The database of databases

Today chemical biology generates new high-throughput methods of studying biomolecules almost as quickly as organic chemists report total syntheses. Whole genome, transcriptome, proteome, lipidome, glycome etc. analyses are flourishing and delivering vast amounts of data. Bioinformaticist are trying to cope with the data flow by archiving them in various databases. This has led to a situation when the number and diversity of databases became incomprehensible for a human being.

Since 1994 Nucleic Acids Research dedicates one issue per year to the overview of new bioinformatic databases and updates on the older ones. It reached 1000 database benchmark back in in 2006 and now the journal’s collection consists of 1621 resources. Of course, it’s nice to have all databases on one page but HTML is very limited in terms of information one can put in a document.

So scientist were looking for better way to organize all the databases out there. The problem is that many of them become obsolete or simply irrelevant over time. Besides that, some databases are better curated than the others, and this kind of information is crucial for the end user. Hence, https://bio.tools/ appeared as a community-driven effort to keep up-to-date registry of available bioinformatics resources. Currently the registry lists 1785 resources annotated by a number of categories, which users find relevant. The user interface is straightforward, so it’s easy to find relevant databases for a given subject. The motivation and structural organization of the registry one can find in the latest NAR database issue. Of course, as a wiki-style project, its success largely depends on the enthusiasm of contributing scientists. But it’s a great initiative and the timing is about right, because the data flow is unlikely to slow down any time soon.

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Author: Slava Bernat

I did my PhD in medicinal chemistry/chemical biology of G protein-coupled receptors and then explored some chemical biology of non-coding RNA as a postdoc. Currently I'm working in a small biotech company in San-Francisco Bay area as a research chemist. I'm writing about science, which catches my attention in rss feed reader and some random thoughts or tutorials.

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