hikm2010 - query resolution for biology and medicine
TRANSCRIPT
Customisable Query Resolution in Biology and Medicine
Peter AnsellMicrosoft Queensland University of Technology
eResearch Centre
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
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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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Current data formats
● FASTA● EMBL● GFF● BSML● Genbank● Many other formats, including custom XML
Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
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Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
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Brisbane Health Informatics and Knowledge Management Workshop 21 Jan 2010
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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
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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
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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
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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
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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
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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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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
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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
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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