v1.1.1

What's Changed

• Add frequency column to phenotype pages by @glass-ships in #641
• Search category filter fix by @kevinschaper in #640

Full Changelog: v1.1.0...v1.1.1

v1.1.0

Reminder: shutdown of legacy monarch services including Biolink API, Owlsim, previous.monarchinitiative.org and solr.monarchinitiative.org

Node page enhancements

• Initial support for bringing back ortholog phenotypes
• Showing frequency qualifiers to better avoid the appearance of duplicate phenotype rows
• Phenotypes on Gene and Disease pages are sorted by frequency when available

Alpha release of Monarch-R

• A tidy interface for Monarch KG graph data in R: https://github.com/monarch-initiative/monarchr

Semantic Similarity

• Ability to select which metric is used for phenotype compare and search, with a choice of Ancestor Information Content, Phenodigm or Jaccard
• Multi-compare semsim API endpoint for comparing one phenotype profile against a group of phenotype profiles, with phenogrid support to follow in the next release
• Improved sync to browser url, meaning that navigating away from phenotype explorer will no longer clear the phenotype entry fields (this applies beyond phenotype explorer, but is most significantly felt on phenotype explorer)
• Phenogrid labels are no longer truncated in

Improved CONTRIBUTING.md

Mappings

Added NCBI to PomBase gene mapping (monarch-initiative/monarch-mapping-commons#53)
Repaired CHEBI-MESH mapping generation process

Graph updates

• Repair of CHEBI-MESH SSSOM mappings brings in 5,640 Chemical biolink:treats_or_applied_or_studied_to_treat Disease associations from CTD
• Phenio support for DDPHENO ontology brings in 1,216 Gene to Phenotype associations for Dictyostelium discoideum from dictyBase
• Full change stats can be found on the Monarch-QC Dashboard

Full monarch-app release notes below

• Using Enums in SolrImplementation functions by @glass-ships in #576
• Add Triptych for set to set comparison by @kevinschaper in #591
• update publications and citation page by @glass-ships in #609
• Update citations by @glass-ships in #611
• Turn off autoplay on ios video by @vincerubinetti in #610
• Compact associations by @glass-ships in #602
• Update citations by @glass-ships in #617
• semsim multi-compare by @kevinschaper in #612
• Fix table format for associations by @glass-ships in #603
• Add --traverse-orthologs flag for assoc table by @glass-ships in #616
• Add InstanceType for defineExpose'd components by @glass-ships in #623
• Relax codecov by @amc-corey-cox in #625
• Rename ortholog phenotype checkbox by @kevinschaper in #627
• update resources.json by @glass-ships in #628
• Multicompare API update by @kevinschaper in #631
• Node/Yarn to Bun by @vincerubinetti in #624
• Adds frequency_quantifier mixin fields as defined by biolink-model by @kevinschaper in #606
• Sync url by @vincerubinetti in #621
• Improve README and CONTRIBUTING to make the project more accessible. by @amc-corey-cox in #632
• Add option to select metric for semsim search/compare by @glass-ships in #635
• Untruncate labels for phenogrid export by @vincerubinetti in #619
• AppRing updates by @glass-ships in #637

Full Changelog: v1.0.0...v1.1.0

Full monarch-ingest release notes for 2024-03-18

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

v1.0.0

What's Changed

• Skip delete SSH keys when none are present by @glass-ships in #540
• Ff pheno fix by @vincerubinetti in #543
• update PFR page by @glass-ships in #561
• fix download=false still downloading by @glass-ships in #563
• Increase grounding precision by @kevinschaper in #565
• add subj/obj taxon, category, namespace to assoc api endpoint by @glass-ships in #548
• Add google group button by @glass-ships in #573
• Add button to run Text Annotator by @glass-ships in #569
• handle inconsistent annotations by @madanucd in #574
• back merge soft-break message into main by @kevinschaper in #580
• 554 coverage by @amc-corey-cox in #582
• fix entity overlap by @madanucd in #584
• Test coverage by @amc-corey-cox in #583
• add color to category icons by @vincerubinetti in #545
• Fixes how we do OR expansion of filter queries based on lists by @kevinschaper in #585
• fix tally in set to set compare func by @vincerubinetti in #590
• Update checkout action by @glass-ships in #592
• Improve pheno explorer examples by @amc-corey-cox in #596
• Add workflow to upload coverage for main by @amc-corey-cox in #598
• has_phenotype expansion in node schema, semsim autocomplete and boosting tweaks by @kevinschaper in #581

