Web Services

For us, Web services are Web-accessible tools that deliver data in easy-to-parse, machine-readable formats suitable for import into third-party visualization software and data analysis environments, or even custom programs. We want to deliver data in formats that will make it easier to try out new types of data exploration and data mining techniques, and we think that Web services are a good strategy to achieve this goal.

We are using Web services strategies for delivering data in machine-readable formats: a ReST-style strategy. To find out how to use this different types of service, read on:

The ReST Style

We provide access to "raw" expression values and KS quality control test statistics for ATH1 microarray data in our database via a simple, easy-to-use, ReST-style Web service.

The acryonym ReST stands for Representational State Transfer, and it refers to an architectural style of organizing and indexing information on the Web. In a nutshell, a ReST approach treats data sets as having unique addresses, typically using identifiers or names as part of URLs to make it easier to access the data. Typically, a ReST service would return data in an XML (Extended Markup Language) format, but since many programs you might want to use can't easily import XML, our ReST-style service outputs simple comma-separated, plain text. This is why we call our service "ReST-Style" instead of just ReST, because our service doesn't fully conform to the ReST way of doing things.

To access the data via this Web service, you just need to know how to formulate URL queries.

The syntax is:

http://www.cressexpress.org/cgi-bin/getExpVals.py?pss=[ps1,ps2,..,psN]&version=[v][&desc=1]

where [ps1,ps2.,,,psN] is a comma-separated list of probe set ids on the ATH1 array, version [v] corresponds to one of the data releases listed here. Legal values for version include 2_0, 3_0, 3_1, and 3_2. Note desc is optional parameter. If a non-zero value is provided then it returns description of experiment.

For example, the following URL retrieves expression data for two redundant probe sets that measure transcript variants from Arabidopsis locus AT5G35980, which encodes a putative protein kinase with two alternative three prime ends.

http://www.cressexpress.org/cgi-bin/getExpVals.py?pss=249678_at,249679_at&version=2_0

http://www.cressexpress.org/cgi-bin/getExpVals.py?pss=249678_at,249679_at&version=2_0&desc=1

When you click the above URL, the Web service will run and send the output to your browser window. The results are returned as comma-separated plain text table of data. You can then save what appears in your browser as a plain text file and open it later in Excel, R, TableView, or any other program that can handle this simple, table-based format.

Each row in the returned data represents a single 'CEL' file or slide. Columns (and headings) include:

Here is some R code showing how you might use the R statistical analysis environment to access and plot data using the ReST-style Web service:

You can directly run example using command source("http://cressexpress.org/exampleR.R") in your R interpreter