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[bioontology-support] Question about technical requirements to submit ontology

John Graybeal jgraybeal at stanford.edu
Tue Jun 6 14:25:44 PDT 2017


Hi Dawid,

If what you already have is a list of terms and definitions, there are a few paths that could turn that into SKOS or OWL, which in theory could be imported into BioPortal. But there are no trivial paths guaranteed to get you what you need—really an understanding of RDF at least, and probably SKOS or OWL, is important for you to go forward.

A tool that can be used to import tables into OWL form is CELLFIE (https://github.com/protegeproject/cellfie-plugin/wiki/Grocery-Tutorial), which is capable of doing the transformation when run as part of Protege (https://protegewiki.stanford.edu/wiki/Main_Page). But it really expects you to understand OWL in order to follow the instructions.

Another tool that I know about offhand is MMI's ORR (https://mmisw.org), which was built to let people manage their vocabuaries in a way that aligns with the semantic web. The ORR takes a tab-delimited text file and turns it into SKOS, which I have verified can be imported into BioPortal in a way that is useful. I would not expect full interoperability with CPT, as that's not based on SKOS, but the BioPortal features will be usable. You might want to keep your vocabulary private on that system, as it's not (Conflict alert, I volunteer as manager of ORR in my spare time.)

A quick search found the answer https://stackoverflow.com/questions/13147864/how-to-create-an-ontology-from-raw-data-csv?rq=1, which helps you appreciate the options a little more perhaps.

And while I find the W3C specifications _and related documents_ of OWL and related standards very readable (see in particular https://www.w3.org/TR/owl2-overview/#Documentation_Roadmap), if you want a well-written guide to this whole technology, I'd recommend Semantic Web for the Working Ontologist by Dean Allemang and Jim Hendler, it's very approachable.

Best of luck.

John






On Jun 6, 2017, at 11:20 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Dawid,

BioPortal allows for uploads of ontologies developed in OWL, OBO, or SKOS format.

You can submit a new ontology via the BioPortal user interface, by clicking the “Submit New Ontology” button on the Browse page (http://bioportal.bioontology.org/ontologies/).

The CPT ontology currently in BioPortal (http://bioportal.bioontology.org/ontologies/CPT) was imported from the UMLS (https://www.nlm.nih.gov/research/umls/). The UMLS publishes releases twice per year, and we have a special process for importing their data. We convert from UMLS format to RDF using our own custom scripts (available in our GitHub repository: https://github.com/ncbo/umls2rdf).

Not sure if that information helps?

Kind regards,
Jennifer


On Jun 6, 2017, at 12:19 AM, VAN STRAATEN D E A <36313327 at mylife.unisa.ac.za<mailto:36313327 at mylife.unisa.ac.za>> wrote:

To whom it may concern,

I want to find out how do you submit an ontology? We are currently talking to SAMA (South African Medical Association) about submitting the CPT codes we are using in South Africa. They are different from the CPTs used in America. Would we need to encode the codes into XML or JSON and then submit them? What are the technical requirements from our side?

Regards,

<image001.png>

Dawid van Straaten
ANSA administrative assistant
Tel: +27 73 197 1024
Email: dawid at ansa.org.za<mailto:dawid at ansa.org.za>



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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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