1. Using NCBO Web services
Nigam Shah

2. NCBO: Key activities
We create and maintain a library of biomedical ontologies.
We build tools and Web services to enable the use of ontologies [for several tasks].
We collaborate with scientific communities that develop and use ontologies.

4. Ontology services
Accessing, browsing, searching and traversing ontologies in Your application

5. Documentation: www.bioontology.org/wiki/index.php/NCBO_REST_services

6. Code
Specific UI

8. http://rest. bioontology. org/bioportal/search/melanoma/

10. UNDER CONSTRUCTION: http://rest. bioontology

11. Annotator Service
Using Ontologies to Annotate Your Data

12. Annotator: The Basic Idea
Process textual metadata to automatically tag text with as many ontology terms as possible.
We want to process the text and assign “tags” to each element in public repositories.

13. Annotator: http://bioportal.bioontology.org/annotate
Give your text as input
Select your parameters
Get your results… in text or XML

14. An example
“Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye”.
NCI/C , Melanocyte in NCI Thesaurus
39228/DOID:1909, Melanoma in Human Disease
Is_a closure expansion
39228/DOID:191, Melanocytic neoplasm, direct parent of Melanoma in Human Disease
39228/DOID: , cell proliferation disease, grand parent of Melanoma in Human Disease
Mapping expansion
FMA/C , Melanocyte in Foundational Model of Anatomy, concept mapped to NCI/C in UMLS.

15. Code
Specific UI

16. More at … www.bioontology.org/wiki/index.php/Annotator_Web_service
Documentation
User Guide
Sample clients in Java and Perl

17. Data Service Using Ontologies to Access Public Data
The screen shots I was showing you are the UI for a project called OBR at the NCBO. The Goal of the OBR project is to enable the use of ontologies to access public data at multiple levels of abstraction.

18. Resources index: The Basic Idea
Search:
GEO has > 13 datasets on retroperitoneal tumors, none show up without an ontology based search!
- Did you know that GEO contains more public datasets on drug – gene expression information that Connectivity map?
Data mining:
- Extraction of Conditional Probabilities of the Relationships between Drugs, Diseases, and Genes from PubMed guided by relationships in PharmGKB in AMIA spring translational bioinformatics 2009.
The index can be used for:
Search
Data mining

19. Example
Indexing an element from GEO. The GEO element GDS1989 is annotated according to its title and its description, as well as by the ontology elements that comprise the transitive closure over the parent–child relationships subsumed by the direct annotations.

20. Code
Specific UI

21. More at …
Documentation
User Guide

22. Cfl1 : G-n Cfl1 : G-n Cfl1 : G-n
Cofilin is a widely distributed intracellular actin-modulating protein that binds and depolymerizes filamentous F-actin and inhibits the polymerization of monomeric G-actin in a pH-dependent manner. It is involved in the translocation of actin-cofilin complex from cytoplasm to nucleus. … The sequence variation of human CFL1 gene is a genetic modifier for spina bifida risk in California population
Cfl1 :
G-n
Some text …
Cfl1
spina bifida :
G-n
Some disease condition
Cfl1
spina bifida :
G-n
Some disease condition

23. There is a lot more!

24. Credits NIH Roadmap grant U54 HG004028 Mark Musen, PI
The
NIH Roadmap grant U54 HG004028