BiodivPortal
Browse
Search
Mappings
Recommender
Annotator
Projects
Landscape
Login
Support
Submit Feedback
Documentation
Help
Release Notes
Publications
×
Loading
×
Annotator
Get annotations for biomedical text with classes from the ontologies
insert sample text
Show advanced options >>
Match longest only
Match partial words
Include mappings
Exclude numbers
Exclude synonyms
Select ontologies
Thysanoptera Ontology (THYSANOPTERA)
Bohlmann Ontology (BOHLMANN)
The lithologs rock names ontology for igneous rocks (LIT_I)
IHO World Seas (IHO)
Plant Trait Ontology (PTO)
Schema.org Vocabulary (SCHEMAORG)
The Extensible Observation Ontology (OBOE)
Chemical Entities of Biological Interest Ontology (CHEBI)
Quantities, Units, Dimensions, and Types Ontology (QUDT)
Biological Collections Ontology (BCO)
The Environment Ontology (ENVO)
I-ADOPT Framework ontology (I-ADOPT)
Phenotypic Quality Ontology (PATO)
Kingdom Ontology (KINGDOM)
The Geonames ontology (GEONAMES)
Oribatida Ontology (ORIBATIDA)
GFBio Agreed Vocabulary for RecordBasis (RECORDBASIS)
AMMOD Metabarcoding Ontology (BIOBANK)
Flora Phenotype Ontology (FLOPO)
Ecological Trait-data Standard (ETS)
AMMOD IOC World Bird List (IOC)
Integrated Taxonomic Information System (ITIS)
Semantic Web for Earth and Environment Technology Ontology (SWEET)
Animal Trait Ontology for Livestock (ATOL)
ISO3166 Countries and Subdivisions (ISOCOUNTRIES)
Trichoptera Ontology (TRICHOPTERA)
ABCD Base Ontology (ABCD)
German River Names (RIVERS_DE)
Plant Ontology (PO)
Start typing to select ontologies or leave blank to use all
Include ancestors up to level
none
1
2
3
4
5
6
7
8
9
10
all
Include score
none
old
cvalue
cvalueh
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
Get annotations
Annotations
Results are filtered by
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