OLS software 4.0.1

What's Changed

• Add classes to individual table by @haideriqbal in #862
• Add domain and range columns for Properties by @haideriqbal in #866
• Fix failing class expression by @haideriqbal in #867
• Add term size config by @haideriqbal in #852
• Workaround for PRIDE ontology not using BFO:0000050. by @henrietteharmse in #872
• Fix NodePort for backend and frontend by @haideriqbal in #875
• Update ictv purl by @haideriqbal in #878
• Add mondo international version by @haideriqbal in #883
• Add definition properties to description by @haideriqbal in #882
• Update Ingress by @haideriqbal in #884
• Update Ingress to handle routing by @haideriqbal in #885
• Add new Graph and remove old graph component by @haideriqbal in #869
• Privacy notices migrated from being centralised to being localized. by @henrietteharmse in #887
• Add synonym info to docs by @haideriqbal in #891
• Add crt ontology by @haideriqbal in #896
• update id for credit by @haideriqbal in #900
• Update label annotator by @haideriqbal in #901
• TESTCASES: Fix label property by @haideriqbal in #902
• Fix label property api testcases by @haideriqbal in #903
• Add support for embeddings using the neo4j and solr vector stores by @jamesamcl in #881
• Mount prod NFS path by @haideriqbal in #913
• Enhance Ontology Fallback Mechanism by @haideriqbal in #905
• Add configuration for MeSH by @cthoyt in #909
• Add mount paths for webprod by @haideriqbal in #914
• Add missing nfs volume mount by @haideriqbal in #920
• Fix the broken checkbox to toggle showing obsolete classes by @jamesamcl in #927
• Add configurations for WikiPathways, HGNC, ComplexPortal, and ROR by @cthoyt in #931
• Add new component for property views by @haideriqbal in #921
• Update swagger version by @haideriqbal in #934
• Set EVORAO definition property to skos:definition by @Angatar in #941
• Update tree structure for direct children by @haideriqbal in #910
• Update README by @jamesamcl in #946
• Changed purl links to w3id for EMI ontology by @mdrishti in #947
• Force local file overwrite by @haideriqbal in #948
• add GOLD by @jamesamcl in #953
• changed ols redirection by @mdrishti in #954
• Fix unknown expression issue by @haideriqbal in #959
• remove complex by @haideriqbal in #962
• update testcase output by @jamesamcl in #943
• Stable by @jamesamcl in #967
• Add MCP server by @jamesamcl in #966
• Make sure synonym is always array by @haideriqbal in #961
• Tests fix synonym array by @haideriqbal in #969
• Tests api fix synonym array by @haideriqbal in #968
• Add comprehensive GitHub Copilot instructions for OLS4 development workflow by @jamesamcl with @Copilot in #972
• Add min width to svg by @haideriqbal in #974
• Remove wikipathway by @haideriqbal in #979
• Fix base_uri configuration for obo-db-ingest ontologies by @cthoyt in #980
• Add custom resource not found exception by @haideriqbal in #983
• load aro locally by @haideriqbal in #986
• Add support for "-" in entity links by @haideriqbal in #987
• Fix broken dbxrefs tests by @haideriqbal in #988
• Fix broken dbxrefs api tests by @haideriqbal in #989
• Update aro purl by @haideriqbal in #990
• Improve CI/CD by @cthoyt in #997
• Enable testing on PRs (retrry) by @cthoyt in #1006
• Update backend memory by @haideriqbal in #1012
• Stable by @haideriqbal in #1014
• Add reporting service to RDF2JSON by @haideriqbal in #1008
• Add misx ontology by @haideriqbal in #1026
• Add hgnc gene group ontology by @haideriqbal in #1027
• Add Claude Code GitHub Workflow by @haideriqbal in #1043
• Increase backend memory by @haideriqbal in #1041
• Add security scanning by @haideriqbal in #1023
• Add international version of doid by @haideriqbal in #1020
• Remove relatedfrom field from _json in dataload by @haideriqbal in #1046
• Remove Claude code review. CLAUDE IS EXPENSIVE by @haideriqbal in #1086
• bugfix: change last loaded field from anchor to paragraph by @brunopma in #1024
• Add configuration for EC by @cthoyt in #1087
• Add accent normalisation to Solr by @haideriqbal in #1022
• Add embeddings download link by @haideriqbal in #1019
• Remove dependabot by @haideriqbal in #1119
• Fix ontology filter on search by @haideriqbal in #1103
• Update FMA purl by @haideriqbal in #1122
• Make controller methods package private by @haideriqbal in #1126
• Mcp prod by @jamesamcl in #1128
• Stop adding comments to github issues by @haideriqbal in #1135
