[Bio-software] An Open Content Directory for the Life Sciences and
jon.rees at oxfordinformatics.com
Fri Jun 2 04:56:09 EST 2006
An Open Content Directory for the Life Sciences and Medical Sciences
Jon Rees PhD, Oxford Informatics Ltd, the Open Content Company for Life
Sciences and Medical Sciences
49, Swinburne Road, Oxford
Tel: 44 (0) 79 70 89 33 71, E-mail: jon.rees at oxfordinformatics.com
BioDirectory is a new online resource for Life Scientists and Medical
Scientists which is a uniquely "open content" database of tools,
databases and resources of value to the scientific community both in
academia and industry.
The BioDirectory contains resource information aggregated from
Bioinformatics.Net and the life and medical sciences parts of Open
Directory, creating a definitive directory containing more than 7950
categories containing 34500 entries.
Whereas the Open Directory may contain around 16.5% bad links,
including perhaps about 11.4% dead links [1,2], the BioDirectory data
(both public feed and web site) excludes dead links each time the
directory is re-built fortnightly, improving the user's experience.
The automated curation of entries is facilitated by a web crawler,
BioZilla, which spiders through a subject-specific tunnel of life
science and medical sciences web sites, while a search engine has also
been created to allow users to full-text search across more than 86,000
web resources (fast growing), with more results and more relevant
results than are provided by the Open Directory search facility.
There is an ongoing effort to interlink life sciences informatics,
bioinformatics, cheminformatics and medical sciences informatics
categories to the relevant categories to integrate access to knowledge
about subjects, species, and clinical areas with the resources, tools
and databases which can be used to study them
Example: "Nematodes" and "Nematode zoonoses" - the BioDirectory section
on nematodes is linked both to a section on nematode genomics, as well
as a further medical section on nematode zoonoses.
A key goal for BioDirectory is to interlink information on subjects
written from biological, medical and technological perspectives, which
provides alternative routes into knowledge bases for scientists-in-
training, from undergraduates through to post-doctoral scientists.
There is also an on-going effort to create starting points for research
in several new technology areas, which will be announced through our
newsletter as they are launched.
BioDirectory features a search engine with better results than Open
Directory search, and an easier to navigate structure and accessible
design than BioWareDB 
An important feature is that BioDirectory is Open Content, so that both
scientists and the general public can contribute, learn, share and
OpenContent's only excuse for existing is to "facilitate the prolific
creation of freely available, high-quality, well-maintained Content."
This Content can then be used in an infinity of ways, restricted only
by the imagination of the user. One of the most significant uses may be
supporting instruction and helping people learn. Every section of
BioDirectory is available as an RSS feed.
I look forward to hearing your constructive feedback on this new
endeavour, including your suggestions as to how we can best turn this
in to an online community, and how to extend the availability of the
PS. Since opening the site to the public on May 7th 2006, more than
25,000 user visits have been recorded.
 Percentage of dead links was determined from a random sample of
1000 taken from the Life and Medical Sciences subsection of the Open
Directory as measured by our web crawler, using a 12 hour old RDF dump
 So much for the ODP then? An article by Phil Craven from
 Matthiessen MW. 2003. BioWareDB: the biomedical software and
database search engine. Bioinformatics. 2003 Nov 22;19(17):2319-20.
 Fox JA, Butland SL, McMillan S, Campbell G, Ouellette BF. 2005. The
Bioinformatics Links Directory: a compilation of molecular biology web
servers. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W3-24.
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