Annotator

The StagePortal Annotator processes text submitted by users, recognizes relevant ontology terms in the text and returns the annotations to the user. Use the interface below to submit sample text to get ontology-based annotations. Hover the mouse pointer on any button to see what it does.

Tchechmedjiev, A., Abdaoui, A., Emonet, V., Zevio, S., & Jonquet, C. (2018). SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes. BMC bioinformatics, 19(1), 405.

insert sample text

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Select ontologies Start typing to select ontologies or leave blank to use all

Select UMLS semantic types Start typing to select UMLS semantic types or leave blank to use all

Select UMLS semantic groups Start typing to select UMLS semantic groups or leave blank to use all

Include ancestors up to level

Include score Score annotations following the previous 2009 NCBO measure (old) or the C-Value measure (cvalue). If hierarchy expansion is used, then prefer cvalueh.

Filter by score threshold Specify the minimum score value for annotations

Filter confidence threshold Specify the minimum position in the scoring distribution (between 1 and 100)

FastContext Enable FastContext to detect : if a concept has been negated (affirmed, negated), who experienced the found concept (patient, other), when the annotated concept occurred (recent, historical, hypothetical), and/or if the annotated concept is uncertain (certain, uncertain).

Lemmatize Enable Lemmatize to lemmatize the submitted text and use a lemmatized dictionary for the annotations

Annotations

Class filter	Ontology filter	Type filter	UMLS Sem Type	Context	Matched Class filter	Matched Ontology filter	Score	Negation	Experiencer	Temporality	Certainty

Format results as

Reproduce these results using the

Additional parameters explained at Annotator API documentation