Difference between revisions of "UniProt Paper - Gene - Data Type"
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PPI: | PPI: | ||
− | ?Interaction -> Interaction_type Physical | + | ?Interaction -> Interaction_type Physical |
− | + | -> Interactor_overlapping_gene | |
− | + | -> Paper | |
Phenotype: | Phenotype: | ||
− | ?RNAi -> Inhibits | + | ?RNAi -> Inhibits |
− | |||
− | |||
− | |||
− | |||
-> Phenotype | -> Phenotype | ||
-> Reference | -> Reference | ||
+ | |||
+ | ?Variation -> Affects | ||
+ | -> Phenotype | ||
+ | -> Reference | ||
Disease: | Disease: | ||
− | ?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence | + | ?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence |
− | + | -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence | |
Expression: | Expression: | ||
− | ?Expr_pattern -> Expression_of -> Gene | + | ?Expr_pattern -> Expression_of -> Gene |
− | + | -> Reference | |
Sequence: | Sequence: | ||
− | ?Variation -> Affects | + | ?Variation -> Affects |
− | + | -> Nonsense | |
− | + | -> Missense | |
− | + | -> Silent Any one of these filled in | |
− | + | -> Splice_site | |
− | + | -> Frameshift | |
− | + | -> Readthrough | |
− | + | -> Reference |
Revision as of 18:34, 19 May 2015
Original file generated for UniProt:
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/uniprot.cgi
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
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
The Categories would be gene-specific and we will supply information for:
GO:PPI;Phenotype;Disease;Expression;Sequence
How to map this onto our data types from each WS release:
GO:
?GO_annotation -> Gene -> Reference
PPI:
?Interaction -> Interaction_type Physical -> Interactor_overlapping_gene
-> Paper
Phenotype:
?RNAi -> Inhibits -> Phenotype -> Reference
?Variation -> Affects -> Phenotype -> Reference
Disease:
?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence
Expression:
?Expr_pattern -> Expression_of -> Gene -> Reference
Sequence:
?Variation -> Affects -> Nonsense -> Missense -> Silent Any one of these filled in -> Splice_site -> Frameshift -> Readthrough -> Reference