NCBO Open-Biomedical Annotator Web Service

Welcome to the OBA v1.1 REST Service API

Contact: jonquet@stanford.edu

The service is currently deployed with the basis URL: http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/oba/

Documentation is available here: http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm

Test the Open Biomedical Annotator here:

longestOnly true false [default: false]
(i.e., do you want the concept recognizer to match the longest sentence only or not.)

wholeWordOnly true false [default: true]
(i.e., do you want the concept recognizer to match whole word only.)

stopWords [default: empty]
(i.e., list of stop words to use (i.e., not to use for annotation) separated with comma (without spaces) e.g., in,am,be,is.
withDefaultStopWords true false [default: false]
(i.e., do you want to use our default stop word list available here: /obs/stopwords . This cancel the above one.)

minTermSize [default: 0]
(i.e., the minimum size (or equal) a term must have to be included in the annotations.)

scored true false [default: true]
(i.e., do you want the annotations to be scored by relevance.)

withSynonyms true false [default: true]
(i.e., do you want to keep the annotations done with synonyms terms or not.)

localOntologyIDs [default: all]
(i.e., list of ontologies you want to use separated with comma (without spaces) e.g., SNOMEDCT,NCI,MSH.
You can find the list of localOntologyIDs available here: /obs/ontologies)

localSemanticTypeIDs [default: all]
(i.e., list of UMLS semantic types you want to use separated with comma (without spaces) e.g., T047,T048,T191.
You can find the list of localSemanticTypeIDs available here: /obs/semanticTypes)

levelMin [default: 0]
levelMax [default: 0]
(i.e., the level you want the isa-transitive-closure expansion component to be restricted to.)

activateMappings true false [default: false]
(i.e., do you want to use mappings is the semantic expansion.)
mappingTypes [default: all]
(i.e., list of mapping types you want to use for the mapping expansion component separated with comma (without spaces) e.g., inter-cui,from-mrrel.
You can find the list of mapping types available here: /obs/mappingTypes). Note if you use the keyword null in your list, it will disable the mapping expansion component.

text (i.e., the text you want to annotate.) [default: empty]
Be careful to remove end-of-lines caracters from your text.
format (i.e., the format of the results.) [default: asXml]
asText
asTabDelimited (annotations only)
asXML
asOWL

How to use the Open Biomedical Annotator:

To embed the OBA web service is your application, you just have to write a HttpClient which POST its values to the basis URL. The variables are previously denoted in bold with their possible values.