Annotation Conf. Call 2019-07-09
From GO Wiki
github submission for InterPro2GO mappings
- Tagging InterPro in issues
- Lorna has requested that we tag InterPro curators so they can be alerted to issues relevant to them (can find relevant gitHub handles on the group-contacts.yaml file: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv)
- Please also add the InterPro mapping label (always good practice to add labels)
Protein oligomerization terms in GO
- Follow up to 2019-06-11 annotation conference call to review recommendations and actions
- Proposal and Recommendations
- Biological Process Annotations
- Molecular Function Annotations
- Protein Dimerization Activity (includes regulation of activity)
- For MF annotations using the IPI evidence code, we are proposing term merges, so curators hopefully will not have to do manual revision here (programmatic upgrades can be done locally?)
- For example, protein homodimerization activity, should be handled by merging into 'identical protein binding'
- However, there are some evidence code issues/questions that we should review
- For IC, NAS, and TAS evidence codes, recommend upgrading to an experimentally supported annotation or removing
- For IDA annotations, we'd like to convert as many of those as possible into IPI, even if the With field will contain the same ID as the annotated entity. This allows for consistent representation of binding annotations in GO.
- ~1200 IDA annotations to 'protein homodimerization activity'. These should be automatically converted (locally) to 'identical protein binding' using IPI and the annotated entity in the With field.
- ~350 IDA annotations to 'protein heterodimerization activity'. Are these all cases where the interactor could not be assigned an ID? Or are these cases where curators didn't feel the assay fit with IPI?
- There are also IGI, IMP, and RCA annotations - can any of these be converted to IPI (if there isn't a corresponding IPI already)
- IGI (4) to 'protein heterodimerization activity' - are these supporting evidence in addition to IPI? Or something else?
- IMP (133) to one of the MF terms - are these supporting evidence in addition to IPI? Or something else?
- RCA (21) to one of the MF terms - most of these are older annotations from Gramene, a handful from AgBase
- Gitter question from Petra
Matrix QC checks
- How is this work going for people?
- Questions, comments?
GO-CAMs and Annotation Extensions
- After USC hackathon in June, we formed a small working group to fully articulate the GO-CAM model specifications
- This will allow uniform QC across workbenches, projects (e.g. Reactome and MOD imports)
- Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation
- Present: Birgit, Bob, Colin, David, Dmitry, Edith, Giulia, Harold, Karen, Kimberly, Laurent-Philippe, Midori, Pascale, Petra, Sabrina, Stacia, Seth, Suzi A, Tanya, Tom, Ruth, Patrick N