Dear Team,
I am currently working towards my PhD looking at a large-scale
systematic analysis of genotype-phenotype correlations and have been
using Taverna as the means of implementing this using workflows.
Over the past year I have managed to implement a novel means of
identifying candidate genes involved in the expression of a phenotype
and have obtained some significant biological results, which are being
put forward for being published at the moment in biology and
bioinformatics journals. These workflows utilised the BioMart Ensembl
processor available in Taverna.
However, since BioMart dramatically changed the schema, the
implementation of BioMart in Taverna can no longer run, which in turn
means that these workflows are not currently runnable. As you can
appreciate, this has had a disastrous knock-on effects for both my own
and for the Wellcome Trust Pathogen-Host project who wished to use my
workflows for processing their data. It has also meant that I am not
able to submit my papers to the proposed journals until I can verify
that the workflows are functional again and provide the same means of
data analysis. Being on the Taverna users list I have also noticed a
number of other researchers have had workflows fail because of BioMart.
The Taverna BioMart developer (David Cc'd) has provided me with a
runnable version of BioMart 0.5, however, a number of attributes have
now disappeared that are vital to my methodology, including Cow-Human
Ensembl gene homologues. These issues are on the BioMart end and not
Taverna.
I am very grateful for the web service the BioMart team has provided and
the continual co-operation the BioMart developers have had with the
myGrid team, and hope to continue to use it for the remainder of my PhD.
However, as this is a large user group I think it would really benefit
both the myGrid developers and in turn the end users if some means of
email notification were provided on the Taverna mailing lists, and
likewise to subsequent high usage mailing lists to notify people of any
dramatic changes which may affect future research.
sincerely,
Paul Fisher.
- [mart-dev] BioMart and Taverna Paul Fisher
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