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
2

3. Current data formats
● FASTA
● EMBL
● GFF
● BSML
● Genbank
● Many other formats, including custom XML
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
3

4. Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
4

5. Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
5

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
6

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
7

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
8

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
9

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
10

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
11

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
12

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
13

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
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
14