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[bioontology-support] new Bio API

Darren Weber dlweber at stanford.edu
Wed Feb 26 14:25:49 PST 2014



Also see
http://data.bioontology.org/metrics

The ontology URI is in the links for each entry of the array.

-- Darren



On 2/26/14, 2:17 PM, Ray Fergerson wrote:
>
> Bob,
>
> Thanks. This is very helpful. The metrics are available for any 
> particular ontology with the call:
>
> http://data.bioontology.org/ontologies/SNOMEDCT/metrics
>
> This call is always very fast because the metrics are all 
> precalculated. If you have a fixed set of ontologies this this is what 
> you should use.
>
> If instead you want to loop over all ontologies and look at their 
> metrics (this sounds like what you want) then you need to make a 
> single call to get back all ontology objects and then traverse to the 
> “metrics” link in each and make that call for each ontology (the URL 
> there is the same form as the one above but there is no reason to 
> build it yourself since we have already done so.
>
> http://data.bioontology.org/ontologies
>
> and then traverse to the “metrics” link on each ontology.
>
> It is easiest to look at this in a browser like Chrome and see the 
> results and then generate the code accordingly.
>
> This should all work fairly quickly. The list of ontologies may take a 
> few seconds to retrieve but the metrics calls are all sub-second.
>
> We would be happy to hear more success stories about the annotator or 
> BioPortal in general. If you can point us to a talk or journal article 
> that we can read that would be great!
>
> Ray
>
> *From:*Bob Stanley [mailto:rstanley at io-informatics.com]
> *Sent:* Wednesday, February 26, 2014 12:21 PM
> *To:* Ray Fergerson; Sergey Nikitin; support at bioontology.org
> *Cc:* musen at stanford.edu; Erich Gombocz
> *Subject:* RE: new Bio API
>
> 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 
> <mailto:support at bioontology.org>
> *Cc:* Bob Stanley; musen at stanford.edu <mailto: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"
>
>         ],
>
> ·
>
> 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",
>
>         ·*"**@type**"*: "http://data.bioontology.org/metadata/User",
>
>         ·
>
>         *"**@context**"*: {
>
>         o*"**@vocab**"*: "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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