New life science demo for Apache Stanbol

[Rupert Westenthaler <ru...@gmail.com>]

Hi Stanbol community

There is a new Stanbol demonstration that shows how one can customize
Apache Stanbol to be used in the life science domain. It is based on
the following public available data sets

* Dailymed [1]: Published by the National Library of Medicine, this
dataset provides high quality information about marketed drugs.
* SIDER [2]: SIDER contains information on marketed drugs and their
adverse effects. The information is extracted from public documents
and package inserts.
* Diseasome [3]: The human disease network publishes a network of
4,300 disorders and disease genes linked by known disorder-gene
associations for exploring all known phenotype and disease gene
associations, indicating the common genetic origin of many diseases.
* DrugBank [4]: A repository of almost 5000 FDA-approved small
molecule and biotech drugs. It contains detailed information about
drugs including chemical, pharmacological and pharmaceutical data;
along with comprehensive drug target data such as sequence, structure,
and pathway information.

Note that the RDF versions of this dataset used by this demos are
maintained and hosted by the Freie Universität Berlin [5]. While they
are all public available commercial usage may require explicit
permissions for some of the datasets.

You can find the Demo at

   http://svn.apache.org/repos/asf/incubator/stanbol/trunk/demos/ehealth/

If you checkout the Stanbol trunk (required to build the demo) you
will find the demo at

    {stanbol}/demo/ehealth

All the rest is explained by the README.md file in this directory. A
nicely formatted version is available via Github [6]. However not that
the 2nd part of the README "Backround information about this demo" is
still work in progress.


For all that directly want to try such things the demo is also
available on the Stanbol Demo server hosted by the IKS project.

This includes the following three services:

(1) By default the Stanbol Enhancer on the dev server extracts drugs
and diseases based on there preferred labels.

   http://dev.iks-project.eu:8081/enhancer

(2) The ehealth enhancement chain can find more stuff because it also
uses alternate labels. This is exact the same EnhancementChain that is
also used by the demo.

   http://dev.iks-project.eu:8081/enhancer/chain/ehealth

(3) The health dataset can also be directly used via the Apache
Stanbol Entityhub.

   http://dev.iks-project.eu:8081/entityhub/site/ehealth/

NOTE: If you use the UI make sure that the language field is empty, as
this datasets do not define language information.

e.g. the following query will search for drugs with the name "Aspirin"
and return all information that would be also be printed on the drug
description

   http://dev.iks-project.eu:8081/entityhub/site/ehealth/find?name=Aspirin&field=dailymed:name&ldpath=dailymed:name;rdfs:comment;dailymed:warning;dailymed:precaution;dailymed:description;dailymed:adverseReaction

by default returned data will be of some JSON format. But any RDF
serialization is supported if the Accept header is set accordingly.
Note that with Stanbol HTTP headers can also be parsed as query
parameter by using:

   header_{header}={value}

will result in the header

   {header}: {value}

e.g. the above query to returned as "application/rdf+xml"

   http://dev.iks-project.eu:8081/entityhub/site/ehealth/find?name=Aspirin&field=dailymed:name&ldpath=dailymed:name;rdfs:comment;dailymed:warning;dailymed:precaution;dailymed:description;dailymed:adverseReaction&header_Accept=application/rdf%2Bxml


If there are any questions feel free to ask. Any kind of suggestions
are also very welcome!

best
Rupert Westenthaler




[1] http://dailymed.nlm.nih.gov/dailymed/
[2] http://sideeffects.embl.de/
[3] http://www.nd.edu/~networks/Publication%20Categories/03%20Journal%20Articles/Biology/HumanDisease_PNAS-V104-p8685(14My07).pdf
[4] http://www.drugbank.ca/
[5] http://www.wiwiss.fu-berlin.de/en/institute/pwo/bizer/

[6] https://github.com/apache/stanbol/blob/ae91bf9d0661ef8f714c5836875ecf364bf89a51/demos/ehealth/README.md
-- 
| Rupert Westenthaler             rupert.westenthaler@gmail.com
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