0, name = "protobuf" version = "4.25.1" description = "" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1466,6 +1573,7 @@ files = [ name = "pyasn1" version = "0.5.1" description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)" +category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -1477,6 +1585,7 @@ files = [ name = "pyasn1-modules" version = "0.3.0" description = "A collection of ASN.1-based protocols modules" +category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -1491,6 +1600,7 @@ pyasn1 = ">=0.4.6,<0.6.0" name = "pydantic" version = "1.10.13" description = "Data validation and settings management using python type hints" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1543,6 +1653,7 @@ email = ["email-validator (>=1.0.3)"] name = "pygments" version = "2.17.2" description = "Pygments is a syntax highlighting package written in Python." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1558,6 +1669,7 @@ windows-terminal = ["colorama (>=0.4.6)"] name = "pyjsg" version = "0.11.10" description = "Python JSON Schema Grammar interpreter" +category = "main" optional = false python-versions = "*" files = [ @@ -1573,6 +1685,7 @@ jsonasobj = ">=1.2.1" name = "pymdown-extensions" version = "10.4" description = "Extension pack for Python Markdown." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1591,6 +1704,7 @@ extra = ["pygments (>=2.12)"] name = "pyparsing" version = "3.1.1" description = "pyparsing module - Classes and methods to define and execute parsing grammars" +category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -1605,6 +1719,7 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyproject-api" version = "1.6.1" description = "API to interact with the python pyproject.toml based projects" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1624,6 +1739,7 @@ testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytes name = "pyshex" version = "0.8.1" description = "Python ShEx Implementation" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1646,6 +1762,7 @@ urllib3 = "*" name = "pyshexc" version = "0.9.1" description = "PyShExC - Python ShEx compiler" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1665,6 +1782,7 @@ shexjsg = ">=0.8.1" name = "pystow" version = "0.5.2" description = "Easily pick a place to store data for your python package." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1689,6 +1807,7 @@ xml = ["lxml"] name = "pytest" version = "7.4.3" description = "pytest: simple powerful testing with Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1711,6 +1830,7 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-logging" version = "2015.11.4" description = "Configures logging and allows tweaking the log level with a py.test flag" +category = "main" optional = false python-versions = "*" files = [ @@ -1724,6 +1844,7 @@ pytest = ">=2.8.1" name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -1738,6 +1859,7 @@ six = ">=1.5" name = "pytrie" version = "0.4.0" description = "A pure Python implementation of the trie data structure." +category = "main" optional = false python-versions = "*" files = [ @@ -1751,6 +1873,7 @@ sortedcontainers = "*" name = "pytz" version = "2023.3.post1" description = "World timezone definitions, modern and historical" +category = "main" optional = false python-versions = "*" files = [ @@ -1762,6 +1885,7 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1811,6 +1935,7 @@ files = [ name = "pyyaml-env-tag" version = "0.1" description = "A custom YAML tag for referencing environment variables in YAML files. " +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1825,6 +1950,7 @@ pyyaml = "*" name = "rdflib" version = "6.3.2" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." +category = "main" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -1846,6 +1972,7 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"] name = "rdflib-jsonld" version = "0.6.1" description = "rdflib extension adding JSON-LD parser and serializer" +category = "main" optional = false python-versions = "*" files = [ @@ -1860,6 +1987,7 @@ rdflib = ">=5.0.0" name = "rdflib-shim" version = "1.0.3" description = "Shim for rdflib 5 and 6 incompatibilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1875,6 +2003,7 @@ rdflib-jsonld = "0.6.1" name = "referencing" version = "0.31.0" description = "JSON Referencing + Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1890,6 +2019,7 @@ rpds-py = ">=0.7.0" name = "requests" version = "2.31.0" description = "Python HTTP for Humans." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1911,6 +2041,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "requests-oauthlib" version = "1.3.1" description = "OAuthlib authentication support for Requests." +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1929,6 +2060,7 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"] name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1943,6 +2075,7 @@ six = "*" name = "rfc3987" version = "1.3.8" description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)" +category = "main" optional = false python-versions = "*" files = [ @@ -1954,6 +2087,7 @@ files = [ name = "rpds-py" version = "0.13.1" description = "Python bindings to Rust's persistent data structures (rpds)" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2062,6 +2196,7 @@ files = [ name = "rsa" version = "4.9" description = "Pure-Python RSA implementation" +category = "dev" optional = false python-versions = ">=3.6,<4" files = [ @@ -2076,6 +2211,7 @@ pyasn1 = ">=0.1.3" name = "ruamel-yaml" version = "0.18.5" description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2094,6 +2230,7 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] name = "ruamel-yaml-clib" version = "0.2.8" description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2139,6 +2276,7 @@ files = [ name = "schemasheets" version = "0.1.24" description = "Package to author schemas using spreadsheets" +category = "dev" optional = false python-versions = ">=3.9,<4.0" files = [ @@ -2157,6 +2295,7 @@ ontodev-cogs = ">=0.3.3,<0.4.0" name = "setuptools" version = "69.0.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2173,6 +2312,7 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "shexjsg" version = "0.8.2" description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language" +category = "main" optional = false python-versions = "*" files = [ @@ -2187,6 +2327,7 @@ pyjsg = ">=0.11.10" name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -2198,6 +2339,7 @@ files = [ name = "sortedcontainers" version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" +category = "main" optional = false python-versions = "*" files = [ @@ -2209,6 +2351,7 @@ files = [ name = "soupsieve" version = "2.5" description = "A modern CSS selector implementation for Beautiful Soup." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2220,6 +2363,7 @@ files = [ name = "sparqlslurper" version = "0.5.1" description = "SPARQL Slurper for rdflib" +category = "main" optional = false python-versions = ">=3.7.4" files = [ @@ -2236,6 +2380,7 @@ sparqlwrapper = ">=1.8.2" name = "sparqlwrapper" version = "2.0.0" description = "SPARQL Endpoint interface to Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2256,6 +2401,7 @@ pandas = ["pandas (>=1.3.5)"] name = "sqlalchemy" version = "2.0.23" description = "Database Abstraction Library" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2339,10 +2485,22 @@ postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"] pymysql = ["pymysql"] sqlcipher = ["sqlcipher3-binary"] +[[package]] +name = "stringcase" +version = "1.2.0" +description = "String case converter." +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "stringcase-1.2.0.tar.gz", hash = "sha256:48a06980661908efe8d9d34eab2b6c13aefa2163b3ced26972902e3bdfd87008"}, +] + [[package]] name = "tabulate" version = "0.9.0" description = "Pretty-print tabular data" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2357,6 +2515,7 @@ widechars = ["wcwidth"] name = "termcolor" version = "2.3.0" description = "ANSI color formatting for output in terminal" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2371,6 +2530,7 @@ tests = ["pytest", "pytest-cov"] name = "tomli" version = "2.0.1" description = "A lil' TOML parser" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2382,6 +2542,7 @@ files = [ name = "tox" version = "4.11.3" description = "tox is a generic virtualenv management and test command line tool" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2409,6 +2570,7 @@ testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pol name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2429,6 +2591,7 @@ telegram = ["requests"] name = "types-python-dateutil" version = "2.8.19.14" description = "Typing stubs for python-dateutil" +category = "main" optional = false python-versions = "*" files = [ @@ -2440,6 +2603,7 @@ files = [ name = "typing-extensions" version = "4.8.0" description = "Backported and Experimental Type Hints for Python 3.8+" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2451,6 +2615,7 @@ files = [ name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ @@ -2462,6 +2627,7 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2476,6 +2642,7 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "uritemplate" version = "4.1.1" description = "Implementation of RFC 6570 URI Templates" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2487,6 +2654,7 @@ files = [ name = "urllib3" version = "2.1.0" description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2503,6 +2671,7 @@ zstd = ["zstandard (>=0.18.0)"] name = "virtualenv" version = "20.24.7" description = "Virtual Python Environment builder" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2523,6 +2692,7 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess name = "watchdog" version = "3.0.0" description = "Filesystem events monitoring" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2562,6 +2732,7 @@ watchmedo = ["PyYAML (>=3.10)"] name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2577,6 +2748,7 @@ tests = ["pytest", "pytest-cov"] name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2656,6 +2828,7 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2673,4 +2846,4 @@ docs = ["linkml"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "c8f07bf023a635f14193c21359465608bb86c0917669b364d7b901686a540893" +content-hash = "a8747a38f7aebb817224851818ba30afa9254584e6c6d20fdfb463c797c1aec7" diff --git a/project/excel/translator_testing_model.xlsx b/project/excel/translator_testing_model.xlsx index 6a69d10..9b026df 100644 Binary files a/project/excel/translator_testing_model.xlsx and b/project/excel/translator_testing_model.xlsx differ diff --git a/project/graphql/translator_testing_model.graphql b/project/graphql/translator_testing_model.graphql index 953a3b7..3c8bbbc 100644 --- a/project/graphql/translator_testing_model.graphql +++ b/project/graphql/translator_testing_model.graphql @@ -20,6 +20,11 @@ type AcceptanceTestAsset testReference: Uriorcurie runnerSettings: [String]! testMetadata: TestMetadata! + biolinkQualifiedPredicate: Uriorcurie + biolinkSubjectAspectQualifier: String + biolinkSubjectDirectionQualifier: String + biolinkObjectAspectQualifier: String + biolinkObjectDirectionQualifier: String id: Uriorcurie! tags: [String] mustPassDate: Date @@ -212,6 +217,11 @@ type TestAsset testReference: Uriorcurie runnerSettings: [String]! testMetadata: TestMetadata! + biolinkQualifiedPredicate: Uriorcurie + biolinkSubjectAspectQualifier: String + biolinkSubjectDirectionQualifier: String + biolinkObjectAspectQualifier: String + biolinkObjectDirectionQualifier: String id: Uriorcurie! tags: [String] } @@ -269,6 +279,11 @@ type TestEdgeData testReference: Uriorcurie runnerSettings: [String]! testMetadata: TestMetadata! + biolinkQualifiedPredicate: Uriorcurie + biolinkSubjectAspectQualifier: String + biolinkSubjectDirectionQualifier: String + biolinkObjectAspectQualifier: String + biolinkObjectDirectionQualifier: String id: Uriorcurie! tags: [String] } diff --git a/project/jsonld/translator_testing_model.context.jsonld b/project/jsonld/translator_testing_model.context.jsonld index 4267351..9d86ab2 100644 --- a/project/jsonld/translator_testing_model.context.jsonld +++ b/project/jsonld/translator_testing_model.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-12-07T10:24:07", + "generation_date": "2024-03-04T11:39:59", "source": "translator_testing_model.yaml" }, "@context": { @@ -15,6 +15,12 @@ "association": { "@type": "@id" }, + "biolink_predicate": { + "@type": "@id" + }, + "biolink_qualified_predicate": { + "@type": "@id" + }, "components": { "@context": { "@vocab": "@null", diff --git a/project/jsonld/translator_testing_model.jsonld b/project/jsonld/translator_testing_model.jsonld index 1269edf..d7e592e 100644 --- a/project/jsonld/translator_testing_model.jsonld +++ b/project/jsonld/translator_testing_model.jsonld @@ -631,24 +631,14 @@ { "name": "ComponentEnum", "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/ComponentEnum", + "description": "Translator components are identified by their InfoRes identifiers.", "from_schema": "https://w3id.org/TranslatorSRI/TranslatorTestingModel", - "permissible_values": [ - { - "text": "arax" - }, - { - "text": "aragorn" - }, - { - "text": "ars" - }, - { - "text": "bte" - }, - { - "text": "improving" - } - ] + "reachable_from": { + "source_ontology": "biolink", + "source_nodes": [ + "biolink:infores" + ] + } }, { "name": "TestPersonaEnum", @@ -1140,6 +1130,80 @@ "range": "string", "@type": "SlotDefinition" }, + { + "name": "biolink_predicate", + "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_predicate", + "description": "the predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.", + "from_schema": "https://w3id.org/TranslatorSRI/TranslatorTestingModel", + "slot_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_predicate", + "range": "uriorcurie", + "@type": "SlotDefinition" + }, + { + "name": "biolink_subject_aspect_qualifier", + "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_subject_aspect_qualifier", + "description": "The aspect of the subject of the test asset predicate", + "from_schema": "https://w3id.org/TranslatorSRI/TranslatorTestingModel", + "slot_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_subject_aspect_qualifier", + "owner": "TestAsset", + "domain_of": [ + "TestAsset" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "biolink_subject_direction_qualifier", + "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_subject_direction_qualifier", + "description": "The direction of the subject of the test asset predicate", + "from_schema": "https://w3id.org/TranslatorSRI/TranslatorTestingModel", + "slot_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_subject_direction_qualifier", + "owner": "TestAsset", + "domain_of": [ + "TestAsset" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "biolink_object_aspect_qualifier", + "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_object_aspect_qualifier", + "description": "The aspect of the object of the test asset predicate", + "from_schema": "https://w3id.org/TranslatorSRI/TranslatorTestingModel", + "slot_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_object_aspect_qualifier", + "owner": "TestAsset", + "domain_of": [ + "TestAsset" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "biolink_object_direction_qualifier", + "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_object_direction_qualifier", + "description": "The direction of the object of the test asset predicate", + "from_schema": "https://w3id.org/TranslatorSRI/TranslatorTestingModel", + "slot_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_object_direction_qualifier", + "owner": "TestAsset", + "domain_of": [ + "TestAsset" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "biolink_qualified_predicate", + "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_qualified_predicate", + "description": "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.", + "from_schema": "https://w3id.org/TranslatorSRI/TranslatorTestingModel", + "slot_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/biolink_qualified_predicate", + "owner": "TestAsset", + "domain_of": [ + "TestAsset" + ], + "range": "uriorcurie", + "@type": "SlotDefinition" + }, { "name": "output_id", "definition_uri": "https://w3id.org/TranslatorSRI/TranslatorTestingModel/output_id", @@ -2122,6 +2186,11 @@ "test_reference", "TestAsset_runner_settings", "test_metadata", + "biolink_qualified_predicate", + "biolink_subject_aspect_qualifier", + "biolink_subject_direction_qualifier", + "biolink_object_aspect_qualifier", + "biolink_object_direction_qualifier", "TestAsset_id", "TestAsset_tags" ], @@ -2156,6 +2225,11 @@ "test_reference", "TestAsset_runner_settings", "test_metadata", + "biolink_qualified_predicate", + "biolink_subject_aspect_qualifier", + "biolink_subject_direction_qualifier", + "biolink_object_aspect_qualifier", + "biolink_object_direction_qualifier", "TestAsset_id", "TestAsset_tags", "must_pass_date", @@ -2200,6 +2274,11 @@ "test_reference", "TestAsset_runner_settings", "test_metadata", + "biolink_qualified_predicate", + "biolink_subject_aspect_qualifier", + "biolink_subject_direction_qualifier", + "biolink_object_aspect_qualifier", + "biolink_object_direction_qualifier", "TestAsset_id", "TestAsset_tags" ], @@ -2599,9 +2678,9 @@ ], "metamodel_version": "1.7.0", "source_file": "translator_testing_model.yaml", - "source_file_date": "2023-12-07T10:23:17", - "source_file_size": 26460, - "generation_date": "2023-12-07T10:24:08", + "source_file_date": "2024-03-04T11:39:55", + "source_file_size": 27623, + "generation_date": "2024-03-04T11:40:00", "@type": "SchemaDefinition", "@context": [ "project/jsonld/translator_testing_model.context.jsonld", diff --git a/project/jsonschema/translator_testing_model.schema.json b/project/jsonschema/translator_testing_model.schema.json index b5b6a5c..4222936 100644 --- a/project/jsonschema/translator_testing_model.schema.json +++ b/project/jsonschema/translator_testing_model.schema.json @@ -12,6 +12,26 @@ "description": "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement", "type": "string" }, + "biolink_object_aspect_qualifier": { + "description": "The aspect of the object of the test asset predicate", + "type": "string" + }, + "biolink_object_direction_qualifier": { + "description": "The direction of the object of the test asset predicate", + "type": "string" + }, + "biolink_qualified_predicate": { + "description": "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.", + "type": "string" + }, + "biolink_subject_aspect_qualifier": { + "description": "The aspect of the subject of the test asset predicate", + "type": "string" + }, + "biolink_subject_direction_qualifier": { + "description": "The direction of the subject of the test asset predicate", + "type": "string" + }, "description": { "description": "A human-readable description for a Test Entity", "type": "string" @@ -379,14 +399,7 @@ "type": "object" }, "ComponentEnum": { - "description": "", - "enum": [ - "arax", - "aragorn", - "ars", - "bte", - "improving" - ], + "description": "Translator components are identified by their InfoRes identifiers.", "title": "ComponentEnum", "type": "string" }, @@ -874,6 +887,26 @@ "description": "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement", "type": "string" }, + "biolink_object_aspect_qualifier": { + "description": "The aspect of the object of the test asset predicate", + "type": "string" + }, + "biolink_object_direction_qualifier": { + "description": "The direction of the object of the test asset predicate", + "type": "string" + }, + "biolink_qualified_predicate": { + "description": "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.", + "type": "string" + }, + "biolink_subject_aspect_qualifier": { + "description": "The aspect of the subject of the test asset predicate", + "type": "string" + }, + "biolink_subject_direction_qualifier": { + "description": "The direction of the subject of the test asset predicate", + "type": "string" + }, "description": { "description": "A human-readable description for a Test Entity", "type": "string" @@ -1238,6 +1271,26 @@ "description": "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement", "type": "string" }, + "biolink_object_aspect_qualifier": { + "description": "The aspect of the object of the test asset predicate", + "type": "string" + }, + "biolink_object_direction_qualifier": { + "description": "The direction of the object of the test asset predicate", + "type": "string" + }, + "biolink_qualified_predicate": { + "description": "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.", + "type": "string" + }, + "biolink_subject_aspect_qualifier": { + "description": "The aspect of the subject of the test asset predicate", + "type": "string" + }, + "biolink_subject_direction_qualifier": { + "description": "The direction of the subject of the test asset predicate", + "type": "string" + }, "description": { "description": "A human-readable description for a Test Entity", "type": "string" diff --git a/project/owl/translator_testing_model.owl.ttl b/project/owl/translator_testing_model.owl.ttl index 5d5f710..232275b 100644 --- a/project/owl/translator_testing_model.owl.ttl +++ b/project/owl/translator_testing_model.owl.ttl @@ -12,10 +12,10 @@ ttm:AcceptanceTestCase a owl:Class, linkml:ClassDefinition ; rdfs:label "AcceptanceTestCase" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom ttm:AcceptanceTestAsset ; owl:onProperty ttm:test_assets ], [ a owl:Restriction ; - owl:allValuesFrom ttm:AcceptanceTestAsset ; + owl:minCardinality 1 ; owl:onProperty ttm:test_assets ], ttm:TestCase ; skos:definition "See AcceptanceTestAsset above for more details." ; @@ -36,7 +36,25 @@ ttm:BenchmarkTestSuite a owl:Class, ttm:ComplianceTestCase a owl:Class, linkml:ClassDefinition ; rdfs:label "ComplianceTestCase" ; - rdfs:subClassOf ttm:TestCase ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:trapi_version ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:trapi_version ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:biolink_version ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:biolink_version ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:trapi_version ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:biolink_version ], + ttm:TestCase ; skos:definition "TRAPI and Biolink Model standards compliance test" ; skos:inScheme . @@ -79,10 +97,34 @@ ttm:TestRunSession a owl:Class, linkml:ClassDefinition ; rdfs:label "TestRunSession" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; + owl:onProperty ttm:timestamp ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:timestamp ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_results ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty ttm:test_entities ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:test_runner_name ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty ttm:test_runner_name ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestCaseResult ; + owl:onProperty ttm:test_case_results ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_runner_name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Datetime ; + owl:onProperty ttm:timestamp ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; owl:onProperty ttm:test_entities ], ttm:TestEntity ; skos:definition "A single invocation of a TestRunner." ; @@ -92,307 +134,637 @@ ttm:TestRunnerConfiguration a owl:Class, linkml:ClassDefinition ; rdfs:label "TestRunnerConfiguration" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_run_parameters ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:test_run_parameters ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ttm:tags ], + owl:onProperty ttm:test_run_parameters ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty ttm:tags ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:tags ], ttm:TestEntity ; skos:definition "General configuration parameters and test data input for a single invocation of a TestRunner." ; skos:inScheme . -ttm:answer_informal_concept a owl:ObjectProperty, +ttm:biolink_predicate a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "answer_informal_concept" ; - rdfs:range linkml:String ; - skos:definition "An answer that is returned from the test case, note: this must be combined with the expected_result to form a complete answer. It might make sense to couple these in their own object instead of strictly sticking to the flat schema introduced by the spreadsheet here: https://docs.google.com/spreadsheets/d/1yj7zIchFeVl1OHqL_kE_pqvzNLmGml_FLbHDs-8Yvig/edit#gid=0" ; + rdfs:label "biolink_predicate" ; + rdfs:range linkml:Uriorcurie ; + skos:definition "the predicate in Biolink model corresponding to the shorthand predicate name used in the test asset." ; skos:inScheme . -ttm:aragorn a owl:ObjectProperty, +ttm:results a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "aragorn" ; + rdfs:label "results" ; + rdfs:range ttm:TestOutput ; + skos:definition "The results of a TestRunner run of one specific TestCase." ; skos:inScheme . -ttm:arax a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "arax" ; +ttm:AcceptanceTestAsset a owl:Class, + linkml:ClassDefinition ; + rdfs:label "AcceptanceTestAsset" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:query_node ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:expected_result ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:NodeEnum ; + owl:onProperty ttm:query_node ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Integer ; + owl:onProperty ttm:top_level ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:string_entry ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:ExpectedResultsEnum ; + owl:onProperty ttm:expected_result ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:expected_result ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:query_node ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:scientific_question ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:notes ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:answer_informal_concept ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestEnvEnum ; + owl:onProperty ttm:must_pass_environment ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:DirectionEnum ; + owl:onProperty ttm:direction ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:top_level ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:must_pass_date ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:answer_informal_concept ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:must_pass_environment ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:string_entry ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:direction ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:must_pass_date ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:string_entry ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:notes ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:scientific_question ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:notes ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:direction ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:top_level ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:scientific_question ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:must_pass_environment ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:answer_informal_concept ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Date ; + owl:onProperty ttm:must_pass_date ], + ttm:TestAsset ; + skos:definition "Model derived from Jenn's test asset design and Shervin's runner JSON here as an example." ; skos:inScheme . -ttm:association a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "association" ; - rdfs:range ttm:association_category ; - skos:definition "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement" ; +ttm:KnowledgeGraphNavigationTestCase a owl:Class, + linkml:ClassDefinition ; + rdfs:label "KnowledgeGraphNavigationTestCase" ; + rdfs:subClassOf ttm:TestCase ; + skos:definition "Knowledge Graph navigation integration test" ; skos:inScheme . -ttm:biolink_version a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "biolink_version" ; - skos:definition "Biolink Model release (SemVer string)" ; - skos:inScheme . + a owl:Class, + ttm:QueryTypeEnum ; + rdfs:label "treats" ; + rdfs:subClassOf ttm:QueryTypeEnum . -ttm:bte a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "bte" ; +ttm:TestOutput a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestOutput" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:pks ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_id ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestResultPKSet ; + owl:onProperty ttm:pks ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:test_case_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case_id ], + ttm:TestEntity ; + skos:definition "The output of a TestRunner run of one specific TestCase." ; skos:inScheme . -ttm:components a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "components" ; - rdfs:range ttm:ComponentEnum ; - skos:definition "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; - skos:inScheme . +ttm:ComponentEnum a owl:Class, + linkml:EnumDefinition . -ttm:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - skos:definition "A human-readable description for a Test Entity" ; - skos:inScheme . + a owl:Class, + ttm:DirectionEnum ; + rdfs:label "decreased" ; + rdfs:subClassOf ttm:DirectionEnum . -ttm:direction a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "direction" ; - rdfs:range ttm:DirectionEnum ; - skos:definition "The direction of the expected query result triple" ; - skos:inScheme . + a owl:Class, + ttm:DirectionEnum ; + rdfs:label "increased" ; + rdfs:subClassOf ttm:DirectionEnum . -ttm:expected_output a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "expected_output" ; - skos:altLabel "Expected Output" ; - skos:inScheme . + a owl:Class, + ttm:ExpectedOutputEnum ; + rdfs:label "Acceptable" ; + rdfs:subClassOf ttm:ExpectedOutputEnum . -ttm:expected_result a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "expected_result" ; - rdfs:range ttm:ExpectedResultsEnum ; - skos:definition "The expected result of the query" ; - skos:inScheme . + a owl:Class, + ttm:ExpectedOutputEnum ; + rdfs:label "BadButForgivable" ; + rdfs:subClassOf ttm:ExpectedOutputEnum . -ttm:improving a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "improving" ; - skos:inScheme . + a owl:Class, + ttm:ExpectedOutputEnum ; + rdfs:label "NeverShow" ; + rdfs:subClassOf ttm:ExpectedOutputEnum . -ttm:in_v1 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "in_v1" ; - rdfs:range linkml:Boolean ; - skos:altLabel "In v1" ; - skos:inScheme . + a owl:Class, + ttm:ExpectedOutputEnum ; + rdfs:label "TopAnswer" ; + rdfs:subClassOf ttm:ExpectedOutputEnum . -ttm:input_category a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_category" ; - rdfs:range ttm:concept_category ; - skos:altLabel "SubjectCategory" ; - skos:inScheme . + a owl:Class, + ttm:ExpectedResultsEnum ; + rdfs:label "exclude_bad" ; + rdfs:subClassOf ttm:ExpectedResultsEnum . -ttm:input_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:Uriorcurie ; - skos:altLabel "InputID, node normalized", - "SubjectID" ; - skos:inScheme . + a owl:Class, + ttm:ExpectedResultsEnum ; + rdfs:label "include_good" ; + rdfs:subClassOf ttm:ExpectedResultsEnum . -ttm:input_name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_name" ; - skos:altLabel "InputName (user choice)", - "SubjectName" ; - skos:inScheme . + a owl:Class, + ttm:FileFormatEnum ; + rdfs:label "JSON" ; + rdfs:subClassOf ttm:FileFormatEnum . -ttm:merged_pk a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "merged_pk" ; - skos:inScheme . + a owl:Class, + ttm:FileFormatEnum ; + rdfs:label "TSV" ; + rdfs:subClassOf ttm:FileFormatEnum . -ttm:must_pass_date a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "must_pass_date" ; - rdfs:range linkml:Date ; - skos:definition "The date by which this test must pass" ; - skos:inScheme . + a owl:Class, + ttm:FileFormatEnum ; + rdfs:label "YAML" ; + rdfs:subClassOf ttm:FileFormatEnum . -ttm:must_pass_environment a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "must_pass_environment" ; - rdfs:range ttm:TestEnvEnum ; - skos:definition "The deployment environment within which this test must pass." ; - skos:inScheme . + a owl:Class, + ttm:NodeEnum ; + rdfs:label "object" ; + rdfs:subClassOf ttm:NodeEnum . -ttm:name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "name" ; - skos:definition "A human-readable name for a Test Entity" ; - skos:inScheme . + a owl:Class, + ttm:NodeEnum ; + rdfs:label "subject" ; + rdfs:subClassOf ttm:NodeEnum . -ttm:notes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "notes" ; - rdfs:range linkml:String ; - skos:definition "The notes of the query" ; +ttm:Precondition a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Precondition" ; + rdfs:subClassOf ttm:TestEntity ; + skos:definition "Represents a precondition for a TestCase" ; skos:inScheme . -ttm:output_category a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "output_category" ; - rdfs:range ttm:concept_category ; - skos:altLabel "ObjectCategory" ; +ttm:Qualifier a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Qualifier" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:value ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:parameter ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:parameter ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:parameter ], + ttm:TestEntityParameter ; skos:inScheme . -ttm:output_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "output_id" ; - rdfs:range linkml:Uriorcurie ; - skos:altLabel "ObjectID", - "OutputID" ; - skos:inScheme . + a owl:Class, + ttm:SemanticSeverityEnum ; + rdfs:label "High" ; + rdfs:subClassOf ttm:SemanticSeverityEnum . -ttm:output_name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "output_name" ; - skos:altLabel "ObjectName", - "OutputName" ; + a owl:Class, + ttm:SemanticSeverityEnum ; + rdfs:label "Low" ; + rdfs:subClassOf ttm:SemanticSeverityEnum . + + a owl:Class, + ttm:SemanticSeverityEnum ; + rdfs:label "NotApplicable" ; + rdfs:subClassOf ttm:SemanticSeverityEnum . + +ttm:TestCaseResult a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestCaseResult" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:test_suite_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestCase ; + owl:onProperty ttm:test_case ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_result ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case_result ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestCaseResultEnum ; + owl:onProperty ttm:test_case_result ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_suite_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_suite_id ], + ttm:TestEntity ; + skos:definition "The outcome of a TestRunner run of one specific TestCase." ; skos:inScheme . -ttm:parent_pk a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "parent_pk" ; + a owl:Class, + ttm:TestCaseResultEnum ; + rdfs:label "test_failed" ; + rdfs:subClassOf ttm:TestCaseResultEnum . + + a owl:Class, + ttm:TestCaseResultEnum ; + rdfs:label "test_passed" ; + rdfs:subClassOf ttm:TestCaseResultEnum . + + a owl:Class, + ttm:TestCaseResultEnum ; + rdfs:label "test_skipped" ; + rdfs:subClassOf ttm:TestCaseResultEnum . + +ttm:TestEntityParameter a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestEntityParameter" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:value ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:parameter ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:parameter ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:parameter ] ; + skos:definition "A single 'tag = value' pair (where 'value' is a simple string)." ; skos:inScheme . -ttm:pks a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "pks" ; - rdfs:range ttm:TestResultPKSet ; + a owl:Class, + ttm:TestEnvEnum ; + rdfs:label "ci" ; + rdfs:subClassOf ttm:TestEnvEnum . + + a owl:Class, + ttm:TestEnvEnum ; + rdfs:label "dev" ; + rdfs:subClassOf ttm:TestEnvEnum . + + a owl:Class, + ttm:TestEnvEnum ; + rdfs:label "prod" ; + rdfs:subClassOf ttm:TestEnvEnum . + + a owl:Class, + ttm:TestEnvEnum ; + rdfs:label "test" ; + rdfs:subClassOf ttm:TestEnvEnum . + + a owl:Class, + ttm:TestIssueEnum ; + rdfs:label "TMKP" ; + rdfs:subClassOf ttm:TestIssueEnum . + + a owl:Class, + ttm:TestIssueEnum ; + rdfs:label "category too generic" ; + rdfs:subClassOf ttm:TestIssueEnum . + + a owl:Class, + ttm:TestIssueEnum ; + rdfs:label "causes not treats" ; + rdfs:subClassOf ttm:TestIssueEnum . + + a owl:Class, + ttm:TestIssueEnum ; + rdfs:label "chemical roles" ; + rdfs:subClassOf ttm:TestIssueEnum . + + a owl:Class, + ttm:TestIssueEnum ; + rdfs:label "contraindications" ; + rdfs:subClassOf ttm:TestIssueEnum . + + a owl:Class, + ttm:TestIssueEnum ; + rdfs:label "test_issue" ; + rdfs:subClassOf ttm:TestIssueEnum . + + a owl:Class, + ttm:TestObjectiveEnum ; + rdfs:label "AcceptanceTest" ; + rdfs:subClassOf ttm:TestObjectiveEnum . + + a owl:Class, + ttm:TestObjectiveEnum ; + rdfs:label "BenchmarkTest" ; + rdfs:subClassOf ttm:TestObjectiveEnum . + + a owl:Class, + ttm:TestObjectiveEnum ; + rdfs:label "QuantitativeTest" ; + rdfs:subClassOf ttm:TestObjectiveEnum . + + a owl:Class, + ttm:TestPersonaEnum ; + rdfs:label "All" ; + rdfs:subClassOf ttm:TestPersonaEnum . + + a owl:Class, + ttm:TestPersonaEnum ; + rdfs:label "Clinical" ; + rdfs:subClassOf ttm:TestPersonaEnum . + + a owl:Class, + ttm:TestPersonaEnum ; + rdfs:label "LookUp" ; + rdfs:subClassOf ttm:TestPersonaEnum . + + a owl:Class, + ttm:TestPersonaEnum ; + rdfs:label "Mechanistic" ; + rdfs:subClassOf ttm:TestPersonaEnum . + +ttm:TestResultPKSet a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestResultPKSet" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:improving ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:unsecret ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:aragorn ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:bte ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:arax ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:improving ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:improving ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:bte ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:merged_pk ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:bte ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:merged_pk ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:merged_pk ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:aragorn ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:parent_pk ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:arax ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:arax ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:aragorn ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:parent_pk ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:unsecret ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:parent_pk ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:unsecret ], + ttm:TestEntity ; skos:definition "Primary keys for a given ARA result set from a SmokeTest result for a given TestCase." ; skos:inScheme . -ttm:preconditions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "preconditions" ; - rdfs:range ttm:Precondition ; - skos:inScheme . + a owl:Class, + ttm:TestSourceEnum ; + rdfs:label "BenchMark" ; + rdfs:subClassOf ttm:TestSourceEnum . -ttm:predicate_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate_id" ; - rdfs:range ttm:predicate_type ; - skos:altLabel "Predicate" ; - skos:inScheme . + a owl:Class, + ttm:TestSourceEnum ; + rdfs:label "SME" ; + rdfs:subClassOf ttm:TestSourceEnum . -ttm:predicate_name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate_name" ; - skos:altLabel "Query", - "Relationship" ; - skos:inScheme . + a owl:Class, + ttm:TestSourceEnum ; + rdfs:label "SMURF" ; + rdfs:subClassOf ttm:TestSourceEnum . -ttm:qualifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifiers" ; - rdfs:range ttm:Qualifier ; - skos:definition "Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot." ; - skos:inScheme . + a owl:Class, + ttm:TestSourceEnum ; + rdfs:label "TACT" ; + rdfs:subClassOf ttm:TestSourceEnum, + . -ttm:query_node a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "query_node" ; - rdfs:range ttm:NodeEnum ; - skos:definition "The node of the (templated) TRAPI query to replace" ; - skos:inScheme . + a owl:Class, + ttm:TestSourceEnum ; + rdfs:label "TestDataLocation" ; + rdfs:subClassOf ttm:TestSourceEnum . -ttm:query_type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "query_type" ; - rdfs:range ttm:QueryTypeEnum ; - skos:definition "Type of TestCase query." ; - skos:inScheme . + a owl:Class, + ttm:TestSourceEnum ; + rdfs:label "TranslatorTeam" ; + rdfs:subClassOf ttm:TestSourceEnum . -ttm:results a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "results" ; - rdfs:range ttm:TestOutput ; - skos:definition "The results of a TestRunner run of one specific TestCase." ; +ttm:TestSuiteSpecification a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestSuiteSpecification" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_data_file_format ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_data_file_locator ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:test_data_file_locator ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_data_file_format ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:FileFormatEnum ; + owl:onProperty ttm:test_data_file_format ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_data_file_locator ], + ttm:TestEntity ; + skos:definition "Parameters for a Test Case instances either dynamically generated from some external source of Test Assets." ; skos:inScheme . -ttm:scientific_question a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scientific_question" ; - rdfs:range linkml:String ; - skos:definition "The full human-readable scientific question a SME would ask, which is encoded into the test asset." ; - skos:inScheme . + a owl:Class, + ttm:TrapiTemplateEnum ; + rdfs:label "ameliorates" ; + rdfs:subClassOf ttm:TrapiTemplateEnum . -ttm:semantic_severity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "semantic_severity" ; - rdfs:range ttm:SemanticSeverityEnum ; - skos:altLabel "Semantic Severity" ; - skos:inScheme . + a owl:Class, + ttm:TrapiTemplateEnum ; + rdfs:label "drug-to-gene" ; + rdfs:subClassOf ttm:TrapiTemplateEnum . -ttm:string_entry a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "string_entry" ; - rdfs:range linkml:String ; - skos:altLabel "disease", - "trapi node 2" ; - skos:definition "The object of the core triple to be tested" ; - skos:inScheme . + a owl:Class, + ttm:TrapiTemplateEnum ; + rdfs:label "drug_treats_rare_disease" ; + rdfs:subClassOf ttm:TrapiTemplateEnum . -ttm:test_annotations a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "test_annotations" ; - rdfs:subPropertyOf ttm:test_entity_parameters ; - skos:definition "Metadata annotation." ; - skos:inScheme . + a owl:Class, + ttm:TrapiTemplateEnum ; + rdfs:label "three_hop" ; + rdfs:subClassOf ttm:TrapiTemplateEnum . -ttm:test_case a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "test_case" ; - rdfs:range ttm:TestCase ; - skos:definition "Slot referencing a single TestCase." ; - skos:inScheme . + a owl:Class, + ttm:TrapiTemplateEnum ; + rdfs:label "treats" ; + rdfs:subClassOf ttm:TrapiTemplateEnum . -ttm:test_case_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "test_case_id" ; - rdfs:range linkml:String ; - skos:definition "CURIE id of a TestCase registered in the system." ; - skos:inScheme . +ttm:association_category a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf ttm:category_type . -ttm:test_case_input_id a owl:ObjectProperty, +ttm:category_type a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf linkml:Uriorcurie . + +ttm:components a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_case_input_id" ; - rdfs:range linkml:Uriorcurie ; - skos:altLabel "InputID, node normalized", - "SubjectID" ; + rdfs:label "components" ; + rdfs:range ttm:ComponentEnum ; + skos:definition "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; skos:inScheme . -ttm:test_case_objective a owl:ObjectProperty, +ttm:pks a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_case_objective" ; - rdfs:range ttm:TestObjectiveEnum ; - skos:definition "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + rdfs:label "pks" ; + rdfs:range ttm:TestResultPKSet ; + skos:definition "Primary keys for a given ARA result set from a SmokeTest result for a given TestCase." ; skos:inScheme . -ttm:test_case_predicate_id a owl:ObjectProperty, +ttm:preconditions a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_case_predicate_id" ; - skos:altLabel "Predicate" ; + rdfs:label "preconditions" ; + rdfs:range ttm:Precondition ; skos:inScheme . -ttm:test_case_predicate_name a owl:ObjectProperty, +ttm:predicate_type a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf linkml:Uriorcurie . + +ttm:qualifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_case_predicate_name" ; - skos:altLabel "Predicate" ; + rdfs:label "qualifiers" ; + rdfs:range ttm:Qualifier ; + skos:definition "Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot." ; skos:inScheme . -ttm:test_case_result a owl:ObjectProperty, +ttm:runner_settings a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_case_result" ; - rdfs:range ttm:TestCaseResultEnum ; - skos:definition "Encoded result of a single test run of a given test case" ; + rdfs:label "runner_settings" ; + rdfs:range linkml:String ; + skos:altLabel "Settings" ; + skos:definition "Settings for the test harness for TestAsset" ; skos:inScheme . ttm:test_case_results a owl:ObjectProperty, @@ -410,13 +782,6 @@ ttm:test_case_runner_settings a owl:ObjectProperty, skos:definition "Settings for the test harness for TestCase" ; skos:inScheme . -ttm:test_case_source a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "test_case_source" ; - rdfs:range ttm:TestSourceEnum ; - skos:definition "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; - skos:inScheme . - ttm:test_cases a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "test_cases" ; @@ -424,478 +789,757 @@ ttm:test_cases a owl:ObjectProperty, skos:definition "List of explicitly enumerated Test Cases." ; skos:inScheme . -ttm:test_data_file_format a owl:ObjectProperty, +ttm:test_entities a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_data_file_format" ; - rdfs:range ttm:FileFormatEnum ; - skos:definition "File format of test entity data (e.g. TSV, YAML or JSON)" ; + rdfs:label "test_entities" ; + rdfs:range ttm:TestEntity ; + skos:definition "One or more instances of TestEntity, generally of class TestAsset, TestCase or TestSuite." ; + skos:inScheme . + +ttm:test_entity_parameters a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_entity_parameters" ; + rdfs:range ttm:TestEntityParameter ; + skos:definition "One or more parameters documenting target characteristics of a TestEntity." ; + skos:inScheme . + +ttm:TestAsset a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestAsset" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:Boolean ; + owl:onProperty ttm:well_known ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:biolink_qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:predicate_name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:biolink_object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ttm:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:in_v1 ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:expected_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:test_reference ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ttm:runner_settings ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:predicate_name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:in_v1 ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:output_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:input_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:biolink_subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:semantic_severity ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:biolink_qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:biolink_object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:input_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:output_id ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:SemanticSeverityEnum ; + owl:onProperty ttm:semantic_severity ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:biolink_subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:tags ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestMetadata ; + owl:onProperty ttm:test_metadata ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:semantic_severity ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:output_name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:output_category ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:output_name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:output_name ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:predicate_type ; + owl:onProperty ttm:predicate_id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_issue ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:biolink_subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:association_category ; + owl:onProperty ttm:association ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:output_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:biolink_object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:input_id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:well_known ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:predicate_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:biolink_subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ttm:test_metadata ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:Qualifier ; + owl:onProperty ttm:qualifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_issue ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:expected_output ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_metadata ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:biolink_object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Boolean ; + owl:onProperty ttm:in_v1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:biolink_object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:runner_settings ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:input_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:output_category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:biolink_subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:biolink_subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:well_known ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:biolink_qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:concept_category ; + owl:onProperty ttm:input_category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:input_category ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_reference ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:concept_category ; + owl:onProperty ttm:output_category ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:input_id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:association ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:predicate_name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:predicate_id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:qualifiers ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:tags ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_reference ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:biolink_object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:association ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestIssueEnum ; + owl:onProperty ttm:test_issue ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:input_name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:expected_output ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:input_category ], + ttm:TestEntity ; + skos:definition "Represents a Test Asset, which is a single specific instance of TestCase-agnostic semantic parameters representing the specification of a Translator test target with inputs and (expected) outputs." ; + skos:inScheme . + +ttm:TestMetadata a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestMetadata" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:test_annotations ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_annotations ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestSourceEnum ; + owl:onProperty ttm:test_source ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_reference ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_reference ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_source ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:test_reference ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_objective ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_objective ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_source ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestObjectiveEnum ; + owl:onProperty ttm:test_objective ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_annotations ], + ttm:TestEntity ; + skos:definition "Represents metadata related to (external SME, SMURF, Translator feedback, large scale batch, etc.) like the provenance of test assets, cases and/or suites." ; + skos:inScheme . + + a owl:Class, + ttm:TestSourceEnum ; + rdfs:label "GitHubUserFeedback" ; + rdfs:subClassOf ttm:TestSourceEnum . + +ttm:TestSuite a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestSuite" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ttm:test_metadata ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestSuiteSpecification ; + owl:onProperty ttm:test_suite_specification ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_metadata ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_suite_specification ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_suite_specification ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_cases ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestMetadata ; + owl:onProperty ttm:test_metadata ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_persona ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestCase ; + owl:onProperty ttm:test_cases ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestPersonaEnum ; + owl:onProperty ttm:test_persona ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_persona ], + ttm:TestEntity ; + skos:definition "Specification of a set of Test Cases, one of either with a static list of 'test_cases' or a dynamic 'test_suite_specification' slot values. Note: at least one slot or the other, but generally not both(?) needs to be present." ; skos:inScheme . -ttm:test_data_file_locator a owl:ObjectProperty, +ttm:answer_informal_concept a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_data_file_locator" ; - rdfs:range linkml:Uriorcurie ; - skos:definition "An web accessible file resource link to test entity data (e.g. a web accessible text file of Test Asset entries)" ; + rdfs:label "answer_informal_concept" ; + rdfs:range linkml:String ; + skos:definition "An answer that is returned from the test case, note: this must be combined with the expected_result to form a complete answer. It might make sense to couple these in their own object instead of strictly sticking to the flat schema introduced by the spreadsheet here: https://docs.google.com/spreadsheets/d/1yj7zIchFeVl1OHqL_kE_pqvzNLmGml_FLbHDs-8Yvig/edit#gid=0" ; skos:inScheme . -ttm:test_env a owl:ObjectProperty, +ttm:aragorn a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_env" ; - rdfs:range ttm:TestEnvEnum ; - skos:definition "Deployment environment within which the associated TestSuite is run." ; + rdfs:label "aragorn" ; skos:inScheme . -ttm:test_issue a owl:ObjectProperty, +ttm:arax a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_issue" ; - rdfs:range ttm:TestIssueEnum ; - skos:altLabel "issue label" ; + rdfs:label "arax" ; skos:inScheme . -ttm:test_metadata a owl:ObjectProperty, +ttm:association a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_metadata" ; - rdfs:range ttm:TestMetadata ; - skos:definition "Test metadata describes the external provenance, cross-references and objectives for a given test." ; + rdfs:label "association" ; + rdfs:range ttm:association_category ; + skos:definition "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement" ; skos:inScheme . -ttm:test_objective a owl:ObjectProperty, +ttm:biolink_object_aspect_qualifier a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_objective" ; - rdfs:range ttm:TestObjectiveEnum ; - skos:definition "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + rdfs:label "biolink_object_aspect_qualifier" ; + skos:definition "The aspect of the object of the test asset predicate" ; skos:inScheme . -ttm:test_persona a owl:ObjectProperty, +ttm:biolink_object_direction_qualifier a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_persona" ; - rdfs:range ttm:TestPersonaEnum ; - skos:definition "A Test persona describes the user or operational context of a given test." ; + rdfs:label "biolink_object_direction_qualifier" ; + skos:definition "The direction of the object of the test asset predicate" ; skos:inScheme . -ttm:test_reference a owl:ObjectProperty, +ttm:biolink_qualified_predicate a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_reference" ; + rdfs:label "biolink_qualified_predicate" ; rdfs:range linkml:Uriorcurie ; - skos:altLabel "GitHubIssue" ; - skos:definition "Document URL where original test source particulars are registered (e.g. Github repo)" ; + skos:definition "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset." ; skos:inScheme . -ttm:test_run_parameters a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "test_run_parameters" ; - rdfs:subPropertyOf ttm:test_entity_parameters ; - skos:definition "Parameters for TestRunnerConfiguration that inform the TestHarness and TestRunners about the general characteristics of a test run." ; - skos:inScheme . - -ttm:test_runner_name a owl:ObjectProperty, +ttm:biolink_subject_aspect_qualifier a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_runner_name" ; - skos:definition "Global system name of a TestRunner." ; + rdfs:label "biolink_subject_aspect_qualifier" ; + skos:definition "The aspect of the subject of the test asset predicate" ; skos:inScheme . -ttm:test_source a owl:ObjectProperty, +ttm:biolink_subject_direction_qualifier a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_source" ; - rdfs:range ttm:TestSourceEnum ; - skos:definition "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + rdfs:label "biolink_subject_direction_qualifier" ; + skos:definition "The direction of the subject of the test asset predicate" ; skos:inScheme . -ttm:test_suite_id a owl:ObjectProperty, +ttm:biolink_version a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_suite_id" ; - rdfs:range linkml:Uriorcurie ; - skos:definition "CURIE id of a TestSuite registered in the system." ; + rdfs:label "biolink_version" ; + skos:definition "Biolink Model release (SemVer string)" ; skos:inScheme . -ttm:test_suite_specification a owl:ObjectProperty, +ttm:bte a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_suite_specification" ; - rdfs:range ttm:TestSuiteSpecification ; - skos:definition "Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source." ; + rdfs:label "bte" ; skos:inScheme . -ttm:timestamp a owl:ObjectProperty, +ttm:description a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "timestamp" ; - rdfs:range linkml:Datetime ; - skos:definition "Date time when a given entity was created." ; + rdfs:label "description" ; + skos:definition "A human-readable description for a Test Entity" ; skos:inScheme . -ttm:top_level a owl:ObjectProperty, +ttm:direction a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "top_level" ; - rdfs:range linkml:Integer ; - skos:definition "The answer must return in these many results" ; + rdfs:label "direction" ; + rdfs:range ttm:DirectionEnum ; + skos:definition "The direction of the expected query result triple" ; skos:inScheme . -ttm:trapi_template a owl:ObjectProperty, +ttm:expected_output a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "trapi_template" ; - rdfs:range ttm:TrapiTemplateEnum ; - skos:definition "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; + rdfs:label "expected_output" ; + skos:altLabel "Expected Output" ; skos:inScheme . -ttm:trapi_version a owl:ObjectProperty, +ttm:expected_result a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "trapi_version" ; - skos:definition "TRAPI version (SemVer string)" ; + rdfs:label "expected_result" ; + rdfs:range ttm:ExpectedResultsEnum ; + skos:definition "The expected result of the query" ; skos:inScheme . -ttm:unsecret a owl:ObjectProperty, +ttm:improving a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "unsecret" ; + rdfs:label "improving" ; skos:inScheme . -ttm:well_known a owl:ObjectProperty, +ttm:in_v1 a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "well_known" ; + rdfs:label "in_v1" ; rdfs:range linkml:Boolean ; - skos:altLabel "Well Known" ; - skos:inScheme . - -ttm:AcceptanceTestAsset a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AcceptanceTestAsset" ; - rdfs:subClassOf ttm:TestAsset ; - skos:definition "Model derived from Jenn's test asset design and Shervin's runner JSON here as an example." ; - skos:inScheme . - -ttm:KnowledgeGraphNavigationTestCase a owl:Class, - linkml:ClassDefinition ; - rdfs:label "KnowledgeGraphNavigationTestCase" ; - rdfs:subClassOf ttm:TestCase ; - skos:definition "Knowledge Graph navigation integration test" ; - skos:inScheme . - -ttm:Precondition a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Precondition" ; - rdfs:subClassOf ttm:TestEntity ; - skos:definition "Represents a precondition for a TestCase" ; - skos:inScheme . - -ttm:Qualifier a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Qualifier" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ttm:parameter ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ttm:parameter ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ttm:value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ttm:value ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ttm:value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ttm:parameter ], - ttm:TestEntityParameter ; - skos:inScheme . - - a owl:Class, - ttm:QueryTypeEnum ; - rdfs:label "treats" . - -ttm:TestCaseResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestCaseResult" ; - rdfs:subClassOf ttm:TestEntity ; - skos:definition "The outcome of a TestRunner run of one specific TestCase." ; + skos:altLabel "In v1" ; skos:inScheme . -ttm:TestMetadata a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestMetadata" ; - rdfs:subClassOf ttm:TestEntity ; - skos:definition "Represents metadata related to (external SME, SMURF, Translator feedback, large scale batch, etc.) like the provenance of test assets, cases and/or suites." ; +ttm:input_category a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "input_category" ; + rdfs:range ttm:concept_category ; + skos:altLabel "SubjectCategory" ; skos:inScheme . -ttm:TestOutput a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestOutput" ; - rdfs:subClassOf ttm:TestEntity ; - skos:definition "The output of a TestRunner run of one specific TestCase." ; +ttm:input_id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "input_id" ; + rdfs:range linkml:Uriorcurie ; + skos:altLabel "InputID, node normalized", + "SubjectID" ; skos:inScheme . -ttm:TestResultPKSet a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestResultPKSet" ; - rdfs:subClassOf ttm:TestEntity ; - skos:definition "Primary keys for a given ARA result set from a SmokeTest result for a given TestCase." ; +ttm:input_name a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "input_name" ; + skos:altLabel "InputName (user choice)", + "SubjectName" ; skos:inScheme . -ttm:TestSuiteSpecification a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestSuiteSpecification" ; - rdfs:subClassOf ttm:TestEntity ; - skos:definition "Parameters for a Test Case instances either dynamically generated from some external source of Test Assets." ; +ttm:merged_pk a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "merged_pk" ; skos:inScheme . -ttm:association_category a owl:Class, - linkml:TypeDefinition ; - rdfs:subClassOf ttm:category_type . - -ttm:predicate_type a owl:Class, - linkml:TypeDefinition ; - rdfs:subClassOf linkml:Uriorcurie . - - a owl:Class, - ttm:ComponentEnum ; - rdfs:label "aragorn" . - - a owl:Class, - ttm:ComponentEnum ; - rdfs:label "arax" . - - a owl:Class, - ttm:ComponentEnum ; - rdfs:label "ars" . - - a owl:Class, - ttm:ComponentEnum ; - rdfs:label "bte" . - - a owl:Class, - ttm:ComponentEnum ; - rdfs:label "improving" . - - a owl:Class, - ttm:DirectionEnum ; - rdfs:label "decreased" . - - a owl:Class, - ttm:DirectionEnum ; - rdfs:label "increased" . - - a owl:Class, - ttm:ExpectedOutputEnum ; - rdfs:label "Acceptable" . - - a owl:Class, - ttm:ExpectedOutputEnum ; - rdfs:label "BadButForgivable" . - - a owl:Class, - ttm:ExpectedOutputEnum ; - rdfs:label "NeverShow" . - - a owl:Class, - ttm:ExpectedOutputEnum ; - rdfs:label "TopAnswer" . - - a owl:Class, - ttm:ExpectedResultsEnum ; - rdfs:label "exclude_bad" . - - a owl:Class, - ttm:ExpectedResultsEnum ; - rdfs:label "include_good" . - - a owl:Class, - ttm:FileFormatEnum ; - rdfs:label "JSON" . - - a owl:Class, - ttm:FileFormatEnum ; - rdfs:label "TSV" . - - a owl:Class, - ttm:FileFormatEnum ; - rdfs:label "YAML" . - - a owl:Class, - ttm:NodeEnum ; - rdfs:label "object" . - - a owl:Class, - ttm:NodeEnum ; - rdfs:label "subject" . - -ttm:QueryTypeEnum a owl:Class, - linkml:EnumDefinition ; - linkml:permissible_values . +ttm:must_pass_date a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "must_pass_date" ; + rdfs:range linkml:Date ; + skos:definition "The date by which this test must pass" ; + skos:inScheme . - a owl:Class, - ttm:SemanticSeverityEnum ; - rdfs:label "High" . +ttm:must_pass_environment a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "must_pass_environment" ; + rdfs:range ttm:TestEnvEnum ; + skos:definition "The deployment environment within which this test must pass." ; + skos:inScheme . - a owl:Class, - ttm:SemanticSeverityEnum ; - rdfs:label "Low" . +ttm:name a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "name" ; + skos:definition "A human-readable name for a Test Entity" ; + skos:inScheme . - a owl:Class, - ttm:SemanticSeverityEnum ; - rdfs:label "NotApplicable" . +ttm:notes a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "notes" ; + rdfs:range linkml:String ; + skos:definition "The notes of the query" ; + skos:inScheme . - a owl:Class, - ttm:TestCaseResultEnum ; - rdfs:label "test_failed" . +ttm:output_category a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "output_category" ; + rdfs:range ttm:concept_category ; + skos:altLabel "ObjectCategory" ; + skos:inScheme . - a owl:Class, - ttm:TestCaseResultEnum ; - rdfs:label "test_passed" . +ttm:output_id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "output_id" ; + rdfs:range linkml:Uriorcurie ; + skos:altLabel "ObjectID", + "OutputID" ; + skos:inScheme . - a owl:Class, - ttm:TestCaseResultEnum ; - rdfs:label "test_skipped" . +ttm:output_name a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "output_name" ; + skos:altLabel "ObjectName", + "OutputName" ; + skos:inScheme . -ttm:TestEntityParameter a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestEntityParameter" ; - skos:definition "A single 'tag = value' pair (where 'value' is a simple string)." ; +ttm:parent_pk a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "parent_pk" ; skos:inScheme . - a owl:Class, - ttm:TestEnvEnum ; - rdfs:label "ci" . +ttm:predicate_id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "predicate_id" ; + rdfs:range ttm:predicate_type ; + skos:altLabel "Predicate" ; + skos:inScheme . - a owl:Class, - ttm:TestEnvEnum ; - rdfs:label "dev" . +ttm:predicate_name a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "predicate_name" ; + skos:altLabel "Query", + "Relationship" ; + skos:inScheme . - a owl:Class, - ttm:TestEnvEnum ; - rdfs:label "prod" . +ttm:query_node a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "query_node" ; + rdfs:range ttm:NodeEnum ; + skos:definition "The node of the (templated) TRAPI query to replace" ; + skos:inScheme . - a owl:Class, - ttm:TestEnvEnum ; - rdfs:label "test" . +ttm:query_type a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "query_type" ; + rdfs:range ttm:QueryTypeEnum ; + skos:definition "Type of TestCase query." ; + skos:inScheme . - a owl:Class, - ttm:TestIssueEnum ; - rdfs:label "TMKP" . +ttm:scientific_question a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scientific_question" ; + rdfs:range linkml:String ; + skos:definition "The full human-readable scientific question a SME would ask, which is encoded into the test asset." ; + skos:inScheme . - a owl:Class, - ttm:TestIssueEnum ; - rdfs:label "category too generic" . +ttm:semantic_severity a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "semantic_severity" ; + rdfs:range ttm:SemanticSeverityEnum ; + skos:altLabel "Semantic Severity" ; + skos:inScheme . - a owl:Class, - ttm:TestIssueEnum ; - rdfs:label "causes not treats" . +ttm:string_entry a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "string_entry" ; + rdfs:range linkml:String ; + skos:altLabel "disease", + "trapi node 2" ; + skos:definition "The object of the core triple to be tested" ; + skos:inScheme . - a owl:Class, - ttm:TestIssueEnum ; - rdfs:label "chemical roles" . +ttm:test_annotations a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_annotations" ; + rdfs:subPropertyOf ttm:test_entity_parameters ; + skos:definition "Metadata annotation." ; + skos:inScheme . - a owl:Class, - ttm:TestIssueEnum ; - rdfs:label "contraindications" . +ttm:test_case a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case" ; + rdfs:range ttm:TestCase ; + skos:definition "Slot referencing a single TestCase." ; + skos:inScheme . - a owl:Class, - ttm:TestIssueEnum ; - rdfs:label "test_issue" . +ttm:test_case_id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case_id" ; + rdfs:range linkml:String ; + skos:definition "CURIE id of a TestCase registered in the system." ; + skos:inScheme . - a owl:Class, - ttm:TestObjectiveEnum ; - rdfs:label "AcceptanceTest" . +ttm:test_case_input_id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case_input_id" ; + rdfs:range linkml:Uriorcurie ; + skos:altLabel "InputID, node normalized", + "SubjectID" ; + skos:inScheme . - a owl:Class, - ttm:TestObjectiveEnum ; - rdfs:label "BenchmarkTest" . +ttm:test_case_objective a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case_objective" ; + rdfs:range ttm:TestObjectiveEnum ; + skos:definition "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + skos:inScheme . - a owl:Class, - ttm:TestObjectiveEnum ; - rdfs:label "QuantitativeTest" . +ttm:test_case_predicate_id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case_predicate_id" ; + skos:altLabel "Predicate" ; + skos:inScheme . - a owl:Class, - ttm:TestPersonaEnum ; - rdfs:label "All" . +ttm:test_case_predicate_name a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case_predicate_name" ; + skos:altLabel "Predicate" ; + skos:inScheme . - a owl:Class, - ttm:TestPersonaEnum ; - rdfs:label "Clinical" . +ttm:test_case_result a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case_result" ; + rdfs:range ttm:TestCaseResultEnum ; + skos:definition "Encoded result of a single test run of a given test case" ; + skos:inScheme . - a owl:Class, - ttm:TestPersonaEnum ; - rdfs:label "LookUp" . +ttm:test_case_source a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_case_source" ; + rdfs:range ttm:TestSourceEnum ; + skos:definition "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + skos:inScheme . - a owl:Class, - ttm:TestPersonaEnum ; - rdfs:label "Mechanistic" . +ttm:test_data_file_format a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_data_file_format" ; + rdfs:range ttm:FileFormatEnum ; + skos:definition "File format of test entity data (e.g. TSV, YAML or JSON)" ; + skos:inScheme . - a owl:Class, - ttm:TestSourceEnum ; - rdfs:label "BenchMark" . +ttm:test_data_file_locator a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_data_file_locator" ; + rdfs:range linkml:Uriorcurie ; + skos:definition "An web accessible file resource link to test entity data (e.g. a web accessible text file of Test Asset entries)" ; + skos:inScheme . - a owl:Class, - ttm:TestSourceEnum ; - rdfs:label "GitHubUserFeedback" . +ttm:test_env a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_env" ; + rdfs:range ttm:TestEnvEnum ; + skos:definition "Deployment environment within which the associated TestSuite is run." ; + skos:inScheme . - a owl:Class, - ttm:TestSourceEnum ; - rdfs:label "SME" . +ttm:test_issue a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_issue" ; + rdfs:range ttm:TestIssueEnum ; + skos:altLabel "issue label" ; + skos:inScheme . - a owl:Class, - ttm:TestSourceEnum ; - rdfs:label "SMURF" . +ttm:test_objective a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_objective" ; + rdfs:range ttm:TestObjectiveEnum ; + skos:definition "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + skos:inScheme . - a owl:Class, - ttm:TestSourceEnum ; - rdfs:label "TACT" . +ttm:test_persona a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_persona" ; + rdfs:range ttm:TestPersonaEnum ; + skos:definition "A Test persona describes the user or operational context of a given test." ; + skos:inScheme . - a owl:Class, - ttm:TestSourceEnum ; - rdfs:label "TestDataLocation" . +ttm:test_run_parameters a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_run_parameters" ; + rdfs:subPropertyOf ttm:test_entity_parameters ; + skos:definition "Parameters for TestRunnerConfiguration that inform the TestHarness and TestRunners about the general characteristics of a test run." ; + skos:inScheme . - a owl:Class, - ttm:TestSourceEnum ; - rdfs:label "TranslatorTeam" . +ttm:test_runner_name a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_runner_name" ; + skos:definition "Global system name of a TestRunner." ; + skos:inScheme . - a owl:Class, - ttm:TrapiTemplateEnum ; - rdfs:label "ameliorates" . +ttm:test_source a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_source" ; + rdfs:range ttm:TestSourceEnum ; + skos:definition "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + skos:inScheme . - a owl:Class, - ttm:TrapiTemplateEnum ; - rdfs:label "drug-to-gene" . +ttm:test_suite_id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_suite_id" ; + rdfs:range linkml:Uriorcurie ; + skos:definition "CURIE id of a TestSuite registered in the system." ; + skos:inScheme . - a owl:Class, - ttm:TrapiTemplateEnum ; - rdfs:label "drug_treats_rare_disease" . +ttm:test_suite_specification a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_suite_specification" ; + rdfs:range ttm:TestSuiteSpecification ; + skos:definition "Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source." ; + skos:inScheme . - a owl:Class, - ttm:TrapiTemplateEnum ; - rdfs:label "three_hop" . +ttm:timestamp a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "timestamp" ; + rdfs:range linkml:Datetime ; + skos:definition "Date time when a given entity was created." ; + skos:inScheme . - a owl:Class, - ttm:TrapiTemplateEnum ; - rdfs:label "treats" . +ttm:top_level a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "top_level" ; + rdfs:range linkml:Integer ; + skos:definition "The answer must return in these many results" ; + skos:inScheme . -ttm:category_type a owl:Class, - linkml:TypeDefinition ; - rdfs:subClassOf linkml:Uriorcurie . +ttm:trapi_template a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "trapi_template" ; + rdfs:range ttm:TrapiTemplateEnum ; + skos:definition "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; + skos:inScheme . -ttm:concept_category a owl:Class, - linkml:TypeDefinition ; - rdfs:subClassOf ttm:category_type . +ttm:trapi_version a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "trapi_version" ; + skos:definition "TRAPI version (SemVer string)" ; + skos:inScheme . -ttm:runner_settings a owl:ObjectProperty, +ttm:unsecret a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "runner_settings" ; - rdfs:range linkml:String ; - skos:altLabel "Settings" ; - skos:definition "Settings for the test harness for TestAsset" ; + rdfs:label "unsecret" ; skos:inScheme . -ttm:test_entities a owl:ObjectProperty, +ttm:well_known a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_entities" ; - rdfs:range ttm:TestEntity ; - skos:definition "One or more instances of TestEntity, generally of class TestAsset, TestCase or TestSuite." ; + rdfs:label "well_known" ; + rdfs:range linkml:Boolean ; + skos:altLabel "Well Known" ; skos:inScheme . -ttm:test_entity_parameters a owl:ObjectProperty, +ttm:QueryTypeEnum a owl:Class, + linkml:EnumDefinition ; + linkml:permissible_values . + +ttm:concept_category a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf ttm:category_type . + +ttm:test_assets a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_entity_parameters" ; - rdfs:range ttm:TestEntityParameter ; - skos:definition "One or more parameters documenting target characteristics of a TestEntity." ; + rdfs:label "test_assets" ; + rdfs:range ttm:TestAsset ; + skos:definition "List of explicitly enumerated Test Assets. The class attributes of TestAsset would be included in the TestCase versus being referred to by the identifier (curie) of the TestAsset. That is, this would be a list of objects (in JSONSchema serialization) versus a list of strings (where each string is an identifier pointing to another class)." ; skos:inScheme . ttm:DirectionEnum a owl:Class, @@ -916,41 +1560,6 @@ ttm:NodeEnum a owl:Class, linkml:permissible_values , . -ttm:TestAsset a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestAsset" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ttm:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ttm:tags ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ttm:runner_settings ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ttm:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ttm:tags ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty ttm:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty ttm:runner_settings ], - ttm:TestEntity ; - skos:definition "Represents a Test Asset, which is a single specific instance of TestCase-agnostic semantic parameters representing the specification of a Translator test target with inputs and (expected) outputs." ; - skos:inScheme . - -ttm:TestSuite a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestSuite" ; - rdfs:subClassOf ttm:TestEntity ; - skos:definition "Specification of a set of Test Cases, one of either with a static list of 'test_cases' or a dynamic 'test_suite_specification' slot values. Note: at least one slot or the other, but generally not both(?) needs to be present." ; - skos:inScheme . - ttm:id a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "id" ; @@ -964,6 +1573,21 @@ ttm:parameter a owl:ObjectProperty, skos:definition "Name of a TestParameter." ; skos:inScheme . +ttm:test_metadata a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_metadata" ; + rdfs:range ttm:TestMetadata ; + skos:definition "Test metadata describes the external provenance, cross-references and objectives for a given test." ; + skos:inScheme . + +ttm:test_reference a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "test_reference" ; + rdfs:range linkml:Uriorcurie ; + skos:altLabel "GitHubIssue" ; + skos:definition "Document URL where original test source particulars are registered (e.g. Github repo)" ; + skos:inScheme . + ttm:value a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "value" ; @@ -992,6 +1616,115 @@ ttm:SemanticSeverityEnum a owl:Class, , . +ttm:TestCase a owl:Class, + linkml:ClassDefinition ; + rdfs:label "TestCase" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case_predicate_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:components ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_source ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_env ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:preconditions ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:test_case_runner_settings ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestSourceEnum ; + owl:onProperty ttm:test_case_source ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:ComponentEnum ; + owl:onProperty ttm:components ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_predicate_id ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:Precondition ; + owl:onProperty ttm:preconditions ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestEnvEnum ; + owl:onProperty ttm:test_env ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:test_case_predicate_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_input_id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:trapi_template ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case_predicate_id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_predicate_name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:tags ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:test_case_predicate_id ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TrapiTemplateEnum ; + owl:onProperty ttm:trapi_template ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:QueryTypeEnum ; + owl:onProperty ttm:query_type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ttm:test_case_runner_settings ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:tags ], + [ a owl:Restriction ; + owl:allValuesFrom ttm:TestObjectiveEnum ; + owl:onProperty ttm:test_case_objective ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:trapi_template ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case_objective ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case_input_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:test_case_source ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:test_case_input_id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ttm:test_assets ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_env ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:query_type ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty ttm:test_assets ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:query_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:test_case_objective ], + ttm:TestEntity ; + skos:definition "Represents a single enumerated instance of Test Case, derived from a given collection of one or more TestAsset instances (the value of the 'test_assets' slot) which define the 'inputs' and 'outputs' of the TestCase, used to probe a particular test condition." ; + skos:inScheme . + ttm:TestCaseResultEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -999,11 +1732,10 @@ ttm:TestCaseResultEnum a owl:Class, , . -ttm:test_assets a owl:ObjectProperty, +ttm:tags a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "test_assets" ; - rdfs:range ttm:TestAsset ; - skos:definition "List of explicitly enumerated Test Assets. The class attributes of TestAsset would be included in the TestCase versus being referred to by the identifier (curie) of the TestAsset. That is, this would be a list of objects (in JSONSchema serialization) versus a list of strings (where each string is an identifier pointing to another class)." ; + rdfs:label "tags" ; + skos:definition "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; skos:inScheme . ttm:TestObjectiveEnum a owl:Class, @@ -1021,32 +1753,43 @@ ttm:TestPersonaEnum a owl:Class, , . -ttm:ComponentEnum a owl:Class, - linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - -ttm:TestCase a owl:Class, +ttm:TestEntity a owl:Class, linkml:ClassDefinition ; - rdfs:label "TestCase" ; + rdfs:label "TestEntity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty ttm:test_assets ], + owl:maxCardinality 1 ; + owl:onProperty ttm:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:description ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ttm:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ttm:tags ], + owl:onProperty ttm:name ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ttm:test_assets ], + owl:onProperty ttm:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ttm:description ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ttm:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ttm:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; + owl:onProperty ttm:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty ttm:tags ], - ttm:TestEntity ; - skos:definition "Represents a single enumerated instance of Test Case, derived from a given collection of one or more TestAsset instances (the value of the 'test_assets' slot) which define the 'inputs' and 'outputs' of the TestCase, used to probe a particular test condition." ; + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ttm:tags ] ; + skos:definition "Abstract global 'identification' class shared as a parent with all major model classes within the data model for Translator testing." ; skos:inScheme . ttm:TestEnvEnum a owl:Class, @@ -1066,12 +1809,6 @@ ttm:TrapiTemplateEnum a owl:Class, , . -ttm:tags a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "tags" ; - skos:definition "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - skos:inScheme . - ttm:TestIssueEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -1093,12 +1830,6 @@ ttm:TestSourceEnum a owl:Class, , . -ttm:TestEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TestEntity" ; - skos:definition "Abstract global 'identification' class shared as a parent with all major model classes within the data model for Translator testing." ; - skos:inScheme . - a owl:Ontology ; rdfs:label "Translator-Testing-Model" ; dcterms:license "MIT" ; diff --git a/project/protobuf/translator_testing_model.proto b/project/protobuf/translator_testing_model.proto index be7c114..3b0f95d 100644 --- a/project/protobuf/translator_testing_model.proto +++ b/project/protobuf/translator_testing_model.proto @@ -21,6 +21,11 @@ message AcceptanceTestAsset uriorcurie testReference = 0 repeated string runnerSettings = 0 testMetadata testMetadata = 0 + uriorcurie biolinkQualifiedPredicate = 0 + string biolinkSubjectAspectQualifier = 0 + string biolinkSubjectDirectionQualifier = 0 + string biolinkObjectAspectQualifier = 0 + string biolinkObjectDirectionQualifier = 0 uriorcurie id = 0 repeated string tags = 0 date mustPassDate = 0 @@ -207,6 +212,11 @@ message TestAsset uriorcurie testReference = 0 repeated string runnerSettings = 0 testMetadata testMetadata = 0 + uriorcurie biolinkQualifiedPredicate = 0 + string biolinkSubjectAspectQualifier = 0 + string biolinkSubjectDirectionQualifier = 0 + string biolinkObjectAspectQualifier = 0 + string biolinkObjectDirectionQualifier = 0 uriorcurie id = 0 repeated string tags = 0 } @@ -264,6 +274,11 @@ message TestEdgeData uriorcurie testReference = 0 repeated string runnerSettings = 0 testMetadata testMetadata = 0 + uriorcurie biolinkQualifiedPredicate = 0 + string biolinkSubjectAspectQualifier = 0 + string biolinkSubjectDirectionQualifier = 0 + string biolinkObjectAspectQualifier = 0 + string biolinkObjectDirectionQualifier = 0 uriorcurie id = 0 repeated string tags = 0 } diff --git a/project/shacl/translator_testing_model.shacl.ttl b/project/shacl/translator_testing_model.shacl.ttl index 747ba2d..a1f88e6 100644 --- a/project/shacl/translator_testing_model.shacl.ttl +++ b/project/shacl/translator_testing_model.shacl.ttl @@ -8,86 +8,102 @@ ttm:AcceptanceTestCase a sh:NodeShape ; sh:closed true ; sh:description "See AcceptanceTestAsset above for more details." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; + sh:property [ sh:datatype xsd:string ; + sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; + sh:order 15 ; + sh:path schema1:additionalType ], + [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path ttm:trapi_template ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:test_case_input_id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ttm:test_case_predicate_id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path ttm:test_case_predicate_name ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; - sh:order 15 ; - sh:path schema1:additionalType ], - [ sh:class ttm:AcceptanceTestAsset ; - sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection." ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ttm:test_assets ], - [ sh:description "Deployment environment within which the associated TestSuite is run." ; - sh:in ( "dev" "ci" "test" "prod" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:test_env ], [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path ttm:test_case_objective ], + [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path ttm:test_case_source ], [ sh:datatype xsd:string ; - sh:description "Settings for the test harness for TestCase" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path ttm:test_case_runner_settings ], + sh:maxCount 1 ; + sh:order 9 ; + sh:path ttm:test_case_predicate_id ], + [ sh:description "Deployment environment within which the associated TestSuite is run." ; + sh:in ( "dev" "ci" "test" "prod" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:test_env ], [ sh:class ttm:Precondition ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path ttm:preconditions ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path ttm:test_case_input_id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path schema1:name ], + [ sh:class ttm:AcceptanceTestAsset ; + sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path ttm:test_assets ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 14 ; sh:path schema1:description ], - [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; - sh:in ( "arax" "aragorn" "ars" "bte" "improving" ) ; - sh:order 5 ; - sh:path ttm:components ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path schema1:name ], - [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; - sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; + sh:description "Settings for the test harness for TestCase" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path ttm:test_case_runner_settings ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 7 ; - sh:path ttm:test_case_source ], + sh:order 8 ; + sh:path ttm:test_case_predicate_name ], [ sh:description "Type of TestCase query." ; sh:in ( "treats" ) ; sh:maxCount 1 ; sh:order 1 ; - sh:path ttm:query_type ] ; + sh:path ttm:query_type ], + [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; + sh:in [ rdf:rest () ] ; + sh:order 5 ; + sh:path ttm:components ] ; sh:targetClass ttm:AcceptanceTestCase . ttm:AcceptanceTestSuite a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "A Test persona describes the user or operational context of a given test." ; + sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:test_persona ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], + [ sh:class ttm:TestSuiteSpecification ; + sh:description "Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path ttm:test_suite_specification ], + [ sh:datatype xsd:string ; sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; sh:order 5 ; @@ -96,11 +112,11 @@ ttm:AcceptanceTestSuite a sh:NodeShape ; sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; sh:order 7 ; sh:path schema1:additionalType ], - [ sh:description "A Test persona describes the user or operational context of a given test." ; - sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:test_persona ], + [ sh:class ttm:TestCase ; + sh:description "List of explicitly enumerated Test Cases." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path ttm:test_cases ], [ sh:class ttm:TestMetadata ; sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; sh:maxCount 1 ; @@ -108,27 +124,11 @@ ttm:AcceptanceTestSuite a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path ttm:test_metadata ], - [ sh:class ttm:TestCase ; - sh:description "List of explicitly enumerated Test Cases." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ttm:test_cases ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 6 ; - sh:path schema1:description ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:class ttm:TestSuiteSpecification ; - sh:description "Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path ttm:test_suite_specification ] ; + sh:path schema1:description ] ; sh:targetClass ttm:AcceptanceTestSuite . ttm:BenchmarkTestSuite a sh:NodeShape ; @@ -141,194 +141,219 @@ ttm:ComplianceTestCase a sh:NodeShape ; sh:closed true ; sh:description "TRAPI and Biolink Model standards compliance test" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 12 ; - sh:path ttm:test_case_input_id ], - [ sh:datatype xsd:string ; - sh:description "Settings for the test harness for TestCase" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path ttm:test_case_runner_settings ], - [ sh:class ttm:Precondition ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path ttm:preconditions ], - [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; - sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ttm:test_case_source ], - [ sh:datatype xsd:string ; + sh:property [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; + sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path ttm:test_case_predicate_id ], - [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; - sh:in ( "arax" "aragorn" "ars" "bte" "improving" ) ; - sh:order 7 ; - sh:path ttm:components ], - [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; - sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; + sh:order 6 ; + sh:path ttm:trapi_template ], + [ sh:description "Type of TestCase query." ; + sh:in ( "treats" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path ttm:test_case_objective ], + sh:order 3 ; + sh:path ttm:query_type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path schema1:name ], - [ sh:description "Deployment environment within which the associated TestSuite is run." ; - sh:in ( "dev" "ci" "test" "prod" ) ; + sh:description "Biolink Model release (SemVer string)" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path ttm:test_env ], + sh:order 1 ; + sh:path ttm:biolink_version ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; - sh:order 17 ; - sh:path schema1:additionalType ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 16 ; sh:path schema1:description ], - [ sh:datatype xsd:string ; + [ sh:description "Deployment environment within which the associated TestSuite is run." ; + sh:in ( "dev" "ci" "test" "prod" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:test_case_predicate_name ], + sh:order 2 ; + sh:path ttm:test_env ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path ttm:test_case_input_id ], [ sh:datatype xsd:string ; - sh:description "Biolink Model release (SemVer string)" ; + sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; + sh:order 17 ; + sh:path schema1:additionalType ], + [ sh:datatype xsd:string ; + sh:description "TRAPI version (SemVer string)" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:biolink_version ], + sh:order 0 ; + sh:path ttm:trapi_version ], [ sh:class ttm:TestAsset ; sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection." ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path ttm:test_assets ], - [ sh:description "Type of TestCase query." ; - sh:in ( "treats" ) ; + [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; + sh:in [ rdf:rest () ] ; + sh:order 7 ; + sh:path ttm:components ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 3 ; - sh:path ttm:query_type ], + sh:order 10 ; + sh:path ttm:test_case_predicate_name ], + [ sh:class ttm:Precondition ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path ttm:preconditions ], [ sh:datatype xsd:string ; - sh:description "TRAPI version (SemVer string)" ; + sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:trapi_version ], - [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; - sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; + sh:order 15 ; + sh:path schema1:name ], + [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path ttm:trapi_template ] ; + sh:order 9 ; + sh:path ttm:test_case_source ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path ttm:test_case_predicate_id ], + [ sh:datatype xsd:string ; + sh:description "Settings for the test harness for TestCase" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path ttm:test_case_runner_settings ], + [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path ttm:test_case_objective ] ; sh:targetClass ttm:ComplianceTestCase . ttm:KnowledgeGraphNavigationTestCase a sh:NodeShape ; sh:closed true ; sh:description "Knowledge Graph navigation integration test" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + sh:property [ sh:description "Deployment environment within which the associated TestSuite is run." ; + sh:in ( "dev" "ci" "test" "prod" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:test_env ], + [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; sh:maxCount 1 ; sh:order 7 ; sh:path ttm:test_case_source ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ttm:test_case_predicate_id ], + sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; + sh:order 15 ; + sh:path schema1:additionalType ], + [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; + sh:in [ rdf:rest () ] ; + sh:order 5 ; + sh:path ttm:components ], [ sh:class ttm:TestAsset ; sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection." ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path ttm:test_assets ], - [ sh:class ttm:Precondition ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path ttm:preconditions ], - [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; - sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path ttm:trapi_template ], - [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; - sh:in ( "arax" "aragorn" "ars" "bte" "improving" ) ; - sh:order 5 ; - sh:path ttm:components ], + sh:order 14 ; + sh:path schema1:description ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path ttm:test_case_input_id ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path schema1:identifier ], - [ sh:description "Type of TestCase query." ; - sh:in ( "treats" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:query_type ], - [ sh:description "Deployment environment within which the associated TestSuite is run." ; - sh:in ( "dev" "ci" "test" "prod" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:test_env ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; + [ sh:class ttm:Precondition ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path ttm:preconditions ], + [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; + sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path schema1:description ], + sh:order 4 ; + sh:path ttm:trapi_template ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path schema1:name ], + [ sh:description "Type of TestCase query." ; + sh:in ( "treats" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:query_type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 8 ; sh:path ttm:test_case_predicate_name ], - [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; - sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path ttm:test_case_objective ], [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; - sh:order 15 ; - sh:path schema1:additionalType ], + sh:maxCount 1 ; + sh:order 9 ; + sh:path ttm:test_case_predicate_id ], [ sh:datatype xsd:string ; sh:description "Settings for the test harness for TestCase" ; sh:minCount 1 ; sh:order 11 ; sh:path ttm:test_case_runner_settings ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:test_case_input_id ] ; + [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path ttm:test_case_objective ] ; sh:targetClass ttm:KnowledgeGraphNavigationTestCase . ttm:OneHopTestCase a sh:NodeShape ; sh:closed true ; sh:description "'One Hop' Knowledge Graph navigation integration test" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path ttm:test_case_predicate_name ], - [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; - sh:in ( "arax" "aragorn" "ars" "bte" "improving" ) ; + sh:property [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; + sh:in [ rdf:rest () ] ; sh:order 5 ; sh:path ttm:components ], + [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path ttm:test_case_source ], [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path ttm:trapi_template ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path ttm:test_case_predicate_name ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 14 ; sh:path schema1:description ], + [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path ttm:test_case_objective ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path schema1:name ], + [ sh:description "Deployment environment within which the associated TestSuite is run." ; + sh:in ( "dev" "ci" "test" "prod" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:test_env ], [ sh:class ttm:Precondition ; sh:nodeKind sh:IRI ; sh:order 3 ; @@ -339,52 +364,27 @@ ttm:OneHopTestCase a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path ttm:test_assets ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path schema1:identifier ], - [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; - sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path ttm:test_case_source ], - [ sh:description "Deployment environment within which the associated TestSuite is run." ; - sh:in ( "dev" "ci" "test" "prod" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:test_env ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ttm:test_case_predicate_id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path schema1:name ], [ sh:description "Type of TestCase query." ; sh:in ( "treats" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path ttm:query_type ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path ttm:test_case_input_id ], [ sh:datatype xsd:string ; sh:description "Settings for the test harness for TestCase" ; sh:minCount 1 ; sh:order 11 ; sh:path ttm:test_case_runner_settings ], - [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; - sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path ttm:test_case_objective ], [ sh:datatype xsd:string ; sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; sh:order 15 ; sh:path schema1:additionalType ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:test_case_input_id ] ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path ttm:test_case_predicate_id ] ; sh:targetClass ttm:OneHopTestCase . ttm:OneHopTestSuite a sh:NodeShape ; @@ -396,6 +396,21 @@ ttm:OneHopTestSuite a sh:NodeShape ; sh:maxCount 1 ; sh:order 6 ; sh:path schema1:description ], + [ sh:description "A Test persona describes the user or operational context of a given test." ; + sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:test_persona ], + [ sh:class ttm:TestCase ; + sh:description "List of explicitly enumerated Test Cases." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path ttm:test_cases ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], [ sh:class ttm:TestMetadata ; sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; sh:maxCount 1 ; @@ -403,15 +418,6 @@ ttm:OneHopTestSuite a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path ttm:test_metadata ], - [ sh:description "A Test persona describes the user or operational context of a given test." ; - sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:test_persona ], - [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 7 ; - sh:path schema1:additionalType ], [ sh:class ttm:TestSuiteSpecification ; sh:description "Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source." ; sh:maxCount 1 ; @@ -423,241 +429,259 @@ ttm:OneHopTestSuite a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path schema1:name ], - [ sh:class ttm:TestCase ; - sh:description "List of explicitly enumerated Test Cases." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ttm:test_cases ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ] ; + [ sh:datatype xsd:string ; + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 7 ; + sh:path schema1:additionalType ] ; sh:targetClass ttm:OneHopTestSuite . ttm:QuantitativeTestCase a sh:NodeShape ; sh:closed true ; sh:description "Assumed additional model from Shervin's runner JSON here as an example. This schema is not yet complete." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ttm:test_case_predicate_id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "Settings for the test harness for TestCase" ; + sh:property [ sh:class ttm:TestAsset ; + sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection." ; sh:minCount 1 ; - sh:order 11 ; - sh:path ttm:test_case_runner_settings ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path ttm:test_assets ], [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; - sh:in ( "arax" "aragorn" "ars" "bte" "improving" ) ; + sh:in [ rdf:rest () ] ; sh:order 5 ; sh:path ttm:components ], - [ sh:description "Deployment environment within which the associated TestSuite is run." ; - sh:in ( "dev" "ci" "test" "prod" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:test_env ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path schema1:identifier ], - [ sh:class ttm:Precondition ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path ttm:preconditions ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:test_case_input_id ], [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path ttm:trapi_template ], + [ sh:datatype xsd:string ; + sh:description "Settings for the test harness for TestCase" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path ttm:test_case_runner_settings ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a Test Entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path schema1:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path schema1:name ], + [ sh:class ttm:Precondition ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path ttm:preconditions ], + [ sh:datatype xsd:string ; + sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; + sh:order 15 ; + sh:path schema1:additionalType ], [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; sh:maxCount 1 ; sh:order 7 ; sh:path ttm:test_case_source ], - [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; - sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path ttm:test_case_objective ], [ sh:description "Type of TestCase query." ; sh:in ( "treats" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path ttm:query_type ], - [ sh:class ttm:TestAsset ; - sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection." ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ttm:test_assets ], - [ sh:datatype xsd:string ; + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path ttm:test_case_input_id ], + [ sh:description "Deployment environment within which the associated TestSuite is run." ; + sh:in ( "dev" "ci" "test" "prod" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path ttm:test_case_predicate_name ], + sh:order 0 ; + sh:path ttm:test_env ], [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; - sh:order 15 ; - sh:path schema1:additionalType ], + sh:maxCount 1 ; + sh:order 9 ; + sh:path ttm:test_case_predicate_id ], + [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path ttm:test_case_objective ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path schema1:description ] ; + sh:order 8 ; + sh:path ttm:test_case_predicate_name ] ; sh:targetClass ttm:QuantitativeTestCase . ttm:StandardsComplianceTestSuite a sh:NodeShape ; sh:closed true ; sh:description "Test suite for testing Translator components against releases of standards like TRAPI and the Biolink Model." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:description ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:description "A Test persona describes the user or operational context of a given test." ; - sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:test_persona ], - [ sh:class ttm:TestMetadata ; + sh:property [ sh:class ttm:TestMetadata ; sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path ttm:test_metadata ], + [ sh:datatype xsd:string ; + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 7 ; + sh:path schema1:additionalType ], [ sh:class ttm:TestSuiteSpecification ; sh:description "Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path ttm:test_suite_specification ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 7 ; - sh:path schema1:additionalType ], + sh:description "A human-readable description for a Test Entity" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path schema1:description ], + [ sh:description "A Test persona describes the user or operational context of a given test." ; + sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:test_persona ], [ sh:class ttm:TestCase ; sh:description "List of explicitly enumerated Test Cases." ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path ttm:test_cases ] ; + sh:path ttm:test_cases ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path schema1:name ] ; sh:targetClass ttm:StandardsComplianceTestSuite . ttm:TestEdgeData a sh:NodeShape ; sh:closed true ; sh:description "Represents a single Biolink Model compliant instance of a subject-predicate-object edge that can be used for testing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:in ( "High" "Low" "NotApplicable" ) ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path ttm:semantic_severity ], + [ sh:datatype xsd:string ; + sh:description "The direction of the object of the test asset predicate" ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path ttm:biolink_object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The direction of the subject of the test asset predicate" ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path ttm:biolink_subject_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path ttm:in_v1 ], + [ sh:datatype xsd:string ; sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined to specify TestAsset membership in a \"Block List\" collection" ; - sh:order 21 ; + sh:order 26 ; sh:path schema1:additionalType ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:input_name ], + [ sh:in ( "causes not treats" "TMKP" "category too generic" "contraindications" "chemical roles" "test_issue" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path ttm:test_issue ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path ttm:expected_output ], [ sh:maxCount 1 ; sh:order 7 ; sh:path ttm:output_category ], - [ sh:description "A unique identifier for a Test Entity" ; + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path ttm:predicate_id ], + [ sh:description "Document URL where original test source particulars are registered (e.g. Github repo)" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:boolean ; + sh:order 15 ; + sh:path ttm:test_reference ], + [ sh:datatype xsd:string ; + sh:description "The aspect of the object of the test asset predicate" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path ttm:in_v1 ], + sh:order 21 ; + sh:path ttm:biolink_object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The aspect of the subject of the test asset predicate" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path ttm:biolink_subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Settings for the test harness, e.g. \"inferred\"" ; sh:minCount 1 ; sh:order 16 ; sh:path ttm:runner_settings ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:expected_output ], [ sh:description "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement" ; sh:maxCount 1 ; sh:order 8 ; sh:path ttm:association ], - [ sh:in ( "High" "Low" "NotApplicable" ) ; + [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path ttm:semantic_severity ], + sh:minCount 1 ; + sh:order 23 ; + sh:path schema1:identifier ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path ttm:predicate_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a Test Entity" ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path schema1:description ], [ sh:maxCount 1 ; sh:order 0 ; sh:path ttm:input_id ], + [ sh:maxCount 1 ; + sh:order 5 ; + sh:path ttm:output_id ], + [ sh:description "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path ttm:biolink_qualified_predicate ], + [ sh:datatype xsd:boolean ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path ttm:well_known ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path ttm:input_category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path schema1:name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 6 ; sh:path ttm:output_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path schema1:description ], [ sh:class ttm:Qualifier ; sh:description "Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot." ; sh:nodeKind sh:BlankNode ; sh:order 9 ; sh:path ttm:qualifiers ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:input_name ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ttm:input_category ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ttm:predicate_id ], - [ sh:maxCount 1 ; - sh:order 5 ; - sh:path ttm:output_id ], - [ sh:in ( "causes not treats" "TMKP" "category too generic" "contraindications" "chemical roles" "test_issue" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path ttm:test_issue ], [ sh:class ttm:TestMetadata ; sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path ttm:test_metadata ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path schema1:name ], - [ sh:description "Document URL where original test source particulars are registered (e.g. Github repo)" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path ttm:test_reference ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ttm:predicate_name ], - [ sh:datatype xsd:boolean ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path ttm:well_known ] ; + sh:path ttm:test_metadata ] ; sh:targetClass ttm:TestEdgeData . ttm:TestOutput a sh:NodeShape ; @@ -665,79 +689,79 @@ ttm:TestOutput a sh:NodeShape ; sh:description "The output of a TestRunner run of one specific TestCase." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 5 ; - sh:path schema1:additionalType ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; + sh:description "CURIE id of a TestCase registered in the system." