0.1.0

What's Changed

• General cleanup and documentation updates by @caufieldjh in #381
• Fix some URLs by @caufieldjh in #384
• Remove DuckDB backend and database sync by @caufieldjh in #385
• Add microbiomekg by @caufieldjh in #388
• Add insight page by @caufieldjh in #389
• Add toxin page by @caufieldjh in #390
• Updates for stale warning cleanup and Product consistency across Resource pages by @caufieldjh in #392
• Remove duplicate gwascatalog entries; update gwascatalog page by @caufieldjh in #393
• Add epigraphdb page by @caufieldjh in #395
• General cleanup: URL fixes, metadata updates, and new pages (itis, alliance, hmdb) by @caufieldjh in #396
• General cleanup: remove excess warnings and notifications; add pages for aop-db and aop-wiki by @caufieldjh in #397
• Fix and catch yaml parsing errors during build by @caufieldjh in #399
• Remove comments from resource layout by @caufieldjh in #401
• Add pages for rnacentral, intact, cosmic, and 1000genomes by @caufieldjh in #402
• General updates: add pages for pharmdb, 5srrnadb, and biogps by @caufieldjh in #403
• Add pages for dorothea and phosphositeplus by @caufieldjh in #404
• Add page for globi by @caufieldjh in #406
• Add pages for bioportal, cancer-genome-interpreter, circbase, compartments, and toxcast by @caufieldjh in #407
• Stub page updates by @caufieldjh in #409
• Fix #410: secondary products are being incorrectly included among primary products by @caufieldjh in #411
• Add category for BER-relevant resources; add to those Resource pages by @caufieldjh in #413
• Add functions to retrieve metadata from OBO Foundry by @caufieldjh in #414
• Restructuring, better counts, and more filtering options for the main page by @caufieldjh in #415
• Make Ontology and OntologyProduct classes; apply to records by @caufieldjh in #417
• Stub updates: connectivitymap, clue, dictybase, flybase, genecards by @caufieldjh in #418
• Improvements for build process performance and efficiency by @caufieldjh in #419
• Add page for PDBe by @caufieldjh in #420
• Stub updates: crd, ena, eupathdb, malacards, mesh, mgnify by @caufieldjh in #422
• Stub updates: mirtarbase, modomics, mirgenedb, sckan, rdp, rediportal by @caufieldjh in #423
• Stub updates for 9 resources by @caufieldjh in #427
• Stub updates: ribovision, snodb, srpdb, tarbase, snopy, repohub by @caufieldjh in #429
• Add resource page for TERA by @caufieldjh in #430
• Stub updates: glycordf, glycocoo, motrpac, ttd, zwd, rfam, goa by @caufieldjh in #431
• Update artifacts, including new stubs from infores by @caufieldjh in #432
• Updates to many stub pages by @caufieldjh in #433
• Stub updates: faers, homologene, unichem, oxo, cohd, clinicaltrialsgov by @caufieldjh in #434
• Stub updates for 22 Resources by @caufieldjh in #435
• Add imodulondb by @caufieldjh in #437
• Stub updates for 7 resources by @caufieldjh in #438
• Add pistoia-pgo by @caufieldjh in #439
• Add 9 pages, update others by @caufieldjh in #440
• Restructure KG-Registry-KG interface and views by @caufieldjh in #441
• Update stubs for 9 resources by @caufieldjh in #442
• Stub updates and addition of curation challenge logging by @caufieldjh in #445
• KG-Registry-KG updates: export options, icons, examples, and docs by @caufieldjh in #447
• [WIP] Add iBKH resource to the registry by @caufieldjh with @Copilot in #451
• Add iBKH (integrative Biomedical Knowledge Hub) resource by @caufieldjh in #449
• Stub updates and a new directory for organization pages by @caufieldjh in #452
• Add AGENTS.md by @caufieldjh in #454
• Recategorize ARAX as Aggregator with proper Translator metadata by @caufieldjh with @Copilot in #455
• Add previously curated KG resources and update some stubs by @caufieldjh in #456
• Update KG-Microbe resource page by @caufieldjh in #457
• Stub updates and two new organizations by @caufieldjh in #458
• Stub updates by @caufieldjh in #461
• Update URL checker to handle FTP by @caufieldjh in #463
• Add more products to kg-monarch Resource by @caufieldjh in #464
• Add Organizations by @caufieldjh in #465
• Add KGs from Open Knowledge Network by @caufieldjh in #467
• Organization metadata updates by @caufieldjh in #469
• Improve collection viewing - add description, capitalize properly by @caufieldjh in #470
• Update organization metadata for all orgs with generic descriptions by @caufieldjh in #472
