Difference between revisions of "UniProt Paper - Gene - Data Type"
(Created page with "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.") |
|||
Line 4: | Line 4: | ||
Updates to file will now include data types curated for a given gene. | 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 |
Revision as of 18:32, 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