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path schema1:name ], + sh:order 0 ; + sh:path ttm:test_case_id ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path schema1:identifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path schema1:description ], + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 5 ; + sh:path schema1:additionalType ], [ sh:class ttm:TestResultPKSet ; sh:description "Primary keys for a given ARA result set from a SmokeTest result for a given TestCase." ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path ttm:pks ], [ sh:datatype xsd:string ; - sh:description "CURIE id of a TestCase registered in the system." ; + sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:test_case_id ] ; + sh:order 4 ; + sh:path schema1:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path schema1:name ] ; sh:targetClass ttm:TestOutput . ttm:TestRunSession a sh:NodeShape ; sh:closed true ; sh:description "A single invocation of a TestRunner." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ttm:TestCaseResult ; - sh:description "One or more instances of TestCaseResult." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ttm:test_case_results ], + sh:property [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], [ sh:datatype xsd:dateTime ; sh:description "Date time when a given entity was created." ; sh:maxCount 1 ; sh:order 3 ; sh:path ttm:timestamp ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], [ sh:class ttm:TestEntity ; sh:description "Different TestRunners may expect specific kinds of TestEntity as input. These 'test_entities' one or more instances of TestAsset, TestCase or TestSuite." ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path ttm:test_entities ], [ sh:datatype xsd:string ; - sh:description "Global system name of a TestRunner." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:test_runner_name ], + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 7 ; + sh:path schema1:additionalType ], + [ sh:class ttm:TestCaseResult ; + sh:description "One or more instances of TestCaseResult." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path ttm:test_case_results ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; sh:order 5 ; sh:path schema1:name ], + [ sh:datatype xsd:string ; + sh:description "Global system name of a TestRunner." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:test_runner_name ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 6 ; - sh:path schema1:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 7 ; - sh:path schema1:additionalType ] ; + sh:path schema1:description ] ; sh:targetClass ttm:TestRunSession . ttm:TestRunnerConfiguration a sh:NodeShape ; @@ -745,24 +769,24 @@ ttm:TestRunnerConfiguration a sh:NodeShape ; sh:description "General configuration parameters and test data input for a single invocation of a TestRunner." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally identify the TestRunner(s) using this configuration." ; - sh:order 4 ; - sh:path schema1:additionalType ], + sh:description "A human-readable description for a Test Entity" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path schema1:description ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path schema1:description ], [ sh:class ttm:TestEntityParameter ; sh:description "Parameters for TestRunnerConfiguration that inform the TestHarness and TestRunners about the general characteristics of a test run." ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path ttm:test_run_parameters ], + [ sh:datatype xsd:string ; + sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally identify the TestRunner(s) using this configuration." ; + sh:order 4 ; + sh:path schema1:additionalType ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; @@ -774,7 +798,22 @@ ttm:TestSuite a sh:NodeShape ; sh:closed true ; sh:description "Specification of a set of Test Cases, one of either with a static list of 'test_cases' or a dynamic 'test_suite_specification' slot values. Note: at least one slot or the other, but generally not both(?) needs to be present." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class ttm:TestCase ; + sh:description "List of explicitly enumerated Test Cases." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path ttm:test_cases ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], + [ sh:description "A Test persona describes the user or operational context of a given test." ; + sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:test_persona ], + [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 6 ; @@ -784,10 +823,6 @@ ttm:TestSuite a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 7 ; - sh:path schema1:additionalType ], [ sh:class ttm:TestMetadata ; sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; sh:maxCount 1 ; @@ -795,82 +830,54 @@ ttm:TestSuite a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path ttm:test_metadata ], - [ sh:class ttm:TestCase ; - sh:description "List of explicitly enumerated Test Cases." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ttm:test_cases ], - [ sh:description "A Test persona describes the user or operational context of a given test." ; - sh:in ( "All" "Clinical" "LookUp" "Mechanistic" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:test_persona ], + [ sh:datatype xsd:string ; + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 7 ; + sh:path schema1:additionalType ], [ sh:class ttm:TestSuiteSpecification ; sh:description "Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path ttm:test_suite_specification ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ] ; + sh:path ttm:test_suite_specification ] ; sh:targetClass ttm:TestSuite . ttm:AcceptanceTestAsset a sh:NodeShape ; sh:closed true ; sh:description "Model derived from Jenn's test asset design and Shervin's runner JSON here as an example." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 13 ; - sh:path ttm:predicate_id ], + sh:property [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path ttm:input_name ], [ sh:datatype xsd:string ; - sh:description "The notes of the query" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path ttm:notes ], - [ sh:datatype xsd:integer ; - sh:description "The answer must return in these many results" ; + sh:order 16 ; + sh:path ttm:output_name ], + [ sh:description "The deployment environment within which this test must pass." ; + sh:in ( "dev" "ci" "test" "prod" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path ttm:top_level ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:input_id ], - [ sh:datatype xsd:date ; - sh:description "The date by which this test must pass" ; + sh:order 1 ; + sh:path ttm:must_pass_environment ], + [ sh:datatype xsd:string ; + sh:description "The full human-readable scientific question a SME would ask, which is encoded into the test asset." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:must_pass_date ], - [ sh:class ttm:Qualifier ; - sh:description "Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot." ; - sh:nodeKind sh:BlankNode ; - sh:order 19 ; - sh:path ttm:qualifiers ], - [ sh:class ttm:TestMetadata ; - sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; + sh:order 2 ; + sh:path ttm:scientific_question ], + [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path ttm:test_metadata ], - [ sh:maxCount 1 ; - sh:order 17 ; - sh:path ttm:output_category ], + sh:order 33 ; + sh:path schema1:identifier ], [ sh:datatype xsd:string ; + sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined to specify TestAsset membership in a \"Block List\" collection" ; + sh:order 36 ; + sh:path schema1:additionalType ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path ttm:expected_output ], - [ sh:description "The node of the (templated) TRAPI query to replace" ; - sh:in ( "subject" "object" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path ttm:query_node ], - [ sh:description "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path ttm:association ], + sh:order 35 ; + sh:path schema1:description ], [ sh:datatype xsd:boolean ; sh:maxCount 1 ; sh:order 23 ; @@ -879,116 +886,138 @@ ttm:AcceptanceTestAsset a sh:NodeShape ; sh:maxCount 1 ; sh:order 22 ; sh:path ttm:semantic_severity ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path ttm:input_name ], - [ sh:description "A unique identifier for a Test Entity" ; + [ sh:class ttm:TestMetadata ; + sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 28 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined to specify TestAsset membership in a \"Block List\" collection" ; - sh:order 31 ; - sh:path schema1:additionalType ], - [ sh:datatype xsd:string ; - sh:description "The full human-readable scientific question a SME would ask, which is encoded into the test asset." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path ttm:test_metadata ], + [ sh:datatype xsd:boolean ; sh:maxCount 1 ; - sh:order 2 ; - sh:path ttm:scientific_question ], + sh:order 24 ; + sh:path ttm:well_known ], + [ sh:maxCount 1 ; + sh:order 13 ; + sh:path ttm:predicate_id ], [ sh:in ( "causes not treats" "TMKP" "category too generic" "contraindications" "chemical roles" "test_issue" ) ; sh:maxCount 1 ; sh:order 21 ; sh:path ttm:test_issue ], + [ sh:datatype xsd:string ; + sh:description "The direction of the subject of the test asset predicate" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path ttm:biolink_subject_direction_qualifier ], + [ sh:description "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path ttm:association ], + [ sh:datatype xsd:string ; + sh:description "The object of the core triple to be tested" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path ttm:string_entry ], [ sh:description "The direction of the expected query result triple" ; sh:in ( "increased" "decreased" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path ttm:direction ], + [ sh:datatype xsd:integer ; + sh:description "The answer must return in these many results" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path ttm:top_level ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; + sh:description "The notes of the query" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path ttm:notes ], + [ sh:datatype xsd:date ; + sh:description "The date by which this test must pass" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:must_pass_date ], + [ sh:maxCount 1 ; + sh:order 17 ; + sh:path ttm:output_category ], + [ sh:datatype xsd:string ; + sh:description "The aspect of the subject of the test asset predicate" ; sh:maxCount 1 ; sh:order 29 ; - sh:path schema1:name ], + sh:path ttm:biolink_subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Settings for the test harness, e.g. \"inferred\"" ; - sh:minCount 1 ; - sh:order 26 ; - sh:path ttm:runner_settings ], - [ sh:description "The deployment environment within which this test must pass." ; - sh:in ( "dev" "ci" "test" "prod" ) ; + sh:description "The direction of the object of the test asset predicate" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:must_pass_environment ], + sh:order 32 ; + sh:path ttm:biolink_object_direction_qualifier ], [ sh:datatype xsd:string ; + sh:description "The aspect of the object of the test asset predicate" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path ttm:predicate_name ], + sh:order 31 ; + sh:path ttm:biolink_object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 16 ; - sh:path ttm:output_name ], + sh:order 20 ; + sh:path ttm:expected_output ], + [ sh:description "The expected result of the query" ; + sh:in ( "include_good" "exclude_bad" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path ttm:expected_result ], [ sh:description "Document URL where original test source particulars are registered (e.g. Github repo)" ; sh:maxCount 1 ; sh:order 25 ; sh:path ttm:test_reference ], + [ sh:description "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path ttm:biolink_qualified_predicate ], [ sh:datatype xsd:string ; sh:description "An answer that is returned from the test case, note: this must be combined with the expected_result to form a complete answer. It might make sense to couple these in their own object instead of strictly sticking to the flat schema introduced by the spreadsheet here: https://docs.google.com/spreadsheets/d/1yj7zIchFeVl1OHqL_kE_pqvzNLmGml_FLbHDs-8Yvig/edit#gid=0" ; sh:maxCount 1 ; sh:order 5 ; sh:path ttm:answer_informal_concept ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path ttm:output_id ], + [ sh:datatype xsd:string ; + sh:description "Settings for the test harness, e.g. \"inferred\"" ; + sh:minCount 1 ; + sh:order 26 ; + sh:path ttm:runner_settings ], + [ sh:class ttm:Qualifier ; + sh:description "Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot." ; + sh:nodeKind sh:BlankNode ; + sh:order 19 ; + sh:path ttm:qualifiers ], [ sh:maxCount 1 ; sh:order 12 ; sh:path ttm:input_category ], - [ sh:description "The expected result of the query" ; - sh:in ( "include_good" "exclude_bad" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path ttm:expected_result ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path ttm:input_id ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path schema1:description ], - [ sh:datatype xsd:boolean ; + sh:order 14 ; + sh:path ttm:predicate_name ], + [ sh:description "The node of the (templated) TRAPI query to replace" ; + sh:in ( "subject" "object" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path ttm:well_known ], + sh:order 8 ; + sh:path ttm:query_node ], [ sh:datatype xsd:string ; - sh:description "The object of the core triple to be tested" ; + sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path ttm:string_entry ], - [ sh:maxCount 1 ; - sh:order 15 ; - sh:path ttm:output_id ] ; + sh:order 34 ; + sh:path schema1:name ] ; sh:targetClass ttm:AcceptanceTestAsset . ttm:TestCaseResult a sh:NodeShape ; sh:closed true ; sh:description "The outcome of a TestRunner run of one specific TestCase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path schema1:identifier ], - [ sh:description "Encoded result of a single test run of a given test case" ; - sh:in ( "test_passed" "test_failed" "test_skipped" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ttm:test_case_result ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path schema1:name ], - [ sh:description "CURIE id of a TestSuite registered in the system." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:test_suite_id ], - [ sh:class ttm:TestCase ; + sh:property [ sh:class ttm:TestCase ; sh:description "Slot referencing a single TestCase." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -1002,7 +1031,26 @@ ttm:TestCaseResult a sh:NodeShape ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 5 ; - sh:path schema1:description ] ; + sh:path schema1:description ], + [ sh:description "Encoded result of a single test run of a given test case" ; + sh:in ( "test_passed" "test_failed" "test_skipped" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path ttm:test_case_result ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path schema1:identifier ], + [ sh:description "CURIE id of a TestSuite registered in the system." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:test_suite_id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path schema1:name ] ; sh:targetClass ttm:TestCaseResult . ttm:TestEntity a sh:NodeShape ; @@ -1014,10 +1062,6 @@ ttm:TestEntity a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path schema1:name ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; sh:order 3 ; @@ -1026,7 +1070,11 @@ ttm:TestEntity a sh:NodeShape ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 2 ; - sh:path schema1:description ] ; + sh:path schema1:description ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path schema1:identifier ] ; sh:targetClass ttm:TestEntity . ttm:TestResultPKSet a sh:NodeShape ; @@ -1035,51 +1083,51 @@ ttm:TestResultPKSet a sh:NodeShape ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 3 ; - sh:path ttm:arax ], + sh:order 0 ; + sh:path ttm:parent_pk ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path ttm:bte ], + sh:order 8 ; + sh:path schema1:name ], [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 10 ; - sh:path schema1:additionalType ], + sh:description "A human-readable description for a Test Entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path schema1:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 4 ; sh:path ttm:unsecret ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 6 ; sh:path ttm:improving ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:parent_pk ], + sh:order 3 ; + sh:path ttm:arax ], [ sh:datatype xsd:string ; + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 10 ; + sh:path schema1:additionalType ], + [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path ttm:aragorn ], + sh:minCount 1 ; + sh:order 7 ; + sh:path schema1:identifier ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path ttm:merged_pk ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path schema1:name ], + sh:order 5 ; + sh:path ttm:bte ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path schema1:description ] ; + sh:order 2 ; + sh:path ttm:aragorn ] ; sh:targetClass ttm:TestResultPKSet . ttm:TestEntityParameter a sh:NodeShape ; @@ -1087,142 +1135,165 @@ ttm:TestEntityParameter a sh:NodeShape ; sh:description "A single 'tag = value' pair (where 'value' is a simple string)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "(String) value of a TestParameter." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:value ], - [ sh:datatype xsd:string ; sh:description "Name of a TestParameter." ; sh:maxCount 1 ; sh:order 0 ; - sh:path ttm:parameter ] ; + sh:path ttm:parameter ], + [ sh:datatype xsd:string ; + sh:description "(String) value of a TestParameter." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:value ] ; sh:targetClass ttm:TestEntityParameter . ttm:Qualifier a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The 'parameter' of a Qualifier should be a `qualifier` slot name from the Biolink Model ('biolink' namespace) 'biolink:qualifier' hierarchy." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:parameter ], - [ sh:datatype xsd:string ; sh:description "The 'value' of should be a suitable value generally drawn from an applicable Biolink Model (\"Enum\") value set of the specified Qualifier." ; sh:maxCount 1 ; sh:order 1 ; - sh:path ttm:value ] ; + sh:path ttm:value ], + [ sh:datatype xsd:string ; + sh:description "The 'parameter' of a Qualifier should be a `qualifier` slot name from the Biolink Model ('biolink' namespace) 'biolink:qualifier' hierarchy." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:parameter ] ; sh:targetClass ttm:Qualifier . ttm:TestSuiteSpecification a sh:NodeShape ; sh:closed true ; sh:description "Parameters for a Test Case instances either dynamically generated from some external source of Test Assets." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An web accessible file resource link to test entity data (e.g. a web accessible text file of Test Asset entries)" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable description for a Test Entity" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path schema1:description ], + [ sh:description "File format of test entity data (e.g. TSV, YAML or JSON)" ; + sh:in ( "TSV" "YAML" "JSON" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:test_data_file_format ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path schema1:identifier ], + [ sh:description "An web accessible file resource link to test entity data (e.g. a web accessible text file of Test Asset entries)" ; sh:maxCount 1 ; sh:order 0 ; sh:path ttm:test_data_file_locator ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path schema1:name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 5 ; + sh:path schema1:additionalType ] ; + sh:targetClass ttm:TestSuiteSpecification . + +ttm:TestAsset a sh:NodeShape ; + sh:closed true ; + sh:description "Represents a Test Asset, which is a single specific instance of TestCase-agnostic semantic parameters representing the specification of a Translator test target with inputs and (expected) outputs." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The direction of the subject of the test asset predicate" ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path ttm:biolink_subject_direction_qualifier ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path ttm:input_id ], + [ sh:datatype xsd:string ; + sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined to specify TestAsset membership in a \"Block List\" collection" ; + sh:order 26 ; + sh:path schema1:additionalType ], + [ sh:description "Document URL where original test source particulars are registered (e.g. Github repo)" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path ttm:test_reference ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path ttm:output_category ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path ttm:predicate_id ], + [ sh:class ttm:Qualifier ; + sh:description "Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot." ; + sh:nodeKind sh:BlankNode ; + sh:order 9 ; + sh:path ttm:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The direction of the object of the test asset predicate" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path schema1:description ], + sh:order 22 ; + sh:path ttm:biolink_object_direction_qualifier ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; + sh:order 23 ; sh:path schema1:identifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path schema1:name ], - [ sh:description "File format of test entity data (e.g. TSV, YAML or JSON)" ; - sh:in ( "TSV" "YAML" "JSON" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:test_data_file_format ], - [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 5 ; - sh:path schema1:additionalType ] ; - sh:targetClass ttm:TestSuiteSpecification . - -ttm:TestAsset a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a Test Asset, which is a single specific instance of TestCase-agnostic semantic parameters representing the specification of a Translator test target with inputs and (expected) outputs." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 25 ; sh:path schema1:description ], [ sh:maxCount 1 ; - sh:order 7 ; - sh:path ttm:output_category ], - [ sh:datatype xsd:boolean ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path ttm:well_known ], - [ sh:in ( "causes not treats" "TMKP" "category too generic" "contraindications" "chemical roles" "test_issue" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path ttm:test_issue ], + sh:order 2 ; + sh:path ttm:input_category ], [ sh:maxCount 1 ; sh:order 5 ; sh:path ttm:output_id ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path schema1:identifier ], [ sh:datatype xsd:string ; - sh:description "Settings for the test harness, e.g. \"inferred\"" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path ttm:runner_settings ], + sh:description "The aspect of the object of the test asset predicate" ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path ttm:biolink_object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path ttm:well_known ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 24 ; sh:path schema1:name ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ttm:input_id ], - [ sh:datatype xsd:string ; + [ sh:description "The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:input_name ], + sh:order 18 ; + sh:path ttm:biolink_qualified_predicate ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 10 ; - sh:path ttm:expected_output ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ttm:input_category ], - [ sh:description "Document URL where original test source particulars are registered (e.g. Github repo)" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path ttm:test_reference ], + sh:order 4 ; + sh:path ttm:predicate_name ], [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined to specify TestAsset membership in a \"Block List\" collection" ; - sh:order 21 ; - sh:path schema1:additionalType ], + sh:maxCount 1 ; + sh:order 6 ; + sh:path ttm:output_name ], [ sh:in ( "High" "Low" "NotApplicable" ) ; sh:maxCount 1 ; sh:order 12 ; sh:path ttm:semantic_severity ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ttm:predicate_name ], + sh:description "Settings for the test harness, e.g. \"inferred\"" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path ttm:runner_settings ], [ sh:description "Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement" ; sh:maxCount 1 ; sh:order 8 ; sh:path ttm:association ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; sh:maxCount 1 ; - sh:order 6 ; - sh:path ttm:output_name ], + sh:order 13 ; + sh:path ttm:in_v1 ], + [ sh:in ( "causes not treats" "TMKP" "category too generic" "contraindications" "chemical roles" "test_issue" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path ttm:test_issue ], [ sh:class ttm:TestMetadata ; sh:description "Test metadata describes the external provenance, cross-references and objectives for a given test." ; sh:maxCount 1 ; @@ -1230,98 +1301,99 @@ ttm:TestAsset a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path ttm:test_metadata ], - [ sh:class ttm:Qualifier ; - sh:description "Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot." ; - sh:nodeKind sh:BlankNode ; - sh:order 9 ; - sh:path ttm:qualifiers ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ttm:predicate_id ], - [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 13 ; - sh:path ttm:in_v1 ] ; + sh:order 10 ; + sh:path ttm:expected_output ], + [ sh:datatype xsd:string ; + sh:description "The aspect of the subject of the test asset predicate" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path ttm:biolink_subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:input_name ] ; sh:targetClass ttm:TestAsset . ttm:TestCase a sh:NodeShape ; sh:closed true ; sh:description "Represents a single enumerated instance of Test Case, derived from a given collection of one or more TestAsset instances (the value of the 'test_assets' slot) which define the 'inputs' and 'outputs' of the TestCase, used to probe a particular test condition." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; - sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; + sh:property [ sh:description "Type of TestCase query." ; + sh:in ( "treats" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path ttm:test_case_objective ], + sh:order 1 ; + sh:path ttm:query_type ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path ttm:test_case_predicate_id ], + sh:order 13 ; + sh:path schema1:name ], + [ sh:class ttm:Precondition ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path ttm:preconditions ], [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path schema1:description ], + sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; + sh:order 15 ; + sh:path schema1:additionalType ], + [ sh:datatype xsd:string ; + sh:description "Settings for the test harness for TestCase" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path ttm:test_case_runner_settings ], [ sh:class ttm:TestAsset ; sh:description "One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection." ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path ttm:test_assets ], - [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; - sh:in ( "arax" "aragorn" "ars" "bte" "improving" ) ; - sh:order 5 ; - sh:path ttm:components ], - [ sh:datatype xsd:string ; + [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path ttm:test_case_predicate_name ], + sh:order 6 ; + sh:path ttm:test_case_objective ], [ sh:description "Deployment environment within which the associated TestSuite is run." ; sh:in ( "dev" "ci" "test" "prod" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path ttm:test_env ], - [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; - sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path ttm:test_case_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; + sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path schema1:name ], - [ sh:description "Type of TestCase query." ; - sh:in ( "treats" ) ; + sh:order 14 ; + sh:path schema1:description ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:query_type ], + sh:order 9 ; + sh:path ttm:test_case_predicate_id ], [ sh:maxCount 1 ; sh:order 10 ; sh:path ttm:test_case_input_id ], - [ sh:datatype xsd:string ; - sh:description "Settings for the test harness for TestCase" ; + [ sh:description "The component that this test case is intended to run against. Most often this is the ARS for acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX." ; + sh:in [ rdf:rest () ] ; + sh:order 5 ; + sh:path ttm:components ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path ttm:test_case_runner_settings ], - [ sh:class ttm:Precondition ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path ttm:preconditions ], - [ sh:datatype xsd:string ; - sh:description "One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection." ; - sh:order 15 ; - sh:path schema1:additionalType ], + sh:order 12 ; + sh:path schema1:identifier ], + [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; + sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path ttm:test_case_source ], [ sh:description "A template for a query, which can be used to generate a query for a test case. note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template. Templates themselves are currently stored in the config/[source_name]/templates directory." ; sh:in ( "ameliorates" "treats" "three_hop" "drug_treats_rare_disease" "drug-to-gene" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path ttm:trapi_template ], - [ sh:description "A unique identifier for a Test Entity" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path schema1:identifier ] ; + sh:order 8 ; + sh:path ttm:test_case_predicate_name ] ; sh:targetClass ttm:TestCase . ttm:Precondition a sh:NodeShape ; @@ -1329,67 +1401,67 @@ ttm:Precondition a sh:NodeShape ; sh:description "Represents a precondition for a TestCase" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 3 ; - sh:path schema1:additionalType ], + sh:description "A human-readable name for a Test Entity" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path schema1:name ], [ sh:description "A unique identifier for a Test Entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for a Test Entity" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:name ], [ sh:datatype xsd:string ; sh:description "A human-readable description for a Test Entity" ; sh:maxCount 1 ; sh:order 2 ; - sh:path schema1:description ] ; + sh:path schema1:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 3 ; + sh:path schema1:additionalType ] ; sh:targetClass ttm:Precondition . ttm:TestMetadata a sh:NodeShape ; sh:closed true ; sh:description "Represents metadata related to (external SME, SMURF, Translator feedback, large scale batch, etc.) like the provenance of test assets, cases and/or suites." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; + sh:property [ sh:description "Document URL where original test source particulars are registered (e.g. Github repo)" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path ttm:test_reference ], + [ sh:description "Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative)" ; sh:in ( "AcceptanceTest" "BenchmarkTest" "QuantitativeTest" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path ttm:test_objective ], + [ sh:description "A unique identifier for a Test Entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path schema1:identifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable description for a Test Entity" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path schema1:description ], [ sh:description "Provenance of a specific set of test assets, cases and/or suites. Or, the person who cares about this, know about this. We would like this to be an ORCID eventually, but currently it is just a string." ; sh:in ( "SME" "SMURF" "GitHubUserFeedback" "TACT" "BenchMark" "TranslatorTeam" "TestDataLocation" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path ttm:test_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; + sh:order 7 ; + sh:path schema1:additionalType ], [ sh:datatype xsd:string ; sh:description "A human-readable name for a Test Entity" ; sh:maxCount 1 ; sh:order 5 ; sh:path schema1:name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable description for a Test Entity" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path schema1:description ], - [ sh:description "Document URL where original test source particulars are registered (e.g. Github repo)" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ttm:test_reference ], [ sh:class ttm:TestEntityParameter ; sh:description "Metadata annotation." ; sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path ttm:test_annotations ], - [ sh:description "A unique identifier for a Test Entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path schema1:identifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists." ; - sh:order 7 ; - sh:path schema1:additionalType ] ; + sh:path ttm:test_annotations ] ; sh:targetClass ttm:TestMetadata . diff --git a/project/shex/translator_testing_model.shex b/project/shex/translator_testing_model.shex index b5f5b05..6ddf9cd 100644 --- a/project/shex/translator_testing_model.shex +++ b/project/shex/translator_testing_model.shex @@ -184,6 +184,11 @@ linkml:Sparqlpath xsd:string @linkml:Uriorcurie ? ; @linkml:String + ; @ ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; + @linkml:String ? ; + @linkml:String ? ; + @linkml:String ? ; schema1:additionalType @linkml:String * ) ; rdf:type [ ] diff --git a/project/sqlschema/translator_testing_model.sql b/project/sqlschema/translator_testing_model.sql index 19c20b3..db751a7 100644 --- a/project/sqlschema/translator_testing_model.sql +++ b/project/sqlschema/translator_testing_model.sql @@ -187,6 +187,11 @@ CREATE TABLE "AcceptanceTestAsset" ( well_known BOOLEAN, test_reference TEXT, test_metadata TEXT NOT NULL, + biolink_qualified_predicate TEXT, + biolink_subject_aspect_qualifier TEXT, + biolink_subject_direction_qualifier TEXT, + biolink_object_aspect_qualifier TEXT, + biolink_object_direction_qualifier TEXT, id TEXT NOT NULL, must_pass_date DATE, must_pass_environment VARCHAR(4), @@ -263,6 +268,11 @@ CREATE TABLE "TestAsset" ( well_known BOOLEAN, test_reference TEXT, test_metadata TEXT NOT NULL, + biolink_qualified_predicate TEXT, + biolink_subject_aspect_qualifier TEXT, + biolink_subject_direction_qualifier TEXT, + biolink_object_aspect_qualifier TEXT, + biolink_object_direction_qualifier TEXT, id TEXT NOT NULL, PRIMARY KEY (id), FOREIGN KEY(test_metadata) REFERENCES "TestMetadata" (id) @@ -301,6 +311,11 @@ CREATE TABLE "TestEdgeData" ( well_known BOOLEAN, test_reference TEXT, test_metadata TEXT NOT NULL, + biolink_qualified_predicate TEXT, + biolink_subject_aspect_qualifier TEXT, + biolink_subject_direction_qualifier TEXT, + biolink_object_aspect_qualifier TEXT, + biolink_object_direction_qualifier TEXT, id TEXT NOT NULL, PRIMARY KEY (id), FOREIGN KEY(test_metadata) REFERENCES "TestMetadata" (id) @@ -337,7 +352,7 @@ CREATE TABLE "TestSuite" ( CREATE TABLE "AcceptanceTestCase_components" ( backref_id TEXT, - components VARCHAR(9), + components VARCHAR, PRIMARY KEY (backref_id, components), FOREIGN KEY(backref_id) REFERENCES "AcceptanceTestCase" (id) ); @@ -358,7 +373,7 @@ CREATE TABLE "AcceptanceTestCase_tags" ( CREATE TABLE "ComplianceTestCase_components" ( backref_id TEXT, - components VARCHAR(9), + components VARCHAR, PRIMARY KEY (backref_id, components), FOREIGN KEY(backref_id) REFERENCES "ComplianceTestCase" (id) ); @@ -379,7 +394,7 @@ CREATE TABLE "ComplianceTestCase_tags" ( CREATE TABLE "KnowledgeGraphNavigationTestCase_components" ( backref_id TEXT, - components VARCHAR(9), + components VARCHAR, PRIMARY KEY (backref_id, components), FOREIGN KEY(backref_id) REFERENCES "KnowledgeGraphNavigationTestCase" (id) ); @@ -400,7 +415,7 @@ CREATE TABLE "KnowledgeGraphNavigationTestCase_tags" ( CREATE TABLE "OneHopTestCase_components" ( backref_id TEXT, - components VARCHAR(9), + components VARCHAR, PRIMARY KEY (backref_id, components), FOREIGN KEY(backref_id) REFERENCES "OneHopTestCase" (id) ); @@ -428,7 +443,7 @@ CREATE TABLE "Precondition_tags" ( CREATE TABLE "QuantitativeTestCase_components" ( backref_id TEXT, - components VARCHAR(9), + components VARCHAR, PRIMARY KEY (backref_id, components), FOREIGN KEY(backref_id) REFERENCES "QuantitativeTestCase" (id) ); @@ -449,7 +464,7 @@ CREATE TABLE "QuantitativeTestCase_tags" ( CREATE TABLE "TestCase_components" ( backref_id TEXT, - components VARCHAR(9), + components VARCHAR, PRIMARY KEY (backref_id, components), FOREIGN KEY(backref_id) REFERENCES "TestCase" (id) ); diff --git a/pyproject.toml b/pyproject.toml index f3563e5..1b93b00 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,6 +19,7 @@ linkml-runtime = "^1.6.1" linkml = "^1.6.1" pandas = "^2.1.2" pydantic = "^1.10.13" +bmt = "^1.2.1" [tool.poetry-dynamic-versioning] enable = true diff --git a/src/translator_testing_model/datamodel/pydanticmodel.py b/src/translator_testing_model/datamodel/pydanticmodel.py index 9f24818..5a63e36 100644 --- a/src/translator_testing_model/datamodel/pydanticmodel.py +++ b/src/translator_testing_model/datamodel/pydanticmodel.py @@ -2,7 +2,7 @@ from datetime import datetime, date from enum import Enum from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field +from pydantic import BaseModel as BaseModel, ConfigDict, Field import sys if sys.version_info >= (3, 8): from typing import Literal @@ -184,19 +184,12 @@ class TrapiTemplateEnum(str, Enum): -class ComponentEnum(str, Enum): - - - arax = "arax" - - aragorn = "aragorn" - - ars = "ars" - - bte = "bte" - - improving = "improving" +class ComponentEnum(str): + """ + Translator components are identified by their InfoRes identifiers. + """ + dummy = "dummy" class TestPersonaEnum(str, Enum): @@ -285,6 +278,11 @@ class TestAsset(TestEntity): test_reference: Optional[str] = Field(None, description="""Document URL where original test source particulars are registered (e.g. Github repo)""") runner_settings: List[str] = Field(default_factory=list, description="""Settings for the test harness, e.g. \"inferred\"""") test_metadata: TestMetadata = Field(..., description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""") + biolink_qualified_predicate: Optional[str] = Field(None, description="""The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.""") + biolink_subject_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the subject of the test asset predicate""") + biolink_subject_direction_qualifier: Optional[str] = Field(None, description="""The direction of the subject of the test asset predicate""") + biolink_object_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the object of the test asset predicate""") + biolink_object_direction_qualifier: Optional[str] = Field(None, description="""The direction of the object of the test asset predicate""") id: str = Field(..., description="""A unique identifier for a Test Entity""") name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""") description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""") @@ -323,6 +321,11 @@ class AcceptanceTestAsset(TestAsset): test_reference: Optional[str] = Field(None, description="""Document URL where original test source particulars are registered (e.g. Github repo)""") runner_settings: List[str] = Field(default_factory=list, description="""Settings for the test harness, e.g. \"inferred\"""") test_metadata: TestMetadata = Field(..., description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""") + biolink_qualified_predicate: Optional[str] = Field(None, description="""The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.""") + biolink_subject_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the subject of the test asset predicate""") + biolink_subject_direction_qualifier: Optional[str] = Field(None, description="""The direction of the subject of the test asset predicate""") + biolink_object_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the object of the test asset predicate""") + biolink_object_direction_qualifier: Optional[str] = Field(None, description="""The direction of the object of the test asset predicate""") id: str = Field(..., description="""A unique identifier for a Test Entity""") name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""") description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""") @@ -351,6 +354,11 @@ class TestEdgeData(TestAsset): test_reference: Optional[str] = Field(None, description="""Document URL where original test source particulars are registered (e.g. Github repo)""") runner_settings: List[str] = Field(default_factory=list, description="""Settings for the test harness, e.g. \"inferred\"""") test_metadata: TestMetadata = Field(..., description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""") + biolink_qualified_predicate: Optional[str] = Field(None, description="""The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.""") + biolink_subject_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the subject of the test asset predicate""") + biolink_subject_direction_qualifier: Optional[str] = Field(None, description="""The direction of the subject of the test asset predicate""") + biolink_object_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the object of the test asset predicate""") + biolink_object_direction_qualifier: Optional[str] = Field(None, description="""The direction of the object of the test asset predicate""") id: str = Field(..., description="""A unique identifier for a Test Entity""") name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""") description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""") diff --git a/src/translator_testing_model/datamodel/pydanticmodel_v2.py b/src/translator_testing_model/datamodel/pydanticmodel_v2.py index 27c58b2..0d171c5 100644 --- a/src/translator_testing_model/datamodel/pydanticmodel_v2.py +++ b/src/translator_testing_model/datamodel/pydanticmodel_v2.py @@ -2,7 +2,7 @@ from datetime import datetime, date from enum import Enum from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field +from pydantic import BaseModel as BaseModel, ConfigDict, Field import sys if sys.version_info >= (3, 8): from typing import Literal @@ -13,13 +13,13 @@ metamodel_version = "None" version = "0.0.0" -class ConfiguredBaseModel(BaseModel, - validate_assignment = True, - validate_default = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): - pass +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment=True, + validate_default=True, + extra='forbid', + arbitrary_types_allowed=True, + use_enum_values = True) class TestSourceEnum(str, Enum): @@ -180,19 +180,12 @@ class TrapiTemplateEnum(str, Enum): -class ComponentEnum(str, Enum): - - - arax = "arax" - - aragorn = "aragorn" - - ars = "ars" - - bte = "bte" - - improving = "improving" +class ComponentEnum(str): + """ + Translator components are identified by their InfoRes identifiers. + """ + dummy = "dummy" class TestPersonaEnum(str, Enum): @@ -281,6 +274,11 @@ class TestAsset(TestEntity): test_reference: Optional[str] = Field(None, description="""Document URL where original test source particulars are registered (e.g. Github repo)""") runner_settings: List[str] = Field(default_factory=list, description="""Settings for the test harness, e.g. \"inferred\"""") test_metadata: TestMetadata = Field(..., description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""") + biolink_qualified_predicate: Optional[str] = Field(None, description="""The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.""") + biolink_subject_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the subject of the test asset predicate""") + biolink_subject_direction_qualifier: Optional[str] = Field(None, description="""The direction of the subject of the test asset predicate""") + biolink_object_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the object of the test asset predicate""") + biolink_object_direction_qualifier: Optional[str] = Field(None, description="""The direction of the object of the test asset predicate""") id: str = Field(..., description="""A unique identifier for a Test Entity""") name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""") description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""") @@ -319,6 +317,11 @@ class AcceptanceTestAsset(TestAsset): test_reference: Optional[str] = Field(None, description="""Document URL where original test source particulars are registered (e.g. Github repo)""") runner_settings: List[str] = Field(default_factory=list, description="""Settings for the test harness, e.g. \"inferred\"""") test_metadata: TestMetadata = Field(..., description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""") + biolink_qualified_predicate: Optional[str] = Field(None, description="""The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.""") + biolink_subject_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the subject of the test asset predicate""") + biolink_subject_direction_qualifier: Optional[str] = Field(None, description="""The direction of the subject of the test asset predicate""") + biolink_object_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the object of the test asset predicate""") + biolink_object_direction_qualifier: Optional[str] = Field(None, description="""The direction of the object of the test asset predicate""") id: str = Field(..., description="""A unique identifier for a Test Entity""") name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""") description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""") @@ -347,6 +350,11 @@ class TestEdgeData(TestAsset): test_reference: Optional[str] = Field(None, description="""Document URL where original test source particulars are registered (e.g. Github repo)""") runner_settings: List[str] = Field(default_factory=list, description="""Settings for the test harness, e.g. \"inferred\"""") test_metadata: TestMetadata = Field(..., description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""") + biolink_qualified_predicate: