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OGER: OntoGene Entity Recognition


Summary

The OntoGene’s Biomedical Entity Recogniser (OGER) is a RESTful web service, implemented on top of  the Bio Term Hub. OGER allows a remote user to batch annotate a collection of documents. Recently, we have participated in a community-organized evaluation of Bio Text Mining services (BioCreative/TIPS), in which our system obtained the best results according to four of the six evaluation metrics. 


Test it using the web interface

OGER can be accessed either through a web interface for single text annotation, or as a web service (typically for batch annotations).

The base URL is the following, which leads you to the web interface.

https://pub.cl.uzh.ch/projects/ontogene/oger/          <BASE_URL>


Usage as a web service

Different requests can be composed starting from the base URL above and adding specifiers as described here:

https://pub.cl.uzh.ch/projects/ontogene/oger/info

Any incorrect or unspecified specifier will lead you to the same page.

Currently we support two types of requests: fetch and upload.

  • A fetch request will retrieve an existing document from a known source:   
          GET <BASE_URL>/fetch/<SOURCE>/<OUTPUT_FORMAT>/<DOC_ID>
          POST <BASE_URL>/fetch/<SOURCE>/<OUTPUT_FORMAT>/<DOC_ID>

  • An upload request is used to submit a text to be annotated.
          POST <BASE_URL>/upload/<INPUT_FORMAT>/<OUTPUT_FORMAT> [/<DOC_ID>]


The accepted values of SOURCE are currently: pubmed, pmc
 
The accepted values of INPUT_FORMAT are: txt, bioc, pxml, nxml, pxml.gz

The accepted values of OUTPUT_FORMAT are:  bioc, odin, odin_custom, tsv, xml

DOC_ID is a PubMed or PMC numerical identifier in a fetch request. It can also be used as
an optional value in an upload request to specify an ID which will be added as an attribute
value in the output documents formats that contain a document ID (odin, odin_custom).

Check the info page for additional options not yet documented here:

https://pub.cl.uzh.ch/projects/ontogene/oger/info


Examples

An example of a complete request is the following

GET https://pub.cl.uzh.ch/projects/ontogene/oger/fetch/pubmed/tsv/21436587

It retrieves the annotated version of PubMed abstract 21436587 in tsv format. You can get a PMC document by replacing "pubmed" with "pmc" (and using a PMC identifier).

As another example, you can upload an article for annotation:

echo 'tumor cells reduced HSC numbers' | POST https://pub.cl.uzh.ch/projects/ontogene/oger/upload/txt/odin

which returns an XML document with our ODIN XML markup. 

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