• Improve OLS search by @haideriqbal in #1130
• Add NOT IN ontology filter by @haideriqbal in #1134
• Don't load empty ontologies by @haideriqbal in #1124
• Skip obsolete ontologies by @haideriqbal in #1137
• Remove quotation from suggest query by @haideriqbal in #1138
• Convert ontology rdfjson to ebi-search files by @haideriqbal in #1142
• move to defining ontology from imported for is local by @haideriqbal in #1139
• Add synonym information to V1 Search endpoint by @haideriqbal in #1145
• Add PREFER ontology by @haideriqbal in #1147
• Added missing SSSOM predicates by @henrietteharmse in #1143
• Skip notification for deprecated ontologies by @haideriqbal in #1152
• Skip invalid langauge tags by @haideriqbal in #1156
• Fix PREFER labels by @haideriqbal in #1159
• Update solr client by @haideriqbal in #1168
• Fix HRA labels by @haideriqbal in #1166
• Update the way to handle is_deprecated by @haideriqbal in #1158
• Highlight search text by @haideriqbal in #1157
• Update reporting service email logic by @haideriqbal in #1169
• Add image metadata if available by @haideriqbal in #1170
• Update vario purl by @haideriqbal in #1174
• nextflow, full integration tests, semantic search by @jamesamcl in #1171
• Add obsolete entity filtering to MCP search tools by @jamesamcl with @Copilot in #1176
• Text tagger by @jamesamcl in #1177
• Rename ols_to_tsv to extract_strings_from_terms by @jamesamcl with @Copilot in #1182
• Update URI for Orphanet Rare Disease Ontology by @matentzn in #1185
• Update readme by @haideriqbal in #1188
• Add custom curie extractor by @haideriqbal in #1183
• Preserve new line characters by @haideriqbal in #1172
• Update OLS privacy notice by @haideriqbal in #1191
• Update privacy notices by @haideriqbal in #1194
• Update nextflow file by @haideriqbal in #1189
• Update embedding volume by @haideriqbal in #1200
• Fix swagger doc issues by @haideriqbal in #1202
• update local ontology paths & move FTP copy out of nextflow by @haideriqbal in #1208
• Update solr and neo4j storage by @haideriqbal in #1211
• load curated text mappings by @jamesamcl in #1197
• improve curie extraction by @haideriqbal in #1213
• Update swagger docs by @haideriqbal in #1214
• Fixes search issue by @haideriqbal in #1203
• Fix properties endpoint by @haideriqbal in #1219
• Add transform ontology by @haideriqbal in #1221
• Fix ordo ontology by @haideriqbal in #1224
• Add gmho ontology by @haideriqbal in #1223
• Update dataload testcases by @haideriqbal in #1225
• Fix queryField search by @haideriqbal in #1227
• Fix mailing list by @haideriqbal in #1229
• Stable by @haideriqbal in #1230
• Fix mailing list by @haideriqbal in #1231
• Stable by @haideriqbal in #1232
• Embedding fixes for big models by @jamesamcl in #1233
• Update SSSOM mapping by @haideriqbal in #1245
• Make retry logic simple by @haideriqbal in #1244
• Cap MCP version by @haideriqbal in #1247
• Add custom curie extraction by @haideriqbal in #1234
• Fix orcid resolution without leveldb by @haideriqbal in #1235
• Migrate to managed postgres by @jamesamcl in #1236
• fix mixs config (#1136) by @jamesamcl in #1259
• Fix empty curie and short_form columns by @haideriqbal in #1271
• This covers CVE-2026-29063 by @haideriqbal in #1268
• This covers the six Tomcat criticals: CVE-2026-43515, CVE-2026-41293,… by @haideriqbal in #1269
• Update expected dataload fixtures for populated curie/short_form columns by @jamesamcl in #1274
• Fix api tests by @haideriqbal in #1275
• Restore old behavious for q param in classes search by @haideriqbal in #1277
• Restore partial (prefix) match in entity search (#1267) by @jamesamcl in #1273
• Fix #1262: show data release date instead of current timestamp in stats by @haideriqbal in #1279
• Fix #1265: make ontologyId filter case-insensitive in PostgreSQL by @haideriqbal in #1280
• Add . to ontology id validation by @haideriqbal in #1281
• Add cohort ontology (COHO) by @jamesamcl in #1284
• Remove legacy graph view by @haideriqbal in #1285
• Fix case insensitive issue in v1 api by @haideriqbal in #1288
• Fix ontology id index scan issue by @haideriqbal in #1290
• Create index on synonyms and other optimisation fixes. by @haideriqbal in #1291
• Optimise hierarchy joins and add indexes for paginated listings by @haideriqbal in #1293
• Query list was being ignored by @haideriqbal in #1298
