Present: Rama, Rachael, David, Kimberly, Chris, Pascale, Huaiyu, Judy, Suzi
Automated Phenotype-Based GO Annotations
- 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.
- How can we improve phenotype-based GO annotations?
- Downstream effects have long been problematic for phenotype-based GO annotations, especially when these annotations are based on a mapping file (Phenotype Ontology Term : GO Biological Process Term).
- Consider constructing a more rules-based approach to applying the BP annotation.
- To what extent can we make use of the ontology structure (e.g., inter-ontology links) to aid in a rules-based approach?
- To what extent can we improve the mappings between PO and GO terms? Start with molecular processes -> cellular processes -> organismal processes.
- How should we handle cases where a BP annotation is the result of cumulative results, i.e. a summation of phenotypes?
Action Item: Draft a GO_REF for BP annotations inferred from Phenotype Ontology annotations that documents curation pipeline and entities included in the With/From column, e.g. Variation IDs, RNAi experiment IDs, Phenotype Ontology terms, Paper IDs. [Kimberly]
Action Item: Update documentation about what can be included in the With/From column for IMP annotations to include paper identifiers. [Rachael, Rama]
Action Item: Survey existing annotations to find suspect (outlier) BP annotations. [Suzi, Chris]
Action Item: Assemble use cases where phenotype-based annotations would be either misleading or inconsistent with manual GO annotation practices. [GO Curators]
- What are GO's plans for the meeting?
- Would be good to have a coordinated set of talks - start a wiki page for ideas?
- Submit a paper for the Database issue? Just abstracts?
- Who is going to the meeting?
Action Item: Add abstract deadline to GO calendar - DONE [Suzi]
Papers - November 15th, 2013
Abstract for Posters - February 10, 2014
Action Item: Create wiki page for ideas.
Ideas: enrichment analysis strategies, MGI's phenotype to BP pipeline, apoptosis
GO Wiki Editing
- Chris, Seth have added a Plug-in for the Wiki that will force you to add a category for any new page.