Transcript Annotator Service

Using NCBO Web services
Nigam Shah
[email protected]
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.
www.bioontology.org
ONTOLOGY SERVICES
Accessing, browsing, searching and traversing ontologies in Your
application
Documentation: www.bioontology.org/wiki/index.php/NCBO_REST_services
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Code
Specific UI
http://rest.bioontology.org/<SERVICE>
http://rest.bioontology.org/bioportal/ontologies
http://rest.bioontology.org/bioportal/search/melanoma/?ontologyids=1351
http://rest.bioontology.org/bioportal/virtual/ontology/1351/D008545
UNDER CONSTRUCTION:
http://rest.bioontology.org/obs/rootpath/MSH/C0025202
http://rest.bioontology.org/obs/rootpath/1351/D008545
ANNOTATOR SERVICE
Using Ontologies to Annotate Your Data
Annotator: The Basic Idea
Process textual metadata to automatically tag text
with as many ontology terms as possible.
Annotator: http://bioportal.bioontology.org/annotate
• Give your text as
input
• Select your
parameters
• Get your results…
in text or XML
An example
• “Melanoma is a malignant tumor of melanocytes which
are found predominantly in skin but also in the bowel and the
eye”.
• NCI/C0025201, 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:0000818, cell proliferation disease, grand parent
of Melanoma in Human Disease
• Mapping expansion
• FMA/C0025201, Melanocyte in Foundational Model of
Anatomy, concept mapped to NCI/C0025201 in UMLS.
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Code
http://rest.bioontology.org/obs/annotator
Specific UI
More at …
www.google.com/search?q=annotator+web+service
www.bioontology.org/wiki/index.php/Annotator_W
eb_service
• Documentation
• User Guide
• Sample clients in Java and Perl
DATA SERVICE
Using Ontologies to Access Public Data
Resources index: The Basic Idea
• The index can be used for:
• Search
• Data mining
Example
Code
http://rest.bioontology.org/resouce_index/<service>
Specific UI
More at …
www.google.com/search?q=ncbo+biomedical+resources+index
www.bioontology.org/wiki/index.php/NCBO_Biomedi
cal_Resources_Index
• Documentation
• User Guide
Cfl1
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 pHdependent manner. It is involved in the translocation of actincofilin complex from cytoplasm to nucleus. … The sequence
variation of human CFL1 gene is a genetic modifier for spina
bifida risk in California population
:
G-n
Some text …
http://rest.bioontology.org/obs/rootpath/MSH/C0037917
Cfl1
:
G-n
Cfl1
:
G-n
spina bifida
Some disease condition
spina bifida
Some disease condition
There is a lot more!
www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project
Credits
Mark Musen, PI
The team @
www.bioontology.org/project-team
NIH Roadmap grant U54 HG004028
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