New Contributors

• @amc-corey-cox made their first contribution in #582

Full Changelog: v0.20.0...v1.0.0

v0.20.2

Updates link to V2/Biolink API in Fastapi description

v0.20.1

Full Changelog: v0.20.0...v0.20.1

What's Changed

• add soft break message to api description by @kevinschaper in #579

Full Changelog: v0.20.0...v0.20.1

v0.20.0

What's Changed

• Update PageAbout.vue by @glass-ships in #526
• exclude multi-entity association endpoint from api by @glass-ships in #527
• Fix semsim search GET api method, add api tests by @kevinschaper in #529
• Updating to Pydantic v2 by @glass-ships in #495
• add qualifier fields by @kevinschaper in #533
• Update PFR page by @glass-ships in #534
• Update test for changed data by @kevinschaper in #535
• TSV for Downloads by @glass-ships in #530
• add associations tsv download to frontend by @vincerubinetti in #537
• Text annotation v3 by @madanucd in #522
• show phenotype in pheno sem sim group by @vincerubinetti in #538

New Contributors

• @madanucd made their first contribution in #522

Full Changelog: v0.19.2...v0.20.0

v0.19.2

What's Changed

• Fixes searches where no category is specified by @kevinschaper in #520

Full Changelog: v0.19.1...v0.19.2

v0.19.1

What's Changed

• Turns text annotator off again in the UI by @kevinschaper in #518

Full Changelog: v0.19.0...v0.19.1

v0.19.0

What's Changed

• Add Resources (Bang Our Own Drum) by @glass-ships in #463
• add blurb to resources page by @glass-ships in #485
• update resource fixture by @glass-ships in #488
• Fixed text that links to HPO by @nlharris in #455
• Update PFR page by @glass-ships in #492
• add ssh cache and key expiration for deployment workflow by @glass-ships in #491
• Simplify loading of converter in CurieService by @cthoyt in #486
• add send to pheno ex button, obsolete node, misc by @vincerubinetti in #482
• update publications (and makefile/script slightly) by @glass-ships in #493
• Updating Teams Page again by @glass-ships in #487
• Implement SemsimServer search by @glass-ships in #499
• Quick fixes for semsim search / API config by @kevinschaper in #503
• Populate uri for entities when extra=True by @kevinschaper in #502
• Adds a full entity to the semsim search response by @kevinschaper in #504
• Reduce limit on phenotype fetching to the 500 record max by @kevinschaper in #509
• Bring back oak and phenio (text annotator) by @vincerubinetti in #497
• Pass the phenio db path to the oak implementation initializer by @kevinschaper in #510
• remove old ssh keys in action by @glass-ships in #511
• Improve association table search by @kevinschaper in #268
• Replace CuriesService with direct usage of curies.Converter by @cthoyt in #494
• Quick PR to turn off oak init and hide the text annotator endpoints so that we can start up on GCP again. by @kevinschaper in #512
• generate category enums by solr query by @glass-ships in #515
• Semantic Search UI by @kevinschaper in #514
• Fixes specifying categories on the search endpoint by @kevinschaper in #517

New Contributors

• @cthoyt made their first contribution in #486

Full Changelog: v0.18.1...v0.19.0

v0.18.1

What's Changed

• Update Overview page by @glass-ships in #472

Full Changelog: v0.18.0...v0.18.1