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Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
Linking Text Mining Efforts to
Semantic Web
Jin...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
Agenda
● PubAnnotation
● OntoFinder/OntoFactory...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
PubAnnotation
● Storage/Repository
● Platform/E...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
PubAnnotation
● Demo
✔ Is available at YouTube
...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
PubAnnotation
● Example of complex annotation
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
Interconnection and synergy
PubAnnotation Core
...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
GATA3-Driven Th2 Responses Inhibit TGF-1Induced...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
PubAnnotation
● Open Architecture (REST API)
Bi...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
PubAnnotation
● Aims at improving
✔ the product...
Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
Agenda
● PubAnnotation
● OntoFinder/OntoFactory...
OntoFinder/Factory/Cloud
● OntoFinder
✔ Ontology search (REST interface)
● OntoFactory
✔ Ontology term collection (User In...
Ontology production
based on BioPortal
BioPortalBioPortal
Ontology selectionOntology selection Term selectionTerm selectio...
OntoFactory
OntoCloud
Conclusion
● PubAnnotation
● OntoFinder/Factory/Cloud
● LODQA
Productivity
autonomous of content-holders
Welcome!
Pubannotation ontocloud-lodqa
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Pubannotation ontocloud-lodqa

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As an research & development activities toward linking text mining efforts to semantic web, PubAnnotation, an annotation storage&platform is introduced with a system demo. In the end, some other related systems, OntoFinder/Factory/Cloud and LODQA briefly are introduced.

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Transcript of "Pubannotation ontocloud-lodqa"

  1. 1. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS Linking Text Mining Efforts to Semantic Web Jin-Dong Kim DBCLS
  2. 2. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS Agenda ● PubAnnotation ● OntoFinder/OntoFactory/OntoCloud ● LODQA
  3. 3. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS PubAnnotation ● Storage/Repository ● Platform/Environment for Literature Annotation
  4. 4. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS PubAnnotation ● Demo ✔ Is available at YouTube ➔ http://www.youtube.com/watch?v=lXFCXKxuCgE
  5. 5. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS PubAnnotation ● Example of complex annotation
  6. 6. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS Interconnection and synergy PubAnnotation Core - annotation repository - search engine (SQL, SPARQL) - alignment of annotation Annotation Visualizers/Editors TextAE, ... Automatic Annotator Ontofinder, ... XMLizer BioC, ... RDFizer BioInterchange, ... ... (CSV, JSON, BioNLP-ST, …)
  7. 7. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS GATA3-Driven Th2 Responses Inhibit TGF-1Induced FOXP3 Expression and the Formation of Regulatory T Cells Transcription factors act in concert to induce lineage commitment towards Th1, Th2, or T regulatory (Treg) cells, and their counter-regulatory mechanisms were shown to be critical for polarization between Th1 and Th2 phenotypes. FOXP3 is an essential transcription factor for natural, thymus-derived (nTreg) and inducible Treg (iTreg) commitment; however, the mechanisms regulating its expression are as yet unknown. We describe a mechanism controlling iTreg polarization, which is overruled by the Th2 differentiation pathway. We demonstrated that interleukin 4 (IL-4) present at the time of T cell priming inhibits FOXP3. This inhibitory mechanism was also confirmed in Th2 cells and in T cells of transgenic mice overexpressing GATA-3 in T cells, which are shown to be deficient in transforming growth factor (TGF) β-mediated FOXP3 induction. This inhibition is mediated by direct binding of GATA3 to the FOXP3 promoter, which represses its transactivation process. ... PubAnnotation ● Powerful alignment of annotation This inhibitory mechanism was also confirmed in Th2 cells and in T cells of transgenic mice over-expressing GATA-3 in T cells, which are shown to be deficient in transforming growth factor (TGF)-beta-mediated FOXP3 induction. PubAnnotation Local Annotation Upload & align 107-113, Protein 208-213, Protein 838-833, Protein 936-941, Protein
  8. 8. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS PubAnnotation ● Open Architecture (REST API) BioInterchange OpenLinguistics NLP2RDF BioC Genia AlvisAE brat knowtator
  9. 9. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS PubAnnotation ● Aims at improving ✔ the productivity of annotation, and ✔ the share-ability of annotation ➔ Including semantic web and LOD community. ● With ✔ Open architecture, and ✔ Open source
  10. 10. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS Agenda ● PubAnnotation ● OntoFinder/OntoFactory/OntoCloud ● LODQA
  11. 11. OntoFinder/Factory/Cloud ● OntoFinder ✔ Ontology search (REST interface) ● OntoFactory ✔ Ontology term collection (User Interface) ● OntoCloud ✔ Visualization of ontologies
  12. 12. Ontology production based on BioPortal BioPortalBioPortal Ontology selectionOntology selection Term selectionTerm selection Ontology developmentOntology development Base ontologies seed ontology my ontology Ontology registrationOntology registration OntoFinder/OntoFactoryOntoFinder/OntoFactory
  13. 13. OntoFactory
  14. 14. OntoCloud
  15. 15. Conclusion ● PubAnnotation ● OntoFinder/Factory/Cloud ● LODQA Productivity autonomous of content-holders
  16. 16. Welcome!
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