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NASC

The European Arabidopsis Stock Centre

NASC Data And Webservices

NASC provides programmatic access to various data resources and analysis tools via Webservice technologies. Webservices technologies enable integration and inter-operation between client and server software. The technology is built on open standards: Representational state transfer (REST): a software architecture style. Simple Object Access Protocol (SOAP): a messaging protocol for transporting information. Web Service Description Language (WSDL): a method for describing Webservices and their capabilities. A list and description of Webservices provided by NASC follows:
Germplasm Webservices
Genomic Webservices
Transcriptomics Webservices
Soaplab2 Webservices
RESTful Services
 

Germplasm Webservices

Seed Stocks

The NASC stock catalogue holds over 800,000 accessions of Arabidopsis thaliana. This includes a wealth of characterised mutants and multiple markers; a wide variety of enhancer and promoter trap lines (both GUS and GFP), suitable for expression studies; several mapping populations and hundreds of ecotypes, which are of particular interest to post genomic research and offer a reservoir of natural genetic variation. Collections from the SALK Institute, GABI-Kat, Syngenta SAIL T-DNA, Wisc DS Lox, John Innes Centre together with the IMA (Institute for Molecular Agrobiology) lines from Singapore and similar lines from the CSHL (Cold Spring Harbor Laboratory) constitute a very large number of sequenced characterised insertion lines suitable for reverse genetics. Data associated with NASC stocks are available via webservices.

Ontologies

In an effort to augment the depth and quality of the data, NASC has utilised various ontologies and standards, giving the research community a controlled and structured vocabulary to describe and represent their data. NASC has adopted the Plant Ontology in its Germplasm database to structure and annotate its phenotypic descriptions. These immediately benefit the plant research community by allowing users to query the database via webservices using defined terminologies.

 

Genomic Webservices (LEGACY)

AtEnsembl (LEGACY)

AtEnsembl was NASC's pioneering genome browser for Arabidopsis thaliana. It combined positional information for all publicly available DNA tagging programmes in Arabidopsis and in its last incarnation integrated these directly with TAIR8 (NOTE: as of September 2008) and MIPS (NOTE: as of September 2008) Arabidopsis genome annotations. No additional genebuilds were carried out after 2008 but a series of alignments were done to provide Affymetrix gene probes, UniProt hits, and other similarity data up until 2010. We currently recommend the following public browser: Araport and the excellent subscription service at TAIR.

Webservices accessing the AtEnsembl database are no longer available. If you would like a webservice to access legacy data from AtEnsembl, please contact the Bioinformatics team.

 

Transcriptomics Webservices (LEGACY)

The NASC Arabidopsis Microarray service (NASCarrays) closed (2002-2013). The transcriptomics webservices accessing these data have also been retired.

All plant affymetrix data in NASCArrays has gone to GEO throughout the lifetime of the service (as required by many journals) where it should be accessible to all for the foreseeable future.

CEL files from NASCArrays are also available at the Iplant cloud Data Store, and are accessible using the DAVIS web interface. From here, the data can be accessed by all Iplant technologies.

Please also feel free to use our Link index to NASCarrays data on iPlant sorted by experiment number.


 

Soaplab2 Webservices

SoaplabSOAPLAB2, was developed at the European Bioinformatics Institute (EBI), and is a SOAP-based analysis webservice that is used to wrap command-line applications so they can be used as webservices.

NASC has used SOAPLab to deploy most of its webservices. See the NASC SOAP services link for a list of all NASC SOAP webservices.

SOAPLab ships with its own client, SPINET, where webservices can be tested using a browser. This page - NASC SOAP services - is provided mainly as a link to available NASC webservices, a brief description of what each one does, and an example input that can be used. There is also WSDL link alongside each service name.

 

RESTful Webservices

REST stands for Representational State Transfer, first described by Ron Fielding, and inspired by the development of Hypertext Transfer Protocol (HTTP).

NASC's RESTful webservices API allows access to the NASC stock catalog and related data, via a set of URLs with a fixed pattern showed below. The query parameters are shown in curly brackets. The results of the webservices are returned in JSON format for simple consumption. NASC RESTful services will also help to meet integration requirements for large cross continental projects such as the Arabidopsis Information Portal that build systems where data can be easily combined and extended.

REST features include:

These features are part of the HTTP design, thus HTTP can be considered a REST protocol and REST services are based on HTTP. Using URLs to identify resources, MIME types to identify types of data representation and using requests that contain all the state required to process the request.

The data returned by a RESTful service can be in a variety of MIME formats. NASC data is currently returned in standard JSON (JavaScript Object Notation) format.

NASC RESTful webservices

The basic format of a NASC RESTful webservice is as follows:

http://webservices.arabidopsis.info:3000/{tablename}

For example: http://webservices.arabidopsis.info:3000/stock

You can invoke a REST webservice simply by using it's URI. For a simple example of how to invoke a NASC webservice, please follow this link.

Beloow are some examples of querying the RESTful webservices:

Service URI Description Using curl Using wget
http://webservices.arabidopsis.info:3000/stock Fetch all Stocks curl 'http://webservices.arabidopsis.info:3000/stock' -H 'Content-type:application/json' wget -q -header='Content-type:application/json' 'http://webservices.arabidopsis.info:3000/stock' -0 -

Taverna

TavernaTaverna has been created by the myGrid team. This project makes it possible to create workflows by chaining the output of one service to the input of another. Taverna is available for download from the Taverna homepage.

Developing workflows using Taverna is a simple way of making use of NASC webservices; making it possible to combine them with other diverse available webservices. It provides a practical and useful way to document and share workflows and their design.


Contact

Please email all comments or problems to the bioinformatics team.

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