Eutils.org Service

NCBI E-utilities, as a RESTful API, and providing RDF for the Semantic Web.

This service is deployed as a proof-of-concept to http://eutils.org.

Documentation, including instructions on how to use the service, is on the site itself. This README page describes implementation and deployment details.

This project is registered with BioPortal here.

To do

See GitHub issues.

Installation

Download the eXist database server.

Run the installer:

java -jar eXist-db-setup-2.1-rev18721.jar

Accept all the defaults.

Change to the webapp directory under the eXist installation, and then clone this repo:

cd *exist-install-dir*/webapp
git clone https://github.com/Klortho/eutils-org.git

Start the server:

cd *exist-install-dir*
bin/startup.sh

Point your browser at http://localhost:8080/exist/eutils-org/app/.

Outstanding API design issues

• All of the WebEnv/query_key stuff has been left out. We can do that later if we want.
• Also left out epost
• For queries that would result in URLs longer than 2k, use the "POST/Create/Redirect" pattern
• Interaction with user's query history
• EPOST equivalent
• Handling resources with > 1 object type (like dbGaP)
• Is search technology an implementation detail? (rather than /entrez, maybe /data/gene/?term=cat&search=entrez|solr, etc.)

Anatomy of the app

The application is designed to be deployed under the eXist database, and is written in XQuery and XSLT.

The main controller is controller.xql, and uses features of eXist described in the documentation, URL Rewriting and MVC Framework.

References

• NCBI. Entrez Programming Utilities Help. 2010.

• Biotea: RDFizing PubMed Central in Support for the Paper as an Interface to the Web of Data, Garcia Castro, L J; McLaughlin, C; Garcia, A. 2012.

• From Markup to Linked Data: Mapping NISO JATS v1.0 to RDF using the SPAR (Semantic Publishing and Referencing) Ontologies, Peroni S, Lapeyre DA, Shotton D., 2012

• W3C. Cool URIs for the Semantic Web. 2008.

• Heath, Tom and Bizer, Christian (2011). Linked Data: Evolving the Web into a Global Data Space Accessed: 2013-06-09. (WebCite)

• Berners-Lee, Tim (2006). Linked Data - Design Issues. Accessed: 2013-06-09. (WebCite)

• Biohackathon 2013 Wiki pages (on GitHub)

• Identifiers.org

• Resource description framework technologies in chemistry - paper by Egon Willighagen

Archives

There is a paper that describes the first incarnation of the service, the rationale behind it, and details about how it worked: EutilsRDF Web Service: an RDF interface to NCBI Entrez Utilities.