Asymmetries in Retrieval of Gene Function Information

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Asymmetries in Retrieval of Gene Function
Information

• Timothy B. Patrick, PhD1,
• Lillian C. Folk, MS2,
• Catherine K. Craven, MLS3
• 1Healthcare Administration and Informatics,
  University of Wisconsin-Milwaukee
• 2College Of Veterinary Medicine, 3Health
  Management and Informatics,
• University of Missouri-Columbia

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Acknowledgements

• 2004 Donald A. B. Lindberg Research Fellowship
• University of Missouri National Library of
  Medicine Biomedical and Health Informatics
  Research Training grant

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Overview

• Background
• What is an asymmetry in retrieval of gene
  function information?
• Life science information retrieval and processing
  workflows
• Example of asymmetrical workflows
• Compare three apparently equivalent asymmetrical
  workflows
• Conclusion
• Documentation standards
• Multidisciplinary teams for life science workflows

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What is an Asymmetry in Retrieval?

• Taking different paths to get the same kind of
  information about a given biological object
• Life science information retrieval and processing
  workflows

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Complex Information Retrieval

• May involve the use of multiple information
  resources databases and analysis tools, in
  combination
• Such combinations of resources are often
  represented as workflows.

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Workflow Standards

• Business Process Execution Language for Web
  Services Version 1.1
• http//www-128.ibm.com/developerworks/library/spec
  ification/ws-bpel/
• Simple Conceptual Unified Flow Language (SCUFL)
• Taverna Workbench
• http//taverna.sourceforge.net/

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Logical Workflows

• A logical workflow is sort of like a logical
  process model, with processes, data links, and
  control links
• Key aspects of the workflow are inputs, outputs
  and processes that transform the data

Sequence ID
Sequence string
get DNA sequence
Similarity search
results
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Physical Workflows

• A physical workflow is like a physical process
  model, with processes, data links, and control
  links

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Physical Workflow
Antoon Goderis, Ulrike Sattler and Carole Goble,
Applying DLs to workflow reuse and repurposing
Description Logics workshop, Edinburgh, Scotland,
24-26 July 2005
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Asymmetry

• Asymmetry means the paths or workflows are
  different from the same set of potential inputs
  about some biological object they take different
  paths to produce the same kind of results.
• Asymmetrical workflows are equivalent if they do
  produce the same results.

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This Study

• Example of asymmetrical workflows that might look
  to a user to be equivalent but which are not
  equivalent due to various features of the
  resources involved.
• Knowledge that they are not equivalent requires
  knowledge of metadata about the resources.

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Three Workflows
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http//www.affymetrix.com/corporate/media/genechip
_essentials/gene_expression/Features_and_probes.af
fx
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http//www.mygrid.org.uk/images/pagemaster/GravesD
iseasescenario_1.png
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http//www.mygrid.org.uk/images/pagemaster/GravesD
iseasescenario_1.png
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Three Workflows
Affymetrix
Affymetrix
Affymetrix
Genbank Accession number
Genbank Accession number
Genbank Accession number
Nucleotide
Gene
Pubmed links
Pubmed links
Pubmed
Pubmed
Pubmed
Pubmed ID
Pubmed ID
Pubmed ID
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Methods

• We first collected representative DNA Accession
  numbers associated with genes expressed in a
  microarray experiment designed to identify
  changes in gene expression associated with
  skeletal muscle recovery from immobilization-induc
  ed sarcopenia. This experiment sought, using a
  mouse model, to identify differences in gene
  expression associated with successful recovery
  from sarcopenia in young muscle as compared to
  failed recovery in old muscle.
• NIH grant AG18881
• Pattison JS, Folk LC, Madsen RW, Childs TE, Booth
  FW. Transcriptional profiling identifies
  extensive downregulation of extracellular matrix
  gene expression in sarcopenic rat soleus muscle.
  Physiological Genomics 15(1)34-43, 2003.
• Pattison JS, Folk LC, Madsen RW, Booth FW.
  Selected Contribution Identification of
  differentially expressed genes between young and
  old rat soleus muscle during recovery from
  immobilization-induced atrophy. Journal of
  Applied Physiology 95(5)2171-9, 2003.
• Pattison JS, Folk LC, Madsen RW, Childs TE,
  Spangenburg EE, Booth FW. Expression profiling
  identifies dysregulation of myosin heavy chains
  IIb and IIx during limb immobilization in the
  soleus muscles of old rats. Journal of Physiology
  553(Pt 2)357-68, 2003.

