Cshals Tech Talk
21
SciVerse Platform Embraces Semantic Applications Vishal Gupta [email protected] @Visha1Gupta Ari Tuchman [email protected]
-
Upload
visha1gupta -
Category
Documents
-
view
655 -
download
1
description
Talk given at the CSHALS 2011 conference at Boston
Transcript of Cshals Tech Talk
Researchers are looking for tools to help them find, integrate, and re‐use content
“Scientific innovation depends onusing the
Scientific innovation depends on finding, integrating, and re‐using the products of previous research... Our semantic enhancements led to the creation of a whole “ecosystem” of articles, documents, spreadsheets, data fusions related to that original work...frictionless interoperability between papers and datasets is highly desirable.”
D. et al, Adventures in Semantic Publishing: Shotton D. et al, Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Comput Biol 5(4)
Elsevier’s SciVerse platform delivers the right information and tools, at the right time, g
ScienceDirectScienceDirect ScopusScopusAPPAPP
APP pp
APPAPP
APP
10 MILLION FULL TEXT ARTICLES
15 THOUSANDE‐BOOKS
41 MILLIONABSTRACTS
Web/Third Party ContentWeb/Third Party Content SciTopicsSciTopics
300 MILLION 13 SOURCES
APPAPP
APP
APP PAGESWRITTEN BY SCIENTIFIC
EXPERTS ONLY18 INSTITUTIONSINTL REPOSITORY
23 MILLIONPATENT FILES
WEB PAGES SOCIETY
SHARE YOUR KNOWLEDGE AND LEARN FROM
OTHERSAPPAPP APP
EXPERTS ONLYINTL. REPOSITORY PATENT FILES OTHERS
The Developer Network beta provides developers access to resources and community
Developers can access content APIs and download SDKs to get started…
…with a variety of options, depending on the use case
Some of our APIs beyond the framework
SciVerse Applications beta to provide access to applications developed by the scientific community
SciVerse Applications gallery will make available a constantly expanding universe of applications
NCBO, Stanford semantic search app
Trusted academic and corporate partners are already beginning to drive innovation
Understanding by visualizing big picture context –
trends, clusters, correlations
.... and providing tools to rapidly drill down on high‐value details.
Search for Warfarin (Coumadin)
• Identify salient data types for analyzing query topic {Phrase, gram/sec, Molar…}• Aggregate data values of learned type.U t d i l t d h
• Identify salient data types for analyzing query topic {Phrase, gram/sec, Molar…}• Aggregate data values of learned type.U t d i l t d h• Uncover trends in related phrases.• Uncover trends in related phrases.
Examine Landscape of Dosages
• Visualize landscape of numeric data.• Intuitive displays of clusters, standard values, and ranges. •Recognize whitespace and zoom in to desired parameter space
• Visualize landscape of numeric data.• Intuitive displays of clusters, standard values, and ranges. •Recognize whitespace and zoom in to desired parameter space•Recognize whitespace and zoom in to desired parameter space.•Recognize whitespace and zoom in to desired parameter space.
Focus on High‐Impact Patient Studies
• Filter clinical studies by patient number.• Identify clusters and correlations between axes• Filter clinical studies by patient number.• Identify clusters and correlations between axes• Identify clusters and correlations between axes.• Identify clusters and correlations between axes.
Correlate Warfarin Dosages with Individual Genes
• Extract linkages between specific genes and optimum dosages.• Extract linkages between specific genes and optimum dosages.
Timeline of Genes Associated with Warfarin
Genes listed in orderof most recent appearancein corpus.
• Chart all genes in the literature that are investigated in the context of Warfarin S t b fi t/l t d t i th
• Chart all genes in the literature that are investigated in the context of Warfarin S t b fi t/l t d t i th
DATE
• Sort by fist/last appearance date in the corpus.• Analyze genes by degree of correlation (“friend‐of‐friend” genes).• Sort by fist/last appearance date in the corpus.• Analyze genes by degree of correlation (“friend‐of‐friend” genes).