• Add text tagger grant on db by @haideriqbal in #1299
• add mepto ontology by @haideriqbal in #1300
• Fix exact match missing search fields by @haideriqbal in #1302
• Fix index and db pool by @haideriqbal in #1304
• Fix ictv filter properties by @haideriqbal in #1307
• Update container security-container-scan.yml by @haideriqbal in #1310
• Fix orcid tests by @haideriqbal in #1316
• build(backend): slim runtime image by @haideriqbal in #1319
• build(embed): slim runtime image by @haideriqbal in #1320
• fix(embed): cap duckdb memory in per-ontology parquet OOM by @haideriqbal in #1324
• fix(dataload): broadcast global filter-property list to json2postgres by @haideriqbal in #1325
• fix(dataload): add prefix and ontology fields to SSSOM other block by @haideriqbal in #1326
• build(dataload): slim runtime image by @haideriqbal in #1322
• fix(frontend): restore public/ as source for static assets by @haideriqbal in #1329
• Link and document MCP tools on MCP server page by @haideriqbal in #1330
• fix(dataload): exclude obsolete terms from SSSOM extract by @haideriqbal in #1328
• fix(dataload): stop cross-ontology curie leaking onto shared IRIs by @haideriqbal in #1335
• fix(backend): make v1 search groupField collapse results by IRI by @haideriqbal in #1336
• Add UOGTO ontology by @haideriqbal in #1337
• fix(docs): correct searchFields example to singular synonym field by @haideriqbal in #1338
• fix(frontend): correct OLS downloads links to match real release, drop Solr by @haideriqbal in #1339
• fix(backend): case-insensitive + field-restricted search fixes (#1309, #1308, #1312) by @haideriqbal in #1340
• Fix localization of mixed ontology metadata arrays by @haideriqbal in #1343
• Stabilize autocomplete search under broad prefixes by @haideriqbal in #1346
• Fix configured definition property handling by @haideriqbal in #1344
• Add AIO (Artificial Intelligence Ontology) to ebi_ontologies.json by @turbomam in #1332
• fix: restore exact fuzzy autosuggest matching, cache results by @haideriqbal in #1347
• Add REHABO ontology by @haideriqbal in #1348
• Add Value Sets ontology by @haideriqbal in #1349
• Add local cmpo ontology file by @haideriqbal in #1350
• fix(dataload): add ontology IRI to SSSOM metadata by @haideriqbal in #1353
• fix(dataload): remediate reporting image dependencies by @haideriqbal in #1354
• perf(autosuggest): fix /api/suggest cold-start latency by @haideriqbal in #1357
• Fix object-valued filter property loading by @haideriqbal in #1358
• Fix V2 ontology dynamic parameter binding by @haideriqbal in #1359
• Preserve API client error statuses by @haideriqbal in #1360
• Fix repeated dynamic filter values by @haideriqbal in #1361
• Honor safe PostgreSQL search sorting by @haideriqbal in #1362
• Apply explicit PostgreSQL boost fields by @haideriqbal in #1363
• Add V2 ontology backend testing pilot by @haideriqbal in #1364
• Add V1 ontology controller test coverage by @haideriqbal in #1365
• Exclude facetFields from dynamic filters by @haideriqbal in #1366
• Exclude sort from dynamic filters by @haideriqbal in #1367
• Add V2 entity controller layered test coverage by @haideriqbal in #1368
• Add V1 term controller layered test coverage by @haideriqbal in #1369
• Test V2 property controller by @haideriqbal in #1370
• Map V1 property status flags by @haideriqbal in #1371
• Add layered V1 property controller tests by @haideriqbal in #1372
• Restrict V2 class hierarchy results to classes by @haideriqbal in #1373
• test: cover V2 class controller by @haideriqbal in #1374
• Filter obsolete class individuals by @haideriqbal in #1375
• test: cover v2 individual controller by @haideriqbal in #1376
• Map V1 individual status flags by @haideriqbal in #1377
• Test V1 individual controller by @haideriqbal in #1378
• Fix IRI queries in v1 search and select by @haideriqbal in #1379
• test: cover V2 statistics controller by @haideriqbal in #1380
• fix: preserve V1 suggest start offset by @haideriqbal in #1381
• fix: explain invalid ontology ids by @haideriqbal in #1382
• test: cover v1 suggest controller by @haideriqbal in #1383
• Fix inclusive V1 hierarchy search by @haideriqbal in #1384
• test: cover v1 search controller by @haideriqbal in #1385
• Fix V1 select pagination offset by @haideriqbal in #1386
• Fix ontology-scoped individual identifier lookup by @haideriqbal in #1388
• Test V1 select controller across layered backend suites by @haideriqbal in #1387
