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[bioontology-support] Status of annotation expansions with mappings using NCBO Annotator

manuelso manuelso at stanford.edu
Thu Nov 21 08:52:57 PST 2013


Hi Clement,

At the moment the annotator only returns manual mappings (CUI, OBO-XREF and REST). Our mapping database for automatic mappings (LOOM and URIs) has been growing very fast and including automatic mappings in the annotator incurs in responses that are expensive to generate and difficult to consume. To work around this issue one would need to perform additional calls to the mapping endpoint, for example [1].

For the term melanoma in NCIT I believe we only have mappings to MESH via LOOM hence the absence of mappings for that call.

I hope this helps,

Manuel

[1] http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3224/mappings?no_context=true&no_links=true

On Nov 21, 2013, at 2:02 AM, Clement Jonquet <jonquet at lirmm.fr> wrote:

> Hi there,
>  
> What is the status of the mapping extension using the Annotator.
> It does not seems to work for now:
>  
> http://data.bioontology.org/annotator?text=Melanoma&ontologies=NCIT,MESH&max_level=0&mapping_types=automatic&apikey=24e03810-54e0-11e0-9d7b-005056aa3316
>  
> Should return annotations made through the existing mappings btw NCIT and MESH
> http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMSH%2FD008545#mappings
>  
> Also, did you get my other message related to the score option ?
>  
> Clement
>  
>  
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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