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Alliance

The Alliance of Genome Resources contains a subset of model organism data from member databases that is harmonized to the same model. Over time, as the alliance adds additional data types, individual MOD ingests can be replaced by collective Alliance ingest. The Alliance has bulk data downloads, ingest data formats, and an API. The preference should be bulk downloads first, followed by ingest formats, finally by API calls. In some cases it may continue to be more practical to load from individual MODs when data is not yet fully harmonized in the Alliance.

Gene Information

Genes for all Alliance species (Human, Rat, Mouse, Fish, Fly, Worm, Yeast, Frog) are loaded using the BGI formatted ingest files, as there are no Gene export files.

Biolink captured

  • biolink:Gene
    • id
    • symbol
    • name
    • in_taxon
    • source
    • synonyms
    • xref

Gene to Phenotype

Phenotype for the subset of Alliance species which use phenotype ontologies (Human, Rat, Mouse, Worm) are loaded using the phenotype ingest format, since there is not yet a phenotype export file from the Alliance. This file contains both Gene and Allele phenotypes, so a single column TSV is produced from BGI files listing Gene IDs to check the category and only genes are included. Environmental conditions are present for some species and are captured using the qualifier.

Biolink captured

  • biolink:GeneToPhenotypicFeatureAssociation
    • id (random uuid)
    • subject (gene.id)
    • predicate (has_phenotype)
    • object (phenotypicFeature.id)
    • publications
    • qualifiers (condition terms)
    • aggregating_knowledge_source (["infores:monarchinitiative", "infores:alliancegenome"])
    • primary_knowledge_source (infores mapped from row['Source'])

Gene Expression

This is the full data model of the Alliance file ingested; however, not all fields are currently used in the current ingest (in most cases, these fields are not yet set in the input data sets; see the gene_to_expression.yaml file)

  • Species
  • SpeciesID
  • GeneID
  • GeneSymbol
  • Location
  • StageTerm
  • AssayID
  • AssayTermName
  • CellularComponentID
  • CellularComponentTerm
  • CellularComponentQualifierIDs
  • CellularComponentQualifierTermNames
  • SubStructureID
  • SubStructureName
  • SubStructureQualifierIDs
  • SubStructureQualifierTermNames
  • AnatomyTermID
  • AnatomyTermName
  • AnatomyTermQualifierIDs
  • AnatomyTermQualifierTermNames
  • SourceURL
  • Source
  • Reference

Discussion Group: https://www.alliancegenome.org/working-groups#expression

Download: https://www.alliancegenome.org/downloads#expression

Biolink captured

  • biolink:Gene

    • id (row['GeneID'])
    • name (row['GeneSymbol'])
    • in taxon (row['SpeciesID'])
    • source (infores mapped from row['Source'])

  • biolink:AnatomicalEntity

    • id (row['AnatomyTermID'])
    • name (row['AnatomyTermName'])
    • source (infores mapped from row['Source'])

  • biolink:CellularComponent # is_a: anatomical entity...

    • id (row['CellularComponentID'])
    • name (row['CellularComponentTerm'])
    • source (infores mapped from row['Source'])

  • biolink:LifeStage

    • id (CURIE heuristically inferred from row['SpeciesID'] and row['StageTerm'])
    • name (row['StageTerm'])
    • in taxon (row['SpeciesID'])
    • source (infores mapped from row['Source'])

  • biolink:GeneToExpressionSiteAssociation

    • id (random uuid)
    • subject (Gene.id)
    • predicates (biolink:expressed_in)
    • object (AnatomicalEntity.id or CellularComponent.id)
    • stage qualifier (LifeStage.id) # if specified; None otherwise
    • has evidence (row['AssayID']) # e.g. taken from MMO - "measurement method ontology"
    • publications (row['Reference'])
    • aggregating_knowledge_source (["infores:monarchinitiative", "infores:alliancegenome"])
    • primary_knowledge_source (infores mapped from row['Source'])

Literature

The Alliance has a well defined literature ingest format that aligns publications from MOD members.

Mapping of Alliance publication category to biolink category

Alliance category Biolink publication type
Research Article IAO:0000013
Review Article IAO:0000013
Thesis IAO:0000311
Book IAO:0000311
Other IAO:0000311
Preprint IAO:0000013
Conference Publication IAO:0000311
Personal Communication IAO:0000311
Direct Data Submission IAO:0000311
Internal Process Reference IAO:0000311
Unknown IAO:0000311
Retraction IAO:0000311

This ingest doesn't make an effort to sort these publication categories into more specific classes than biolink:Publication, but does set the type.

Biolink captured

  • biolink:Publication
    • id (primaryId)
    • name (title)
    • summary (abstract)
    • authors (authors.name flattened as a comma separated string)
    • xref (crossReferences.id)
    • mesh terms (meshTerms.meshHeadingTerm , meshTerms.meshQualifierTerm)
    • type (IAO:0000311 for publication, IAO:0000013 for article)
    • creation date (datePublished)
    • keywords (keywords)

Citation

Harmonizing model organism data in the Alliance of Genome Resources. 2022. Alliance of Genome Resources Consortium. Genetics, Volume 220, Issue 4, April 2022. Published Online: 25 February 2022. doi: doi.org/10.1093/genetics/iyac022. PMID: 35380658; PMCID: PMC8982023.