Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] New rest API

Paul R Alexander palexander at stanford.edu
Wed Dec 11 11:56:15 PST 2013


Lori,

On item 1., you are correct that the id is now a URI. Not all ontologies follow the format you lay out below. Many OBO ontologies, for example, have URIs that end CODE:12345 and it gets translated to CODE_12345. OWL ontologies can include a namespace prefix in the old non-URI ids. These non-URI ids may be available in the skos:notation property for some ontologies.

For 2., you can include the “parents” property on class calls. For example, the class link you provided would look like this (to get prefLabel and the parents):
http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F706898?include=prefLabel,parents

What used to be provided in relations is now available in an attribute called ‘properties’:
http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F706898?include=properties

You can ignore the OrphanClass and treat the class as if it has no parents. The OrphanClass will be removed in the release coming out this week.

Paul


On Dec 11, 2013, at 6:49 AM, Phillips, Lori C. <LCPHILLIPS at PARTNERS.ORG> wrote:

> Hi,
> I use bioportal to extract terms for a given ontology.  I need to know term names, ids and relationships such as parent ids.
> I plan to use something analogous to this: http://data.bioontology.org/ontologies/RXNORM/classes and page through the data.
> I am looking at the new interface…  I can handle format changes.. but have a few questions about the data being returned.
>  
> 1.       IDs
> In the past we had <id> and <fullId>.
>  
> Looks like the new interface uses the old fullId as the new <id>
> I can parse out the info I need
>                 <id>http://purl.bioontology.org/ontology/RXNORM/706898</id>  would become id = 706898.
> But I need to  know if all the ontologies follow this format.
>  
> 2.       For each term I need to know its parent.
> In the past I extracted this info from the <relation><entry> lists.
> Now it looks like I have to follow a link to get this info?  I’ve tried that and I seem to end up with an orphanClass.
>  
> Page 1 of RXNORM gives me Fentanyl as the first term.
> Which has :
> <parents href=http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F706898/parents
>  
> When I go to this page I get:
> "@id": "http://bioportal.bioontology.org/ontologies/umls/OrphanClass",
>  
>  
> Thanks,
> Lori Phillips
>  
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20131211/2b1e269b/attachment-0001.html>


More information about the bioontology-support mailing list