2024-11-19

What's Changed

• Populate publications for GO annotation ingest, plus update tests & doc to match by @kevinschaper in #603
• Add missing function call by @ptgolden in #602
• Updates phenio.db association population to gene & disease phenotype associations by @kevinschaper in #601
• Bring ncbi gene nodes in from modular ingest by @kevinschaper in #604
• Bring in modular hpoa by @kevinschaper in #605
• Remove non modular hpoa by @kevinschaper in #606
• update to move go annotations to modularized version by @AO33 in #607
• Add maxo ingest edges to ingests.yaml by @kevinschaper in #608
• Add species context qualifier, update closurizer by @kevinschaper in #609

New Contributors

• @ptgolden made their first contribution in #602
• @AO33 made their first contribution in #607

Full Changelog: 2024-08-12...2024-11-19

2024-10-16

What's Changed

• Populate publications for GO annotation ingest, plus update tests & doc to match by @kevinschaper in #603
• Add missing function call by @ptgolden in #602
• Updates phenio.db association population to gene & disease phenotype associations by @kevinschaper in #601
• Bring ncbi gene nodes in from modular ingest by @kevinschaper in #604
• Bring in modular hpoa by @kevinschaper in #605
• Remove non modular hpoa by @kevinschaper in #606

New Contributors

• @ptgolden made their first contribution in #602

Full Changelog: 2024-08-12...2024-10-16

2024-09-12

What's Changed

• linkml solr upgrade by @kevinschaper in #589
• Create exploded association exports that traverses closures by @kevinschaper in #588
• Add modular genotype & variant ingests by @kevinschaper in #590
• Use duckdb for jsonl conversion to fit into memory by @kevinschaper in #591
• Repair zeroes in phenotype.hpoa, update PKS by @kevinschaper in #595
• Removed taxon-labels map requirement from hgnc gene ingest. by @DnlRKorn in #598
• Populate type for HGNC & Alliance gene nodes by @kevinschaper in #599

New Contributors

• @DnlRKorn made their first contribution in #598

Full Changelog: 2024-05-22...2024-09-11

2024-08-12

What's Changed

• linkml solr upgrade by @kevinschaper in #589
• Create exploded association exports that traverses closures by @kevinschaper in #588
• Add modular genotype & variant ingests by @kevinschaper in #590
• Use duckdb for jsonl conversion to fit into memory by @kevinschaper in #591
• Repair zeroes in phenotype.hpoa, update PKS by @kevinschaper in #595

Full Changelog: 2024-05-22...2024-08-12

2024-05-22

What's Changed

• Update Koza, imports, and tests. Fix lint/format make targets by @glass-ships in #587

Full Changelog: 2024-04-17...2024-05-22

2024-04-18

What's Changed

• Fix upload and index to KGHub by @glass-ships in #580
• add step to upload index.html generated by multi-indexer by @glass-ships in #581
• Use sudo when downloading solr.tar.gz onto the solr dev instance by @kevinschaper in #579
• Use systematic id for empty gene names by @glass-ships in #582
• cat-merge update by @kevinschaper in #583
• Add knowledge level & agent type, plus constraint improvements by @kevinschaper in #584

Full Changelog: 2024-03-18...2024-04-17

2024-03-18

What's Changed

• Download mappings from data.mi.org by @glass-ships in #562
• Include human gene expression from bGee by @kevinschaper in #563
• Adds lowercase keyword grounding field to Solr entity collection by @kevinschaper in #564
• Adds copy-field declarations for the full_name field which stores the long name of genes by @kevinschaper in #565
• Add denormalized node output file produced by closurizer with has_phenotype expansions and load it into Solr by @kevinschaper in #567
• Update closurizer to 0.5.1 by @kevinschaper in #568
• Upload/Update dev solr service by @glass-ships in #570
• Add script to create github release via jenkins job by @glass-ships in #566
• Updates to latest biolink, adds frequency quantifier fields to hpoa d2p by @kevinschaper in #571
• Write data and package versions to data/output by @glass-ships in #561
• fix write-metadata params in Jenkinsfiles by @kevinschaper in #572
• Upload data to archive bucket on release by @glass-ships in #573
• Fix release script not running in jenkins job by @glass-ships in #574
• Treats refactor / Biolink 4.1.x update by @kevinschaper in #577
• Add object taxon info for gene to gene association export by @kevinschaper in #576
• Restore onset_qualifier, plus HPOA DB_reference -> publication and doc cleanup by @kevinschaper in #578

Full Changelog: 2024-01-13...2024-03-18

2024-01-13

Phenio: 2024-01-12
Mondo: 2024-01-03
HPO: 2024-01-11

What's Changed

• Interactions Cleanup by @kevinschaper in #558

Full Changelog: 2023-12-16...2024-01-13

2023-12-16

Data Versions

Phenio: 20231213
Mondo: 2023-12-12
HPO: 2023-10-09

What's Changed

• Attempt to update to Pydantic v2 by @glass-ships in #551
• Update Reactome ingests to use Reactome as a prefix rather than REACT by @kevinschaper in #556
• Update the phenio.db term association population to point to db files in output subdir by @kevinschaper in #554
• add additional entity field tokenizations by @kevinschaper in #541
• Monarch-App Issue 438 add BioGRID ingest by @RichardBruskiewich in #549
• Adds a notebook experiment for replacing closurizer's use of petl by @kevinschaper in #538
• Flesh out pheno README by @RichardBruskiewich in #546
• notebook - KG diff from stats by @madanucd in #550
• Update the gene mapping file to match the new name with the .sssom.tsv suffix. by @kevinschaper in #557

Full Changelog: https://github.com/monarch-initiative/monarch-ingest/commits/2023-12-16