In Summaryy
• Discover:
Quantifind App on SciVerse Applications Marketplace
D l• Develop:
Start Building an App for your institution on the Developer Network | Elsevier|
• Share:
Vishal [email protected]
@Visha1Gupta
Forces that shape research
Government Policies
l b lLEANTechnology Global
Competition
LEANRESEARCH
Trend exacerbated by economic downturnWorkflow Inefficiencies
Web of linked data and knowledge outside the formal literature is growing exponentiallyg g p y
BBC PaycountData
BBC PaycountData
FlickrFlickr
LIBRISLIBRISRDF ohlohRDF ohloh
BBC MusicBBC Music
MySpace WrapperMySpace Wrapper
Audio‐ScrobblerAudio‐
Scrobbler
Music‐brainzMusic‐brainz
FOAF profilesFOAF profiles
cexporter
cexporter
ACMACM
DBLP RKB DBLP RKB
RAE 2001RAE 2001
National Science
Foundation
National Science
Foundation
RDF Book MashupRDF Book Mashup
rieseriese
BBCProgrammes
BBCProgrammes
Geo‐namesGeo‐names
ProjectGuten‐berg
ProjectGuten‐berg
Open CalaisOpen Calais
ExplorerExplorereprintseprints
Virtuoso SpongerVirtuoso Sponger CORDISCORDIS
DBpediaDBpedia
Linked GeoDataLinked GeoData
US Census Data
US Census Data
W3CWorldNet
W3CWorldNet
LinkedCTLinkedCT
DBLP BerlinDBLP Berlin UniParcUniParc
FreebaseFreebase
ReactomeReactome
DBLP HanoverDBLP
Hanover
TaxonomyTaxonomyPROSITEPROSITE
CiteSEERCiteSEER
UniRefUniRef
Homolo Gene
Homolo Gene
GeneIDGeneID
ChEBIChEBIGene
OntologyGene
Ontology
KEGGKEGG
OMIMOMIM
UniProtUniProt
PROSITEPROSITE
PfamPfam ProDomProDomCASCAS
Source: Richard Cyganiak and Anja Jentzsch – linkeddata.org (as of July 2009)
UniSTSUniSTSHGNCHGNC MGIMGI
PubMed
PubMed
PDBPDB
Linked data is also clouded by spam
BBC PaycountData
BBC PaycountData
FlickrFlickr
LIBRISLIBRISRDF ohlohRDF ohlohSPAMSPAM
SPAMSPAM
BBC MusicBBC Music
MySpace WrapperMySpace Wrapper
Audio‐ScrobblerAudio‐
Scrobbler
Music‐brainzMusic‐brainz
FOAF profilesFOAF profiles
cexporter
cexporter
ACMACM
DBLP RKB DBLP RKB
RAE 2001RAE 2001
National Science
Foundation
National Science
Foundation
SPAMSPAMSPAMSPAM
SPAMSPAMSPAMSPAM
SPAMSPAM
“Approximately 90% of the 10 billion pages that will be added to the web over the next year to be spam The massive flooding of the web with
RDF Book MashupRDF Book Mashup
rieseriese
BBCProgrammes
BBCProgrammes
Geo‐namesGeo‐names
ProjectGuten‐berg
ProjectGuten‐berg
Open CalaisOpen Calais
ExplorerExplorereprintseprints
Virtuoso SpongerVirtuoso Sponger CORDISCORDIS
SPAMSPAM
SPAMSPAMSPAMSPAM
SPAMSPAM
SPAMSPAM
spam… The massive flooding of the web with endless copies and permutations and shadows of existing things is what is pulling the rug out from under link‐based search rankings... Links don't
DBpediaDBpedia
Linked GeoDataLinked GeoData
US Census Data
US Census Data
W3CWorldNet
W3CWorldNet
LinkedCTLinkedCT
DBLP BerlinDBLP Berlin UniParcUniParc
FreebaseFreebase
ReactomeReactome
DBLP HanoverDBLP
Hanover
TaxonomyTaxonomyPROSITEPROSITE
CiteSEERCiteSEER
UniRefUniRef
SPAMSPAM
SPAMSPAMSPAMSPAM
SPAMSPAMSPAMSPAM
grepresent a human voting on the quality of a site anymore.”
Ri h Sk t CEO f Bl kk
Homolo Gene
Homolo Gene
GeneIDGeneID
ChEBIChEBIGene
OntologyGene
Ontology
KEGGKEGG
OMIMOMIM
UniProtUniProt
PROSITEPROSITE
PfamPfam ProDomProDomCASCASSPAMSPAM
SPAMSPAM
SPAMSPAMSPAMSPAM
Rich Skrenta, CEO of BlekkoThe "Useless Garbage" Of The Web, Jan 10, 2011
UniSTSUniSTSHGNCHGNC MGIMGI
PubMed
PubMed
PDBPDBSPAMSPAM
