Over the last 3 decades, many Genes have been identified as the source of many forms of cancer. Many Projects attempt to catalog all the newly available research data, including the Cancer Genome Project (CGP). CGP is using the human genome sequence and high throughput mutation detection techniques to identify somatically acquired sequence variants/mutations that are central in the development of human cancers. A new addition to their data is the Catalog of Somatics Mutations in Cancer (COSMIC).
The following information on mutant Cancer-causing genes is from the CGP's Gene Census at the Sanger Center. The available data table were converted directly into RDF (source), the Semantic Web format, using Babel. The RDF is rendered as an interactive web page using Exhibit. The various row colors represent those cancer-causing Kinases.
What is noteworthy here is that this data could have dynamically come from a database or a spreadsheet (in this case it was a .xls file from CGP), but once converted into Semantic RDF, it is more re-useable by both local viewers and tools, as well as from a distance (referentially). No additional code needs to be added to handle the identifiers (e.g., to create web links); they ARE the links! (Eventually when we all adopt one URI model for all molecular identifiers, this step will become even easier, and globally referential!) So please feel free and use this data in any way you wish-- you could for example, take the data (as RDF or JSON or tab-separated) and the source code of this viewer and re-mash them to make them more useful for your own work!
Feel free to send me any questions or suggestions you may have on this data viewer.
How to use the Exhibit View: Click on the table headers to sort a column in descending or ascending order. The various links in the cells are either semantic node links (in which case if the mutant gene is identified with a kinase, you will see ALL the semantically combined info!), or links to other resources such as Entrez-Gene. The facet views on the right represent the different types of Tissues, Chromosome location, somatic or gemerline mutation, DNA mutation type, Cancer genetics, somatic tumor phenotypes, germline tumor phenotypes and cancer syndromes . By selecting any combination of their listed types, the view will display only those filtered entries. The numbers left of each type indicate how many visible entries match each type. Alternative pivot-plots can be viewed by clicking on the above menus; for example, you can click on SOMATIC X GERMLINE Tumors see what genes give rise to both germline and somatic malignancies. Current views are underlined in red and preserve the facets already selected. You can shift to the Kinase View by clicking on the link below. A snap-shot of any current data view can be "copied" as RDF by clicking on the scissor icon above.
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