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[bioontology-support] [BioPortal] Feedback from Chao-Kung Chen

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Feb 16 15:31:23 PST 2017


Hello Chao-Kung,


On Feb 16, 2017, at 4:21 AM, Chao-Kung Chen <ckchen at ebi.ac.uk<mailto:ckchen at ebi.ac.uk>> wrote:


Hi Jennifer:

Thank you very much indeed for your help.

After obtaining the api key, I can now access the page:

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

and when the page is loaded, it says on top
  *   page": 1,
  *   "pageCount": 27

So I guess I would expect 27 pages of mappings.
But starting from page 8, it becomes empty. Would you explain what this means?


This appears to be a bug in our system.  Apologies for this inconvenience.  I’ve entered an issue in our public issue tracker.  You can follow the progress here if you’d like:

https://github.com/ncbo/ontologies_linked_data/issues/66




What I try to achieve is for each Mesh term I get from pubmed for a paper, I want to convert it to an MP, if available.
Do you think this url is the best way to achieve this?


There are a lot of different ways to retrieve mappings in BioPortal.  Given a particular MESH term (e.g.: “Myopia"), you can use a REST call to get all the mappings for that term:

http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD009216/mappings<http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D009216/mappings>

You could iterate through the result set and select only those mappings from the MP ontology.

The various ways to retrieve mappings are detailed on the documentation page:

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


I am also not sure the best way to traverse the tree to obtain the mapping for the Mesh terms not in the given url above?


As I mentioned above, this looks like a bug in our system that we’ll need to investigate and fix.

Kind regards,
Jennifer

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