Tip of the Week: Varietas. A plaid database.
For this week’s Tip of the Week I’ll introduce Varietas, a resource that integrates human variation information such as SNP and CNV data, and offers a handy tabular output with links to additional databases that will enable researchers to quickly explore other sources of information about the variations or regions of interest.
I think this is the first resource I’ve used from Finland. And it’s definitely the first resource I have used that is plaid. But it struck me that plaid is a pretty good conceptualization of the variations that we see in the genomes. Some are a single thread, some are larger sections, and the overlaps between the variations we observed in the genome are important to our understanding of them as well. And the history of computation leads back to textile manufacturing, in fact. So I thought it was a pretty good concept.
But let’s explore the threads of Varietas. You can read the paper which is linked below, but here I’ll just summarize some of the main features. First let me say the focus of this database appears to be human variation. Although you wouldn’t know that from the site very clearly. As far as I could tell there wasn’t any other species data. But if you want human variation data, you’ll find a variety of threads available to you. If you check out the About page, you’ll see the source data available includes Ensembl, the NHGRI GWAS catalog, SNPedia, and GAD. These sources also provide OMIM data, HGNC nomenclature, phenotypes, and MeSH terms. And the threads out include dbSNP, PubMed, SNPedia, and WikiGenes as well. This is also summarized nicely in Figure 1 of their paper.
It’s a very straightforward interface. There is a basic search with a text box for quick searching, and you select the type of data you are starting with: SNPs, genes, keywords, or locations. And the output will be a table with the results that correspond to your query.
If you have larger sets of features that you want to interrogate you can use the advanced forms to enter more data.
The tabular output can be viewed on the web with all the handy links. Or you can download the data as a text file to be used in other ways.
I’ll demonstrate the sample search for the movie, but you won’t see the full range of data that’s available there. I wish they had samples for each type of search. But I found one sample that will also show CNV results: choose the Location radio button and enter this location range to see some CNV samples 6:1234-123400
Varietas home page: http://kokki.uku.fi/bioinformatics/varietas/
PubMed record for the paper: http://www.ncbi.nlm.nih.gov/pubmed/20671203
Paananen, J., Ciszek, R., & Wong, G. (2010). Varietas: a functional variation database portal Database, 2010 DOI: 10.1093/database/baq016