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monarch-initiative
Data Ingestion Pipeline for Monarch
```turtle . . . . ``` => some variant of SMC2 has-phenotype Haplotype HH3 (I don't think a haplotype is a phenotype but let's put that to the side or...
```turtle . . . . ``` Which translates to: 'Collie eye anomaly in dog' has-disposition obsolete autosomal recessive inheritance http://purl.obolibrary.org/obo/GENO_0000150 replaced by http://purl.obolibrary.org/obo/GENO_0000148 1. we should have a general check...
There are lot's of drops in frog and rat data. In some cases this is due to the taxon not being linked to the gene, so the data is still...
The reactome to ensembl file contains both gene and transcript ids. We should make sure these get different handling (eg don't categorize transcripts as genes)
for example see https://monarchinitiative.org/phenotype/HP:0000023 this is likely not a dipper bug but triaging here until we can investigate further credit to @iimpulse for finding this
Flybase alleles would be more accurately typed as "variant allele" instead of "allele"
On both production and beta we have nodes categorized as both genes and variants, for example: https://scigraph-data.monarchinitiative.org/scigraph/graph/neighbors?id=MGI%3A3811864&depth=1&blankNodes=false&relationshipType=sameAs&direction=BOTH&entail=false&project=* which comes from mgi.ttl: http://www.informatics.jax.org/allele/MGI:3811865 owl:sameAs http://www.informatics.jax.org/marker/MGI:3811864 Is this accurate? cc @mbrush
omim.ttl has classes which have multiple rdfs:label annotations, such as: ``` ORPHA:118231 a owl:Class ; rdfs:label "Capillary malformation-arteriovenous malformation", "Parkes Weber syndrome" ; biolink:category biolink:Disease . ``` By my regex...
On https://archive.monarchinitiative.org/beta/rdf/ucscbands.ttl we have ``` NCBIGenome: a SO:0001505, "_:NCBITaxon:7955genome" ; rdfs:label "NCBI build " ; RO:0002162 NCBITaxon:7955 ; dc:description "biolink:GenomeBuild" ; biolink:category biolink:GenomeBuild . ``` Couple weird things: - curie...
we should have some methods to create regions of sequence relatedness. the same model should accomodate both syntenic regions (across species), genome-duplications within the same species, and [pseudoautosomal regions](http://en.wikipedia.org/wiki/Pseudoautosomal_region) (such...
