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Participants:  
[[Category:GO_Managers_Meetings]]
Participants: Pascale, Midori, Chris, Suzi, Mike, David, Jen, Jane


Agenda: Jen
Agenda: Jane


Minutes: David
Minutes: Pascale


==Action items from previous calls ==
==Action items from previous calls ==


*'''David, Tanya, Jane:''' Compose wiki documentation for ontology editors, with step-by-step instructions on making cross-products - in progress (will start this week)
*'''David, Tanya, Jane:''' Compose wiki documentation for ontology editors, with step-by-step instructions on making cross-products - in progress (will start this week)
** David says they need the new OBO-edit to do it.
** Chris says that there wont be new GUI changes that would affect the screen shots.
*'''Jen:''' Draft wiki page to summarize motivation for MF-BP links - in progress
*'''Jen:''' Draft wiki page to summarize motivation for MF-BP links - in progress
*'''Managers:''' Comment on draft proposal that Suzi will circulate (content meetings, RefGen annotations, etc.) - not sent
*'''Managers:''' Comment on draft proposal that Suzi will circulate (content meetings, RefGen annotations, etc.) - not sent
*'''Pascale:''' Confirm date of Geneva annotation camp - 14th-17th June at SIB - sent to GO-Top and only Judy responded. GO-Top to confirm.
*'''Midori, Jane, David, Tanya, Chris:''' Midori to resend draft (DONE), others to comment - sent - some comments received. In progress.
* '''Chris''' filter IEAs from GAF inference. do we need more detailed evidence codes - e.g. IC-derived-from-ISS - in progress
*'''Chris''' report on aligning Reactome and GO - in progress
*'''Emily:''' We can use this text http://wiki.geneontology.org/index.php/GAF_2.0 to make documentation of GAF 2.0 for the website. Perhaps Emily and Amelia would like to work together on that.- in progess
*'''Emily:''' Send a mail to GO-friends to advertise GAF 2.0 and to show the docs.- in progress


==Discussion items==
==Discussion items==


* CHEBI XPs. The classification of some chemical entities such as "carbohydrate" in CHEBI is radically from GO (for example, in CHEBI, nucleotide is_a carbohydrate). Should we just adopt their classification wholesale? This would radically reorganize GO in places (Chris)
===GOC moving over to using extended GO===
Main issue seems to be with has_part - visualization, queries etc. How should we handle this? (the email was actually only asking about inter-ontology links, I know, but we should address this anyway).
** Chris says that not everyone needs to move to the extended GO - only people who understand the new file.
[ACTION ITEM]: Jane will send another email to clarify this.
** Eurie sent questions about how annotations will get displayed, etc. Jane suggests we have a FAQ
** Chris: previously we used to summarize by ontology (F, P), but it's now possible to do to differently, so that
we need to resolve some issue related to how we summarize annotations.  At first we probably should not change anything.
** AmiGO, GO term finder tools? Does anything to be changed here?


Right now, we seem to be at a bit of sticking point on this. It seems that CHEBI and GO want to have a different view of complex molecules. CHEBI wants a structural view and GO wants a metabolic/biochemical view. CHEBI classifies every carbohydrate-containing molecule a carbohydrate, but this causes problems when GO represents the metabolism/biosynthesis/catabolism of these molecules. We will continue to try to work with CHEBI to align our views.
===Term changes and term provenance issues===
* Based on the recent e-mail discussion about annotators knowing about ontology changes, we should bring up the idea of term changes and term provenance again. We really should come up with a way to record information about the creation of a term and the changes that have been made to it over time and to store that information in one place.
* Jane suggests the tool OnEX :
http://aprilia.izbi.uni-leipzig.de:8080/onex/
(go to concept-based analysis)
* Pascale: it would be nice to have the relevant documentation linked from the terms, for example to GO nuts.  
* Chris: we should consider applying 'upper level' decisions to all relevant terms
* David doesn't want another place where to write documentation
* [ACTION ITEM ]Jane suggests to move this to the meeting agenda for the next GO consortium meeting


* UniProtKB IDs. (Chris)
===Internal cross-products to be released===
* First internal cross-products to be released into extended GO on Monday, Jan. 18th. Announcement to GO Friends: http://fafner.stanford.edu/pipermail/gofriends/2010-January/001691.html
* Midori asks who will do the editing. David suggests GOA, so that it would be online sort at the middle of the day.
* First will add the 'regulation' set.
[ACTION ITEM] Midori : release first set of cross products, Jan 18 (regulation)
[ACTION ITEM] Midori : add this to GO news on Monday.


