Web Services
GeneCruiser 3 provides an application programming interface
(API) that allows programmers to access GeneCruiser functionality
from within their own applications. GeneCruiser provides this API
using web services.
GeneCruiser has two categories of web services: new web
services and legacy web services. The new web services are
implemented using a REST-like
architecture. The legacy web services were created using SOAP
(Apache Axis). The web services are described below in more detail.
New Web Services
GeneCruiser 3 includes new web services that provide the same
functionality as the
Find Variations and
Variations to Genes pages. In addition, this version also provides
web services for:
- Retrieving Genes by genomic identifier (i.e., gene,
transcript, or translation identifier)
- Retrieving Genes by genomic location
- Retrieving Variations by name (e.g., dbSNP RS number)
These new web services are implemented using a REST-like
architecture. Queries are performed using an URL and the response is
formatted as XML. For example, to retrieve a gene using a HGNC Gene
Symbol:
http://genecruiser.broad.mit.edu/genecruiser3_services/rest/gene/byGenomicId?idType=HGNC_GENE&
id=BRCA1&firstResult=0&email=joe@example.com
Note that the email address must be the address for a
registered GeneCruiser user. The response to the query is an XML structure.
Full documentation for the new web services can be found
here:GeneCruiser3WebServices.pdf
Haploview is one of the projects that has
integrated GeneCruiser to their software. As Haploview is
open-source, you can view their Java based implementation of
GeneCruiser client at Haploview SourceForge
project site.
Legacy Web Services
The GeneCruiser legacy web services provide the same
functionality as the
Annotate Probes and
Convert genes pages. These web services were created using SOAP
(Apache Axis).
Note: Any service that handles identifiers
from disparate sources must be able to recognize the context or
scope of the identifiers. The GeneCruiser legacy web servies use
Life Science Identifiers (LSIDs) to unambiguously identify
Affymetrix probe IDs. For more information, see Liefeld,
et al. (2005).
View the GeneCruiser
Legacy Web Service WSDL. We plan to replace these Legacy web
services with a REST style implementation in a future version of
GeneCruiser.
