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.
See GitHub issues.
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.
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)
Biohackathon 2013 Wiki pages (on GitHub)
Resource description framework technologies in chemistry - paper by Egon Willighagen
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.