Difference between revisions of "UniProt Paper - Gene - Data Type"
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Revision as of 19:29, 19 May 2015
Original file generated for UniProt:
Updates to file will now include data types curated for a given gene.
What we currently supply:
WBGene WBPaperID PMID
Not sure how this is generated - before my time.
What we need to add:
WBGene WBPaperID PMID Category
The Categories would be gene-specific and we will supply information for:
WBGene00003508 WBPaper00003680 pmid10517638 GO;Phenotype;Disease;Expression;Sequence
Strategy: Several possible strategies - not sure which is best.
Easiest to get everything from WS or a mixture of WS and postgres?
Some things, like GO, RNAi and Variation Phenotypes, need to be from WS
1) Start with Paper object and then trace the data types in the Refers_to tag - this works for everything but Disease
2) Look at each object in each relevant class - this seems computationally very intensive
How to map this onto our data types from each WS release:
?GO_annotation -> Gene -> Reference
?Interaction -> Interaction_type Physical -> Interactor_overlapping_gene -> Paper
?RNAi -> Inhibits -> Phenotype -> Reference
?Variation -> Affects -> Phenotype -> Reference
?Expr_pattern -> Expression_of -> Gene -> Reference
?Variation -> Affects
-> Nonsense -> Missense -> Silent Any one of these filled in -> Splice_site -> Frameshift -> Readthrough
?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence