OEWG 20090407

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GOC Meeting OE Cake

OBO-Edit Working Group, Tuesday April 7th, 2009 9.30 a.m. PST

Conference call details:
US: 1-888-727-6732
Outside US: 1-719-867-3417
pin: 601425

Agenda/Chair: Midori
Minutes: Jen

Action items carried over

  • Amina and Chris
    • Document ID Fixer, Cross Product pages, Semantic Parser manager.

Feature progress

not done yet

Amina now working on 2.1 which will include new features for cross products show implied links feature, where there are check boxes to choose which links to assert. These show up in a pop up windows which freezes the other window. That is no use to Amina is changing assert implied links into a separate component. The terms invovled will be highlighted in all the other components too.

Amina will put in 2.0.1 in the tracker menus so we can categorise our requests correctly.

  • Amina
    • Release notes need to acknowledge known issues
    • RC announcement on sourceforge, oboedit.org and the wiki.
  • Loading_a_History_File.htm - check for accuracy, especially in light of SF 2526247 bug report
  • Amina plans to make the graph viewer work the same as the graph editor (I think this has to do with imlpied links, reasoner, etc. but A will put all in documentation)
  • user dictionary fix in progress
  • Documentation - pending user guide pages
  • Misc user issues - Colin, other non-wg users

Colin's feedback:

Action: Any chance of Colin sending these test ontologies in case they would be useful to keep?

They're attached to the tracker item!Batchelorc 03:40, 8 April 2009 (PDT)

David's feedback:

Dangling reference issues (references to terms that don't have their own stanza in any of the files loaded)
One problem with dangling references is that they cause the display of a java pointer in the XP tab when used as part of an XP def - possible example in Colin's bug report here:

David gave up including dangling references as it is currently too difficult in OBO-Edit - both because of this issue and because of display of blank nodes in graphs and trees.

Importing whole ontologies slows things down terribly and is not feasible. Chris mentions an option to have selective imports of ontologies. David has also using this. Something similar is being considered for OE 2.01.
David's system just grabs is_a path to root for every term he uses.

Discussion items

  • GOC Meeting
  • OBO-Edit 2.0 Release and next steps

Release plans:

Amina confirms that we will go stright from rc 1 to release. Karen says that as long as Chris's scripts to remove created by and creation date tags are in place then we can start committing directly from OE2 to the live repository. Chris confirms that this is in place so we are good to go. General agreement that we should be able to commit from OE2 immediately after release.

Midori proposes that she will email everybody to say that we will switch on date: x unless complains. Karen suggests that we just do one commit in the editorial office and then no one else commit this day until we see what happens overnight. That was we can check for difficulties. Midori says this is unlikely to be a problem as few people currently commit the live file. Karen says that the small change needs to be a new term creation so we can see the creation tags being removed.

Karen is happy for this to happen any time after the release takes place. Midori will figure out a time/day to do it. The release is due tomorrow, so she will think about doing it the next day.

Amina mentions that we will have different config folders so people might like to import the configuration folders. Amina recommends that we post a how-to on the release notes. Perhaps also mention that this is present when we send a mail to the lists.

Midori has action item to write to GO-Editors for when to freeze and when to switch to OE2 and she will also mention config files then.

Test resources in OBO-Edit

Test resources distributed with OBO-Edit:
We don't want too many of these in the executable so we should just choose two or three tiny ontologies.
Make it easy to select one of the existing ontologies, like sequence, so-xp or the editors’ one.
We can make a url that will always point to the latest version.
Amina will organise this.

  • config directory changes for version progressions


  • Update test ontologies distributed with release under test_resources for new users to poke around with.
  • Close/ update out of date tracker items

Questions from Jen on how OBO-Edit should behave:

1a) In OBOMerge if a term in the parent file has two relationships, and one gets deleted in the branch file and the other gets deleted in the output file, then the term is currently left with no relationships at all in the output file.

This is because leaving a relationship in is not considered by OBO-Edit to be a concrete decision that would be in conflict with the other decision to delete the relationship. The rules of precedence are not invoked and the deletion is automatically accepted, regardless of which file has precedence.

Is this what we want? It means that very occasionally OBOMerge might produce unexpected orphan children, though these would be very obvious to the user in the output file. Perhaps a warning message would be appreciated?

Action: Warning message to be added

1b)We have the same behavior with substitution tags. If a term had two replaced_by tags and one was deleted in the live file and the other was deleted in the branch file, then there would be none in the output file.

What behavior do we want to see? Would it be best just to have a verification check for obsolete terms with no substitution tags?

Action: Warning message to be added

2) If a term mentioned in a substitution tag is subsumed in a merge my tests show that the substitution tag is not currently updated to show the new primary id and term name. Would we like this to happen automatically or should there just be a dialog box to say that substitution tags need updating?

Action: Automatically update ids

Dbxref library Feature request

David's feature request on dbxref library:

David has big libraries already set up. He wonders about searching these or importing standard file formats. Amina says that search and autocomplete are easy to implement. Colin says that the ids he uses are DOIs but he doesn't know if there is look up for ISBNs. David says ‘yes there are’ and he can send some along. David says endnote exports standard formats and BibTeX is a common one. He says maybe there are standard java libraries too. Short term, could the sort order be on the description field rather than id.
Midori: Or maybe have an option? Configurable could be good.


David has a grant to write an ontology-linked atlas of the fly brain. Should give lots of opportunities for testing OBO-Edit. Will involved bringing in bulk data on connectivity and lineage.

Congratulations to David on the grant.

Action Items


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