Tag Archives: biodata mining

Tip of the Week: Ratmine

Ratmine is a ‘data warehouse’ that allows the user to construct queries across different areas of biological knowledge from SNPs to Pathways. It’s developed by the people at RGD and uses Intermine a project developed for Flymine and as part of a project between RGD, SGD and ZFIN to implement Intermine for these databases and ” develop new methods of interoperability for cross-organism research.” We’ve mentioned Intermine before and it’s also used in ModEncode Intermine is going to have to be a subject of a later post I think :).

This tip is actually a video done by the RGD group and one of those gems I’ve found at SciVee in our attempts to integrate our tips at SciVee (which will be coming). We occasionally will highlight a short tutorial done by someone else here at our tips (occasionally) and since I’ve found this gem and just got back from vacation in Florida :)…
Btw, while you are at it, you might want to check out this interesting set of tutorials on biomedical ontologies.

Biodata mining

Recently Mary pointed me to this journal that came out this year, I thought I’d pass it on to you: BioData Mining. The journal is open access and housed at BioMed Central and the focus:

…all aspects of data mining applied to high-dimensional biological and biomedical data, focusing on computational aspects of knowledge discovery from large-scale genetic, transcriptomic, genomic, proteomic, and metabolomic data.

There are some interesting articles in there, for example, this one on a new software developed gene ontology based  clustering for microarray experiments. They publish papers on resources, methodologies and scientific results from mined data. Could be a journal to keep an eye on.