What inputs

1
Provenance of e-Science Experiments experience
from bioinformatics
The myGrid project aims to provide middleware
layers that make the Information Grid appropriate
for the needs of bioinformatics. Provenance
management is one of the services provided to
support scientific method and best practice found
at the bench but often neglected at the
workstation. Provenance metadata records the
materials, methods and results of in silico
experiments as well as scientists' notes about
experiments. This information is essential if
experiments are to be validated and verified by
others. It is also important in assessing the
quality and timeliness of results. The large
amount of provenance data required to verify
others' experiments means that as much as
possible must be automatically and systematically
collected. Sets of provenance data provide a
store of know-how that can be mined to provide
users with views of their virtual organisation,
including suggestions based on past experience.
Bioinformatics analyses typically involve
visiting many data resources and analytical
tools. These in silico experiments can be created
as pipelines or workflows in the Taverna
editor.
Claire Jennings
Gene ID 504_at
who
2003/08/15 2025
What (inputs)
Provenance metadata includes standard
annotations, e.g. who performed the in silico
experiment and when. Scientists can also provide
additional context information such as
hypotheses, conclusions and related literature
when
what
The provenance record of a workflow run is a
convenient way of automatically and
systematically recording the derivation path by
which results are generated from input data.
The workflow, services and input data in a
workflow provenance record are all items which
have their own provenance
how
why
Services
What (outputs)
The use of semantically rich provenance metadata
expressed using ontologies enables the creation
of a web of scientific holdings where items are
linked by related concepts
Acknowledgements This work is supported by the UK
e-Science programme EPSRC GR/R67743, DARPA DAML
subcontract PY-1149, Stanford University. The
Graves Disease case study is from Simon Pearce
and Claire Jennings, Institute of Human Genetics,
School of Clinical Medical Sciences, University
of Newcastle.
The myGrid team Matthew Addis, Nedim Alpdemir,
Rich Cawley, Vijay Dialani, Alvaro Fernandes,
Justin Ferris, Rob Gaizauskas, Kevin Glover,
Carole Goble (director), Chris Greenhalgh, Mark
Greenwood, Ananth Krishna, Phil Lord, Xiaojian
Liu, Darren Marvin, Karon Mee, Simon Miles, Luc
Moreau, Tom Oinn, Juri Papay, Norman Paton, Steve
Pettifer, Milena Radenkovic, Peter Rice, Angus
Roberts, Alan Robinson, Martin Senger, Nick
Sharman, Robert Stevens, Paul Watson, Anil Wipat
Chris Wroe.