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File Date Author Commit
docs 2011-02-23 Paul Boddie Paul Boddie [c55024] Added some documentation, copyright and licensi...
submissions 2011-04-12 Paul Boddie Paul Boddie [fc994c] Updated the "Name" element as suggested by Ian.
templates 2012-01-09 Paul Boddie Paul Boddie [39438c] Updated the template for iRefIndex 9.0 and adde...
.hgtags 2012-01-09 Paul Boddie Paul Boddie [919aeb] Added tag snapshot-2012-01-09-iRefIndex-9-0 for...
README.txt 2012-01-09 Paul Boddie Paul Boddie [39438c] Updated the template for iRefIndex 9.0 and adde...
make_linkout.py 2011-02-23 Paul Boddie Paul Boddie [c55024] Added some documentation, copyright and licensi...

Read Me

The NCBI services offer a mechanism through which external providers can
submit links to their own services which then appear in certain records
retrieved from the NCBI services concerned. The script and templates supplied
here provide a means of generating the files which describe iRefWeb as a
provider (providerinfo.xml) along with the Entrez Gene records that should be
decorated with links to iRefWeb pages (resources.xml).

Generating the Files
--------------------

To generate the XML files which should then be transferred to NCBI, run the
following command...

  python make_linkout.py genes.txt resources.xml providerinfo.xml providerid

...substituting the appropriate filename for genes.txt in order to provide a
list of gene identifiers (one identifier per line in a text file) to the
program, and substituting an NCBI-assigned provider identifier for providerid.

For iRefWeb, the following command should be used:

  python make_linkout.py genes.txt resources.xml providerinfo.xml 7847

Generating a Gene Identifier List
---------------------------------

One way of building a list of gene identifiers is to process the MITAB files
generated by iRefIndex using the iRefIndex MITAB parser:

  http://irefindex.uio.no/wiki/iRefIndex_MITAB2.6_Parser

The export_all_genes.sql report will provide such a list which can then be
used directly with the above command. This report may require the
populate_interactor_genes.sql template to be applied to the database first.

Validating the Resources File
-----------------------------

Once a resources.xml file has been produced, it is possible to validate it
against the LinkOut DTD by using the following service:

  http://www.ncbi.nlm.nih.gov/projects/linkout/doc/validate.shtml

The type of the input file should be specified as "General" in the case of
iRefWeb.

Updating the Release Information
--------------------------------

The templates/providerinfo.xml file needs to be changed when a new release of
iRefIndex is made so that the release number corresponds to that of the new
release.

References
----------

"Information for Other Resource Providers"
http://www.ncbi.nlm.nih.gov/books/NBK3802/

"Technical Information"
http://www.ncbi.nlm.nih.gov/books/NBK3807/

Contact, Copyright and Licence Information
------------------------------------------

The current Web page for this software at the time of release is:

http://irefindex.uio.no/wiki/iRefWeb_LinkOut_Generator

The author can be contacted at the following e-mail address:

paul.boddie@biotek.uio.no

Copyright and licence information can be found in the docs directory - see
docs/COPYING.txt and docs/gpl-3.0.txt for more information.