Merge Ontologies into Functional and reclassify HPA tissue

catalog.json

@@ -620,9 +620,9 @@
   {
     "id": "go_bp_uniprot_tfidf_svd256",
     "name": "GO TF-IDF SVD-256",
-    "category": "Ontologies",
+    "category": "Functional",
     "category_source": "manual",
-    "modality": "Ontologies",
+    "modality": "Functional",
     "algorithm": "binary GO Biological Process profile + TF-IDF + TruncatedSVD-256",
     "description": "Ontology-based representation built from direct, non-negated Gene Ontology Biological Process annotations, weighted with TF-IDF and reduced to 256 dimensions by SVD.",
     "n_genes": 16833,
@@ -731,7 +731,7 @@
   },
   {
     "algorithm": "HPA normal tissue immunohistochemistry annotations. maximum ordinal protein-expression level across annotated cell types within each tissue. HPA Level encoded as Not detected=0, Low=1, Medium=2, High=3. For each gene and tissue, maximum level across annotated cell types was used. Tissue columns were z-scored across mapped genes.",
-    "category": "Functional",
+    "category": "Expression",
     "category_source": "manual",
     "community_contribution": false,
     "coverage_pct": 66.78,
@@ -740,7 +740,7 @@
     "id": "hpa_normal_ihc_tissue_level_zscore",
     "license": "Original source / license terms",
     "metadata_url": "https://huggingface.co/datasets/embeddingsSSRF/gene_embeddings/blob/326b257a20e73df337ece40bb82401e277851f5b/data/embeddings/hpa_normal_ihc_tissue_level_zscore/metadata.json",
-    "modality": "Functional",
+    "modality": "Expression",
     "n_dims": 59,
     "n_genes": 13420,
     "name": "HPA tissue",
@@ -951,7 +951,7 @@
   },
   {
     "algorithm": "NEWT component embedding (checkpoint: not applicable). precomputed component embedding table.",
-    "category": "Ontologies",
+    "category": "Functional",
     "category_source": "manual",
     "community_contribution": false,
     "coverage_pct": 68.61,
@@ -960,7 +960,7 @@
     "id": "newt_go_256",
     "license": "Original source / license terms",
     "metadata_url": "https://huggingface.co/datasets/embeddingsSSRF/gene_embeddings/blob/326b257a20e73df337ece40bb82401e277851f5b/data/embeddings/newt_go_256/metadata.json",
-    "modality": "Ontologies",
+    "modality": "Functional",
     "n_dims": 256,
     "n_genes": 13788,
     "name": "NEWT GO-256",
@@ -973,7 +973,7 @@
   },
   {
     "algorithm": "NEWT component embedding (checkpoint: not applicable). precomputed component embedding table.",
-    "category": "Ontologies",
+    "category": "Functional",
     "category_source": "manual",
     "community_contribution": false,
     "coverage_pct": 68.61,
@@ -982,7 +982,7 @@
     "id": "newt_go_graph",
     "license": "Original source / license terms",
     "metadata_url": "https://huggingface.co/datasets/embeddingsSSRF/gene_embeddings/blob/326b257a20e73df337ece40bb82401e277851f5b/data/embeddings/newt_go_graph/metadata.json",
-    "modality": "Ontologies",
+    "modality": "Functional",
     "n_dims": 256,
     "n_genes": 13788,
     "name": "NEWT GO graph",
@@ -1061,7 +1061,7 @@
   },
   {
     "algorithm": "OPA2Vec.",
-    "category": "Ontologies",
+    "category": "Functional",
     "category_source": "manual",
     "community_contribution": false,
     "coverage_pct": 92.85,
@@ -1070,7 +1070,7 @@
     "id": "opa2vec_goa_human",
     "license": "Original source / license terms",
     "metadata_url": "https://huggingface.co/datasets/embeddingsSSRF/gene_embeddings/blob/326b257a20e73df337ece40bb82401e277851f5b/data/embeddings/opa2vec_goa_human/metadata.json",
-    "modality": "Ontologies",
+    "modality": "Functional",
     "n_dims": 200,
     "n_genes": 18660,
     "name": "OPA2Vec",

index.html

@@ -38,12 +38,7 @@
       <h1>Gene Embeddings</h1>
 
       <p class="lead">
-          Browse standardized gene-level representations spanning
-          protein sequence, DNA sequence, RNA sequence, expression,
-          biomedical text, functional data, networks, ontologies,
-          regulatory genomics, knowledge graphs, single-cell, and
-          multimodal representations.
-      </p>
+          Browse standardized gene-level representations spanning protein sequence, DNA sequence, RNA sequence, expression, biomedical text, functional, networks, regulatory genomics, knowledge graphs, single-cell, and multimodal representations.</p>
       <div class="actions">
         <a
           class="button primary"