From: SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes
Description | Example | % in EMEA (14 FP & 36 FN) | % in MEDLINE (15FP & 35 FN) | |
---|---|---|---|---|
FP | Annotation with a concept that was not covered in the gold standard | “évaluant la douleur”/Proc. (i.e., “pain evaluation”) matched but not in gold standard. | 10 | 10 |
Partial annotation on some but not all of the expected tokens | “sytème nerveux central” recognized instead of “signes du système nerveux central” (spelling) | 10 | 12 | |
Incorrect Semantic Group annotation | “rein” (kidney) annotated with DISO. instead of ANAT. Generates both an FP and an FN. | 8 | 8 | |
Concept missing from the French ontologies in the portal | Expected annotation: “canaux” (canals), but the SIFR Annotator dictionary only contains “canal, sai” (canal unspecified), which cannot match | 34 | 12 | |
FN | Morphosyntactic variation | Expected annotation “sériques” (an adjectivation of sérum) as ANAT, whereas the ontology label is “sérum” (the noun). | 18 | 26 |
Formulation different from concept labels (synonym, paraphrase) | Expected annotation “flacon” (vial), while the ontology concept label read “bouteille” (bottle). | 14 | 22 | |
Incorrect Semantic Group | “rein” (kidney) annotated with DISO instead of ANAT. Generates both an FP and an FN. | 6 | 10 | |
Unrecognized acronym or medical abbreviation | The gold standard expects “SNM” to be annotated with DISO, while the ontologies only contain “syndrome malin des neuroleptiques”. | 2 | 0 |