02 January 2006

Nucleic Acids Research: Database Issue 2006

Nucleic Acids Research The new database issue of Nucleic Acids Research was released this week. The current issue is the largest yet and presents 94 new databases and updates of 68 existing databases. But as a bioinformatician, how can I know about all the content, all the difference about all this new stuff ? what are the redundancies ? what is really new ? where is the you-must-use-this-amazing-tool ? is this database built by a postdoc that will move to another lab next month ? what will be out of fund next year ?

In 2005, Nature contacted 89 databases listed in the Molecular Biology Database Collection (Nucl. Acids Res.28 1−7; 2000) to see how many still have funding five years on [ref].
"Of these, 51 reported that they are struggling financially. Seven of these have closed; the rest are being updated sporadically in their owners' spare time.
Not all these databases necessarily deserve to receive continued funding, especially as technology advances and competing resources are set up. But bioinformaticists are concerned by the sheer number that cannot find the money to provide an ongoing service."

Connotea might be a good way to find out what is really important among the 163 abstracts published in the NAR issue if several users add comments about each papers, so I imported all the abstracts into connotea.

BTW: I did this using the XML output format from ncbi/pubmed, the XSLT stylesheet below and xsltproc. The result was a RIS file that can be imported into connotea.

<?xml version='1.0' ?>
<xsl:stylesheet xmlns:xsl='http://www.w3.org/1999/XSL/Transform' version='1.0'>
<xsl:output method='text'/>

<xsl:template match='PubmedArticleSet'>
<xsl:apply-templates select='PubmedArticle'/>

<xsl:template match='PubmedArticle'>
JO - <xsl:value-of select='.//Journal/ISOAbbreviation'/>
N1 - <xsl:value-of select='.//AbstractText'/>
<xsl:apply-templates select='.//PMID'/>
TI - <xsl:value-of select='.//ArticleTitle'/>
<xsl:apply-templates select='.//AuthorList'/>
<xsl:apply-templates select='.//DescriptorName'/>
KW - NAR Database Issue 2006
KW - Bioinformatics
KW - Database
ER -

<xsl:template match='PMID'>
UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=<xsl:apply-templates/>

<xsl:template match='AuthorList'>
<xsl:apply-templates select='Author' />

<xsl:template match='Author'>
AU - <xsl:value-of select='LastName'/>, <xsl:value-of select='ForeName'/>

<xsl:template match='DescriptorName'>
KW - <xsl:apply-templates/>


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