[Bio-software] An Open Content Directory for the Life Sciences and Medical Sciences

Jon Rees 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 [3]

An important feature is that BioDirectory is Open Content, so that both 
scientists and the general public can contribute, learn, share and 
research freely.

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.[5]

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 


Best wishes,

Jon Rees

PS. Since opening the site to the public on May 7th 2006, more than 
25,000 user visits have been recorded.


[1] 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 
from http://rdf.dmoz.org 
[2] So much for the ODP then? An article by Phil Craven from 
[3] Matthiessen MW. 2003. BioWareDB: the biomedical software and 
database search engine. Bioinformatics. 2003 Nov 22;19(17):2319-20.
[4] 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.
[5] OpenContent.org

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