For information about OGER see 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. Check our screencast introduction to BTH and OGER (180MB: it might take a while to load). NEWS: In 2019 we participated in the CRAFT shared task, about large scale NER, with excellent results. Find here our paper. Use OGER through 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> IMPORTANT: the base URL has changed! It is now https://oger.nlp.idsia.ch/ Use OGER as a web service The complete documentation of the OGER REST API can be found here. You can easily construct simple queries adding specifiers to the <BASE_URL> mentioned above. Currently we support two types of requests: fetch and upload. Check also the eamples at the bottom of this page.
POST <BASE_URL>/fetch/<SOURCE>/<OUTPUT_FORMAT>/<DOC_ID>
Any incorrect or unspecified specifier will lead to an error page providing some basic information. The accepted values of SOURCE are currently:
DOC_ID is a PubMed or PubMed Central numerical identifier (depending on which SOURCE option has been provided) 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). The accepted values of INPUT_FORMAT are:
Check the info page below for additional options not yet documented here: https://github.com/OntoGene/OGER/wiki/REST-API Examples An example of a complete request is the following curl -X 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). Another similar example, using as output json format for PubAnnotation: curl -X GET https://pub.cl.uzh.ch/projects/ontogene/oger/fetch/pubmed/pubanno_json/6234315 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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