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Methods

• Next, we retrieved the Unique Identifiers (UIs)
  of Entrez Pubmed citations that were associated
  with the Accession numbers by each of the three
  Entrez resources.
• Directly in the case of Entrez Pubmed
• Indirectly, via Pubmed links in the case of
  Entrez Nucleotide and Entrez Gene
• Next, we compared the number of Pubmed ID's
  retrieved by the three resources for each of the
  Accession numbers.

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Three Workflows
Affymetrix
Affymetrix
Affymetrix
Genbank Accession number
Genbank Accession number
Genbank Accession number
Nucleotide
Gene
Pubmed links
Pubmed links
Pubmed
Pubmed
Pubmed
Pubmed ID
Pubmed ID
Pubmed ID
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Three Workflows
Affymetrix
Affymetrix
Affymetrix
Genbank Accession number
Genbank Accession number
Genbank Accession number
Nucleotide
Gene
Pubmed links
Pubmed links
Pubmed
Pubmed
Pubmed
Pubmed ID
Pubmed ID
Pubmed ID
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Three Workflows
Affymetrix
Affymetrix
Affymetrix
Genbank Accession number
Genbank Accession number
Genbank Accession number
Nucleotide
Gene
Pubmed links
Pubmed links
Pubmed
Pubmed
Pubmed
Pubmed ID
Pubmed ID
Pubmed ID
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Three Workflows
Affymetrix
Affymetrix
Affymetrix
Genbank Accession number
Genbank Accession number
Genbank Accession number
Nucleotide
Gene
Pubmed links
Pubmed links
Pubmed
Pubmed
Pubmed
Pubmed ID
Pubmed ID
Pubmed ID
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Summary of Pubmed IDs by Accession Number
Pubmed
Nucleotide
Gene
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Methods

• Compared number of Pubmed IDs produced for each
  Accession number by each workflow.
• Applied non-parametric test Kendalls W
• Pubmed versus Nucleotide versus Gene
• p lt .05

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The Three Workflows Are Not Equivalent
?
?
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The SI field identifies secondary source
databanks and accession numbers of outside
resources discussed in MEDLINE articles. The
field is composed of the source followed by a
slash followed by an accession number and can be
searched with one or both components, e.g.,
genbank si, AF001892 si, genbank/AF001892
si. The SI field and the Entrez sequence
database links are not linked. The PubMed links
to these databases are created from the reference
field of the GenBank or GenPept flat file. These
references include citations that discuss the
specific sequence presented in these flat files.
http//www.ncbi.nlm.nih.gov/books/bv.fcgi?ridhelp
pubmed.box.pubmedhelp.Box_1_Search_Field_Dpubmedh
elp.Secondary_Source_ID_
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Conclusions
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Need for Documentation

• The first conclusion I take from this project is
  that there is a need for documentation of
  workflow details.
• In another study we look at the character of
  documentation of information processing and
  retrieval methods in published reports of
  microarray experiments

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Multidisciplinary Teams for Workflows

• The second conclusion I take is that the
  development of workflows requires
  multidisciplinary teams.

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domain expert (scientist)
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domain metadata expert (information specialist)
domain expert (scientist)
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KNOWLEDGE-ENABLED WORKFLOWS
METADATA
domain metadata expert (information specialist)
TOOLS
domain expert (scientist)
INFORMATION ITEMS
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