flair.datasets.biomedical#

`ANAT_EM`	Corpus for anatomical named entity mention recognition.
`AZDZ`	Arizona Disease Corpus from the Biomedical Informatics Lab at Arizona State University.
`BC2GM`	Original BioCreative-II-GM corpus containing gene annotations.
`BIGBIO_NER_CORPUS`	This class implements an adapter to data sets implemented in the BigBio framework.
`BIOBERT_CHEMICAL_BC4CHEMD`	BC4CHEMD corpus with chemical annotations as used in the evaluation of BioBERT.
`BIOBERT_CHEMICAL_BC5CDR`	BC5CDR corpus with chemical annotations as used in the evaluation of BioBERT.
`BIOBERT_DISEASE_BC5CDR`	BC5CDR corpus with disease annotations as used in the evaluation of BioBERT.
`BIOBERT_DISEASE_NCBI`	NCBI disease corpus as used in the evaluation of BioBERT.
`BIOBERT_GENE_BC2GM`	BC4CHEMD corpus with gene annotations as used in the evaluation of BioBERT.
`BIOBERT_GENE_JNLPBA`	JNLPBA corpus with gene annotations as used in the evaluation of BioBERT.
`BIOBERT_SPECIES_LINNAEUS`	Linneaeus corpus with species annotations as used in the evaluation of BioBERT.
`BIOBERT_SPECIES_S800`	S800 corpus with species annotations as used in the evaluation of BioBERT.
`BIONLP2013_CG`	Corpus of the BioNLP'2013 Cancer Genetics shared task.
`BIONLP2013_PC`	Corpus of the BioNLP'2013 Pathway Curation shared task.
`BIOSEMANTICS`	Original Biosemantics corpus.
`BIO_INFER`	Original BioInfer corpus.
`BioBertHelper`	Helper class to convert corpora and the respective train, dev and test split used by BioBERT.
`BioNLPCorpus`	Base class for corpora from BioNLP event extraction shared tasks.
`CDR`	CDR corpus as provided by JHnlp/BioCreative-V-CDR-Corpus.
`CELL_FINDER`	Original CellFinder corpus containing cell line, species and gene annotations.
`CELL_LINE_TAG`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`CEMP`	Original CEMP corpus containing chemical annotations.
`CHEBI`	Original CHEBI corpus containing all annotations.
`CHEMDNER`	Original corpus of the CHEMDNER shared task.
`CHEMICAL_TAG`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`CLL`	Original CLL corpus containing cell line annotations.
`CRAFT`	Original CRAFT corpus (version 2.0) containing all but the coreference and sections/typography annotations.
`CRAFT_V4`	Version 4.0.1 of the CRAFT corpus containing all but the co-reference and structural annotations.
`CoNLLWriter`	Utility class for writing InternalBioNerDataset to CoNLL files.
`DECA`	Original DECA corpus containing gene annotations.
`DISEASE_TAG`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`DpEntry`
`Entity`	Internal class to represent entities while converting biomedical NER corpora to a standardized format.
`FSU`	Original FSU corpus containing protein and derived annotations.
`GELLUS`	Original Gellus corpus containing cell line annotations.
`GENE_TAG`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`GPRO`	Original GPRO corpus containing gene annotations.
`HUNER_ALL_BIOID`
`HUNER_ALL_BIONLP2013_CG`
`HUNER_ALL_BIONLP_ST_2011_ID`
`HUNER_ALL_BIONLP_ST_2013_PC`
`HUNER_ALL_BIORED`
`HUNER_ALL_CDR`	HUNER version of the IEPA corpus containing disease and chemical annotations.
`HUNER_ALL_CELL_FINDER`	HUNER version of the CellFinder corpus containing only gene annotations.
`HUNER_ALL_CHEBI`	HUNER version of the CHEBI corpus containing chemical, gene and species annotations.
`HUNER_ALL_CPI`
`HUNER_ALL_CRAFT_V4`	HUNER version of the CRAFT corpus containing chemical, gene and species annotations.
`HUNER_ALL_DRUGPROT`
`HUNER_ALL_JNLPBA`	HUNER version of the JNLPBA corpus containing gene and cell line annotations.
`HUNER_ALL_LOCTEXT`	HUNER version of the Loctext corpus containing species and protein annotations.
`HUNER_ALL_MIRNA`	HUNER version of the miRNA corpus containing gene, species and disease annotations.