• Fix duplicate collectionMetadata declaration causing syntax error by @caufieldjh in #474
• Add FORUM and related ontologies by @caufieldjh in #475
• Data fixes for invalid format names; general data updates by @caufieldjh in #476
• Add NAMs Network Knowledge Graph resource page by @caufieldjh in #478
• Improvements to KG viz re edge display by @caufieldjh in #479
• Add options to filter by taxon by @caufieldjh in #480
• Add taxon annotations to GLoBI resource (Issue #481) by @caufieldjh in #503
• Add mangal.io ecological networks database to kg-registry (Issue #482) by @caufieldjh in #504
• General data updates for Resources by @caufieldjh in #505
• Add plant-reactome by @caufieldjh in #507
• Add openbiodiv and proton by @caufieldjh in #508
• Add KnowWhereGraph resource entry by @caufieldjh in #509
• Add EOL TraitBank resource entry by @caufieldjh in #511
• Add resources: Open Tree of Life, GBIF, OBIS by @caufieldjh in #512
• Update CAM-KP (Causal Activity Models Knowledge Provider) resource entry by @caufieldjh in #513
• Resource page additions and updates by @caufieldjh in #514
• Fix #510 by @caufieldjh in #515
• Updates for biogrid by @caufieldjh in #516
• Add RDF/TTL serialization by @caufieldjh in #517
• Add automated KG evaluation by @caufieldjh in #519
• Update KG evals by @caufieldjh in #520
• General updates for resources; extra focus on EMI-KG by @caufieldjh in #521
• Replace poetry with uv by @caufieldjh in #525
• Add Resource page for Translator normalized graphs; add drugrephub page; update text-mining-kp by @caufieldjh in #523
• General data fixes and updates; add prokn by @caufieldjh in #526
• Add unibiomap and KG eval by @caufieldjh in #529
• Update STRING products and sources by @caufieldjh in #530
• Update wikidata products and URLs by @caufieldjh in #531
• Updated details by @egonw in #533
• Update metadata for 10 resource stubs by @caufieldjh in #534
• Add data quality dashboard by @caufieldjh in #535
• Stub updates and cleanup by @caufieldjh in #536
• Resource updates: adding publications and products by @caufieldjh in #538
• Pass resource file list in file, not command line by @caufieldjh in #540
• Add MetaTraits microbial trait knowledge graph resource by @caufieldjh with @Copilot in #541
• Add OREGANO knowledge graph resource by @caufieldjh with @Copilot in #543
• Update page dates by @caufieldjh in #545
• Update dates for resources sourced from OBO Foundry ontologies by @caufieldjh in #546
• Update obo-db-ingest, medgen, and complexportal by @caufieldjh in #547
• Fix broken links in Gene Ontology metadata page by @caufieldjh with @Copilot in #549
• Adjust layout to be more mobile-friendly by @caufieldjh in #550
• Add ORKG, DBpedia, and Wikipedia by @caufieldjh with @Copilot in #552
• Performance improvements for the build process by @caufieldjh in #554
• Update license details and docs by @caufieldjh in #555
• Add sync for Translator data releases by @caufieldjh in #556
• Repair misalignment on Resource pages by @caufieldjh in #558
• Add four KG Resources: ckg, hald, kg4sl, and pharmebinet by @caufieldjh in #559
• Fixes and tests for KG-Registry-KG exports by @caufieldjh in #560
• Include Details card on Resource pages by @caufieldjh in #561
• Improve coverage of OMOP standardized vocabularies by @caufieldjh in #562
• Add diagram to enumerate product types and sources on Resource pages by @caufieldjh in #563
• Merge duplicate GO entries; update OBO Foundry sync to merge more cleanly by @caufieldjh in #565
• Fix issue with OBO Foundry sync producing invalid objects by @caufieldjh in #567
• Update licenses for a variety of Resources by @caufieldjh in #568
• Add eKG by @caufieldjh in #571
• Add fix for doc name collisions by @caufieldjh in #572
• Address AOP-Wiki and AOP-DB metadata by @caufieldjh in #574
• Complete IntAct IMEx metadata by @caufieldjh in #575
• Be more specific about relation types between Resources and Products by @caufieldjh in #576
• Follow up typed KG edge relation display by @caufieldjh in #577
• Add skills for agentic curation by @caufieldjh in #578
• Curation and cleanup for several Resource pages by @caufieldjh in #579
• Curation: stub page updates and additions by @caufieldjh in #580
• Curation: stub page updates, revisions, Skill updates, fixes for rendering URLs for product pages by @caufieldjh in #582
• Add Raras by @caufieldjh in #583
• Add interface to compare resources by @caufieldjh in #584
