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[bioontology-support] new Bio API

Bob Stanley rstanley at io-informatics.com
Wed Feb 26 12:20:54 PST 2014


Hi Ray,

Sergey is copying me on these notes so I thought I'd chime in from the user side.  One use case is to run a relatively low-bandwidth query from within our system to return metrics on a specific ontology of interest before attempting to actually download or import it. With a targeted query that completes quickly and brings back ontology metrics (# of classes, etc.), we can get a (admittedly limited, but) better idea for what may actually be there. This allows to avoid putting unnecessary burdens on the environment that can be caused by downloading what may turn out to extremely large, incomplete or un-useful ontologies. Open to other concepts to make it easier to browse useful metrics on selected ontologies or the entire list.

Although we've chatted internally with Sergey about some of the above, I wanted to write you directly also to note that we're also recently exercising Annotator more actively with some positive results.

I'll be mentioning these contributions by Stanford (BioPortal, Annotator) in my talk at the Boston conference on semantic technologies in healthcare / life sciences (CSHALS) this week.

Thanks for all your help!

All the best,

Bob


From: Ray Fergerson [mailto:ray.fergerson at stanford.edu]
Sent: Tuesday, February 25, 2014 2:57 PM
To: Sergey Nikitin; support at bioontology.org
Cc: Bob Stanley; musen at stanford.edu; Erich Gombocz
Subject: RE: new Bio API

Sergey,

This information doesn't get expanded anymore because we thought that very few users would actually want it and it greatly slows down the call for everyone else.

Can you tell me what your use case is for needed the user information for all ontologies? This doesn't seem very common. As an aside, since the user data only very rarely changes, you could instead just get the all user information and cache it on your side. You wouldn't need to retrieve it on every call.

Ray

From: Sergey Nikitin [mailto:snikitin at io-informatics.com]
Sent: Tuesday, February 25, 2014 2:20 AM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Bob Stanley; musen at stanford.edu<mailto:musen at stanford.edu>; Erich Gombocz; ray.fergerson at stanford.edu<mailto:ray.fergerson at stanford.edu>
Subject: new Bio API

Hi Support,

    In the old API the ontologies request returned a lot of information about each item. We are trying to find a way to receive alomost the same results with the new API.

            In the new API one can receive an ontology list in json format using URL: http://data.bioontology.org/ontologies?apikey={api-key}<http://data.bioontology.org/ontologies?apikey=%7bapi-key%7d>

    The result structures contain links to other objects, like:
{
"administeredBy": [
"http://data.bioontology.org/users/pjd"<http://data.bioontology.org/users/pjd>
],
*
o
     Is there a way to receive ontologies with data obtained by following the links in one request? For example:
{
"administeredBy": ["<http://data.bioontology.org/users/pjd>
*         username": "pjd",
*         "email": "pdevries at wisc.edu<mailto:pdevries at wisc.edu>",
*         "role": [
o    "LIBRARIAN"
],
*         "@id": "http://data.bioontology.org/users/pjd"<http://data.bioontology.org/users/pjd>,
*         "@type": "http://data.bioontology.org/metadata/User"<http://data.bioontology.org/metadata/User>,
*
"@context": {
o    "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>
}
],

 Perhaps, this is not the right approach? Then, what you recommend?
 https://bioportal.bioontology.org/ontologies loads pretty fast. We want to achive the same result.

Thanks,
Sergey Nikitin
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