`HUNER_ALL_SCAI`	HUNER version of the SCAI chemicals corpus containing chemical and disease annotations.
`HUNER_ALL_VARIOME`	HUNER version of the Variome corpus containing gene, disease and species annotations.
`HUNER_BIONLP2013_CG`
`HUNER_CELL_LINE`	Union of all HUNER cell line data sets.
`HUNER_CELL_LINE_BIOID`
`HUNER_CELL_LINE_BIORED`
`HUNER_CELL_LINE_CELL_FINDER`	HUNER version of the CellFinder corpus containing only cell line annotations.
`HUNER_CELL_LINE_CLL`	HUNER version of the CLL corpus containing cell line annotations.
`HUNER_CELL_LINE_GELLUS`	HUNER version of the Gellus corpus containing cell line annotations.
`HUNER_CELL_LINE_JNLPBA`	HUNER version of the JNLPBA corpus containing cell line annotations.
`HUNER_CHEBI`	HUNER version of the CHEBI corpus.
`HUNER_CHEMICAL`	Union of all HUNER chemical data sets.
`HUNER_CHEMICAL_BIOID`
`HUNER_CHEMICAL_BIONLP2013_CG`
`HUNER_CHEMICAL_BIONLP_ST_2011_ID`
`HUNER_CHEMICAL_BIONLP_ST_2013_PC`
`HUNER_CHEMICAL_BIORED`
`HUNER_CHEMICAL_CDR`	HUNER version of the IEPA corpus containing chemical annotations.
`HUNER_CHEMICAL_CEMP`	HUNER version of the CEMP corpus containing chemical annotations.
`HUNER_CHEMICAL_CHEBI`	HUNER version of the CHEBI corpus containing chemical annotations.
`HUNER_CHEMICAL_CHEMDNER`	HUNER version of the CHEMDNER corpus containing chemical annotations.
`HUNER_CHEMICAL_CPI`
`HUNER_CHEMICAL_CRAFT_V4`	HUNER version of the CRAFT corpus containing (only) chemical annotations.
`HUNER_CHEMICAL_DRUGPROT`
`HUNER_CHEMICAL_NLM_CHEM`
`HUNER_CHEMICAL_SCAI`	HUNER version of the SCAI chemicals corpus containing chemical annotations.
`HUNER_CRAFT_V4`	HUNER version of the CRAFT corpus containing (only) chemical annotations.
`HUNER_DISEASE`	Union of all HUNER disease data sets.
`HUNER_DISEASE_BIONLP2013_CG`
`HUNER_DISEASE_BIORED`
`HUNER_DISEASE_CDR`	HUNER version of the IEPA corpus containing disease annotations.
`HUNER_DISEASE_MIRNA`	HUNER version of the miRNA corpus containing disease annotations.
`HUNER_DISEASE_NCBI`	HUNER version of the NCBI corpus containing disease annotations.
`HUNER_DISEASE_PDR`	PDR Dataset with only Disease annotations.
`HUNER_DISEASE_SCAI`	HUNER version of the SCAI chemicals corpus containing disease annotations.
`HUNER_DISEASE_VARIOME`	HUNER version of the Variome corpus containing disease annotations.
`HUNER_GENE`	Union of all HUNER gene data sets.
`HUNER_GENE_BC2GM`	HUNER version of the BioCreative-II-GM corpus containing gene annotations.
`HUNER_GENE_BIOID`
`HUNER_GENE_BIONLP2013_CG`
`HUNER_GENE_BIONLP_ST_2011_EPI`
`HUNER_GENE_BIONLP_ST_2011_GE`
`HUNER_GENE_BIONLP_ST_2011_ID`
`HUNER_GENE_BIONLP_ST_2011_REL`
`HUNER_GENE_BIONLP_ST_2013_GE`
`HUNER_GENE_BIONLP_ST_2013_PC`
`HUNER_GENE_BIORED`
`HUNER_GENE_BIO_INFER`	HUNER version of the BioInfer corpus containing only gene/protein annotations.
`HUNER_GENE_CELL_FINDER`	HUNER version of the CellFinder corpus containing only gene annotations.
`HUNER_GENE_CHEBI`	HUNER version of the CHEBI corpus containing gene annotations.
`HUNER_GENE_CPI`
`HUNER_GENE_CRAFT_V4`	HUNER version of the CRAFT corpus containing (only) gene annotations.
`HUNER_GENE_DECA`	HUNER version of the DECA corpus containing gene annotations.
