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[bioontology-support] [BioPortal] Feedback from Marwa

Michael Dorf mdorf at stanford.edu
Mon Jul 27 13:25:28 PDT 2020


Hi Marwa,

Thank you for your questions. In BioPortal there are optional categories that one can assign to his/her ontology during the creation phase. An ontology can belong to multiple categories, but they are not hierarchical. You can obtain the list of available categories by using this API service endpoint:

http://data.bioontology.org/categories

To determine which group an ontology belongs to, you can make this call:

http://data.bioontology.org/ontologies/SNOMEDCT?display=all

The “hasDomain” field contains the list of the categories for a given ontology.

To your second question, our current data store is an RDF database called “4store”:

https://github.com/4store/4store

We do, however, have short-term plans to migrate to AllegroGraph:

https://allegrograph.com/products/allegrograph/

Our Virtual Appliance v3.0, which you can download and install in your own environment, already includes compatibility with AllegroGraph.

As far the direct access to the database, we have a SPARQL endpoint that you can use:

http://sparql.bioontology.org/

Unfortunately, the data contained in that endpoint isn’t regularly synced with our production data, so it will not contain all the ontologies that exist in BioPortal. As part of the near future migration to AllegroGraph, we plan to implement a SPARQL endpoint that mirrors our production data.

Please let me know if I omitted anything or if you have further questions.

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Jul 27, 2020, at 3:50 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Marwa

Email: marwa.abdelrehem at fci.au.edu.eg<mailto:marwa.abdelrehem at fci.au.edu.eg>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies

Feedback:

I am a researcher interested in ontology reuse and especially in bio-ontologies. In a part of my research, I am interested to determine the ontology domain (Category). My question is does bioportal has a hierarchy for those categories? and if so, can I have access to it?
The second question is what is the type of database that you store the ontologies information in? and also can I have access to it?
Thanks in advance.

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