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HIKM2010 - Query Resolution for Biology and Medicine
1. Customisable Query Resolution in
Biology and Medicine
Peter Ansell
Microsoft Queensland University of Technology
eResearch Centre
p.ansell@qut.edu.au
2. Outline
● What data is out there
● Current data formats
● RDF based system
● Biology and Medicine case study
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
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3. Current data formats
● FASTA
● EMBL
● GFF
● BSML
● Genbank
● Many other formats, including custom XML
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5. Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
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6. Linked Data
1) Use URIs as names for things
2) Use HTTP URIs so that people can look up
those names.
3) When someone looks up a URI, provide useful
information, using the standards (RDF, SPARQL)
4) Include links to other URIs. so that they can
discover more things.
http://www.w3.org/DesignIssues/LinkedData.html
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7. Bio2RDF distributed queries
● Assign namespaces to providers and create
URI's based on the namespace
● Just using RDF is not enough, the URI's have
to be transparent enough to be used and
referenced
● Query across relevant providers given a users
query and get results in a single RDF document
● Aggregate all results into a single RDF
document and return to the user
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8. Bio2RDF workflow
Resolved URI: http://bio2rdf.org/label/go:0000345
Host name: http://bio2rdf.org/ Query: label/go:0000345
Regular expression: label/([w-]+):(.+)
http://bio2rdf.org/query:labelsearch
http://bio2rdf.org/query:labelsearchforgo
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9. Demo background
● The background for this hypothetical
demonstration is a patient who has not been
responding well to a particular drug,
Isocarboxazid, as a treatment for their
depression
● The goal is to determine what information is
available to a doctor in changing the treatment
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10. Genomics demo
● http://bio2rdf.org/drugbank_drugs:DB01247
● Isocarboxazid
● http://bio2rdf.org/drugbank_targets:3939
● http://bio2rdf.org/hgnc:6834
● http://bio2rdf.org/geneid:4129
– MAOB
● http://bio2rdf.org/pubmed:10653595
– Localisation of MAOA and MAOB in pancreas, thyroid
and adrenal glands
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11. Drug effects demo
● http://bio2rdf.org/links/drugbank_drugs:DB01247
● http://bio2rdf.org/drugbank_druginteractions:DB00176_DB01247
– Possible adverse effects with Fluvoxamine
● http://bio2rdf.org/sider_drugs:3759
● http://bio2rdf.org/sider_sideeffects:C0027813
– Known possible side effect of Neuritis
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
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12. Alternative drugs demo
● http://bio2rdf.org/drugbank_targets:3939
● http://bio2rdf.org/pfam:PF01593
– Amino oxidase protein family
● http://bio2rdf.org/drugbank_targets:3041
– Similar protein, L-amino-acid oxidase
● http://bio2rdf.org/drugbank_drugs:DB03147
– Drug for similar protein, Flavin-Adenine
Dinucleotide
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13. Private and public data
● Private information could be provided using
current or future access models
● Public information can be linked to make it
explicit what the links are from the private
patient or clinical information to the wider set
of biological and chemical databases are
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14. Conclusion
● Many large distributed datasources
● Single interface, RDF
● Distribute queries efficiently across the
endpoints
● Allow for private data to remain private, but be
linked out to public information
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