Expanding and enriching the representation of alleles in the alliance of genome resources
Year: 2021
Type: other
Abstract: The Alliance of Genome Resources (Alliance) has been working to harmonize the representation of alleles across the member model organism databases (MODs). In the first phase, the focus was on harmonizing and incorporating the minimal set of essential features used in single gene allele annotations including; symbol, CURIE, allele_of relation to a gene, description of the molecular mutation. In the second phase, we expanded the allele representation beyond just single gene alleles to also include transgenic alleles. Transgenic alleles differ from single gene alleles in that they do not require an allele_of relation to a gene and may have a relation to a construct. Constructs were added to the Alliance to capture the features of the transgenic vectors used to create transmissible transgenic alleles. Constructs include fields for documenting the promoters and enhancers used to drive expression and the genes expressed. CURIEs are included for the genes used to supply the promoters, enhancers, and expressed gene sequences whenever available. Inclusion of these CURIEs allows for display of transgenic alleles expressing a gene on relevant Alliance gene pages in a transgenic allele table regardless of the species carrying the transgenic allele. Constructs may be related to zero to many transgenic alleles and transgenic alleles may have relationships to zero to many constructs. In the next phase we are working to further expand the information associated with alleles to cover all types of information annotated by any of the participating MODs. Where possible, we are harmonizing existing MOD specific controlled vocabularies and working to get these terms incorporated in public ontologies. For example, the generation method used to create or identify the alleles is annotated using in-house controlled vocabularies or ontologies by many of the MODs. Thus in MGI and FlyBase there are a terms for all endonuclease techniques - “endonuclease-mediated” in MGI and “site specific cleavage” (FBcv:0003007) in FlyBase - while in FlyBase and ZFIN there are individual terms for the different techniques using endonucleases (e.g. CRISPR/cas, TALENs). From the various in-house vocabularies a consensus list of terms was created and these terms were submitted to the Ontology for Biomedical Investigations (OBI). Work to harmonize additional vocabularies, bring in alleles affecting multiple genes, and incorporate the full range of information about alleles into the Alliance is ongoing.
Authors: Susan M Bello, Yvonne M Bradford, Cynthia L Smith, The Alliance of Genome Resources Disease and Phenotype working group
Institution: Jackson Laboratory
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W3208970993