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Summary of the activities developed by the text mining task force during the BioHackathon 2010http://hackathon3.dbcls.jp/wiki/TextMining
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Semantic Textmining
Goals and achievements
BioHackathon 2010
Team members
bull Hammad
bull Matthias
bull Venkata
bull Heiko
bull YAMAMOTO-san
bull Alberto
Original Proposal
bull Integration of text mining results
ndash Reflect Whatizit Medie
ndash Results as triplets
bull URI and predicates
ndash Implementation with SADI
ndash Result presentation using aTag
bull Explore relations
bull Interfaces
The work done
bull Integration of text mining resultsndash Reflect Whatizit Mediendash Results as triplets
bull URI and predicates
ndash Future BioPython module and REST service
bull Explore relationsndash Sesame endpointndash Biogatewayndash ARQ for federated queries
bull Interfacesndash Result presentation using aTagndash Exhibit faceted interface
httpwhatizitneurocommonsorg
httpwhatizitneurocommonsorg
RDF schema for TM
ltrdfDescriptiongt
ltrdftype rdfresource=httprdfsorgsiocnsItemgt
ltsiocabout rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltsioccontentgtSBMAltsioccontentgt
ltsioctopic rdfresource=httppurluniprotorguniprotP10275gt
ltrdfsseeAlso rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltrdfDescriptiongt
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
Team members
bull Hammad
bull Matthias
bull Venkata
bull Heiko
bull YAMAMOTO-san
bull Alberto
Original Proposal
bull Integration of text mining results
ndash Reflect Whatizit Medie
ndash Results as triplets
bull URI and predicates
ndash Implementation with SADI
ndash Result presentation using aTag
bull Explore relations
bull Interfaces
The work done
bull Integration of text mining resultsndash Reflect Whatizit Mediendash Results as triplets
bull URI and predicates
ndash Future BioPython module and REST service
bull Explore relationsndash Sesame endpointndash Biogatewayndash ARQ for federated queries
bull Interfacesndash Result presentation using aTagndash Exhibit faceted interface
httpwhatizitneurocommonsorg
httpwhatizitneurocommonsorg
RDF schema for TM
ltrdfDescriptiongt
ltrdftype rdfresource=httprdfsorgsiocnsItemgt
ltsiocabout rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltsioccontentgtSBMAltsioccontentgt
ltsioctopic rdfresource=httppurluniprotorguniprotP10275gt
ltrdfsseeAlso rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltrdfDescriptiongt
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
Original Proposal
bull Integration of text mining results
ndash Reflect Whatizit Medie
ndash Results as triplets
bull URI and predicates
ndash Implementation with SADI
ndash Result presentation using aTag
bull Explore relations
bull Interfaces
The work done
bull Integration of text mining resultsndash Reflect Whatizit Mediendash Results as triplets
bull URI and predicates
ndash Future BioPython module and REST service
bull Explore relationsndash Sesame endpointndash Biogatewayndash ARQ for federated queries
bull Interfacesndash Result presentation using aTagndash Exhibit faceted interface
httpwhatizitneurocommonsorg
httpwhatizitneurocommonsorg
RDF schema for TM
ltrdfDescriptiongt
ltrdftype rdfresource=httprdfsorgsiocnsItemgt
ltsiocabout rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltsioccontentgtSBMAltsioccontentgt
ltsioctopic rdfresource=httppurluniprotorguniprotP10275gt
ltrdfsseeAlso rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltrdfDescriptiongt
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
The work done
bull Integration of text mining resultsndash Reflect Whatizit Mediendash Results as triplets
bull URI and predicates
ndash Future BioPython module and REST service
bull Explore relationsndash Sesame endpointndash Biogatewayndash ARQ for federated queries
bull Interfacesndash Result presentation using aTagndash Exhibit faceted interface
httpwhatizitneurocommonsorg
httpwhatizitneurocommonsorg
RDF schema for TM
ltrdfDescriptiongt
ltrdftype rdfresource=httprdfsorgsiocnsItemgt
ltsiocabout rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltsioccontentgtSBMAltsioccontentgt
ltsioctopic rdfresource=httppurluniprotorguniprotP10275gt
ltrdfsseeAlso rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltrdfDescriptiongt
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
httpwhatizitneurocommonsorg
httpwhatizitneurocommonsorg
RDF schema for TM
ltrdfDescriptiongt
ltrdftype rdfresource=httprdfsorgsiocnsItemgt
ltsiocabout rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltsioccontentgtSBMAltsioccontentgt
ltsioctopic rdfresource=httppurluniprotorguniprotP10275gt
ltrdfsseeAlso rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltrdfDescriptiongt
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
httpwhatizitneurocommonsorg
RDF schema for TM
ltrdfDescriptiongt
ltrdftype rdfresource=httprdfsorgsiocnsItemgt
ltsiocabout rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltsioccontentgtSBMAltsioccontentgt
ltsioctopic rdfresource=httppurluniprotorguniprotP10275gt
ltrdfsseeAlso rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltrdfDescriptiongt
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
RDF schema for TM
ltrdfDescriptiongt
ltrdftype rdfresource=httprdfsorgsiocnsItemgt
ltsiocabout rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltsioccontentgtSBMAltsioccontentgt
ltsioctopic rdfresource=httppurluniprotorguniprotP10275gt
ltrdfsseeAlso rdfresource=httpwwwncbinlmnihgovpubmed9002550gt
ltrdfDescriptiongt
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
httpreflectws
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
MEDIE and Enju APIs
bull MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE based on indexing by Natural Language Processing and Text Mining techniques
bull Enju is a syntactic parser for English
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
Medie XML outputhttpwww-tsujiiissu-tokyoacjpmediedbclscgipmid=19116711
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
Enju XML outputhttpdocmandbclsjpmedieconvpmid=17551671
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
httptogowsdbclsjpentrypubmedpmidttl
httpwwwuniprotorguniprotP12345rdf
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
Workflow
Whatizit Reflect Medie
TogoWS
Uniprot
XML XMLXML
RDF
RDF
RDF
Pubmed
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
Substance A
Interacts with
Receptor B
Region C
axonal projections
brain region D
Region D
aversive stimuli
Interlink these entities with
taxonomies amp ontologies
TMOntology
httphackathon3dbclsjpwikiTextMining
TMOntology
httphackathon3dbclsjpwikiTextMining
httphackathon3dbclsjpwikiTextMining
