Add sourced InterPro annotation datasets

README.md

@@ -12,7 +12,7 @@ recovery of curated InterPro classifications, not an experimental assay result.
 
 - InterPro metadata: `https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list`
 - UniProt REST API: `https://rest.uniprot.org/uniprotkb/stream`
-- Card generated (UTC): `2026-10-05`
+- Card generated (UTC): `2026-10-07`
 - Organism Taxonomy ID: `9606` (`all` = all organisms).
 - Review status: `reviewed` (`reviewed` = Swiss-Prot, `unreviewed` = TrEMBL, `all` = both).
 - UniProt query: `(organism_id:9606) AND (reviewed:true)`
@@ -21,41 +21,49 @@ recovery of curated InterPro classifications, not an experimental assay result.
 - Consider entries observed in at least 5 proteins.
 - After splitting, retain entries with at least 20
     positives in training, 3 in validation,
-    and 3 in test.
+    and 3 in test. Because validation and test
+    support select the entries, scores are conditional on that label selection.
 - `targets` is a multi-hot vector ordered by InterPro accession. Accession,
   display name, and type are recorded in `label_vocabulary.json`.
-- Proteins without a retained entry before splitting are dropped; after
-    support filtering, other split variants may contain all-zero targets.
+- Proteins without a retained entry are dropped, both before splitting and
+    again after split-support filtering, so no row has all-zero targets.
+- `id` is the UniProtKB accession of the first entry carrying each unique sequence.
 
 ## Splits
 
-Whole MMseqs2 `easy-linclust` clusters are assigned to splits targeting
-`{'train': 0.8, 'validation': 0.1, 'test': 0.1}`, with minimum identity
-`0.3`, minimum coverage
-`0.8`, and
-`1` thread(s). Seed: `1957723`.
-When `create_split_subsets` is enabled, pooled random, stratified, and
-hold-cluster-out subsets are also included. Hold-cluster-out subsets require
-enough MMseqs clusters to populate all three roles.
+Whole MMseqs2 clusters are assigned to splits targeting
+`{'train': 0.8, 'validation': 0.1, 'test': 0.1}`. Seed: `1957723`. Clustering settings:
+
+- MMseqs workflow: `easy-cluster`
+- Minimum sequence identity (`--min-seq-id`): `0.3`
+- Minimum coverage (`-c`): `0.8`
+- Coverage mode (`--cov-mode`): `1`
+- Threads: `1`
+- Other MMseqs2 options use MMseqs2 defaults.
+
+When `create_split_subsets` is enabled, pooled random, stratified (by each
+protein's globally rarest positive entry), and hold-cluster-out subsets are
+also included. Hold-cluster-out subsets require enough MMseqs clusters to
+populate all three roles.
 The optional maximum sequence length is `None` and is
 applied before vocabulary construction and MMseqs2 clustering.
 
 ## Split sizes
 
-- `test`: 156 rows
-- `test_cluster`: 156 rows
-- `test_random`: 156 rows
-- `test_stratified`: 156 rows
-- `train`: 1251 rows
-- `train_cluster`: 1251 rows
-- `train_random`: 1251 rows
-- `train_stratified`: 1251 rows
-- `validation`: 156 rows
-- `validation_cluster`: 156 rows
-- `validation_random`: 156 rows
-- `validation_stratified`: 156 rows
-
-Vocabulary size: 9.
+- `test`: 116 rows
+- `test_cluster`: 116 rows
+- `test_random`: 116 rows
+- `test_stratified`: 116 rows
+- `train`: 850 rows
+- `train_cluster`: 850 rows
+- `train_random`: 850 rows
+- `train_stratified`: 850 rows
+- `validation`: 118 rows
+- `validation_cluster`: 118 rows
+- `validation_random`: 118 rows
+- `validation_stratified`: 118 rows
+
+Vocabulary size: 10.
 
 ## Dataset statistics
 

data/test-00000-of-00001.parquet

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label_vocabulary.json

@@ -2,16 +2,6 @@
   "dataset_name": "interpro_repeat",
   "vocabulary_version": 1,
   "labels": [
-    {
-      "accession": "IPR000225",
-      "name": "Armadillo",
-      "entry_type": "Repeat"
-    },
-    {
-      "accession": "IPR000884",
-      "name": "Thrombospondin type-1 (TSP1) repeat",
-      "entry_type": "Repeat"
-    },
     {
       "accession": "IPR001611",
       "name": "Leucine-rich repeat",
@@ -27,6 +17,11 @@
       "name": "Ankyrin repeat",
       "entry_type": "Repeat"
     },
+    {
+      "accession": "IPR002165",
+      "name": "Plexin repeat",
+      "entry_type": "Repeat"
+    },
     {
       "accession": "IPR003591",
       "name": "Leucine-rich repeat, typical subtype",
@@ -37,6 +32,16 @@
       "name": "Collagen triple helix repeat",
       "entry_type": "Repeat"
     },
+    {
+      "accession": "IPR018108",
+      "name": "Mitochondrial carrier protein, transmembrane region",
+      "entry_type": "Repeat"
+    },
+    {
+      "accession": "IPR018159",
+      "name": "Spectrin/alpha-actinin",
+      "entry_type": "Repeat"
+    },
     {
       "accession": "IPR019734",
       "name": "Tetratricopeptide repeat",

stats.json

@@ -1,18 +1,19 @@
 {
-  "rows_total": 6252,
+  "rows_total": 4336,
+  "canonical_rows": 1084,
   "rows_by_split": {
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-    "validation": 156,
-    "test": 156,
-    "train_random": 1251,
-    "validation_random": 156,
-    "test_random": 156,
-    "train_stratified": 1251,
-    "validation_stratified": 156,
-    "test_stratified": 156,
-    "train_cluster": 1251,
-    "validation_cluster": 156,
-    "test_cluster": 156
+    "train": 850,
+    "validation": 118,
+    "test": 116,
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+    "validation_random": 118,
+    "test_random": 116,
+    "train_stratified": 850,
+    "validation_stratified": 118,
+    "test_stratified": 116,
+    "train_cluster": 850,
+    "validation_cluster": 118,
+    "test_cluster": 116
   },
   "columns": [
     "id",
@@ -24,184 +25,184 @@
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