cooperl09
commented
8 years ago From @cmungall on May 12, 2015 18:27
Background
importer files are fairly simple, and are very useful standard way of configuring a set of ontologies that are intended to be mutually coherent and used together.
An example:
Standard purls are always used. You can map these to local files (e.g. for a dev instance) using a catalog xml file.
URI
What should be the URI of the root ontology? We could register 'planteome' with obolibrary, but this is maybe not required, as we would not likely put class URIs in this space. Although we should be thinking ahead to all ontologies used in this project and what their ID spaces would be.
It may be simplest to keep the planteome owl file in the po idspace, e.g.
http://purl.obolibrary.org/obo/po/planteome.owl
With the source owl checked in to the po repo (so this ticket may belong in another tracker but that's not important).
Ontologies
- po
- eo (I would really like to change the ID space of this one)
- ro*
- go*
- to
- ncbitaxon*
- ...
For the ones marked * we may want to explore subsets in the future
COs
It is probably simpler if we leave the COs out of the first iteration, but ultimately planteome.owl should cover the plant universe
This should probably go in a separate ticket.
Jenkins job
Once we create the first iteration I'll create a jenkins job that will ensure overall coherence of the whole suite.
AmiGO conf
Once the importer is created, you can simplify your amigo conf by using this one file
To set up a dev instance you could use a catalog file to map the URIs to local files.
From @cooperl09 on May 12, 2015 17:35
Comment from Chris M: planteome needs an importer module. This will simplify configuration for amigo and any other tools that consume planteome ontologies.
The first iteration of this can simply be an OWL file with the header that says:
import po.owl import eo.owl import ro.owl import go.owl import to.owl
etc
Copied from original issue: Planteome/plant-trait-ontology#2