monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza

https://monarchinitiative.org

monarch-initiative/monarch-ingest Issues

G2D Data Source Analysis
Updated 4 months ago2
KG-Hub not showing new builds
Closed 4 months ago9
Drug Central Ingest
Updated 4 months ago4
Update name fields used for genes
Closed 4 months ago2
Get Mondo SSSOM from a better url
Closed 4 months ago3
Evidence based Quality Control for the Monarch Graph
Updated 5 months ago1
Upload/update Solr in Jenkins pipeline
Closed 5 months ago
Redirect _all_ mapping dependencies to Monarch Mapping Commons
Closed 6 months ago
Review Dependabot Warnings
Closed 6 months ago1
Add sources index.md page
Closed 6 months ago1
Assess whether Monarch STRING ingest prioritizes high quality knowledge over computed results
Updated 6 months ago
Review of Evidence Capture for Monarch Ingests
Updated 6 months ago3
Dangling edges for Panther
Updated 6 months ago7
Dangling edges found for STRING.
Updated 6 months ago7
GenCC gene to disease ingest
Updated 7 months ago2
Add the Mouse Missense Mutation Library (MML) https://jcsmr.anu.edu.au/services/libraries-banking/missense-mutation-library
Updated 7 months ago4
Update Koza and move to Pydantic V2
Closed 8 months ago
Stats uploads to KG-Hub need to be publicly accessible
Closed 8 months ago6
Populate term_associations in a phenio.db artifact
Closed 10 months ago1
Will yeast (S. pombe and S. cerevisiae) orthologs be included?
Updated 10 months ago5
HPOA vs. HPO-Annotations
Updated 10 months ago
"Also known as" on gene pages mixes up genes and diseases (suggesting problem in ingest)
Updated 10 months ago1
Poetry can't resolve depenencies
Closed 10 months ago1
Documentation: Phenio
Closed a year ago1
Aspergillus genes are missing from the ncbi gene ingest output
Closed a year ago
Make specific missing node / dangling edge reports for core ingests
Updated a year ago1
Review kg-phenio ID prefix subset
Updated a year ago8
kghub upload is failing
Closed a year ago1
Update StringDB mapping url
Closed a year ago
Update alliance gene expression to capture assay as qualifier, xref as publication
Closed a year ago
Add subject/object taxon fields to denormalized edges
Updated a year ago
Use weaker predicate for CTD
Closed a year ago1
Add HPOA gene to disease ingest (and remove OMIM g2d)
Closed a year ago5
Populate in_taxon_label on genes
Closed a year ago1
Make category single valued in denormalized schema
Closed a year ago2
Docs deploy action is failing
Closed a year ago1
Put merged_graph_stats.yaml into `current/stats` on kg-hub s3 bucket
Closed a year ago1
Treat name as a required field
Updated a year ago
Koza SSSOM rewire feature: document loss of precision
Updated a year ago
Add full category closure to category field in jsonl and neo4j artifacts
Closed a year ago
Add jsonl and nt versions of the final graph
Closed a year ago1
Address Publication ingests
Updated a year ago
HPOA should be using `infores:hpo-annotations` according to biolink
Closed a year ago1
Make sure phenio edges have a valid category
Updated a year ago
Make sure subject is always in subject_closure, object is always in object_closure
Updated a year ago
Update HPOA columns
Updated a year ago
Rescue 112k HPOA d2p edges with ORPHA -> MONDO mapping
Closed a year ago4
Add cli docs for ingest command
Closed a year ago
Document the ingest process
Closed a year ago
Add validation of final KG
Updated a year ago1