monarch-initiative/monarch-ingest

Issues

• Delete incomplete cached file during ingest download?

  #600 opened 2 months ago by ptgolden
  1

• Ingest for HGNC Gene unnecessarily needs taxon-label map

  #597 opened 3 months ago by DnlRKorn
  0

• Monarch KG neo4j dump not working 2023 10 17

  #596 opened 3 months ago by kcortes133
  0

• Create delta between ORION and MONDO

  #594 opened 4 months ago by DnlRKorn
  1

• Add the Mouse Missense Mutation Library (MML) https://jcsmr.anu.edu.au/services/libraries-banking/missense-mutation-library

  #493 opened a year ago by sierra-moxon
  4

• Mondo derived g2d's should not be presented on the website as "associations"

  #592 opened 5 months ago by matentzn
  0

• Will yeast (S. pombe and S. cerevisiae) orthologs be included?

  #520 opened 6 months ago by ValWood
  6

• Address inconsistencies in documentation for HPOA vs. HPO-Annotations

  #523 opened a year ago by glass-ships
  0

• GenCC gene to disease ingest

  #450 opened 8 months ago by kevinschaper
  3

• Create cookiecutter template for modular koza ingests

  #585 opened 6 months ago by glass-ships
  0

• KG-Hub not showing new builds

  #500 opened 8 months ago by justaddcoffee
  9

• Drug Central Ingest

  #457 opened 2 years ago by putmantime
  4

• Update name fields used for genes

  #437 opened 8 months ago by kevinschaper
  2

• Get Mondo SSSOM from a better url

  #445 opened 8 months ago by kevinschaper
  3

• Evidence based Quality Control for the Monarch Graph

  #487 opened a year ago by RichardBruskiewich
  1

• Upload/update Solr in Jenkins pipeline

  #569 opened 9 months ago by glass-ships
  0

• Redirect _all_ mapping dependencies to Monarch Mapping Commons

  #555 opened 10 months ago by matentzn
  0

• Review Dependabot Warnings

  #503 opened 10 months ago by glass-ships
  1

• Add sources index.md page

  #508 opened 10 months ago by glass-ships
  1

• Assess whether Monarch STRING ingest prioritizes high quality knowledge over computed results

  #533 opened a year ago by monicacecilia
  0

• Dangling edges for Panther

  #446 opened 2 years ago by RichardBruskiewich
  7

• Update Koza and move to Pydantic V2

  #542 opened a year ago by glass-ships
  0

• Stats uploads to KG-Hub need to be publicly accessible

  #518 opened a year ago by caufieldjh
  6

• Populate term_associations in a phenio.db artifact

  #517 opened a year ago by kevinschaper
  1

• "Also known as" on gene pages mixes up genes and diseases (suggesting problem in ingest)

  #522 opened a year ago by nlharris
  1

• Poetry can't resolve depenencies

  #513 opened a year ago by glass-ships
  1

• Documentation: Phenio

  #491 opened a year ago by glass-ships
  1

• Aspergillus genes are missing from the ncbi gene ingest output

  #490 opened a year ago by kevinschaper
  0

• Make specific missing node / dangling edge reports for core ingests

  #507 opened a year ago by kevinschaper
  1

• Review kg-phenio ID prefix subset

  #468 opened 2 years ago by kevinschaper
  8

• kghub upload is failing

  #502 opened a year ago by kevinschaper
  1

• Update StringDB mapping url

  #495 opened a year ago by kevinschaper
  0

• Update alliance gene expression to capture assay as qualifier, xref as publication

  #497 opened a year ago by kevinschaper
  0

• Add subject/object taxon fields to denormalized edges

  #485 opened a year ago by kevinschaper
  0

• Use weaker predicate for CTD

  #483 opened a year ago by kevinschaper
  1

• Add HPOA gene to disease ingest (and remove OMIM g2d)

  #444 opened a year ago by kevinschaper
  5

• Populate in_taxon_label on genes

  #471 opened a year ago by kevinschaper
  1

• Make category single valued in denormalized schema

  #472 opened a year ago by kevinschaper
  2

• Docs deploy action is failing

  #470 opened a year ago by kevinschaper
  1

• Put merged_graph_stats.yaml into `current/stats` on kg-hub s3 bucket

  #478 opened a year ago by kevinschaper
  1

• Treat name as a required field

  #475 opened a year ago by kevinschaper
  0

• Koza SSSOM rewire feature: document loss of precision

  #473 opened a year ago by matentzn
  0

• Add full category closure to category field in jsonl and neo4j artifacts

  #463 opened 2 years ago by kevinschaper
  0

• Add jsonl and nt versions of the final graph

  #462 opened 2 years ago by kevinschaper
  1

• Address Publication ingests

  #459 opened 2 years ago by glass-ships
  0

• HPOA should be using `infores:hpo-annotations` according to biolink

  #438 opened 2 years ago by matentzn
  1

• Make sure phenio edges have a valid category

  #458 opened 2 years ago by kevinschaper
  0

• Make sure subject is always in subject_closure, object is always in object_closure

  #454 opened 2 years ago by kevinschaper
  0

• Rescue 112k HPOA d2p edges with ORPHA -> MONDO mapping

  #434 opened 2 years ago by kevinschaper
  4

• Add cli docs for ingest command

  #431 opened 2 years ago by kevinschaper
  0