Ontology meeting 2012-09-05

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30-minute meeting



  • David
  • Heiko
  • Tanya
  • Chris
  • Jane
  • Becky
  • Paola


We haven't been getting them for a while. They were quite useful, could they be reinstated please?

AI: CHRIS to reinstate the 3 emails: obsoleted terms, new terms, changed terms.


  • Reactome are still sending their Xrefs to Amelia's mailbox, and these need adding to the main GO file.
  • Slightly tricky because there's often multiple Xrefs for one term, because they have Reactome Xrefs for each species.
  • Occassionally Reactome Xrefs get added to the main GO file manually (e.g. by Becky for signaling terms: see GO:0036323. Need some way that these aren't over-written (e.g. by submitting them to Reactome for inclusion in their mappings: not optimal though as would need to check these don't get lost).

AI: CHRIS to write a script that updates the main ontology with the Reactome Xrefs from external2go. The script will report differences, which an editor will need to follow up on.

FOLLOW-UP: EC numbers in GO - feasibility study

Carried over from a previous meeting: see Action Items and background here:


Nothing new to report

Future Ontology Editor

From the end of an email I just read from Chris: "We have to get away from asserting these in the editors file though. The options are abandon oboedit or allow Elk to be called from within OE.".

Can Heiko comment on how difficult this would be to do in OE? The problem with Protege 4 is that it has no resources for development, nor is it likely to, so I'm not convinced whole-hearted adoption is the answer right now. Unless there's an option for us to develop P4?

  • Chris and Heiko have an alternate plan, because currently if we assert implied links, we have no way to know if we should remove these at a later date, if the reference ontology changes. So the new plan is to tag the implied links in the OBO file (e.g. tag=is_inferred). Then we can insert the links but if any of the tagged relations change in the external ontology, these implied links can be reviewed.
  • Becky has tested Heiko's new script (it works, just as expected!) but we should hold off adding any implied links until they are tagged.

* AI: CHRIS: Send a warning to gofriends on 28TH SEPTEMBER 2012, that new tags exist in the GO file.

* AI: CHRIS: Add tags to the GO file after everything is moved over to svn (22ND SEPTEMBER 2012).

Projects are being added to JIRA

The ongoing ontology projects have been added to JIRA. Who is going to have access and how will we track them?

We should all be going in and updating progress on the projects that have been assigned to us.

* AI: DAVID: Add in new project 'tRNA metabolism' (project to be led by Harold).

* AI: JANE: Add Harold to the JIRA people list.

* AI: JANE: To dig out the time limits of the projects, previously agreed with Judy. Rough timings are: cardiac conduction (end Sept), apoptosis (end Oct), cell cell cycle (TBC: end Jan?). We also need to add in due-dates for sub-tasks.

* AI: JANE: To rearrange projects on the JIRA page so that they're grouped by timings.

* AI: On the first ontology meeting of the month, we will spend time going through the projects and checking progree.

* AI: BECKY: To check if anything else needs doing for cardiac conduction signaling, and update the progress accordingly.

GO help transition to JIRA

  • Need to retire the Stanford list. We're still waiting for this, but once it's done, we can move everything over to the new JIRA system.

Meissner's corpuscle

Is GO the right ontology for this term? [1]

Isn't this an anatomical structure?

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