import EBI's gene2phenotype

andrewsu commented 6 years ago

https://www.ebi.ac.uk/gene2phenotype/downloads

seems like a reasonably simple data parser to write.

currently 2332 data records with these fields (from https://www.ebi.ac.uk/gene2phenotype/README):


  - gene symbol:                  HGNC gene symbol 
  - gene mim:                     OMIM number for a gene entry
  - disease name:                 Name provided by the curator
  - disease mim:                  OMIM number for a disease entry
  - disease confidence:           One value from the list of possible categories: both DD and IF, confirmed, possible, probable
  - allelic requirement:          comma-separated list of allelic requirement attributes. Possible values are: biallelic, monoallelic (Y),
                                  imprinted, uncertain, monoallelic, hemizygous, x-linked dominant, x-linked over-dominance, mosaic,
                                  mitochondrial, digenic 
  - mutation consequence:         One value from the list of possible consequences: 5_prime or 3_prime UTR mutation, activating,
                                  all missense/in frame, cis-regulatory or promotor mutation, dominant negative, increased gene dosage,
                                  loss of function, part of contiguous gene duplication, part of contiguous genomic interval deletion, uncertain
  - phenotypes:                   semicolon-separated list of HPO (http://www.human-phenotype-ontology.org/) IDs
  - organ specificity list:       semicolon-separated list of organs
  - pmids:                        semicolon-separated list of PMIDs 
  - panel:                        G2P panel: Cancer, Cardiac, DD, Ear, Eye or Skin
  - prev symbols:                 Symbols previously approved by the HGNC for this gene
  - hgnc id:                      HGNC identifier
  - gene disease pair entry date: Entry date for the gene disease pair into the database```

newgene commented 5 years ago

Parser implemented by @namespacestd0 here:

https://github.com/namespacestd0/ebi-data-parser

Pending to include in MyGene.info

sirloon commented 5 years ago

source name: "g2p"

andrewsu commented 5 years ago

any status update on this ticket? If the parser is done, would be great to get it integrated in a future release...

newgene commented 4 years ago

already deployed at https://pending.biothings.io/ebigene2phenotype

biothings / mygene.info

import EBI's gene2phenotype #51