The SIFR BioPortal 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.

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Start typing to select ontologies or leave blank to use all
Start typing to select UMLS semantic types or leave blank to use all
Start typing to select UMLS semantic groups or leave blank to use all
Score annotations following the previous 2009 NCBO measure (old) or the C-Value measure (cvalue). If hierarchy expansion is used, then prefer cvalueh.
Specify the minimum score value for annotations
Specify the minimum position in the scoring distribution (between 1 and 100)
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).
Enable Lemmatize to lemmatize the submitted text and use a lemmatized dictionary for the 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