OntoRest: OntoGene web services

We provide access to some of the text mining capabilities of the OntoGene sytem through RESTful web services. Fundamentally you can send any document (or collection of documents) in BioC format and have it processed by the OntoGene pipeline.

BioC is a new standard for data exchange for text mining systems. It was developed at NLM/NCBI as part of an international collaboration (the OntoGene group is one of the members). It provides a simple format that can be used, among other things, to query a web service. BioC is defined by a simple DTD.

At the moment (September 4, 2014) the following services are available:
  • https://pub.cl.uzh.ch/projects/BioC/chem                 identifies chemical entities
  • https://pub.cl.uzh.ch/projects/BioC/chem+offset      as above, with offsets (position of the term in the document)
  • https://pub.cl.uzh.ch/projects/BioC/disease             identifies diseases
  • https://pub.cl.uzh.ch/projects/BioC/disease+offset  as above, with offsets
  • https://pub.cl.uzh.ch/projects/BioC/gene                 identifies genes
  • https://pub.cl.uzh.ch/projects/BioC/gene+offset      as above, with offsets
  • https://pub.cl.uzh.ch/projects/BioC/ctd                    delivers all the entities above (genes, chemicals, diseases)
  • https://pub.cl.uzh.ch/projects/BioC/ctd+offset         as above, with offsets
  • https://pub.cl.uzh.ch/projects/BioC/ixn                    identifies "action terms" (which describe an interaction type)
  • https://pub.cl.uzh.ch/projects/BioC/ctd+rel              delivers all the entitites (gene, chemical, diseases) and their interactions
  • https://pub.cl.uzh.ch/projects/BioC/ctd+offset+rel  delivers relationships and entities, with offsets

Instructions on how to use the OntoGene RESTful service

In order to use the services, you need to submit a document (or collection) in BioC format (see example here) as a POST request to one of the services above.

There are different utilities that allow the submission of a document as a post request to a remote service. For example, you could use the curl utility and choose one of the following options:

curl SERVICE | curl -d "$(cat FILENAME)" -X POST
cat FILENAME | curl SERVICE -d @- -X POST

If your document is available from a web server, you can submit it for example as follows:

curl DOCURL | curl SERVICE -d @- -X POST

In the examples above, SERVICE is the URL of one of the OntoRest services (see above), DOCURL is the location of a remote document, FILENAME is the path of a local file. Beware that the local file, or the document retrieved at DOCURL, must be in BioC format.

You can either send a single BioC document to an OntoRest service (see example here), or a collection of documents (see example here).

For simple testing you can also use a browser plugin, such as "Poster" for Firefox.  Once installed, you have the enter the url of the OntoRest service that you want to use, and attach the file that you want to analyze; then press the [POST] button.

In case of problems, please contact Fabio Rinaldi (fabio AT ontogene.org).

ODIN web interface

Additionally, you can test the OntoGene text mining capabilities through our web interface called ODIN (OntoGene document inspector). Currently  two versions are publicly available:

  • ODIN CTD (customized for the Comparative Toxicogenomics Database)
  • ODIN RegulonDB (customized for the RegulonDB database)

The implementation of OntoRest is based on PyBioC, a python based implementation of the BioC standard developed at the University of Zurich. For technical details, contact Hernani Marques Madeira (h2m@access.uzh.ch).

Additional information available in the following publications:

Marques, Hernani; Rinaldi, Fabio (2013). PyBioC: a python implementation of the BioC core. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, MD, US, 7 October 2013 - 9 October 2013, 2-4.

Fabio Rinaldi, Simon Clematide,  Hernani Marques, Tilia Ellendorff, Martin Romacker, and Raul Rodriguez-Esteban. OntoGene web services for biomedical text mining. BMC Bioinformatics 2014, 15(Suppl 14):S6  doi:10.1186/1471-2105-15-S14-S6