diff --git a/R/getPathwaysFromIndra.R b/R/getPathwaysFromIndra.R
index 06b1a45..76c654e 100644
--- a/R/getPathwaysFromIndra.R
+++ b/R/getPathwaysFromIndra.R
@@ -107,8 +107,8 @@ getPathwaysFromIndra <- function(annotated_df, main_target = 'MEN1_HUMAN', targe
             edgeToMetadataMapping[[key]]$data$stmt_type <- c(edge$type)
             edgeToMetadataMapping[[key]]$source_id <- source_id
             edgeToMetadataMapping[[key]]$target_id <- obj
-            edgeToMetadataMapping[[key]] <- MSstatsBioNet:::.addAdditionalMetadataToIndraEdge(
-                edgeToMetadataMapping[[key]], annotated_df, namespace
+            edgeToMetadataMapping[[key]] <- .addAdditionalMetadataToIndraEdge(
+                edgeToMetadataMapping[[key]], annotated_df
             )
         }
     }
diff --git a/R/getSubnetworkFromIndra.R b/R/getSubnetworkFromIndra.R
index af40f3f..d8a1896 100644
--- a/R/getSubnetworkFromIndra.R
+++ b/R/getSubnetworkFromIndra.R
@@ -30,6 +30,9 @@
 #' @param force_include_proteins character vector of protein identifiers to exempt 
 #' from all filtering steps. These proteins will be retained regardless of p-value, 
 #' logFC, or other filtering criteria. Default is NULL, i.e. no exemptions.
+#' @param force_include_other character vector of identifiers to include in the
+#' network, regardless if those ids are in the input data. Should be formatted
+#' as "namespace:identifier", e.g. "HGNC:1234" or "CHEBI:4911".
 #'
 #' @return list of 2 data.frames, nodes and edges
 #'
@@ -53,10 +56,11 @@ getSubnetworkFromIndra <- function(input,
                                    correlation_cutoff = 0.3,
                                    sources_filter = NULL,
                                    logfc_cutoff = NULL,
-                                   force_include_proteins = NULL) {
+                                   force_include_proteins = NULL,
+                                   force_include_other = NULL) {
     input <- .filterGetSubnetworkFromIndraInput(input, pvalueCutoff, logfc_cutoff, force_include_proteins)
-    .validateGetSubnetworkFromIndraInput(input, protein_level_data, sources_filter)
-    res <- .callIndraCogexApi(input$HgncId)
+    .validateGetSubnetworkFromIndraInput(input, protein_level_data, sources_filter, force_include_other)
+    res <- .callIndraCogexApi(input$HgncId, force_include_other)
     res <- .filterIndraResponse(res, statement_types, evidence_count_cutoff, sources_filter)
     edges <- .constructEdgesDataFrame(res, input, protein_level_data)
     edges <- .filterEdgesDataFrame(edges, paper_count_cutoff, correlation_cutoff)
diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index cb25998..e514d52 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -2,13 +2,16 @@
 #' @param input dataframe from MSstats groupComparison output
 #' @param protein_level_data dataframe from MSstats dataProcess output
 #' @param sources_filter sources filter
+#' @param force_include_other character vector of identifiers to include in the
+#' network.
 #' @keywords internal
 #' @noRd
-.validateGetSubnetworkFromIndraInput <- function(input, protein_level_data, sources_filter) {
+.validateGetSubnetworkFromIndraInput <- function(input, protein_level_data, sources_filter, force_include_other) {
     if (!"HgncId" %in% colnames(input)) {
         stop("Invalid Input Error: Input must contain a column named 'HgncId'.")
     }
-    if (nrow(input) >= 400) {
+    num_proteins = nrow(input) + ifelse(!is.null(force_include_other), length(force_include_other), 0)
+    if (num_proteins >= 400) {
         stop("Invalid Input Error: INDRA query must contain less than 400 proteins.  Consider lowering your p-value cutoff")
     }
     if (nrow(input) == 0) {
@@ -28,16 +31,26 @@
 
