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.

1. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
Linking Text Mining Efforts to
Semantic Web
Jin-Dong Kim
DBCLS

2. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
Agenda
● PubAnnotation
● OntoFinder/OntoFactory/OntoCloud
● LODQA

3. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
PubAnnotation
● Storage/Repository
● Platform/Environment
for Literature Annotation

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. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
PubAnnotation
● Example of complex annotation

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. 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. 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. 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. Licensed under a Creative Commons Attribution 3.0 Unported License - DBCLS
Agenda
● PubAnnotation
● OntoFinder/OntoFactory/OntoCloud
● LODQA

11. OntoFinder/Factory/Cloud
● OntoFinder
✔ Ontology search (REST interface)
● OntoFactory
✔ Ontology term collection (User Interface)
● OntoCloud
✔ Visualization of ontologies

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. OntoFactory

14. OntoCloud

16. Conclusion
● PubAnnotation
● OntoFinder/Factory/Cloud
● LODQA
Productivity
autonomous of content-holders

17. Welcome!