monarch-initiative monarch-ingest issues

monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza

https://monarchinitiative.org

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issues

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Get output from modular ingests before merge in Jenkins job

#593 glass-ships opened 6 days ago
1
Mondo derived g2d's should not be presented on the website as "associations"

#592 matentzn opened 1 week ago
0
Use duckdb for jsonl conversion to fit into memory

#591 kevinschaper closed 2 days ago
0
Add modular genotype & variant ingests

#590 kevinschaper closed 3 weeks ago
1
linkml solr upgrade

#589 kevinschaper closed 4 weeks ago
0
Create exploded association exports that traverses closures

#588 kevinschaper closed 3 weeks ago
1
Update Koza, imports, and tests. Fix lint/format make targets

#587 glass-ships closed 1 month ago
0
notebook experimenting on using duckdb to merge a kg

#586 kevinschaper opened 2 months ago
0
Create cookiecutter template for modular koza ingests

#585 glass-ships closed 1 month ago
0
Add knowledge level & agent type, plus constraint improvements

#584 kevinschaper closed 2 months ago
0
cat-merge update

#583 kevinschaper closed 3 months ago
0
Use systematic id for empty gene names

#582 glass-ships closed 3 months ago
0
add step to upload index.html generated by multi-indexer

#581 glass-ships closed 3 months ago
1
Fix upload and index to KGHub

#580 glass-ships closed 3 months ago
11
Use sudo when downloading solr.tar.gz onto the solr dev instance

#579 kevinschaper closed 3 months ago
0
Restore onset_qualifier, plus HPOA DB_reference -> publication and doc cleanup

#578 kevinschaper closed 3 months ago
0
Treats refactor / Biolink 4.1.x update

#577 kevinschaper closed 3 months ago
0
Add object taxon info for gene to gene association export

#576 kevinschaper closed 3 months ago
0
Biolink 4.1.x upgrade / treats refactor

#575 kevinschaper closed 3 months ago
0
Fix release script not running in jenkins job

#574 glass-ships closed 3 months ago
0
Upload data to archive bucket on release

#573 glass-ships closed 3 months ago
0
fix write-metadata params in Jenkinsfiles

#572 kevinschaper closed 3 months ago
0
Updates to latest biolink, adds frequency quantifier fields to hpoa d2p

#571 kevinschaper closed 3 months ago
0
Upload/Update dev solr service

#570 glass-ships closed 4 months ago
0
Upload/update Solr in Jenkins pipeline

#569 glass-ships closed 4 months ago
0
Update closurizer to 0.5.1

#568 kevinschaper closed 4 months ago
0
Add denormalized node output file produced by closurizer with has_phenotype expansions and load it into Solr

#567 kevinschaper closed 4 months ago
0
Add script to create github release via jenkins job

#566 glass-ships closed 4 months ago
0
Adds copy-field declarations for the full_name field which stores the long name of genes

#565 kevinschaper closed 5 months ago
0
Adds lowercase keyword grounding field to Solr entity collection

#564 kevinschaper closed 5 months ago
0
Include human gene expression from bGee

#563 kevinschaper closed 5 months ago
1
Download mappings from data.mi.org

#562 glass-ships closed 5 months ago
0
Write data and package versions to data/output

#561 glass-ships closed 3 months ago
5
Bump jinja2 from 3.1.2 to 3.1.3

#560 dependabot[bot] closed 5 months ago
1
Rename GOA to GO

#559 glass-ships closed 5 months ago
0
Interactions Cleanup

#558 kevinschaper closed 5 months ago
0
Update the gene mapping file to match the new name with the .sssom.tsv suffix.

#557 kevinschaper closed 6 months ago
0
Update Reactome ingests to use `Reactome` as a prefix rather than `REACT`

#556 kevinschaper closed 6 months ago
0
Redirect _all_ mapping dependencies to Monarch Mapping Commons

#555 matentzn closed 5 months ago
0
Update the phenio.db term association population to point to db files in output subdir

#554 kevinschaper closed 6 months ago
0
One potential solution to resolve Monarch-App issue#465

#553 RichardBruskiewich closed 6 months ago
1
Restore phenio doc

#552 kevinschaper closed 7 months ago
0
Attempt to update to Pydantic v2

#551 glass-ships closed 6 months ago
1
notebook - KG diff from stats

#550 madanucd closed 6 months ago
0
Monarch-App Issue 438 add BioGRID ingest

#549 RichardBruskiewich closed 6 months ago
1
Keep all phenio node columns

#548 kevinschaper closed 7 months ago
0
Upload data dir to monarch-archive

#547 kevinschaper closed 7 months ago
0
Flesh out pheno README

#546 RichardBruskiewich closed 6 months ago
0
Add TSV export, borrowing from release-utils

#545 kevinschaper closed 7 months ago
0
issue-426-goa-provenance

#543 RichardBruskiewich closed 7 months ago
0