Ontology Working Group GitHub Meeting, Tuesday April 3rd, 2015: Difference between revisions

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* CM: Recommend staying in OBO format for now to facilitate doing the difs, but can do the editing in OBO in Protege 5.0
* CM: Recommend staying in OBO format for now to facilitate doing the difs, but can do the editing in OBO in Protege 5.0
''LM: Looks like Protege 4.3 also allows opening and saving OBO files''
''LM: Looks like Protege 4.3 also allows opening and saving OBO files''
* Advantage of the upcoming Protege 5.0 is that you can import  
* Advantage of the upcoming Protege 5.0 is that you can import other ontologies
*  
* This will be very useful once we start working on the PSO
 
* New Protege 5.0 coming out soon- '''when?'''
 
* Need to specify which format the curators should be saving in.






===Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page===
===Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page===

Revision as of 06:34, 21 April 2015

Agenda and Notes:

Attending: LC, JE, CM, JP

1. Discussion of OWL Tools

  • CM- you can use OWL Tools now to convert OBO to OWL, is now on GitHub, https://github.com/owlcollab
    • help file is there "Command line examples"
  • OWL Tools is undergoing a rewrite, will be called "Robot" (Robot is an OBO tool)

2. Setting up the GitHub Repository

  • CM- Granularity discussion- do we want to have all the ontologies in one repo or have separate repos for each ontology?
    • Question of whether we want the same trackers or separate ones- but we are keeping the ontology trackers at SourceForge
  • If the ontologies are each in their own repo, we can have a separate mini-wiki in the repository
  • See the "GitHub_Possible_Format: where is this?
  • Permissions are controlled per repo, so we probably want to have the reference ontologies in one and the application ontologies in another
  • CM- Recommend not having the different formats in different folders, but think of the source files and the release files. OBO and OWL files should go in the same directory together.
  • source (src) directory- contains the files for the release
  • doc directory contains documentation files in markdown format
  • Commit messages are given specific ids

3. Existing Repositories:

  • plant-trait-ontology- was set up last spring 2014 for the TRY meeting,
    • Using the create repository script, has a number of extra features such as the image and tools folders
    • RW submitted a list of traits from the TRY database, but they have never been added. We should keep this list and eventually get them integrated.
    • This version of the TO is out of sync with the one on our svn.
  • planteome-ontologies (was Ontology-Files)

4. Move to Protege 5.0

  • CM: Recommend staying in OBO format for now to facilitate doing the difs, but can do the editing in OBO in Protege 5.0

LM: Looks like Protege 4.3 also allows opening and saving OBO files

  • Advantage of the upcoming Protege 5.0 is that you can import other ontologies
  • This will be very useful once we start working on the PSO
  • New Protege 5.0 coming out soon- when?
  • Need to specify which format the curators should be saving in.


Back to the Planteome_Ontology_Development_and_Coordination_Working_Group page

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