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GK version 8 release

Ewan Birney birney at
Thu Mar 11 11:13:06 PST 2004

Dear Go(ers)

I'd like to update you on GK (Genome Knowledgebase... which is the
database in search of a better name: something like
ChordatePathwayAtEventLevelDetailBase ... a little too long perhaps)
which is a highly detailed event-orientated database that uses GO
dictionaries but annotates pathways to event-level detail.

We've released version 8 at

With stats of:

                        Core    Expanded

Accessioned Entities    762     1961
Concrete Complexes      446     1345
Generic Complexes       232     569
Concrete Reactions      749     2735
Concrete Pathways       61      277
Generic Reactions       451     1520
Generic Pathways        251     839
Literature References   794     794

Core means authored events by biological experts, predominantly in human.
Expanded is the result of use the Core information to expand to mouse,
rat, zebra fish and fugu using ortholog mappings from Ensembl to deduce
putative orthologous events in other organisms. The key number to track is
core Accessioned Entities which is now "chr 20" sized (previous release it
was chr 22 sized) in terms of overall number of genes. I think we'll be
skipping over chr19 but steadily increasing this year.

GK now also links to both LocusLink and Ensembl from our protein pages,
improving navigation.

We have other pathways in production waiting to be released and some great
visualisation tools in development (watch this space!). GK is completely
open (data and code), uses GO as its source of biological definitions and
is suitable for use in any model organism system, so we would encourage
any collaborators to contact us: human/mammalian focused biologists to
contribute pathways (just contact gkb-dev email cc'd in this email)  or
model organism databases to use GK as a framework for your pathway data or
computational groups wanting a set of "known true" pathway descriptions at
this level of detail.


Ewan Birney

on behalf of the GK development team

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