 #' Call INDRA Cogex API and return response
 #' @param hgncIds list of hgnc ids
+#' @param force_include_other list of identifiers to include in the network
 #' @return list of INDRA statements
 #' @importFrom jsonlite toJSON
 #' @importFrom httr POST add_headers content
 #' @keywords internal
 #' @noRd
-.callIndraCogexApi <- function(hgncIds) {
+.callIndraCogexApi <- function(hgncIds, force_include_other) {
     indraCogexUrl <-
         "https://discovery.indra.bio/api/indra_subnetwork_relations"
 
     groundings <- lapply(hgncIds, function(x) list("HGNC", x))
+    if (!is.null(force_include_other)) {
+        groundings <- c(groundings, lapply(force_include_other, function(x) {
+            parts <- unlist(strsplit(x, ":"))
+            if (length(parts) != 2) {
+                stop(paste0("Invalid identifier format: ", x, ". Expected format is 'namespace:identifier', e.g. 'HGNC:1234' or 'CHEBI:4911'."))
+            }
+            list(parts[1], parts[2])
+        }))
+    }
     groundings <- list(nodes = groundings)
     groundings <- jsonlite::toJSON(groundings, auto_unbox = TRUE)
 
@@ -133,40 +146,31 @@
 #' Add additional metadata to an edge
 #' @param edge object representation of an INDRA statement
 #' @param input filtered groupComparison result
-#' @param source_namespace namespace of the source for evidence URL
 #' @return edge with additional metadata
 #' @keywords internal
 #' @noRd
-.addAdditionalMetadataToIndraEdge <- function(edge, input, source_namespace = "@HGNC") {
+.addAdditionalMetadataToIndraEdge <- function(edge, input) {
     edge$evidence_list <- paste(
         "https://db.indra.bio/statements/from_agents?subject=",
-        edge$source_id, source_namespace, "&object=",
-        edge$target_id, "@HGNC&format=html",
+        edge$source_id, "@", edge$source_ns, "&object=",
+        edge$target_id, "@", edge$target_ns, "&format=html",
         sep = ""
     )
     
     # Convert back to uniprot IDs
-    if (source_namespace == "@HGNC") {
-        matched_rows_source <- input[which(input$HgncId == edge$source_id), ]
+    matched_rows_source <- input[which(input$HgncId == edge$source_id), ]
+    if (nrow(matched_rows_source) != 1) {
+        edge$source_uniprot_id <- edge$source_name
+    } else {
+        edge$source_uniprot_id <- matched_rows_source$Protein
     }
-    matched_rows_target <- input[which(input$HgncId == edge$target_id), ]
-    
-    if ((source_namespace == "@HGNC" && nrow(matched_rows_source) != 1) || nrow(matched_rows_target) != 1) {
-        stop(paste0(
-            "INDRA Exception: Unexpected number of matches for the following HGNC IDs in the input data: ", 
-            edge$source_id, 
-            " or ", 
-            edge$target_id, 
-            ". Each ID must match exactly one entry in the input data, but 0 or multiple matches were found. Please check the input data for duplicates or missing entries."
-        ))
-    } 
     
-    if (source_namespace == "@HGNC") {
-        edge$source_uniprot_id <- matched_rows_source$Protein
+    matched_rows_target <- input[which(input$HgncId == edge$target_id), ]
+    if (nrow(matched_rows_target) != 1) {
+        edge$target_uniprot_id <- edge$target_name
     } else {
-        edge$source_uniprot_id <- edge$source_id
+        edge$target_uniprot_id <- matched_rows_target$Protein
     }
-    edge$target_uniprot_id <- matched_rows_target$Protein
     