• Test V1 ontology individual controller across layered suites by @haideriqbal in #1389
• fix: null-safe hasChildren check in V1ChildrenJsTreeBuilder by @haideriqbal in #1391
• test: cover v1 ontology property controller by @haideriqbal in #1390
• test: cover v1 ontology term controller (milestone 1 of 2+) by @haideriqbal in #1393
• test: cover v1 ontology term controller (milestone 2 of 2) by @haideriqbal in #1395
• test: cover v2 health check controller by @haideriqbal in #1396
• test: cover v2 defined fields controller by @haideriqbal in #1397
• test: cover v2 text tagger controller by @haideriqbal in #1398
• test: cover v2 llm controller by @haideriqbal in #1399
• Fix class tree by fetching individuals separately by @haideriqbal in #1402
• Nest individuals under hierarchical-property parents in the tree (COHO isSubCohortOf) by @jamesamcl in #1404
• Complete V2 individual hierarchy route test coverage by @haideriqbal in #1406
• test: cover AnnotationExtractor by @haideriqbal in #1407
• fix: throw ResourceNotFoundException instead of NPE in McpSearchService.fetch by @haideriqbal in #1416
• test: cover EmbeddingServiceClient by @haideriqbal in #1408
• fix: use HAS_HIERARCHICAL_CHILDREN for hasHierarchicalChildren in V1AncestorsJsTreeBuilder by @haideriqbal in #1427
• fix: update gitIssue502 golden fixture for bioregistry MEDDRA URL drift by @haideriqbal in #1436
• test: cover JooqSupport by @haideriqbal in #1409
• test: cover JsonTransformer by @haideriqbal in #1410
• test: cover ManchesterSyntaxTransform by @haideriqbal in #1411
• test: cover McpClassService by @haideriqbal in #1412
• test: cover McpEmbeddingService by @haideriqbal in #1413
• test: cover McpOntologyService by @haideriqbal in #1414
• test: cover McpSearchService by @haideriqbal in #1415
• test: cover OlsFacetedResultsPage by @haideriqbal in #1417
• test: cover OlsPostgresClient (1/3) by @haideriqbal in #1418
• test: cover OlsPostgresClient (2/3) by @haideriqbal in #1419
• test: cover OlsPostgresClient (3/3) by @haideriqbal in #1420
• test: cover PostgresClient by @haideriqbal in #1421
• test: cover RemoveLiteralDatatypesTransform by @haideriqbal in #1422
• test: cover RemoveReificationTransform by @haideriqbal in #1423
• test: cover ResolveReferencesTransform by @haideriqbal in #1424
• test: cover ShortFormExtractor by @haideriqbal in #1425
• test: cover TextTaggerService by @haideriqbal in #1426
• test: cover V1AncestorsJsTreeBuilder by @haideriqbal in #1428
• test: cover V1GraphRepository by @haideriqbal in #1429
• test: cover V1JsTreeRepository by @haideriqbal in #1430
• test: cover V1OboDefinitionCitationExtractor by @haideriqbal in #1431
• test: cover V1OboSynonymExtractor by @haideriqbal in #1432
• test: cover V1OboXrefExtractor by @haideriqbal in #1433
• test: cover V1OntologyMapper by @haideriqbal in #1434
• test: cover V1TermMapper by @haideriqbal in #1435
• COHO location hierarchy in the tree, and individuals-tree fixes for the Postgres backend by @jamesamcl in #1437
• Add Java dataload executable contract tests by @haideriqbal in #1444
• Freeze OpenAI embeddings, persist embeddings base, default to Harrier by @haideriqbal in #1446
• Fix update_embeddings_prev OOM and container visibility of embeddings_prev by @haideriqbal in #1447
• test: expand RDF2JSON semantic contracts by @haideriqbal in #1448
• test: cover RDF2JSON annotator branches and imports by @haideriqbal in #1450
• test: expand RDF2JSON hierarchy and OWL contracts by @haideriqbal in #1452
• Expand RDF2JSON annotator and import contract coverage by @haideriqbal in #1453
• Add manifest and linker executable contracts by @haideriqbal in #1454
• Execute PostgreSQL indexes preceded by SQL comments by @haideriqbal in #1455
• Test JSON2Postgres and Python loading with PostgreSQL 17 by @haideriqbal in #1456
• Protect per-ontology Nextflow failure isolation by @haideriqbal in #1457
• Automate stable software releases with Zenodo GitHub archiving by @haideriqbal in #1460

New Contributors

• @Angatar made their first contribution in #941
• @mdrishti made their first contribution in #947
• @jamesamcl with @Copilot made their first contribution in #972
• @brunopma made their first contribution in #1024
• @turbomam made their first contribution in #1332

Full Changelog: ols4-paper...v4.0.1

Cite this software release: https://doi.org/10.5281/zenodo.23184948