5-pln-1520-conlon
DESCRIPTION
TRANSCRIPT
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VIVO: Data, Tools and
Community for Research Discovery
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Learned a field, learned the scientific method, did
science
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Science and Scientists
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But then …
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PubMed adds
700,000 articles
each year
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The Problems Got Hard
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Data Got Big (IDR Slide)
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Lots of Competitors
2010 Shanghai ranking of
world universiti
es http://en.wikipedia.org/wiki/Academic_Ranking_of_World_Universities
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How do we respond?
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The FANTOM Consortium & Riken Omics Science Center, The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line Nature Genetics 41, 553 - 562 (2009)
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Clinical Trial
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Collaboration
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Implementation Research
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Mentoring
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How can we know what is going on,
build teams, solve problems?
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Research Discovery
ResearchDiscovery
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… And the connections between them
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How can we create a world platform for research
discovery?
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Data
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Tools
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Community
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VIVO: Data, Tools and Community
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VIVO is open standards and open linked data regarding science – people, papers/products,
funding, events/presentations, resources, projects/studies, data, concepts – and the
relationships between them
VIVO is open source, community maintained software tools for research discovery and
networking
VIVO is a world community of collaborators – scientists, implementers, developers
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Ontology Process
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Harvesting Data
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Simple tools for presentation, traversal,
search
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Tools using linked open data
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ScienceMap. Examine collections of publications for individuals, work groups, institutions
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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 both HTML and RDF
Software reads VIVO RDF and displays
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Augmenting data
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VIVO Searchlight
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This figure at right displays “collaborative publications” found at 2 or more Researcher Networking websites. The idea that institutions don't work together and that biomedical research is conducted in silos is not true. Researchers, even when separated by great distances, are in fact willing to work together, and this visualization demonstrates that they often do.
Contact: Nick Benik ([email protected]), Harvard Medical School, Boston, MA. URL: http://xcite.hackerceo.org/VIVOviz
Inter-institutional Collaboration Explorer
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CTSAs
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USDAUSDA
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APA
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China
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How can you get involved?
Join us at http://vivoweb.org
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Photo Credits2. Jackson Laboratory scientist wins Shaw Prize, "Nobel of the East“ (1960) http://www.jax.org/news/images/pressimages/300dpi_images/coleman/coleman1960.jpg3. Biochemistry at Stanford. From the Stanford Biochemistry web site. 5. Francis Collins. From the NIH web site.7. Courtesy of UF Health Science Center News and Communications14. http://apod.nasa.gov/apod/ap080225.html17. Institut Pasteur Korea Conducts Special 'IPK Life Science Mentoring' Program . http://ip-korea.org 20. Courtesy of Weill Cornell Medical College21. Figure by M. Conlon24. Bruckner Building Supply web site. http://brucknernyc.com/our-products/in-the-yard/25. First annual VIVO Conference. https://
picasaweb.google.com/110849244647388519713/FirstAnnualVIVONationalConference2010?authkey=Gv1sRgCP6K8LDBpOrKLg#551275718424189315438. Abraham Lincoln Building of the Unites States Agricultural Library. http://en.wikipedia.org/wiki/File:United_States_National_Agricultural_Library.jpg40. VIVO map by M. Conlon41. Second annual VIVO conference. Photographs by M. Conlon42. The VIVO team outside the Gaylord during the great DC quake of 2011. 8/22/2011. Photograph courtesy of Michelle Issing.