Ontology Working Group GitHub Meeting, Tuesday April 3rd, 2015
Agenda and Notes:
Attending: LC, JE, CM, JP
- Link to audio recording: File:Github audio 4-03-2015.m4a
- Link to video recording: File:Github video 4-03-2015.mp4
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.
- New Protege 5.0 coming out soon- beta version is available now, just has an issue- https://github.com/protegeproject/protege/issues/151
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
6. Plan of action
- Set up one of the ontologies at Github- Trait Ontology and start testing it and using it
- It makes sense to do the final release of the PO for the PSDS paper,
- 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 Source Tree or can do command line e.g. gitmv
- Need to decide about whether or not we are going to try to keep the history