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monarch-initiative
Data Ingestion Pipeline for Monarch
MONARCH|bbde782a8f9ecffafa1f|rdf|type|OBAN|association MONARCH|bbde782a8f9ecffafa1f|SEPIO|0000015|BNODE|b9b7ce213aedc167a8d1 MONARCH|bbde782a8f9ecffafa1f|OBAN|association_has_subject|ClinVarVariant|88639 MONARCH|bbde782a8f9ecffafa1f|OBAN|association_has_object|OMIM|608516 MONARCH|bbde782a8f9ecffafa1f|SEPIO|0000007|BNODE| be5743009077a95dd715 MONARCH|bbde782a8f9ecffafa1f|SEPIO|0000168| LITERAL| 0 MONARCH|bf4652956c21bb3ccfe4|rdf|type|OBAN| association MONARCH|bf4652956c21bb3ccfe4|SEPIO|0000168| LITERAL|0 MONARCH|bf4652956c21bb3ccfe4 |OBAN|association_has_object|OMIM|608516 MONARCH|bf4652956c21bb3ccfe4 |OBAN|association_has_subject|ClinVarVariant|88640| MONARCH|bf4652956c21bb3ccfe4 |SEPIO|0000007|BNODE|b067af3b72190f23dc61 MONARCH|bf4652956c21bb3ccfe4 |SEPIO|0000015|BNODE|bd5d2ada782c6538bc23 (that is 2 out of 13.5M Monarch Associations)
Such as 'genotype to phenotypic feature association' See https://biolink.github.io/biolink-model/docs/Association.html
https://beta.monarchinitiative.org/anatomy/UBERON:0004819 According to this page, kidney epithelium is linked to 19182 genes. This is meaningless -- where is this coming from?
From a user > Subject: why is Map3k1 a variant of Map3k11? > You have Map3k1 (one) listed as a variant of Map3k11 (eleven). That can't be right. I think...
This ticket is for starting documentation to allow external collaborators to ingest their data sources. This ticket was inspired by Xenbase contacting us requesting help with documentation for the core...
the anx allele (http://www.informatics.jax.org/allele/MGI:1856657) is a locus for which the actual genetic variant is not known. When you go from https://beta.monarchinitiative.org/variant/MGI:1856657 to the gene page, the gene page is empty:...
The following IRIs will not be supported by uPheno anymore: https://github.com/obophenotype/upheno-dev/blob/master/src/curation/qc/required_allele_phenotype.txt https://github.com/obophenotype/upheno-dev/blob/master/src/curation/qc/required_other_classes.txt If anyone cares about them, they should let me know.
Possible to ingest via dipper? https://t.co/4I4isD9Ka7?amp=1 (redirects to a pdf)
I've been working on our gene-variant display and am auditing our data. In doing this I found that we're missing two allele-gene relationships for shha. According to the ZFIN and...
This bug was originally raised by @iimpulse For reference, the query: https://api-dev.monarchinitiative.org/api/bioentity/gene/MGI:98297/variants?fetch_objects=true&start=0&rows=10&facet=true&facet_fields=subject_taxon&taxon=OBI%3A0100026 yields gene to variant associations. But there are some associations where object has a `BNODE` prefix, and a...
