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README.markdown

README.markdown

BioMart Plus Extras

BioMart Plus Extras is based on BioMart release 0.7 www.biomart.org, which is a data query system for large databases, for which we have added several extras in order to power our web-site www.pubmed2ensembl.org.

Additional features of BioMart Plus Extras are:

  • interactive full-text search queries via NCBI's Entrez Utilities
  • support of the DAS 'sources' request
  • annotation of database query results that show on 'mouseover'
  • 'list like' view that shows individual URL link-outs for comma separated data
  • highlighting of alternating rows, depending on the first column's value in a result set

Installation

BioMart Plus Extras extends biomart-perl, and as such, the CVS checkout as described under Section 2.2 in the Biomart 0.7 documentation has to be replaced by the git command:

git clone git@github.com:pubmed2ensembl/biomart-plus-extras.git

After cloning, the installation can be carried out as described in the BioMart 0.7 documentation. However, some hardcoded references exist in our version of BioMart that may need manual adjustments. The references in the source are tailored to work with the Ensembl Mart 56.

In particular, the following files will need manual changes:

  • conf/settings.conf
    • configuration settings depending on the local installation environment
  • conf/templates/default/header.tt
    • fixing of URL link-outs
  • bin/ConfBuilder.pm
    • correction of MAPMASTER link-out
    • adjustments in sub makeSOURCES
  • lib/BioMart/Registry.pm
    • adjustments in sub getDefaultCoordinate
  • and rather specific changes need to be made in the following files that depend on the data sources that have been integrated into the mart, but try to look for "Entrez" and "EMBL" to get an understanding of what needs to be changed
    • conf/template/default/menupanel.tt
    • cgi-bin/features.PLS
    • lib/BioMart/Configurator.pm

Supporting Software

For the pop-ups that occur on 'mouseover' events, we needed to include Walter Zorn's wz_tooltip library. The library is released under LGPL.

License

BioMart 0.7 is released under the LGPL, and we are continuing to adopt this license for BioMart Plus Extras 0.7.1 (see LICENSE).