Manager 19June2013

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GeneDB annotation

  • GeneDB now have two curators that do GO annotation, but neither has been trained properly
  • UniProt-GOA have offered training for them in October
  • Preliminary plan is to integrate Gene DB annotations into UniProt and allow them to use Protein2GO to add new ones, since their curation tool is not up to scratch
  • Their annotations will be subject to all the automatic updates we do on our database (e.g. obsolete GOIDs, secondary UniProt accessions etc.) but GeneDB will do any necessary manual updates
  • Species they have annotations for:

Leishmania braziliensis

Leishmania major

Leishmania mexicana

Schistosoma mansoni

Trypanosoma brucei

Trypanosoma vivax

Although it hasn't yet been decided which they will submit to us, but most likely at least L. major and T. brucei.


Do we need to check their annotations? Which is the most appropriate group to do this?

Do they need to submit their files to the GOC (be species owner?) or is it better for them to come through the UniProt file?

GOhelpDesk move to JIRA @ TAIR

Tanya and BobM at TAIR have setup an instance of JIRA to handle GOHelp. Currently it is set up to receive emails from We have changed gohelp email 2 times in the recent past. Some of us feel it would be nice to have a neutral address and have redirects/alias set up to go into JIRA. Bob tells me we can use and set up an alias to Any thoughts/objections?

GOC meeting

  • What type of breakout sessions will we arrange, e.g. curator-relevant, ontology editor-relevant, programmer-relevant - so people can make travel plans


  • Judy- typically we have curators work one-on-one for training. Are you going to do that?
  • Rachael- do basic training, couple of months. We have a checking period for 2-3 months during which time we check the annotations.
  • R- who can check their annotations?
  • CM - are these parasites? Does WormB look at parasitic nematodes?
  • Jane- they may have new term requests. We may want to set up a custom TermGenie template for adding terms.
  • PS- we can look at their annotations?
  • SL- should we introduce them to PAINT? May be not initially.
  • GOA will dump annotations (like they do for WB/SGD).
  • They are expected to start by end of October.
  • CM- Are there other species/groups that we can nudge to contribute annotations? Bovine, dog are some organisms.
  • RB- Pseudomonas is one group that we might want to reach out. There is one programmer in Fionna's group who is in touch with me, but otherwise, they are not very engaged.
  • SL, Judy- we need to think how to make it attractive for groups to be involved with GOC.
  • Jane- Sara Hunter and Jane are putting a grant together to annotate microbial genomes.


We should keep a generic address ( Are we ready to move to TAIR system? Almost! We will check with Tanya, Bob. We need to close the EBI system and move to TAIR. We won't be able to move the old emails to TAIR (to search the archive). But we will have access to the EBI JIRA system. The other project management stuff won't move out of EBI, just the gohelpdesk is moving.

New Hire

Jane- We hired a new ontology developer. David Sutherland will start soon, and will come to the GOC meeting in October.


  • Test the new site. More instructions coming soon. It will be updated frequently.


Chris has few papers on his plate to give comments on.


Suzi is writing a renewal for Apollo. She will be including some bits about GO inferences.