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This page is to harbour discussions on BioJava topics, especially topics related to development of new features or extension of already present features.

dbSNP objects for BioJava

I started working with a research team focusing in genomics and observed that there is nothing in BioJava to deal with dbSNP infos. I setup a (very) simple NCBIdbSNP class that can fetch single dbSNP entries and represent them as RichSequences. Anybody would have insights on the subject where I could go with this?

–Foisys 21:25, 23 January 2007 (EST)

Sounds interesting. How do you represent the SNP on the RichSequence? Is it a Feature? Does dbSNP contain frequency information for the SNPs? If it does it would be possible to represent each SNP as a Distribution. You could make a simple extension of RichFeature that stores a Distribution or possibly embed it into the RichAnnotation for the feature (best to do it as a string rather than as a Distribution in this case).

–Mark 23:33, 27 January 2007 (EST)

Right now, I have a simple parser that reads the XML file for a given dbSNP and extracts some infos out of it. I want to make each dbSNP entry into a RichSequence (content still in flux). I have not yet settled into the finality of the object: possibly extracting frequencied in populations would be an nice thing to have?

–Foisys 11:13, 29 January 2007 (EST)

For me this class would be particularly interesting. In STRAP users can manually give a list of SNPs http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16322575 abstract which are then projected on the AA-Sequence, NT-Sequence or 3D-structure http://www.proteinscience.org/cgi/content/abstract/15/1/208 publication Your class could help to get it from the databases automatically.

–Christo 05:07, 10 March 2007 (EST)

Data retrival tools for BioJava

It would be very useful to include tools to retrieve data from different databases, in particular from NCBI. Some tools programmed in Java 1 already exist, but it would be great to embed them in BioJava, along with the tools required to parse the data retrieved.

–Ghislain 22:19, 6 July 2008 (UTC)

Hi Ghislain,

I had this little example ready for a while because I had this same exact problem so many years ago ;-) There is also a package to get info from Ensembl (/wiki/BioJava-ensembl) from Thomas Down but I do not know what is its status right now. Thomas: can you give us an update on this?

–Foisys 12:35, 7 July 2008 (UTC)