Gene Expression Atlas 1.1.3

Hello!

We released Atlas 1.1.3 today. The main highlights of this release are:

• A collection of Atlas REST APIs
• A new Atlas DAS Track - view it in Ensembl Genome Browser

There are a number of bug-fixes, also. You can now link to genes on any number of identifiers, including synonyms and alternate names:

• http://www.ebi.ac.uk/gxa/gene/SPAC16A10.06C, for the S. pombe pli2 gene,

and non-specific identifiers:

• http://www.ebi.ac.uk/gxa/gene/IPR001487, for Bromodomain genes, InterPro IPR001487.

Now, a little more detail on the Atlas REST APIs. These will return JSON or XML, and provide a comprehensive programmatic interface to everything you see in the Atlas Web interface. Here are some examples (lots more detail in the API documentation).

Gene and Condition Queries

These queries return gene results as in the Atlas Heatmap or List Views, with complete information on which conditions the matching genes are over/under-expressed in, including the EFO information.

• http://www.ebi.ac.uk/gxa/api?geneGotermIs=p53+binding&geneDisease=cancer
• http://www.ebi.ac.uk/gxa/api?geneIs=ASPM
• http://www.ebi.ac.uk/gxa/api?geneIsNot=cell+cycle
• http://www.ebi.ac.uk/gxa/api?geneIs=ENSMUSG0000012344

• http://www.ebi.ac.uk/gxa/api?upIn=liver
• http://www.ebi.ac.uk/gxa/api?updownInOrganismpart=heart
• http://www.ebi.ac.uk/gxa/api?downInOrganismpart=kidney&upInSex=male
• http://www.ebi.ac.uk/gxa/api?geneIs=p53&downInOrganismpart=kidney&upInSex=male

Try adding "&indent" to the end of these queries to see pretty-printed output.

Experiment Queries

These queries execute searches for experiments, either listing general experiment information, or, if one or more genes are specified, the full experiment/assay/sample relationship matrix is produced together with gene expression values and, if available, the differential expression statistics.

• http://www.ebi.ac.uk/gxa/api?experiment=cancer
• http://www.ebi.ac.uk/gxa/api?experiment=E-AFMX-5&gene=ENSG00000160766&gene=ENSG00000166337&format=xml

Again, "&indent" will pretty-print the results.

We urge you to check out the docs, try these APIs out and get back to us with feedback and requests for further functionality. We'll post here separately the instructions to enable the Gene Expression Atlas DAS Track in Ensembl. For now, here's a screenshot:

Yours,

--Misha Kapushesky and the Atlas Team

Gene Expression Atlas Project Coordinator

Atlas Web Services Alpha

Hello!

A new build is up - 4866. No major visible changes but several important reworkings under the hood:

• Improved caching - hopefully you should notice faster responses
• Better experimental factor ontology (structured vocabulary of experimental variables) expansion - now expands down through all available levels instead of just one as before, and is on by default. Example: search for tumor.
  
• Auto-suggest drop-down works a bit more intuitively, esp. on conditions. You'll see what I mean, just start typing a query.
  

The big deal with this release is, however, the very limited, initial SOAP Web Services API to the Atlas. See http://www.ebi.ac.uk/microarray/doc/atlas/api.html for further detail on this. Among other things it's a step towards batch querying of data.

As always, your feedback is welcome! More interesting and wonderful things are in the works.

--Misha
P.S. It would be easy for us to offer expansion by lots of other ontologies. Would that be useful to users, too?