Manager 6November2013: Difference between revisions
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#Can we allow use of both a published paper and a GO_REF in the same annotation? Cardinality of the reference field can be >1, but the annotation documentation only refers to cases where a publication has identifiers in different databases, e.g. PubMed and a MOD database. I'd like to include a GO_REF for the WormBase Phenotype2GO-based annotations, but also still include the original publication from which the phenotype information was curated. The GO_REF would explain the methodology used to create the resulting Biological Process annotation. [Kimberly] | #Can we allow use of both a published paper and a GO_REF in the same annotation? Cardinality of the reference field can be >1, but the annotation documentation only refers to cases where a publication has identifiers in different databases, e.g. PubMed and a MOD database. I'd like to include a GO_REF for the WormBase Phenotype2GO-based annotations, but also still include the original publication from which the phenotype information was curated. The GO_REF would explain the methodology used to create the resulting Biological Process annotation. [Kimberly] | ||
## Good idea. We can create a new subclass of IMP in ECO and use the [http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt gaf to eco mapping] (which takes a evidence code + reference pair and maps it to an evidence type). But really we need a way to represent combinatorial evidence. This is analogous to F->P and P->C inferences, where we embed the fact an inference was made using assigned_by=GOC, which is not ideal. | |||
Revision as of 02:50, 6 November 2013
Agenda Items
- Can we allow use of both a published paper and a GO_REF in the same annotation? Cardinality of the reference field can be >1, but the annotation documentation only refers to cases where a publication has identifiers in different databases, e.g. PubMed and a MOD database. I'd like to include a GO_REF for the WormBase Phenotype2GO-based annotations, but also still include the original publication from which the phenotype information was curated. The GO_REF would explain the methodology used to create the resulting Biological Process annotation. [Kimberly]
- Good idea. We can create a new subclass of IMP in ECO and use the gaf to eco mapping (which takes a evidence code + reference pair and maps it to an evidence type). But really we need a way to represent combinatorial evidence. This is analogous to F->P and P->C inferences, where we embed the fact an inference was made using assigned_by=GOC, which is not ideal.