• Curation: aop-wiki, oma, reactome, snodb, tarbase; updates to URL checking scripts by @caufieldjh in #585
• Fix for listing primary sources by @caufieldjh in #586
• Curate: update KG resources for provenance and URL fixes by @caufieldjh in #587
• Curate: KG resource updates by @caufieldjh in #588
• Curate: general resources by @caufieldjh in #589
• Curate stale resource metadata and ontology pages by @caufieldjh in #590
• Batch curate KG Registry resource metadata by @caufieldjh in #592
• Add MetaboKG resource by @caufieldjh in #593
• Add KG-FM resource by @caufieldjh in #595
• Fix resource product section grouping by @caufieldjh in #597
• Batch curate KG Registry resources by @caufieldjh in #599
• Curation: stub Resource pages by @caufieldjh in #600
• Restructure Resource domains and map to controlled vocabulary (#601) by @caufieldjh in #602
• Add ICKG resource by @caufieldjh in #609
• Add myAURA KG resource by @caufieldjh in #610
• Add EmeraldGraph resource by @caufieldjh in #611
• Add AcuKG resource by @caufieldjh in #612
• Add CardioKG resource by @caufieldjh in #613
• Consolidate duplicate FooDB resource by @caufieldjh in #614
• Add incremental publication reference validation by @caufieldjh in #616
• Populate corrected publication citations by @caufieldjh in #617
• Align remaining citation labels with cached titles by @caufieldjh in #618
• Make citation warnings nonfatal in metadata build by @caufieldjh in #619
• Add BioBTree resource and its integrated data sources (#620) by @caufieldjh in #621
• Repair publication citation metadata across 50 Resource pages by @caufieldjh in #622
• Fix resource-page errors, harden link checker, and expand GeneCards sources by @caufieldjh in #623
• Fix invalid archive URL halting TTL build (#624) by @caufieldjh in #625
• Metadata curation: dashboard top-10 fixes + citation backfill (160 resources) by @caufieldjh in #626
• Add discovery skills + remote install/discovery (marketplace.json + ARD) by @caufieldjh in #627
• Improve Resource metadata: top dashboard resources, owner propagation, and citations by @caufieldjh in #629
• Metadata curation round 2: dashboard tooling fixes + publications/infores/format/URL backfill by @caufieldjh in #632
• Exclude references_cache from the Jekyll build by @caufieldjh in #633
• bacdive: add primary products (web portal, API, client examples) by @caufieldjh in #634
• biobtree: add KGX human subgraph graph dump (#630) by @caufieldjh in #635
• Metadata curation round 3: dashboard cache fix, top-10 + no-product cleanup, comprehensive KG provenance (62 new source pages) by @caufieldjh in #636
• Distinguish primary/secondary products and add on-demand source view by @caufieldjh in #637
• Add 48 BER-relevant resources to the ber collection by @caufieldjh in #638
• Metadata curation round 4: dashboard top resources + broken-URL batches by @caufieldjh in #639
• Metadata curation round 5: GO foreign-product fixes + publications by @caufieldjh in #640
• Add "use instead" field for pointing to replacement resources (#598) by @caufieldjh in #641
• Metadata curation round 6: top-10 link fixes + KG upstream-source provenance by @caufieldjh in #642
• Fix broken hetnetpy product link (#643) by @caufieldjh in #644
• Metadata curation round 7: fix registry-table count bug + top-10 + KG provenance by @caufieldjh in #645
• Metadata curation: fix data-quality issues on 50 resources by @caufieldjh in #646
• Add ImmPort download-method products (#650) by @caufieldjh in #654
• Add curated data sources to PubChem substance products (#649) by @caufieldjh in #653
• Update NLM-CKN with current repos, products, and processes (#648) by @caufieldjh in #652
• Add BiomarkerKB's own products and metadata updates (#647) by @caufieldjh in #651
• Combine biomarkerkg (BiomarkerKB KG) into biomarker (BiomarkerKB) by @caufieldjh in #657
• Deactivate Dragon AI Agent GitHub Mentions workflow by @caufieldjh in #658
• Speed up main page load and show explicit loading/error states by @caufieldjh in #661
• Render table rows incrementally and start the data fetch earlier by @caufieldjh in #663
• Report render exceptions separately from data load failures by @caufieldjh in #665
• Remove OBO Foundry-specific leftovers (prep for 0.1.0) by @caufieldjh in #666

New Contributors

• @egonw made their first contribution in #533

Full Changelog: 0.0.1...0.1.0