     return(edge)
 }
@@ -258,14 +262,25 @@
 #' @keywords internal
 #' @noRd
 .constructNodesDataFrame <- function(input, edges) {
+    # Get unique nodes from edges
+    node_ids <- unique(c(edges$source, edges$target))
+    
+    # Create base nodes dataframe
     nodes <- data.frame(
-        id = input$Protein,
-        logFC = input$log2FC,
-        adj.pvalue = input$adj.pvalue,
-        hgncName = if ("HgncName" %in% colnames(input) && is.character(input$HgncName)) input$HgncName else NA,
+        id = node_ids,
         stringsAsFactors = FALSE
     )
-    nodes <- nodes[which(nodes$id %in% edges$source | nodes$id %in% edges$target),]
+    
+    # Add attributes from input where available
+    nodes$logFC <- input$log2FC[match(nodes$id, input$Protein)]
+    nodes$adj.pvalue <- input$adj.pvalue[match(nodes$id, input$Protein)]
+    nodes$hgncName <- if ("HgncName" %in% colnames(input) && is.character(input$HgncName)) {
+        hgnc_value <- input$HgncName[match(nodes$id, input$Protein)]
+        ifelse(is.na(hgnc_value), nodes$id, hgnc_value)
+    } else {
+        nodes$id
+    }
+    
     return(nodes)
 }
 
diff --git a/man/getSubnetworkFromIndra.Rd b/man/getSubnetworkFromIndra.Rd
index bc84f34..2fc5e80 100644
--- a/man/getSubnetworkFromIndra.Rd
+++ b/man/getSubnetworkFromIndra.Rd
@@ -14,7 +14,8 @@ getSubnetworkFromIndra(
   correlation_cutoff = 0.3,
   sources_filter = NULL,
   logfc_cutoff = NULL,
-  force_include_proteins = NULL
+  force_include_proteins = NULL,
+  force_include_other = NULL
 )
 }
 \arguments{
@@ -54,6 +55,10 @@ is NULL, i.e. no logFC filtering.}
 \item{force_include_proteins}{character vector of protein identifiers to exempt 
 from all filtering steps. These proteins will be retained regardless of p-value, 
 logFC, or other filtering criteria. Default is NULL, i.e. no exemptions.}
+
+\item{force_include_other}{character vector of identifiers to include in the
+network, regardless if those ids are in the input data. Should be formatted
+as "namespace:identifier", e.g. "HGNC:1234" or "CHEBI:4911".}
 }
 \value{
 list of 2 data.frames, nodes and edges
diff --git a/tests/testthat/test-getSubnetworkFromIndra.R b/tests/testthat/test-getSubnetworkFromIndra.R
index 9e1e487..ddeca35 100644
--- a/tests/testthat/test-getSubnetworkFromIndra.R
+++ b/tests/testthat/test-getSubnetworkFromIndra.R
@@ -2,7 +2,7 @@ test_that("getSubnetworkFromIndra works correctly", {
     input <- data.table::fread(
         system.file("extdata/groupComparisonModel.csv", package = "MSstatsBioNet")
     )
-    local_mocked_bindings(.callIndraCogexApi = function(x) {
+    local_mocked_bindings(.callIndraCogexApi = function(x,y) {
         return(readRDS(system.file("extdata/indraResponse.rds", package = "MSstatsBioNet")))
     })
     suppressWarnings(subnetwork <- getSubnetworkFromIndra(input, statement_types = c("Activation", "Phosphorylation")))
@@ -14,7 +14,7 @@ test_that("getSubnetworkFromIndra with different statement type works correctly"
     input <- data.table::fread(
         system.file("extdata/groupComparisonModel.csv", package = "MSstatsBioNet")
     )
-    local_mocked_bindings(.callIndraCogexApi = function(x) {
+    local_mocked_bindings(.callIndraCogexApi = function(x,y) {
         return(readRDS(system.file("extdata/indraResponse.rds", package = "MSstatsBioNet")))
     })
     suppressWarnings(