It seems that the IDs have been split into SP and TrEMBL records. This is breaking some things in the pipeline. They did this to provide users with info about whether a record was a SP or TrEMBL record. Emily will check into this, but she feels that the UniProt users want to be able to distinguish records. Emily will work out a way to try to keep both groups happy. Perhaps there can be a look-up table to distinguish SP from TrEMBL?
===Paper on "revisability of GO" ===
collaboration with Sabina Leonelli. There's email in the ontology-editors archive, e.g.: http://fafner.stanford.edu/pipermail/ontology-editors/2009-November/000980.html


* Extended GO - we don't advertise this well. There's not even any documentation to say what's in this file and what makes it better than the existing file. What can we do to make this better? (Jane)
===Future content work===
* Jen has some proposed contents but that has not yet been accepted. [ACTION ITEM] Midori will create a new section in the Ontology development page for those types of topics.  


Do we want to make the extended files more prominent. Eventually the extended GO will become the main GO. We will push the consortium to see how close they are to being able to use the extended files.
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[[GO_Managers_conference_call_minutes|Back to minutes list]]
[[GO_Managers_conference_call_minutes|Back to minutes list]]

Latest revision as of 12:31, 30 June 2014

Participants: Pascale, Midori, Chris, Suzi, Mike, David, Jen, Jane

Agenda: Jane

Minutes: Pascale

Action items from previous calls

  • David, Tanya, Jane: Compose wiki documentation for ontology editors, with step-by-step instructions on making cross-products - in progress (will start this week)
    • David says they need the new OBO-edit to do it.
    • Chris says that there wont be new GUI changes that would affect the screen shots.
  • Jen: Draft wiki page to summarize motivation for MF-BP links - in progress
  • Managers: Comment on draft proposal that Suzi will circulate (content meetings, RefGen annotations, etc.) - not sent

Discussion items

GOC moving over to using extended GO

Main issue seems to be with has_part - visualization, queries etc. How should we handle this? (the email was actually only asking about inter-ontology links, I know, but we should address this anyway).

    • Chris says that not everyone needs to move to the extended GO - only people who understand the new file.

[ACTION ITEM]: Jane will send another email to clarify this.

    • Eurie sent questions about how annotations will get displayed, etc. Jane suggests we have a FAQ
    • Chris: previously we used to summarize by ontology (F, P), but it's now possible to do to differently, so that

we need to resolve some issue related to how we summarize annotations. At first we probably should not change anything.

    • AmiGO, GO term finder tools? Does anything to be changed here?

Term changes and term provenance issues

  • Based on the recent e-mail discussion about annotators knowing about ontology changes, we should bring up the idea of term changes and term provenance again. We really should come up with a way to record information about the creation of a term and the changes that have been made to it over time and to store that information in one place.
  • Jane suggests the tool OnEX :

http://aprilia.izbi.uni-leipzig.de:8080/onex/ (go to concept-based analysis)

  • Pascale: it would be nice to have the relevant documentation linked from the terms, for example to GO nuts.
  • Chris: we should consider applying 'upper level' decisions to all relevant terms
  • David doesn't want another place where to write documentation
  • [ACTION ITEM ]Jane suggests to move this to the meeting agenda for the next GO consortium meeting

Internal cross-products to be released

[ACTION ITEM] Midori : release first set of cross products, Jan 18 (regulation) [ACTION ITEM] Midori : add this to GO news on Monday.

Paper on "revisability of GO"

collaboration with Sabina Leonelli. There's email in the ontology-editors archive, e.g.: http://fafner.stanford.edu/pipermail/ontology-editors/2009-November/000980.html

Future content work

  • Jen has some proposed contents but that has not yet been accepted. [ACTION ITEM] Midori will create a new section in the Ontology development page for those types of topics.

Back to minutes list