VIVO: Sharing Data for Research Discovery Mike Conlon University of Florida [email protected].
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Transcript of VIVO: Sharing Data for Research Discovery Mike Conlon University of Florida [email protected].
![Page 1: VIVO: Sharing Data for Research Discovery Mike Conlon University of Florida mconlon@ufl.edu.](https://reader036.fdocuments.in/reader036/viewer/2022062518/56649e8b5503460f94b907f7/html5/thumbnails/1.jpg)
VIVO: Sharing Data for Research
Discovery
Mike ConlonUniversity of Florida
![Page 2: VIVO: Sharing Data for Research Discovery Mike Conlon University of Florida mconlon@ufl.edu.](https://reader036.fdocuments.in/reader036/viewer/2022062518/56649e8b5503460f94b907f7/html5/thumbnails/2.jpg)
Public, structured linked data about investigators interests, activities and accomplishments, and toolsto use thatdata to advancescience
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![Page 4: VIVO: Sharing Data for Research Discovery Mike Conlon University of Florida mconlon@ufl.edu.](https://reader036.fdocuments.in/reader036/viewer/2022062518/56649e8b5503460f94b907f7/html5/thumbnails/4.jpg)
VIVO Searchlight
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![Page 6: VIVO: Sharing Data for Research Discovery Mike Conlon University of Florida mconlon@ufl.edu.](https://reader036.fdocuments.in/reader036/viewer/2022062518/56649e8b5503460f94b907f7/html5/thumbnails/6.jpg)
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Data Production
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Producing Data
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processOrg<-function(uri){ x<-xmlParse(uri) u<-NULL name<-xmlValue(getNodeSet(x,"//rdfs:label")[[1]]) subs<-getNodeSet(x,"//j.1:hasSubOrganization") if(length(subs)==0) list(name=name,subs=NULL) else { for(i in 1:length(subs)){ sub.uri<-getURI(xmlAttrs(subs[[i]])["resource"]) u<-c(u,processOrg(sub.uri)) } list(name=name,subs=u) }}
VIVO produces human and machine
readable formats
Software reads RDF from VIVO
and displays
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Data Sharing
Photograph by J. G. Park. Flicker.com Photograph by Ell Brown Flicker.com
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Information is stored using the Resource Description
Framework (RDF) as subject-predicate-object “triples”
Jane Smith
professor in
author ofhas affiliation with
Dept. of Genetic
s College of
Medicine
Journal article
Book chapte
r
Book
Genetics Institute
Subject Predicate Object
A Web of Data – The Semantic Web
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The Role of the Archive• Collate data, final semantics, ready for
consumption
Data Archive
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Institutions record activities, interests, accomplishments
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Data, Tools and Scientists
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Data Consumption
Photograph by ScoopMedia. Flicker.com
Photograph by Janet Tarbox. Flicker.com
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A Consumption ScenarioFind all faculty members whose genetic work
is implicated in breast cancer
VIVO will store information about faculty and associate to genes. Diseaseome associates genes to diseases.
Query resolves across VIVO and data sources it links to.
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Data ReasoningData integration continues to be a serious bottleneck for the expectations of increased productivity in the pharmaceutical and biotechnology domain.
“Linked Life Data” integrates common public datasets that describe the relationships between gene, protein, interaction, pathway, target, drug, disease and patient and currently consist of more than 5 billion RDF statements.
The dataset interconnects more than 20 complete data sources and helps to understand the “bigger picture” of a research problem by linking previously unrelated data from heterogeneous knowledge.
From the LarKC (Large Knowledge Collider) http://www.larkc.eu/overview/
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http://vivo.ufl.edu/individual/mconlon