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] [BioPortal] Feedback from Amad Hussain

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Mar 21 14:49:05 PDT 2019


Hello Amad,

On Mar 20, 2019, at 11:56 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

I am a part of the Data Science team at the Nationwide Children's Hospital in Columbus, OH. I am trying to gather a list of all of your class and ontology labels for a named-entity recognition task but do not see an easy way to get this information. I looked into your API but I would need to parse through every ontology tree step-by-step in order to get every label (nearly 9 million of them).

For ontologies, you can issue one GET request to retrieve all the ontology names:

http://data.bioontology.org/ontologies

If all you care about are the names, you can make the call more performant by specifying only the attributes you want with the “include” parameter. You can also turn off the JSON-LD and hypermedia link serializations, e.g.:

http://data.bioontology.org/ontologies?include=name,acronym&display_links=false&display_context=false\<http://data.bioontology.org/ontologies?include=name,acronym&display_links=false&display_context=false%5C>

These parameters are documented in the “General Usage” section of our API documentation:

http://data.bioontology.org/documentation#nav_usage

For classes, you can issue one GET request to retrieve all the classes for a particular ontology:

http://data.bioontology.org/ontologies/BRO/classes

Again, if all you care about are the class labels, you can make the call a lot more performant by using the technique I described above:

http://data.bioontology.org/ontologies/BRO/classes?include=prefLabel&display_links=false&display_context=false

In addition, the result set for class retrieval is paged. The default page size is 50 classes, but you can increase the page size using the pagesize parameter (see the API docs I referenced above).


I assume I would not be able to use your API to make this many GET calls and was hoping you could instead direct me towards a download dump where I could get these labels.

Our system handles a fair amount of throughput, e.g., for the last couple of months the REST API has handled anywhere between 14 and 24 million requests per week. Note that we throttle requests to 15 per second per API key. If you don’t already have an API key, you’ll need to get one to use the API: http://bioportal.bioontology.org/help?pop=true#Getting_an_API_key.

Something else you may want to consider is that we offer a CSV format download for most ontologies in BioPortal, e.g.:

http://data.bioontology.org/ontologies/BRO/download?download_format=csv

The CSV files have a “Preferred Label” column from which you could extract all the class labels. Due to licensing restrictions, we’re not able to offer any sort of file downloads for some ontologies, so in those cases you’d have to use the API.


I have tried investigating your documentation and wiki for a solution but I get a 403 error saying I do not have permission to do so.



Apologies that you experienced problems with our wiki yesterday. It’s been restored. In addition to the API documentation I referenced above, we have sample code in various languages for working with the REST services in GitHub:

https://github.com/ncbo/ncbo_rest_sample_code

Kind regards,
Jennifer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20190321/0757e348/attachment.html>


More information about the bioontology-support mailing list