Datasets
With gold named entities | Without gold named entities |
BB-normEntity normalization | BB-norm+nerEntity recognition and normalization |
BB-relRelation extraction | BB-rel+nerEntity recognition and relation extraction |
BB-kbKnowledge graph extraction | BB-kb+nerEntity recognition and knowledge graph extraction |
Normalization resources
NCBI Taxonomy
The Microorganism entities were assigned taxon identifiers from the NCBI Taxonomy as available the 2 February 2019. We provide the downloadable archive as it was provided by the NCBI at that date, and a list of valid identifiers for Microorganism entities.
Note that the NCBI does not provide old versions of the taxonomy. The version currently available version may contain additional identifiers that are not valid in the BB corpus.
OntoBiotope ontology
The Habitat and Phenotype entities were assigned concept identifiers from the OntoBiotope ontology. We provide the version which has been to annotate the BB corpus.
Evaluation software
Get the evaluation software from our GitHub repository.
Annotation guidelines
The annotation guidelines for the BB 2019 corpus can be found here.