A New Year, A New Site, A New Service

It’s the start of a new year, and nothing says New Year like a website refresh. With the rise in the number of visitors to the site using mobile browsers, we’ve updated the site to make it more mobile friendly. Not only is it more easily viewable on smartphones and tablets, but you can add it to your home screen just like any other app.

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That last bit is important because we’re also announcing the launch of a new service simply called Aspen Gene. With it you can look up information on any gene. The service is powered by the MyGene.info web service developed by Chunlei Wu at The Scripps Research Institute’s Su Lab.  To visualize the data, we’ve developed a series of web components and are making them available through the new open source BioPolymer project.

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The Aspen Gene Search interface

Let’s take a look at the service. You start by entering in the symbol for a gene of interest, in this KRAS. Then tap the “Search” button to start the search.  The search results will then appear as a series of cards at the bottom of the screen. Tap on the arrow icon on the result card, and the gene summary will appear as shown below.

Gene Summary

The Summary tab provides an overview of the gene, including its symbol, synonyms, and IDs in related databases.  We’re currently linking to NCBI’s EntrezGene database, the Online Mendelian Inheritance In Man (OMIM), the Human Genome Nomenclature Committee, UniGene, and PharmGKB.  You can tap on the icon to the right of the field to open the record in a new window.

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Gene Summary Tab

Protein Information

The Protein tab shows the UniProt ID, along with a list of InterPro domains found in the protein.  You can tap on any of the domains to see more information.  The Protein Database section shows a list of PDB IDs. You can tap on any ID to display the associated protein structure.

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Protein Information Tab

Pathway Information

The Pathways tab shows a list of all of the pathways that the gene participates in. This includes entries from KEGG, Reactome, PharmGKB, Wikipathways and more. You can tap on any pathway name to see a diagram of the pathway.

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Pathway Information Tab

 

Publications

The Publications tab shows a list of GeneRIF publications. These are References Into Function, or papers that indicate the function of a gene, and are found in the NCBI EntrezGene database. Tap on the card to display the PubMed record for the article.

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Publication Information Tab

So, come visit us, and give our new site (and our new service a try)!

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About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.
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