Ticket #5 (closed enhancement: fixed)

Opened 7 years ago

Last modified 4 years ago

MIX Ontology

Reported by: guest Owned by: pyilmaz
Priority: minor Component: MIMARKS checklist
Version: 2.2 Keywords:
Cc: Sensitive: no


Original Question to Developers list:

Have you guys either made of know of an instance somewhere of the entire GSC list of terms in an ontology (including descriptions etc.)?

Philippe wrote:

Hi Chris,

Good question. I recently went over the MIGS_MIMS_MIENS document + GCDML
schema to have a feel for the vocabulary requirements.
Also, Peter Sterk has compiled a number of terms for GCS consortium which
should probably be reviewed and discussed by the group.

There are also a number of requirements which are not addressed and possibly
gaps. Are you in a similar situation? Would you like to create such a resource?

best wishes


Philippe wrote:

I managed to dig the link about GSC ontology terms collected and created by Peter.


A number of them have already been flagged as available from other resources such as ENVO,PATO, UO, OBI.

If a GSC terminology or application ontology is to be developed, we could/should decide on the format (OBO or OWL), the amount of class metadata (definition, synonyms, source, editors, curation status and example of usage). Relying on OWL and protege would allow relatively straightforward management of import from other resources.



Chris wrote:
The benefits are obvious for development/upkeep of submission tools, but it has to be a bona-fide resource supported and kept updated by, and in-sync with the GSC checklist(s). With this in mind I think Philippe's suggestion of an OWL for easy use in protege would be very appropriate (plus protege is the only one I've ever used so it saves me learning anything new ;-)).

The generation of the OWL ontology should be pretty straight-forward given that all the hard work of defining the terms and which category they are in has already been done for the checklist!. I'm no expert at creating ontologies but I could probably do it if no-one has already done it / is willing to do it?!
But I don't want to waste time creating something that (a) someone has already done, (b) no-one will use, or (c) we (the GSC) can't support.

Is there an "expert" at creating ontologies on this mailing list that can easily create it from the existing(or slightly modified) Excel sheet of terms? If my basic understanding is correct there are tools that can take a "tree" type structure of terms with descriptions from a CSV file to create the basic OWL ontology, it would then need all the relevant links/exclusions mapping in.


Change History

comment:1 Changed 4 years ago by pyilmaz

There is the MIxS as RDF in Bioportal: http://bioportal.bioontology.org/ontologies/3215

and MCV (MIxS) controlled vocabularies created by Doug Wendel: http://bioportal.bioontology.org/ontologies/3000

comment:2 Changed 4 years ago by pyilmaz

  • Status changed from new to closed
  • Resolution set to fixed
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