Xenbase is a web-accessible resource that integrates all the diverse biological, genomic, genotype and phenotype data available from Xenopus research.
This ingest is built against a one-off OBAN formatted file, which makes for a transformation which only requires adding a curie prefix and connecting column names to biolink attributes. Evidence codes are provided as ECO terms but not yet captured in the output.
Biolink captured:
-
biolink:Gene
- id
-
biolink:PhenotypicFeature
- id
-
biolink:GeneToPhenotypicFeatureAssociation
- id (random uuid)
- subject (gene.id)
- predicate (has_phenotype)
- object (phenotypicFeature.id)
- publications
- aggregating_knowledge_source (["infores:monarchinitiative"])
- primary_knowledge_source (infores:xenbase)
Ortholog associations between Xenbase genes and genes from other organisms.
Biolink captured:
-
biolink:Gene
- id
-
biolink:GeneToGeneHomologyAssociation
- id (random uuid)
- subject (gene.id)
- predicate (orthologous_to)
- object (gene.id)
- aggregating_knowledge_source (["infores:monarchinitiative"])
- primary_knowledge_source (infores:xenbase)
Fisher et al. 2023, Genetics, 2023;, iyad018, doi:10.1093/genetics/iyad018
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