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[bioontology-support] A simple (?) question

John Graybeal jgraybeal at stanford.edu
Thu Jun 15 17:42:40 PDT 2017


Jack,

Here are some quick references, which may get you to where you need to go. If you need more specific direction after looking at this documentation, please post back to the list, and we'll see if we can help.

The way BioPortal handles mappings is described at https://www.bioontology.org/wiki/index.php/BioPortal_Mappings, and is helpful background to understand the results.

The UI for looking for mappings between ontologies is at http://bioportal.bioontology.org/mappings; this will give you an idea of the number of mappings between different ontologies, but may not be usefully navigable for your purposes.

The API interface, what you likely want to use, is described generally at http://data.bioontology.org/documentation<http://data.bioontology.org/documentation#Mapping>, and specifically for mappings at http://data.bioontology.org/documentation#Mapping.

We have a SPARQL endpoint that could provide more direct and granular information, but it is a test system that is not kept current with the latest content.

You will find additional mapping examples and information in the mail archives; I've copied two emails from the list below that contain some additional information and links.

John

Hi Manfred,

Currently we don’t offer a way to download mappings as a file.  There are a couple of recent posts on our support list that offer more detail on this topic:

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Downloading-Mappings-in-Bulk-td4655255.html

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Mapping-download-td4655279.html

Mappings for the ontologies you mention below are available in JSON format via our REST API, e.g.:

http://data.bioontology.org/ontologies/ICD9CM/mappings

http://data.bioontology.org/ontologies/ICD10CM/mappings

Alternatively, if you want the results in XML format, you can use the format query string parameter.  Our REST API is documented here:

http://data.bioontology.org/documentation

Kind regards,
Jennifer



Currently we don’t make mappings available as a flat file download.  You can read about the reason for this in a previous post on our support list:

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Downloading-Mappings-in-Bulk-td4655255.html#a4655269

You can however, retrieve all mappings between the MESH and MP ontologies via our REST API, e.g.:

http://data.bioontology.org/mappings?ontologies=MESH,MP



On Jun 15, 2017, at 5:16 PM, Jack Park <jackpark at topicquests.org<mailto:jackpark at topicquests.org>> wrote:

I went looking for a googlegroup or something, and did not find another place to ask this simple (?) question:

We know that there are several ontologies in the biomedical field, each of which might define the same class as another, using a different namespace.

My question is this:

I would like to be able to take a given URI from one ontology, then post an Owl:SameAs query to your portal to enumerate other forms of the same class.

Is that possible?
If so, what procedure to use?

I have a user key to access your data.

Many thanks in advance.

Jack
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski


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