Showing posts with label genbank. Show all posts
Showing posts with label genbank. Show all posts

03 April 2008

Happy Birthday, Open Data

The received wisdom is that open source begat open access, which begat open data, and in broad outline that's true enough. But in one respect it's quite wrong: the first, and arguably most important open data store was set up fully 25 years ago, and is still going from strength to strength:

For a quarter century, GenBank has helped advance scientific discovery worldwide. The nucleic acid sequence database was established by the National Institutes of Health (NIH) in 1982. Since its creation, the GenBank database has grown at an exponential rate. Amazing as it may seem, in 1984, the entirety of GenBank’s data was published in a two volume hardcover book. Today, if the current contents of GenBank’s database were printed, it would fill more than 300 pickup trucks with paper.

Unveiled at the onset of the “Information Age”, GenBank has continued to evolve and incorporate technological innovations. The GenBank database has remained on the cutting edge of technology and illustrates the dynamic changes over the past 25 years in quantity and speed with which information is shared.

GenBank joined with sequence databases in Europe and Japan to form the International Nucleotide Sequence Database Collaboration. GenBank was one of the earliest bioinformatics community projects on the Internet promoting open access communications among bioscientists. In 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information (NCBI) within NIH where it resides today.

31 July 2006

UK PubMed Central: Good News, Bad News?

The US PubMed Central service has become one of the cornerstones of biomedical research, and a major milestone on the way towards full open access to all scientific knowledge.

Just as the world's central genomic database GenBank exists in three global zones - the US, Europe and Japan - so the natural step would be to roll out PubMed Central as an international service. The first move towards that has now been made with the announcement that a consortium of UK institutions has been chosen to set up UK PubMed Central (UKPMC). That's the good news. The bad news - maybe - is that one of them is the British Library.

Why is that bad news, since the British Library is one of the pre-eminent libraries in the world? Well, that may be so, but it is also deeply involved with Microsoft's Open XML, the rival to OpenDocument Format; Microsoft is trying to push Open XML through a standardisation process to match ODF's full ISO status. It is particularly regrettable that the British Library is bolstering this pseudo-standard with its support, rather than wholeheartedly backing ODF, a totally open, vendor-independent standard, and this could be real problem because of the British Library's role in the UKPMC consortium:

In the initial stages of the UKPMC programme, the British Library will lead on setting up the service, developing the process for handling author submissions and marketing the resource to the research community.

It's the "handling authors submissions" that could be bad news: if, for example, the British Library gave any preference for submissions be made in Microsoft's XML format formats, it would be a huge step back for openness. The US PubMed Central does the Right Thing, and takes submissions in either XML or SGML. Let's hope the UK PubMed Central follows suit and goes for a neutral submissions policy. (Via Open Access News.)