Optional[str] = Field(None, description="""The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset.""") + biolink_subject_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the subject of the test asset predicate""") + biolink_subject_direction_qualifier: Optional[str] = Field(None, description="""The direction of the subject of the test asset predicate""") + biolink_object_aspect_qualifier: Optional[str] = Field(None, description="""The aspect of the object of the test asset predicate""") + biolink_object_direction_qualifier: Optional[str] = Field(None, description="""The direction of the object of the test asset predicate""") id: str = Field(..., description="""A unique identifier for a Test Entity""") name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""") description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""") @@ -665,4 +673,4 @@ class TestResultPKSet(TestEntity): TestRunSession.model_rebuild() TestOutput.model_rebuild() TestResultPKSet.model_rebuild() - + diff --git a/src/translator_testing_model/datamodel/translator_testing_model.py b/src/translator_testing_model/datamodel/translator_testing_model.py index a6192f1..15c6a10 100644 --- a/src/translator_testing_model/datamodel/translator_testing_model.py +++ b/src/translator_testing_model/datamodel/translator_testing_model.py @@ -1,5 +1,5 @@ # Auto generated from translator_testing_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-12-07T10:24:11 +# Generation date: 2024-03-04T11:40:04 # Schema: Translator-Testing-Model # # id: https://w3id.org/TranslatorSRI/TranslatorTestingModel @@ -44,7 +44,7 @@ # Types class CategoryType(Uriorcurie): """ A primitive type in which the value denotes a class within the biolink model. The value must be a URI or a CURIE within the 'biolink' namespace. """ - type_class_uri = XSD.anyURI + type_class_uri = XSD["anyURI"] type_class_curie = "xsd:anyURI" type_name = "category_type" type_model_uri = TTM.CategoryType @@ -52,7 +52,7 @@ class CategoryType(Uriorcurie): class PredicateType(Uriorcurie): """ A CURIE from the Biolink Model ('biolink' namespace) 'biolink:related_to' hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats. """ - type_class_uri = XSD.anyURI + type_class_uri = XSD["anyURI"] type_class_curie = "xsd:anyURI" type_name = "predicate_type" type_model_uri = TTM.PredicateType @@ -60,7 +60,7 @@ class PredicateType(Uriorcurie): class ConceptCategory(CategoryType): """ A category type within the Biolink Model ('biolink' namespace) 'biolink:NamedThing' hierarchy. """ - type_class_uri = XSD.anyURI + type_class_uri = XSD["anyURI"] type_class_curie = "xsd:anyURI" type_name = "concept_category" type_model_uri = TTM.ConceptCategory @@ -68,7 +68,7 @@ class ConceptCategory(CategoryType): class AssociationCategory(CategoryType): """ A category type within the Biolink Model ('biolink' namespace) 'biolink:Association' hierarchy. """ - type_class_uri = XSD.anyURI + type_class_uri = XSD["anyURI"] type_class_curie = "xsd:anyURI" type_name = "association_category" type_model_uri = TTM.AssociationCategory @@ -170,7 +170,7 @@ class TestEntityParameter(YAMLRoot): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestEntityParameter + class_class_uri: ClassVar[URIRef] = TTM["TestEntityParameter"] class_class_curie: ClassVar[str] = "ttm:TestEntityParameter" class_name: ClassVar[str] = "TestEntityParameter" class_model_uri: ClassVar[URIRef] = TTM.TestEntityParameter @@ -192,7 +192,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): class Qualifier(TestEntityParameter): _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.Qualifier + class_class_uri: ClassVar[URIRef] = TTM["Qualifier"] class_class_curie: ClassVar[str] = "ttm:Qualifier" class_name: ClassVar[str] = "Qualifier" class_model_uri: ClassVar[URIRef] = TTM.Qualifier @@ -218,7 +218,7 @@ class TestEntity(YAMLRoot): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestEntity + class_class_uri: ClassVar[URIRef] = TTM["TestEntity"] class_class_curie: ClassVar[str] = "ttm:TestEntity" class_name: ClassVar[str] = "TestEntity" class_model_uri: ClassVar[URIRef] = TTM.TestEntity @@ -255,7 +255,7 @@ class TestMetadata(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestMetadata + class_class_uri: ClassVar[URIRef] = TTM["TestMetadata"] class_class_curie: ClassVar[str] = "ttm:TestMetadata" class_name: ClassVar[str] = "TestMetadata" class_model_uri: ClassVar[URIRef] = TTM.TestMetadata @@ -296,7 +296,7 @@ class TestAsset(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestAsset + class_class_uri: ClassVar[URIRef] = TTM["TestAsset"] class_class_curie: ClassVar[str] = "ttm:TestAsset" class_name: ClassVar[str] = "TestAsset" class_model_uri: ClassVar[URIRef] = TTM.TestAsset @@ -320,6 +320,11 @@ class TestAsset(TestEntity): in_v1: Optional[Union[bool, Bool]] = None well_known: Optional[Union[bool, Bool]] = None test_reference: Optional[Union[str, URIorCURIE]] = None + biolink_qualified_predicate: Optional[Union[str, URIorCURIE]] = None + biolink_subject_aspect_qualifier: Optional[str] = None + biolink_subject_direction_qualifier: Optional[str] = None + biolink_object_aspect_qualifier: Optional[str] = None + biolink_object_direction_qualifier: Optional[str] = None tags: Optional[Union[str, List[str]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -388,6 +393,21 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.test_reference is not None and not isinstance(self.test_reference, URIorCURIE): self.test_reference = URIorCURIE(self.test_reference) + if self.biolink_qualified_predicate is not None and not isinstance(self.biolink_qualified_predicate, URIorCURIE): + self.biolink_qualified_predicate = URIorCURIE(self.biolink_qualified_predicate) + + if self.biolink_subject_aspect_qualifier is not None and not isinstance(self.biolink_subject_aspect_qualifier, str): + self.biolink_subject_aspect_qualifier = str(self.biolink_subject_aspect_qualifier) + + if self.biolink_subject_direction_qualifier is not None and not isinstance(self.biolink_subject_direction_qualifier, str): + self.biolink_subject_direction_qualifier = str(self.biolink_subject_direction_qualifier) + + if self.biolink_object_aspect_qualifier is not None and not isinstance(self.biolink_object_aspect_qualifier, str): + self.biolink_object_aspect_qualifier = str(self.biolink_object_aspect_qualifier) + + if self.biolink_object_direction_qualifier is not None and not isinstance(self.biolink_object_direction_qualifier, str): + self.biolink_object_direction_qualifier = str(self.biolink_object_direction_qualifier) + if not isinstance(self.tags, list): self.tags = [self.tags] if self.tags is not None else [] self.tags = [v if isinstance(v, str) else str(v) for v in self.tags] @@ -402,7 +422,7 @@ class AcceptanceTestAsset(TestAsset): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.AcceptanceTestAsset + class_class_uri: ClassVar[URIRef] = TTM["AcceptanceTestAsset"] class_class_curie: ClassVar[str] = "ttm:AcceptanceTestAsset" class_name: ClassVar[str] = "AcceptanceTestAsset" class_model_uri: ClassVar[URIRef] = TTM.AcceptanceTestAsset @@ -468,7 +488,7 @@ class TestEdgeData(TestAsset): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestEdgeData + class_class_uri: ClassVar[URIRef] = TTM["TestEdgeData"] class_class_curie: ClassVar[str] = "ttm:TestEdgeData" class_name: ClassVar[str] = "TestEdgeData" class_model_uri: ClassVar[URIRef] = TTM.TestEdgeData @@ -493,7 +513,7 @@ class Precondition(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.Precondition + class_class_uri: ClassVar[URIRef] = TTM["Precondition"] class_class_curie: ClassVar[str] = "ttm:Precondition" class_name: ClassVar[str] = "Precondition" class_model_uri: ClassVar[URIRef] = TTM.Precondition @@ -518,7 +538,7 @@ class TestCase(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestCase + class_class_uri: ClassVar[URIRef] = TTM["TestCase"] class_class_curie: ClassVar[str] = "ttm:TestCase" class_name: ClassVar[str] = "TestCase" class_model_uri: ClassVar[URIRef] = TTM.TestCase @@ -600,7 +620,7 @@ class AcceptanceTestCase(TestCase): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.AcceptanceTestCase + class_class_uri: ClassVar[URIRef] = TTM["AcceptanceTestCase"] class_class_curie: ClassVar[str] = "ttm:AcceptanceTestCase" class_name: ClassVar[str] = "AcceptanceTestCase" class_model_uri: ClassVar[URIRef] = TTM.AcceptanceTestCase @@ -629,7 +649,7 @@ class QuantitativeTestCase(TestCase): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.QuantitativeTestCase + class_class_uri: ClassVar[URIRef] = TTM["QuantitativeTestCase"] class_class_curie: ClassVar[str] = "ttm:QuantitativeTestCase" class_name: ClassVar[str] = "QuantitativeTestCase" class_model_uri: ClassVar[URIRef] = TTM.QuantitativeTestCase @@ -654,7 +674,7 @@ class ComplianceTestCase(TestCase): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.ComplianceTestCase + class_class_uri: ClassVar[URIRef] = TTM["ComplianceTestCase"] class_class_curie: ClassVar[str] = "ttm:ComplianceTestCase" class_name: ClassVar[str] = "ComplianceTestCase" class_model_uri: ClassVar[URIRef] = TTM.ComplianceTestCase @@ -687,7 +707,7 @@ class KnowledgeGraphNavigationTestCase(TestCase): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.KnowledgeGraphNavigationTestCase + class_class_uri: ClassVar[URIRef] = TTM["KnowledgeGraphNavigationTestCase"] class_class_curie: ClassVar[str] = "ttm:KnowledgeGraphNavigationTestCase" class_name: ClassVar[str] = "KnowledgeGraphNavigationTestCase" class_model_uri: ClassVar[URIRef] = TTM.KnowledgeGraphNavigationTestCase @@ -712,7 +732,7 @@ class OneHopTestCase(KnowledgeGraphNavigationTestCase): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.OneHopTestCase + class_class_uri: ClassVar[URIRef] = TTM["OneHopTestCase"] class_class_curie: ClassVar[str] = "ttm:OneHopTestCase" class_name: ClassVar[str] = "OneHopTestCase" class_model_uri: ClassVar[URIRef] = TTM.OneHopTestCase @@ -737,7 +757,7 @@ class TestSuiteSpecification(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestSuiteSpecification + class_class_uri: ClassVar[URIRef] = TTM["TestSuiteSpecification"] class_class_curie: ClassVar[str] = "ttm:TestSuiteSpecification" class_name: ClassVar[str] = "TestSuiteSpecification" class_model_uri: ClassVar[URIRef] = TTM.TestSuiteSpecification @@ -770,7 +790,7 @@ class TestSuite(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestSuite + class_class_uri: ClassVar[URIRef] = TTM["TestSuite"] class_class_curie: ClassVar[str] = "ttm:TestSuite" class_name: ClassVar[str] = "TestSuite" class_model_uri: ClassVar[URIRef] = TTM.TestSuite @@ -807,7 +827,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): class AcceptanceTestSuite(TestSuite): _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.AcceptanceTestSuite + class_class_uri: ClassVar[URIRef] = TTM["AcceptanceTestSuite"] class_class_curie: ClassVar[str] = "ttm:AcceptanceTestSuite" class_name: ClassVar[str] = "AcceptanceTestSuite" class_model_uri: ClassVar[URIRef] = TTM.AcceptanceTestSuite @@ -830,7 +850,7 @@ class BenchmarkTestSuite(YAMLRoot): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.BenchmarkTestSuite + class_class_uri: ClassVar[URIRef] = TTM["BenchmarkTestSuite"] class_class_curie: ClassVar[str] = "ttm:BenchmarkTestSuite" class_name: ClassVar[str] = "BenchmarkTestSuite" class_model_uri: ClassVar[URIRef] = TTM.BenchmarkTestSuite @@ -843,7 +863,7 @@ class StandardsComplianceTestSuite(TestSuite): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.StandardsComplianceTestSuite + class_class_uri: ClassVar[URIRef] = TTM["StandardsComplianceTestSuite"] class_class_curie: ClassVar[str] = "ttm:StandardsComplianceTestSuite" class_name: ClassVar[str] = "StandardsComplianceTestSuite" class_model_uri: ClassVar[URIRef] = TTM.StandardsComplianceTestSuite @@ -867,7 +887,7 @@ class OneHopTestSuite(TestSuite): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.OneHopTestSuite + class_class_uri: ClassVar[URIRef] = TTM["OneHopTestSuite"] class_class_curie: ClassVar[str] = "ttm:OneHopTestSuite" class_name: ClassVar[str] = "OneHopTestSuite" class_model_uri: ClassVar[URIRef] = TTM.OneHopTestSuite @@ -891,7 +911,7 @@ class TestRunnerConfiguration(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestRunnerConfiguration + class_class_uri: ClassVar[URIRef] = TTM["TestRunnerConfiguration"] class_class_curie: ClassVar[str] = "ttm:TestRunnerConfiguration" class_name: ClassVar[str] = "TestRunnerConfiguration" class_model_uri: ClassVar[URIRef] = TTM.TestRunnerConfiguration @@ -924,7 +944,7 @@ class TestCaseResult(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestCaseResult + class_class_uri: ClassVar[URIRef] = TTM["TestCaseResult"] class_class_curie: ClassVar[str] = "ttm:TestCaseResult" class_name: ClassVar[str] = "TestCaseResult" class_model_uri: ClassVar[URIRef] = TTM.TestCaseResult @@ -959,7 +979,7 @@ class TestRunSession(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestRunSession + class_class_uri: ClassVar[URIRef] = TTM["TestRunSession"] class_class_curie: ClassVar[str] = "ttm:TestRunSession" class_name: ClassVar[str] = "TestRunSession" class_model_uri: ClassVar[URIRef] = TTM.TestRunSession @@ -996,7 +1016,7 @@ class TestOutput(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestOutput + class_class_uri: ClassVar[URIRef] = TTM["TestOutput"] class_class_curie: ClassVar[str] = "ttm:TestOutput" class_name: ClassVar[str] = "TestOutput" class_model_uri: ClassVar[URIRef] = TTM.TestOutput @@ -1028,7 +1048,7 @@ class TestResultPKSet(TestEntity): """ _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = TTM.TestResultPKSet + class_class_uri: ClassVar[URIRef] = TTM["TestResultPKSet"] class_class_curie: ClassVar[str] = "ttm:TestResultPKSet" class_name: ClassVar[str] = "TestResultPKSet" class_model_uri: ClassVar[URIRef] = TTM.TestResultPKSet @@ -1266,15 +1286,12 @@ def _addvals(cls): PermissibleValue(text="drug-to-gene")) class ComponentEnum(EnumDefinitionImpl): - - arax = PermissibleValue(text="arax") - aragorn = PermissibleValue(text="aragorn") - ars = PermissibleValue(text="ars") - bte = PermissibleValue(text="bte") - improving = PermissibleValue(text="improving") - + """ + Translator components are identified by their InfoRes identifiers. + """ _defn = EnumDefinition( name="ComponentEnum", + description="Translator components are identified by their InfoRes identifiers.", ) class TestPersonaEnum(EnumDefinitionImpl): @@ -1407,6 +1424,24 @@ class slots: slots.predicate_name = Slot(uri=TTM.predicate_name, name="predicate_name", curie=TTM.curie('predicate_name'), model_uri=TTM.predicate_name, domain=None, range=Optional[str]) +slots.biolink_predicate = Slot(uri=TTM.biolink_predicate, name="biolink_predicate", curie=TTM.curie('biolink_predicate'), + model_uri=TTM.biolink_predicate, domain=None, range=Optional[Union[str, URIorCURIE]]) + +slots.biolink_subject_aspect_qualifier = Slot(uri=TTM.biolink_subject_aspect_qualifier, name="biolink_subject_aspect_qualifier", curie=TTM.curie('biolink_subject_aspect_qualifier'), + model_uri=TTM.biolink_subject_aspect_qualifier, domain=None, range=Optional[str]) + +slots.biolink_subject_direction_qualifier = Slot(uri=TTM.biolink_subject_direction_qualifier, name="biolink_subject_direction_qualifier", curie=TTM.curie('biolink_subject_direction_qualifier'), + model_uri=TTM.biolink_subject_direction_qualifier, domain=None, range=Optional[str]) + +slots.biolink_object_aspect_qualifier = Slot(uri=TTM.biolink_object_aspect_qualifier, name="biolink_object_aspect_qualifier", curie=TTM.curie('biolink_object_aspect_qualifier'), + model_uri=TTM.biolink_object_aspect_qualifier, domain=None, range=Optional[str]) + +slots.biolink_object_direction_qualifier = Slot(uri=TTM.biolink_object_direction_qualifier, name="biolink_object_direction_qualifier", curie=TTM.curie('biolink_object_direction_qualifier'), + model_uri=TTM.biolink_object_direction_qualifier, domain=None, range=Optional[str]) + +slots.biolink_qualified_predicate = Slot(uri=TTM.biolink_qualified_predicate, name="biolink_qualified_predicate", curie=TTM.curie('biolink_qualified_predicate'), + model_uri=TTM.biolink_qualified_predicate, domain=None, range=Optional[Union[str, URIorCURIE]]) + slots.output_id = Slot(uri=TTM.output_id, name="output_id", curie=TTM.curie('output_id'), model_uri=TTM.output_id, domain=None, range=Optional[Union[str, URIorCURIE]]) diff --git a/src/translator_testing_model/schema/translator_testing_model.yaml b/src/translator_testing_model/schema/translator_testing_model.yaml index 2cd49c7..2c948f8 100644 --- a/src/translator_testing_model/schema/translator_testing_model.yaml +++ b/src/translator_testing_model/schema/translator_testing_model.yaml @@ -129,6 +129,11 @@ classes: - test_reference - runner_settings - test_metadata + - biolink_qualified_predicate + - biolink_subject_aspect_qualifier + - biolink_subject_direction_qualifier + - biolink_object_aspect_qualifier + - biolink_object_direction_qualifier slot_usage: id: aliases: ["AssetIdentifier"] @@ -506,6 +511,31 @@ slots: predicate_name: aliases: ["Query", "Relationship"] + biolink_predicate: + description: the predicate in Biolink model corresponding to the shorthand predicate name used in the test asset. + range: uriorcurie + + biolink_subject_aspect_qualifier: + description: >- + The aspect of the subject of the test asset predicate + + biolink_subject_direction_qualifier: + description: >- + The direction of the subject of the test asset predicate + + biolink_object_aspect_qualifier: + description: >- + The aspect of the object of the test asset predicate + + biolink_object_direction_qualifier: + description: >- + The direction of the object of the test asset predicate + + biolink_qualified_predicate: + description: >- + The qualified_predicate in Biolink model corresponding to the shorthand predicate name used in the test asset. + range: uriorcurie + output_id: aliases: ["OutputID", "ObjectID"] range: uriorcurie diff --git a/src/translator_testing_model/scripts/generate_suite_for_demo.py b/src/translator_testing_model/scripts/generate_suite_for_demo.py index b022640..f0cc656 100644 --- a/src/translator_testing_model/scripts/generate_suite_for_demo.py +++ b/src/translator_testing_model/scripts/generate_suite_for_demo.py @@ -1,8 +1,30 @@ from src.translator_testing_model.datamodel.pydanticmodel import TestAsset, TestCase, TestSuite, TestMetadata import csv import json -import os import requests +import yaml +import bmt +toolkit = bmt.Toolkit() + + +def retrieve_predicate_mapping(): + # URL of the YAML file + predicate_mapping_url = "https://w3id.org/biolink/predicate_mapping.yaml" + + # Fetch the content of the YAML file + request_response = requests.get(predicate_mapping_url) + + # Check if the request was successful + if response.status_code == 200: + # Parse the YAML content into a Python dictionary + predicate_mapping = yaml.safe_load(request_response.content) + + # Return the parsed dictionary + return predicate_mapping + else: + # Handle errors or unsuccessful requests + print(f"Failed to retrieve the file. HTTP Status Code: {request_response.status_code}") + return None def parse_tsv(filename): @@ -26,6 +48,25 @@ def create_test_assets_from_tsv(test_assets): for row in test_assets: if row.get("Relationship") == "": continue + + biolink_qualified_predicate = "" + biolink_object_aspect_qualifier = "" + biolink_object_direction_qualifier = "" + specified_predicate = row.get("Relationship").lower() + if toolkit.get_element(specified_predicate) is not None: + converted_predicate = toolkit.get_element(specified_predicate).name + else: + pred_mapping = toolkit.pmap + for collction in pred_mapping.values(): + for map_item in collction: + if map_item.get("mapped predicate") == specified_predicate: + converted_predicate = map_item.get("mapped predicate") + converted_predicate = "biolink:" + converted_predicate.replace(" ", "_") + biolink_object_aspect_qualifier = map_item.get("biolink:object_aspect_qualifier") + biolink_object_direction_qualifier = map_item.get("biolink:object_direction_qualifier") + biolink_qualified_predicate = map_item.get("biolink:qualified_predicate") + + expected_output = None if row.get("Expected Result / Suggested Comparator") == "4_NeverShow": expected_output = "NeverShow" @@ -38,6 +79,7 @@ def create_test_assets_from_tsv(test_assets): else: print(f"{row.get('id')} has invalid expected output") continue + ta = TestAsset(id=row.get("id").replace(":", "_"), name=expected_output + ': ' + row.get("OutputName").replace(" ", "_") + "_" + row.get("Relationship").lower() + "_" + row.get("InputName (user choice)").replace(" ", "_"), description=row.get("OutputName").replace(" ", "_") + "_" + row.get("Relationship").lower() + "_" + row.get("InputName (user choice)").replace(" ", "_"), @@ -49,10 +91,10 @@ def create_test_assets_from_tsv(test_assets): test_metadata=TestMetadata(id=1), ) ta.input_name = row.get("InputName (user choice)") - if row.get("GitHubIssue") != "" and row.get("GitHubIssue") is not None: + if row.get("Translator GitHubIssue") != "" and row.get("Translator GitHubIssue") is not None: tmd = TestMetadata(id=1, test_source="SMURF", - test_reference=row.get("GitHubIssue"), + test_reference=row.get("Translator GitHubIssue"), test_objective="AcceptanceTest") ta.test_metadata = tmd else: @@ -60,9 +102,12 @@ def create_test_assets_from_tsv(test_assets): test_source="SMURF", test_objective="AcceptanceTest") ta.test_metadata = tmd - ta.output_name = row.get("OutputName") ta.runner_settings = [row.get("Settings").lower()] + if biolink_qualified_predicate != "": + ta.biolink_qualified_predicate = biolink_qualified_predicate + ta.biolink_object_aspect_qualifier = biolink_object_aspect_qualifier + ta.biolink_object_direction_qualifier = biolink_object_direction_qualifier if row.get("Well Known") == "yes": ta.well_known = True else: @@ -125,8 +170,7 @@ def create_test_suite_from_test_cases(test_cases, test_suite_model): if __name__ == '__main__': # Reading the TSV file - tsv_file_path = 'pf_test_assets_2023_11_28.tsv' - print(f"Error: The file {tsv_file_path} does not exist in the directory {os.getcwd()}.") + tsv_file_path = 'pf_test_assets_030424.tsv' tsv_data = parse_tsv(tsv_file_path) # Create TestAsset objects @@ -154,7 +198,7 @@ def create_test_suite_from_test_cases(test_cases, test_suite_model): with open(filename, 'w', encoding='utf-8') as file: json.dump(item.dict(), file, ensure_ascii=False, indent=4) - url = 'https://raw.githubusercontent.com/TranslatorSRI/Benchmarks/main/config/benchmarks.json' + url = 'https://raw.githubusercontent.com/TranslatorSRI/Benchmarks/main/benchmarks_runner/config/benchmarks.json' # Send a GET request to the URL response = requests.get(url) @@ -179,9 +223,11 @@ def create_test_suite_from_test_cases(test_cases, test_suite_model): test_env="ci", components=["ars"], test_case_objective="QuantitativeTest", + test_case_runner_settings=["limit_queries"] ) file_prefix = k - test_cases.append(tc) + if k.startswith("DrugCentral_subset"): + test_cases.append(tc) filename = f"{file_prefix}.json" with open(filename, 'w', encoding='utf-8') as file: json.dump(tc.dict(), file, ensure_ascii=False, indent=4)