`HUNER_GENE_DRUGPROT`
`HUNER_GENE_FSU`	HUNER version of the FSU corpus containing (only) gene annotations.
`HUNER_GENE_GNORMPLUS`
`HUNER_GENE_GPRO`	HUNER version of the GPRO corpus containing gene annotations.
`HUNER_GENE_IEPA`	HUNER version of the IEPA corpus containing gene annotations.
`HUNER_GENE_JNLPBA`	HUNER version of the JNLPBA corpus containing gene annotations.
`HUNER_GENE_LOCTEXT`	HUNER version of the Loctext corpus containing protein annotations.
`HUNER_GENE_MIRNA`	HUNER version of the miRNA corpus containing protein / gene annotations.
`HUNER_GENE_NLM_GENE`
`HUNER_GENE_OSIRIS`	HUNER version of the OSIRIS corpus containing (only) gene annotations.
`HUNER_GENE_PROGENE`
`HUNER_GENE_SETH_CORPUS`
`HUNER_GENE_TMVAR_V3`
`HUNER_GENE_VARIOME`	HUNER version of the Variome corpus containing gene annotations.
`HUNER_JNLPBA`	HUNER version of the JNLPBA corpus.
`HUNER_LOCTEXT`	HUNER version of the Loctext corpus.
`HUNER_MIRNA`	HUNER version of the miRNA corpus.
`HUNER_SPECIES`	Union of all HUNER species data sets.
`HUNER_SPECIES_BIOID`
`HUNER_SPECIES_BIONLP2013_CG`
`HUNER_SPECIES_BIONLP_ST_2011_ID`
`HUNER_SPECIES_BIONLP_ST_2019_BB`
`HUNER_SPECIES_BIORED`
`HUNER_SPECIES_CELL_FINDER`	HUNER version of the CellFinder corpus containing only species annotations.
`HUNER_SPECIES_CHEBI`	HUNER version of the CHEBI corpus containing species annotations.
`HUNER_SPECIES_CRAFT_V4`	HUNER version of the CRAFT corpus containing (only) species annotations.
`HUNER_SPECIES_LINNEAUS`	HUNER version of the LINNEAUS corpus containing species annotations.
`HUNER_SPECIES_LOCTEXT`	HUNER version of the Loctext corpus containing species annotations.
`HUNER_SPECIES_MIRNA`	HUNER version of the miRNA corpus containing species annotations.
`HUNER_SPECIES_S800`	HUNER version of the S800 corpus containing species annotations.
`HUNER_SPECIES_VARIOME`	HUNER version of the Variome corpus containing species annotations.
`HunerDataset`	Base class for HUNER datasets.
`HunerJNLPBA`
`HunerMiRNAHelper`
`HunerMultiCorpus`	Base class to build the union of all HUNER data sets considering a particular entity type.
`IEPA`	IEPA corpus as provided by http://corpora.informatik.hu-berlin.de/.
`InternalBioNerDataset`	Internal class to represent a corpus and it's entities.
`JNLPBA`	Original corpus of the JNLPBA shared task.
`KaewphanCorpusHelper`	Helper class for the corpora from Kaewphan et al., i.e. CLL and Gellus.
`LINNEAUS`	Original LINNEAUS corpus containing species annotations.
`LOCTEXT`	Original LOCTEXT corpus containing species annotations.
`MIRNA`	Original miRNA corpus.
`NCBI_DISEASE`	Original NCBI disease corpus containing disease annotations.
`OSIRIS`	Original OSIRIS corpus containing variation and gene annotations.
`PDR`	Corpus of plant-disease relations.
`S800`	S800 corpus.
`SCAI_CHEMICALS`	Original SCAI chemicals corpus containing chemical annotations.
`SCAI_DISEASE`	Original SCAI disease corpus containing disease annotations.
`SENTENCE_TAG`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`SPECIES_TAG`	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
`ScaiCorpus`	Base class to support the SCAI chemicals and disease corpora.
`VARIOME`	Variome corpus as provided by http://corpora.informatik.hu-berlin.de/corpora/brat2bioc/hvp_bioc.xml.zip.
`bioc_to_internal`	Helper function to parse corpora that are given in BIOC format.
`brat_to_internal`	Helper function to parse corpora that are annotated using BRAT.
`filter_and_map_entities`
`filter_nested_entities`
`merge_datasets`

Table of Contents

flair.datasets.biomedical#