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

From Planteome.org
Jump to navigation Jump to search

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- gSlidesGitHub_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
  • 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

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.

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? Have installed both on my computer.

  • We will save the list of traits from the TRY database that Ramona created in a working/scratch folder. "Done- added the TRY list to the TO folder on SVN"
  • We can get rid of the existing "plant-trait-ontology-TRY" repository (note- I renamed it to avoid confusion)- Who is doing this?.
  • Set up the Plant Trait Ontology at Github and start testing it and using it- but need to import the history- See below and the [All-Hands meeting notes 4-16]
  • Set up 1 repo for the planteome-ref-ontologies (use lower case and dashes to be more "githubby")- Done, renamed the existing repo, but it needs to be reconfigured.
  • 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. "What is the status on this??"


Back to the Planteome_Ontology_Development_and_Coordination_Working_Group page

Retrieved from "https://wiki.planteome.org/index.php?title=Ontology_Working_Group_GitHub_Meeting,_Tuesday_April_3rd,_2015&oldid=1104"