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bibliography of GO usage?

William Bug William.Bug at drexel.edu
Wed May 18 07:45:35 PDT 2005


Dear GO folks,

I was wondering whether their is a list somewhere of published articles 
containing significant scientific questions specifically answered via 
the use of GO?

I realize use of GO in genomics and gene expression studies has become 
so ubiquitous over the past 5 years it may seem a bit ludicrous to even 
try to compile such a list.

However, in the informatics work I - and many others - do lying outside 
the mainstream of genomics/transcriptomics, I find myself often having 
to evangelize on the topic of why it's so crucial to use 
ontologies/controlled vocabularies where ever practical.  Since I'm 
generally in the role of providing informatics infrastructure, when 
asked by an scientific investigator to justify the extra up-front work 
required to use ontologies when managing scientific data, my first 
inclination is to say:
	"If your data is not placed in this formal, systematized context, it 
will be very costly - maybe prohibitively so - to both integrate it 
with other, external related data sets and to provide a means to either 
search or statistically analyze the body of data as a whole without 
resulting in many false negatives - missing data records because they 
were not tagged with deterministic, semantically-relevant labels.  If 
the systems we build to house & manipulate your data are not 
onto-centric (or eschew use of formalized data standards, for that 
matter), it may also be prohibitively expensive to enable those systems 
as a whole to interoperate with related systems providing complementary 
data and services."

Those can be a rather opaque arguments and not particularly compelling 
to a biological scientist.  The true cost of that cautionary argument 
often is not recognized until later, when you try to build such 
search/browse/stats reduction systems.  By then, the cost of 
introducing onto-centric data management practices is much greater, 
than if you do it properly from the outset.

So - I started through the course of my reading to compile a 
bibliography of the sort of examples I describe in the first sentence 
above - compelling exemplars of GO's use to directly answer scientific 
questions.  For example, in this article from last October's 'Genes In 
Action' issue of 'Science' ("A Gene Expression Map for the Euchromatic 
Genome of Drosophila melanogaster", 'Science', v306, n5696, p655, 
2004.), they state on the 2nd pg, 1st col, 2 para:

"We noted that mRNA expression levels for protein-encoding genes varied 
with the protein function assigned in the Drosophila Gene Ontology. For 
example, genes encoding G protein receptors were expressed at 
relatively low levels, whereas genes encoding ribosomal proteins were 
highly expressed.  A gene^Òs expression level was also associated with 
cellular compartmentalization and the biological process it mediates."

I think that is a simple, cogent and compelling example of how critical 
use of GO can be to - in this case - genome-wide - expression analysis.

Then I thought, "wait a minute, the GO Consortium or one of the heavy 
users of GO has probably already pulled together such a bibliography.  
They would be considerably more qualified than I to decide which 
references should be on such a list anyway."

I'm pretty certain the NLM actually compiles such a list for UMLS (the 
Unified Medical Language System).  To use UMLS, you must acquire a 
license from NLM, which obligates you to report back to NLM on a yearly 
basis what research you have done using UMLS.

I went to the GO web site - a beautiful portal, extremely well 
organized, all the tools & resources you need to effectively implement 
a project using GO - all with a well-designed esthetic (pardon the 
editorializing).  There is a thorough, current bibliography of GO 
research - "Publications on GO by members of the GO Consortium" which 
I've used myself a lot, but this isn't really what I need.

That is why I'm posting this request here.

Has anyone compiled a bibliographic reference list on GO usage?  I 
realize again this may seem absurd given how wide-spread use of GO has 
become in bio-molecular informatics.  However, I know being able to 
point people to such a list would be of great value to the work I do.  
It would be even better if such a list were to reside in an 
onto-centric bibliographic database and could be served up dynamically 
via a web site, where an investigator could query for GO usage in their 
field of study.

Many thanks for bearing with me to the end of this message and thanks 
too for any assistance you can provide on this issue.

Cheers,
Bill Bug

Bill Bug
Senior Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA	19129
215 991 8430 (ph)

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