20th GO Consortium Meeting Action Items

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Status Responsible Party Task Comments
In Progress Documentation working group Document annotation SOPs Another factor we have been tracking is when a curator judges that the curation of a gene is ‘comprehensive’, that is, that is accurately represents the biology (irrespective of the number of papers available or read). This appears in the spreadsheets. The guideline is that when there are few papers, all papers should be read; when there are many (a curator can judge what is too many), then a review should be read to find the important primary literature and decide what information needs to be captured. We don’t keep track of whether or not reviews have been read. Wormbase uses textpresso (PMID 15383839), that helps ensuring curators do not overlook information. The ‘comprehensive’ curation status doesn’t get invalidated when a newer paper is published; however, curators may (and are encouraged to) update the date when the newer literature is curated.
Chris Mungall Re-calculate with is_a only paths
Chris Mungall Re-calculate with experimental codes only generate several versions of the data classified by different evidence codes?
Chris Mungall Provide such reports on a regular basis
Judy Blake Contact NCBI/NLM/OMIM to link to reference genome genes
In progress Documentation working group Document Changes to Gene Association File (GAF) column 2 is canonical gene ID; column 17 is thing you are annotating (always required); column 12 matches column 17 and contains SO ID's; add header to gene association file
In progress Documentation working group Document Changes to gp2protein file includes complete gene index (except for pseudogenes and transposons); column 1 is canonical gene ID; column 2 is accession for sequence of longest form of protein from UniProtKB: or NCBI; syntax of gp2protein file will be provided by Mike and Chris
In progress (Jane) write notice of changes to GAF and gp2protein to users
In progress MODs + Ben Hitz make sure that their input matches new GAF and gp2protein requirements
Seth Carbon Have AmiGO show co-occurrency terms similar to function in QuickGO.
Seth Carbon & Val Wood SLIM by SLIM matrix Would be used to review intersections of different cellular processes and look for unexpected intersections which may identify possible errors. Try first applying to function and component terms; outline cells that you expect to be empty, Have these matrices generated automatically from the AmiGO database.
Ben & Mike Get isoforms into GO database
MODs & Chris Consistent use of IMP "with" column Chris will be talking to individual groups with how they use the with column for IMP. Each MOD groups needs to respond to this for Chris.
Michelle Implement Michelle's proposal decide whether to put 'response to drug' ID in column 16 or is separate IC annotation. Annotate to chemical term ‘response to cocaine’, co-annotate with chemical term for now, then later when available, put GO ID for “response to drug’ in column 16 (or separate IC annotation).
pending Midori, David, Chris, Mike Bada Chemical derivatives and metabolism terms Need input from Chris and Mike on how much can be automated; possibly also current and near-future state of ChEBI
MODs & Pascale All groups to check on how they use IGI and update annotations as per Princeton discussion.
Val Circulate draft doc on how contributes_to can & can't be used Will include: "Would this annotation make sense if this subunit was" ... [thought not finished; might be something like "viewed by itself"].
MODs & Pascale Check existing annotations for "contributes_to" with IDA We think only allow contributes_to with IDA. Look into adding to annotation checking script to flag contributes_to.
Jen Implement rules and software for sanity checking automated annotations (species-based trigger file).


Status Responsible Party Task Comments
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