The CIPF RENATO API: A Systems Genomics Time-Saver

Greg Bates, November 5th, 2012

CIPF RENATOThe CIPF (Centro de Investigation Prince Felipe) in Valencia, Spain, is providing a REgulatory Analysis Tool (RENATO) in the form of a RESTful  API to give researchers access to its genomics database.

The bioinfo website notes they are focused on a systems genomics perspective, recognizing that “Genes do not operate alone within the cell, but in an intricate network of interactions,” which is discovering higher-order levels of interaction to the point where even diseases are “starting to be considered from a systems biology perspective.”

The API’s website notes that it currently supports two species, human and mouse, with three main categories in the database, regulatory, genomic and feature. The regulatory category covers regulatory elements such as microRNAs; genomic is a location in the genome; and feature involves any element that has a defined location on the genome.

The API offers 5 subcategories focused on the transcription factor: info, tfbs (transcription factor binding sites), target_gene (those genes regulated by this TF), gene, and pwm (position weight matrices).

The example call given will obtains all the TFBSs in the human BRCA2 gene.

The example code given is in PERL but, they note, the vast majority of programming languages can handle URLs.

The CIPF is a bioimaging bank in Spain that assists in “diagnostic imaging, radiotherapy, and biochemical technologies” in the country.

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One Response to “The CIPF RENATO API: A Systems Genomics Time-Saver”

November 9th, 2012
at 4:34 pm
Comment by: API Spotlight: Social Media Curation Snip.It, Captricity, and Clean Power Estimation.

[...] Of the many APIs we published this week, eighteen were highlighted on the blog by our team of writers. In this post, we’ll shine a spotlight on those eighteen, which included the CIPF RENATO API.  The API allows researches access to the RENATO genomics database and more specifically the analysis of gene interaction within a cell. There are three main categories within the database: regulatory, genomic and feature. The regulatory category covers regulatory elements, genomic is a location in the genome, and feature involves any element that has a defined location on the genome. To learn more about the CIPF RENATO API visit the RENATO site as well as the CIPF RENATO API blog post. [...]

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