The NAR data base issue 2006
The 2006 edition of Nucleic Acids Research's annual data base issue appeared online today. Given modern search engines and a home page for every researcher, one would think that there would be little new servers to be found but from browsing the issue and performing some sample queries I was surprised to learn that many servers are not easily discovered by simple web searches. From experience, I would not attribute the finding to poor quality of the resources as only few external people link to it but rather the effect that we usually believe the search engines too quickly.
One example is the new resource for bacterial insertion sequences (ISfinder), which was hard to find when searching for databases of insertion sequences, even though it provides a comprehensive resource. (It would be even more useful if it would be up to date with the current state of completely sequenced genomes.)
Some of the readers of this blog who venture into chemical space might be interested in the articles describing DrugBank, SuperNatural or GLIDA. SuperNatural is a collection of natural products and their derivatives, aiming to provide easily accessible small molecules. DrugBank combines drug and drug target information for use with e.g. virtual screening. Similarly, the GPCR-ligand data base (GLIDA) explores small molecules and their protein targets within the G-protein coupled receptors, arguably the most important class of therapeutically accessible proteins.
Many resources described in the current issue are geared towards individual genomes or comparative analysis within a limited group. Browsing the list, I wonder why none of additional, genome-independent systems ever replaced the individual developments performed for every new genome or old resources that do not keep up with current trends. Does the plethora of systems for annotations show that the one-size fits all approach has not been developed or is it simply the desire for independence from outside resources? Many of the resources could be easily run by systems such as SRS at the EBI but it would be very difficult for the developers of the resources to be credited for their work.
Reading the web server issue gives a good overview over the state that bioinformatics is in: fragmented, with limited interoperability between individual resources but hosting a lot of interesting data and displaying the desire to create the required structures some time in the future.
One example is the new resource for bacterial insertion sequences (ISfinder), which was hard to find when searching for databases of insertion sequences, even though it provides a comprehensive resource. (It would be even more useful if it would be up to date with the current state of completely sequenced genomes.)
Some of the readers of this blog who venture into chemical space might be interested in the articles describing DrugBank, SuperNatural or GLIDA. SuperNatural is a collection of natural products and their derivatives, aiming to provide easily accessible small molecules. DrugBank combines drug and drug target information for use with e.g. virtual screening. Similarly, the GPCR-ligand data base (GLIDA) explores small molecules and their protein targets within the G-protein coupled receptors, arguably the most important class of therapeutically accessible proteins.
Many resources described in the current issue are geared towards individual genomes or comparative analysis within a limited group. Browsing the list, I wonder why none of additional, genome-independent systems ever replaced the individual developments performed for every new genome or old resources that do not keep up with current trends. Does the plethora of systems for annotations show that the one-size fits all approach has not been developed or is it simply the desire for independence from outside resources? Many of the resources could be easily run by systems such as SRS at the EBI but it would be very difficult for the developers of the resources to be credited for their work.
Reading the web server issue gives a good overview over the state that bioinformatics is in: fragmented, with limited interoperability between individual resources but hosting a lot of interesting data and displaying the desire to create the required structures some time in the future.
spitshine - 2005-12-29 13:49