Biomedical Engineering Reference
In-Depth Information
Figure 9.3
Atlas query results screen
Figure 9.3 presents a selection of results for the search for members of
the EGFR signaling pathway differentially expressed in carcinomas.
Genes are in rows, ranked by the number of found studies, and columns
provide a view of EFO carcinoma hierarchy. The numbers in dark/light
squares indicate numbers of studies with differential expression.
Bioinformaticians and computational biology researchers often need
direct access to the data and analysis results, bypassing the graphical user
interface. For such users, extensive application programming interfaces
(APIs) are provided, enabling them to extract data from the Atlas as
XML or Javascript Object Notation (JSON) feeds. Every result page has
a JSON and XML button providing direct access to these data feeds.
9.3.1 Adapting Atlas for the real (internal) world
In order to adapt the EBI Atlas to standalone deployments, we undertook
a signifi cant engineering effort. The greatest effort was devoted to
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