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Discovery of target url

Hi,


I'm doing some patent searches for specific targets.  I've been able to guess the target url, for example http://rdf.ebi.ac.uk/resource/surechembl/target/TTR and got results.  But sometime I can't seem to guess the URL.


In general, how to I discover the specific target URL for a protein of interest?  I've tried using concept URL's via free-text searching, but of course this doesn't doesn't get me the surechembl url.


Any suggestions would be appreciated.


Carlos S. Zamudio




Hi,

unfortunately, the mappings from proteins to the gene names that are used as queries are currently not automatically performed in the query. The used identifier for the target url is the HGNC symbol, so you could search for the protein of interest here: http://www.genenames.org/.

The current workaround to reach patent data for ConceptWiki targets (ie a text search result) or Uniprot URIs is the following:

Use the URI in MapURL call with http://identifiers.org/entrez.gene/ as targetUriPattern.
With the result, do a MapURL call with http://www.genenames.org/data/hgnc_data.php?hgnc_id= as targetUriPattern. With the result, do a MapURL call with http://info.identifiers.org/hgnc.symbol/ as targetUriPattern. This should work as input for the patent calls.

I hope this helps!
Daniela


Thank you Daniela for the prompt reply.


Yes, this makes sense to me now.  I plan to do exactly as you suggest.  Is there a reference to the full list of http://identifiers.org/* pattens that are available?


Cheers,

Carlos

There's this page:

    URI Spaces Per Graph


Don't know how complete or current this list is.  Check the $id pattern in the "NameSpace" column.  Might be helpful in some cases.


-- Randy

General documentation for identifiers.org is available here http://identifiers.org/documentation, and a full list of all registered patterns is available here http://www.ebi.ac.uk/miriam/main/collections/. I did not find a list yet of all the patterns we support in the Open PHACTS Discovery Platform, but in general you can use the identifiers.org URIs for all our data sources that are registered there. I'll see if I can find a more comprehensive list.

 

I think that is from version 1.5 of the API, so we might have a few more pattern available by now. But it is a very good start, thank you for sharing it!

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