Manager Call 2017-01-18

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GO HelpDesk

  • If we are going to distribute the shifts during the upcoming year, we need a list of people who will be participating.
  • We also need to make sure we have a representative from each curation group on the mailing list, and also with a github account, so when issues come up they can be tagged.
    • For example, right now there is no curator from GOA on the GO help desk mailing list.
    • Current mailing list:
 Anushya Muruganujan
 Mike Cherry
 Chris Mungall
 David OS
 Donghui Li
 Edith Wong
 Harold Drabkin
 Helen Attrill
 Huaiyu Mi
 Eva Huala
 Judy Blake
 Melanie Courtot
 Stuart Miyasato
 Moni Munoz-Torres
 Pascale Gaudet
 Paola Roncaglia
 Paul Thomas
 Petra Fey
 Rachael Huntley
 Rob Nash
 Seth Carbon
 Stacia Engel
 Suzanna Lewis
 Tanya Berardini
 Tony Sawford
 Kimberly Van Auken
 Val Wood

Submission of New Annotation Files

  • GeneDB and EuPathDB would like to start submitting new annotation files
  • Require ORCID?
  • Multiple organizational affiliation
  • Submit gp2protein or gpi?
  • Some of these are for species they previously submitted for, others are new, at least one overlaps with submission from a curation group no longer active
 With 'Sanger GeneDB' affiliation:
 Leishmania braziliensis
 Leishmania donovani
 Leishmania infantum
 Leishmania major - Sanger GeneDB submits, but not recently
 Leishmania mexicana
 Trypanosoma brucei - Sanger GeneDB submits, but not recently
 Trypanosoma congolense
 Trypanosoma cruzi
 Trypanosoma vivax
 Plasmodium falciparum 3D7
 Plasmodium berghei ANKA
 With 'EuPathDB' affiliation:
 Aspergillus fumigatus
 Aspergillus nidulans - currently a file from AspDB
 Aspergillus niger
 Aspergillus oryzae
 Cryptococcus neoformans
 Fusarium graminearum
 Neurospora crassa
 Not sure if you would need a reduced list, as not all of them are model organisms and/or we do not dedicate that much effort to them. A reduced list would be:
 Leishmania major
 Trypanosoma brucei
 Trypanosoma cruzi
 Aspergillus nidulans - currently a file from AspDB
 Cryptococcus neoformans
 Fusarium graminearum
 Neurospora crassa
  • Annotation tools:

​ We are using Artemis+Chado at the moment and we have scripts in place to dump to GAF files​. What other software would you recommend? We are also looking into easy ways of transferring annotations to close orthologs.

WB LEGO Curation

  • Starting a weekly LEGO call at WB to bring more curators on board
  • Discussing strategies
    • Curators take responsibility for specific areas of biology?
    • Approach integrated with AGR? What LEGO models would we like to see on AGR report pages?

Documentation Jamboree

  • On a previous call, Paul T. floated the idea of a documentation jamboree
  • How feasible is this?
  • There is definitely a need wrt pipelines, curation guidelines (conventional and LEGO), FAQs


Participants: Kimberley, David H, Suzi, Judy, Huaiyu, Pascale, Paola, Melanie, Chris.

GO Helpdesk

  • Kimberly brought up the issue that the current rota covers through the end of Jan. How to handle going forward? Need a new list of people from each group. Ideally there should be 10-15 people on the list, so each person can cover about 4 weeks.
  • The other issue is to have a point of contact for every group. They would need to subscribe to Jira and have a github account, so that issues can be easily assigned to them. Currently it is not case. For example, there is no curator from GOA. Paola suggested to talk to Claire.
  • Suzi suggested to discuss this at the GO top call.

New annotation files

  • Kimberly created this item in the agenda. This is the first time an outside group will submit GO annotations. These are procedural questions.
  • Do we require people to have an ORCID? Chris's answer is "yes".
  • How to put multiple organizational affiliation in the file? A ticket was submitted by Kimberly on this. In the GAF file, there is a line to put multiple organizational affiliations. It is not clear whether it can be done in YAML format. Chris: Will look into it.
  • The tool used for these annotation is Artemis+Chado. Suggest to use PAINT for ortholog inference.
  • Aspergillus nidulans is one of the species. GO currently has annotations from AspDB. AspDB is no longer funded. Suzi suggested that the new annotation file should supersede the old ones, and all automated annotations (except for those from interpro) should be deleted.
  • Kimberly will follow up on this with Chris.

WB LEGO curation

  • Redundant work to generate models for different organism. David brought up this issue. For example, David is curating a mouse model, but can only find experimental evidence in a human paper. He will annotate a human gene, and the human model, then use ISO to infer mouse gene function and curate the mouse model. It seems very redundant. He asked if there was a way to clone the model. Huaiyu suggested to use IBA instead of ISO in this case. David argued that the human annotation is a new one, so there is no way to give an IBA inference at the same time.
  • Pascale suggested to curate LEGO models using PTN ids. This is similar to the canonical pathway models in other pathway databases. Huaiyu suggested that Noctua link to PAINT or Pantree to do such curation. This item will be discussed in the future LEGO call.
  • The other issue is multiple organisms in the same LEGO model. Chris thought that the model should be flagged when this happened. He will work on it. David said there is at least one such models in the current database.

Documentation Jamboree

  • Suzi suggested to do this at the next GO meeting.
  • There is a Github project on this already, which contains a list of documents to be created or updated. Huaiyu suggested to complete this list before the GO meeting.
  • Judy suggested to have 2 people working on each doc, and a 3rd person to read it.
  • David suggested that the people involved in GO help are good candidate to participate in this, especially to read those outward-facing documentations.