Ontology Working Group GitHub Meeting, Tuesday April 3rd, 2015

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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
  • Possible way to set up the repos- have a repo for the external ontologies

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)
  • If we have all the ontologies in one repo, then they will be grouped here

4. Moving 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
  • Need to specify which format the curators should be saving in.
  • It makes sense to do the final release of the PO for the PSDS paper, at Github, rather than putting it out and then moving everything

5. Setting up repositories for other parts of the project on GitHub

  • JP- We will need to have a place to put the code for the image annotation developers source
  • Planteome web site- will be doing quite a bit customization, so that will need to be stored somewhere
  • data warehouse code
  • Probably each individual component should be their own repo.
  • Not sure where the association files are going to be stored, as iPlant has said they do not want to store them there- possibly at Github or leave on our SVN?

6. Next Ontology meeting April 7th

  • Elizabeth and Leo will be there
  • CM should be available
  • Need to get the collaborators into the concept of using the repositories.
  • Suggest uploading the Trait Template as a CSV file, as long as it does not have a lot of functions etc.

6. Plan of Action:

  • For ontology editing: Keep working in OBO format for now, to facilitate doing the difs, but start using Protege 5.0

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

  • We will save the list of traits from the TRY database that Ramona created in a working/scratch folder. "Done- added to the TO folder on SVN"
  • and get rid of the existing plant-ontology repo.
  • Set up one of the ontologies at Github- Plant Trait Ontology and start testing it and using it
  • Set up 1 repo for the planteome-ref-ontologies (use lower case and dashes to be more "githubby")
  • Edits can be made in a program like SourceTree or can do command line e.g. gitmv
  • Need to decide about whether or not we are going to try to keep the history- would be a fairly involved
  • Future of SVN needs to be discussed


  • Justin E will make a cleaned-up version of the SVN, so that we can keep the history of the files. And then move them over to GItHub
  • May just make it as a test to see how it will work and then get rid of it.


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