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  • John Snow Labs
  • Nov 06, 2023

English BertForTokenClassification Base Cased model (from leonweber)

  • bert
  • ner
  • open_source
  • en
  • onnx

Description

Pretrained BertForTokenClassification model, adapted from Hugging Face and curated to provide scalability and production-readiness using Spark NLP. bunsen_base_best is a English model originally trained by leonweber.

Predicted Entities

medmentions_full_ner:B-T085), bionlp_st_2013_gro_ner:B-Ribosome), chemdner_TEXT:MESH:D013830), anat_em_ner:O), cellfinder_ner:I-GeneProtein), ncbi_disease_ner:B-CompositeMention), bionlp_st_2013_gro_ner:B-Virus), medmentions_full_ner:I-T129), scai_disease_ner:B-DISEASE), biorelex_ner:B-chemical), chemdner_TEXT:MESH:D011166), medmentions_st21pv_ner:I-T204), chemdner_TEXT:MESH:D008345), bionlp_st_2013_gro_NER:B-RegulationOfFunction), mlee_ner:I-Cell), bionlp_st_2013_gro_NER:I-RNABiosynthesis), biorelex_ner:I-RNA-family), bionlp_st_2013_gro_NER:B-ResponseToChemicalStimulus), bionlp_st_2011_epi_NER:B-Dephosphorylation), chemdner_TEXT:MESH:D003035), chemdner_TEXT:MESH:D013440), chemdner_TEXT:MESH:D037341), chemdner_TEXT:MESH:D009532), chemdner_TEXT:MESH:D019216), chemdner_TEXT:MESH:D036701), chemdner_TEXT:MESH:D011107), bionlp_st_2013_cg_NER:B-Translation), genia_term_corpus_ner:B-cell_component), medmentions_full_ner:I-T065), bionlp_st_2013_gro_ner:B-ProteinBindingSiteOfDNA), anat_em_ner:I-Developing_anatomical_structure), chemdner_TEXT:MESH:D000225), genia_term_corpus_ner:I-ORDNA_domain_or_regionDNA_domain_or_region), medmentions_full_ner:I-T015), chemdner_TEXT:MESH:D008239), bionlp_st_2013_cg_NER:I-Binding), bionlp_st_2013_cg_NER:B-Amino_acid_catabolism), cellfinder_ner:B-CellComponent), bionlp_st_2013_gro_NER:I-MetabolicPathway), bionlp_st_2013_gro_ner:B-ProteinIdentification), bionlp_st_2011_ge_ner:O), bionlp_st_2011_id_ner:B-Organism), bionlp_st_2013_gro_ner:I-ForkheadWingedHelixTF), mirna_ner:B-Relation_Trigger), bionlp_st_2011_ge_NER:B-Regulation), bionlp_st_2013_cg_NER:B-Gene_expression), chemdner_TEXT:MESH:D008055), chemdner_TEXT:MESH:D009944), verspoor_2013_ner:I-gene), bionlp_st_2013_ge_ner:O), meddocan_ner:B-SEXO_SUJETO_ASISTENCIA), chemdner_TEXT:MESH:D003907), mlee_ner:I-Developing_anatomical_structure), chemdner_TEXT:MESH:D010569), mlee_NER:I-Growth), meddocan_ner:B-NUMERO_TELEFONO), chemdner_TEXT:MESH:D036145), medmentions_full_ner:I-T196), ehr_rel_sts:1), bionlp_st_2013_gro_NER:B-CellularComponentOrganizationAndBiogenesis), chemdner_TEXT:MESH:D009285), bionlp_st_2013_gro_NER:B-ProteinMetabolism), chemdner_TEXT:MESH:D016718), bionlp_st_2013_gro_NER:I-BindingOfTFToTFBindingSiteOfProtein), medmentions_full_ner:I-T074), chemdner_TEXT:MESH:D000432), bionlp_st_2013_gro_NER:I-CellFateDetermination), chia_ner:I-Reference_point), bionlp_st_2013_gro_ner:B-Histone), lll_RE:None), scai_disease_ner:B-ADVERSE), medmentions_full_ner:B-T130), bionlp_st_2013_gro_NER:I-CellCyclePhaseTransition), chemdner_TEXT:MESH:D000480), chemdner_TEXT:MESH:D001556), bionlp_st_2013_gro_ner:B-Nucleus), bionlp_st_2013_gro_ner:B-AP2EREBPRelatedDomain), chemdner_TEXT:MESH:D007854), chemdner_TEXT:MESH:D009499), genia_term_corpus_ner:B-polynucleotide), bionlp_st_2013_gro_NER:I-Transcription), chemdner_TEXT:MESH:D007213), bionlp_st_2013_ge_NER:B-Regulation), bionlp_st_2011_epi_NER:B-DNA_methylation), medmentions_st21pv_ner:B-T031), bionlp_st_2013_ge_NER:I-Gene_expression), chemdner_TEXT:MESH:D007651), bionlp_st_2013_gro_NER:B-OrganismalProcess), bionlp_st_2011_epi_COREF:None), medmentions_st21pv_ner:I-T062), chemdner_TEXT:MESH:D002047), chemdner_TEXT:MESH:D012822), mantra_gsc_en_patents_ner:B-DEVI), medmentions_full_ner:I-T071), chemdner_TEXT:MESH:D013739), bionlp_st_2013_gro_NER:B-NegativeRegulationOfGeneExpression), genia_term_corpus_ner:B-other_name), medmentions_full_ner:B-T018), chemdner_TEXT:MESH:D015242), bionlp_st_2013_cg_NER:O), chemdner_TEXT:MESH:D019469), ncbi_disease_ner:B-DiseaseClass), ebm_pico_ner:B-Intervention_Surgical), chemdner_TEXT:MESH:D011422), chemdner_TEXT:MESH:D002112), chemdner_TEXT:MESH:D005682), anat_em_ner:B-Immaterial_anatomical_entity), bionlp_st_2011_epi_ner:B-Entity), medmentions_full_ner:I-T169), mlee_ner:B-Immaterial_anatomical_entity), verspoor_2013_ner:B-Physiology), cellfinder_ner:I-CellType), chemdner_TEXT:MESH:D011122), chemdner_TEXT:MESH:D010622), chemdner_TEXT:MESH:D017378), bionlp_st_2011_ge_RE:Theme), chemdner_TEXT:MESH:D000431), medmentions_full_ner:I-T102), medmentions_full_ner:B-T097), chemdner_TEXT:MESH:D007529), chemdner_TEXT:MESH:D045265), chemdner_TEXT:MESH:D005971), an_em_ner:I-Multi-tissue_structure), genia_term_corpus_ner:I-ANDDNA_family_or_groupDNA_family_or_group), medmentions_full_ner:I-T080), chemdner_TEXT:MESH:D002207), chia_ner:I-Qualifier), bionlp_st_2013_gro_NER:B-NegativeRegulationOfTranscriptionByTranscriptionRepressor), an_em_ner:I-Immaterial_anatomical_entity), biosses_sts:5), chemdner_TEXT:MESH:D000079963), chemdner_TEXT:MESH:D013196), ehr_rel_sts:2), chemdner_TEXT:MESH:D006152), bionlp_st_2013_gro_NER:B-RegulationOfProcess), mlee_NER:I-Development), medmentions_full_ner:B-T197), bionlp_st_2013_gro_ner:B-NucleicAcid), medmentions_st21pv_ner:I-T017), medmentions_full_ner:I-T046), medmentions_full_ner:B-T204), bionlp_st_2013_gro_NER:B-CellularDevelopmentalProcess), bionlp_st_2013_cg_ner:B-Immaterial_anatomical_entity), chemdner_TEXT:MESH:D014212), bionlp_st_2013_cg_NER:B-Protein_processing), chemdner_TEXT:MESH:D008926), chia_ner:B-Visit), bionlp_st_2011_ge_NER:B-Negative_regulation), mantra_gsc_en_medline_ner:I-OBJC), bionlp_st_2013_gro_ner:I-RNAMolecule), chemdner_TEXT:MESH:D014812), linnaeus_filtered_ner:I-species), chebi_nactem_fullpaper_ner:B-Chemical), bionlp_st_2011_ge_NER:I-Positive_regulation), bionlp_st_2013_gro_ner:B-MutantGene), chemdner_TEXT:MESH:D014859), bionlp_st_2019_bb_ner:B-Phenotype), bionlp_st_2013_gro_NER:I-BindingOfTFToTFBindingSiteOfDNA), diann_iber_eval_en_ner:I-Neg), ddi_corpus_ner:B-DRUG_N), meddocan_ner:B-ID_TITULACION_PERSONAL_SANITARIO), bionlp_st_2013_cg_ner:B-Organ), chemdner_TEXT:MESH:D009320), bionlp_st_2013_cg_ner:I-Organism_subdivision), bionlp_st_2013_cg_ner:B-Cellular_component), chemdner_TEXT:MESH:D003188), chemdner_TEXT:MESH:D001241), chemdner_TEXT:MESH:D004811), bioinfer_ner:I-GeneproteinRNA), chemdner_TEXT:MESH:D002248), bionlp_shared_task_2009_NER:B-Negative_regulation), chemdner_TEXT:MESH:D000143), chemdner_TEXT:MESH:D007099), nlm_gene_ner:O), chemdner_TEXT:MESH:D005485), bionlp_st_2013_gro_ner:B-TranscriptionFactorBindingSiteOfDNA), bionlp_st_2013_gro_ner:B-PhysicalContact), medmentions_full_ner:B-T167), medmentions_st21pv_ner:B-T091), seth_corpus_ner:I-Gene), bionlp_st_2011_ge_COREF:coref), bionlp_st_2011_ge_NER:B-Gene_expression), medmentions_full_ner:B-T031), genia_relation_corpus_RE:None), genia_term_corpus_ner:I-ANDDNA_domain_or_regionDNA_domain_or_region), chemdner_TEXT:MESH:D014970), bionlp_st_2013_gro_NER:B-Mutation), bionlp_st_2013_gro_ner:I-TranscriptionActivator), chemdner_TEXT:MESH:D002217), chemdner_TEXT:MESH:D003367), medmentions_full_ner:I-UnknownType), chemdner_TEXT:MESH:D002998), bionlp_st_2013_gro_ner:I-Phenotype), genia_term_corpus_ner:B-ANDDNA_family_or_groupDNA_family_or_group), hprd50_RE:PPI), chemdner_TEXT:MESH:D002118), scai_chemical_ner:B-IUPAC), bionlp_st_2013_gro_ner:I-ProteinBindingSiteOfProtein), verspoor_2013_ner:B-mutation), chemdner_TEXT:MESH:D011719), chemdner_TEXT:MESH:D013729), bionlp_shared_task_2009_ner:O), chemdner_TEXT:MESH:D005840), chemdner_TEXT:MESH:D009287), medmentions_full_ner:B-T029), chemdner_TEXT:MESH:D037742), medmentions_full_ner:I-T200), chemdner_TEXT:MESH:D012503), bionlp_st_2013_gro_ner:B-ComplexOfProteinAndRNA), mirna_ner:I-Non-Specific_miRNAs), bionlp_st_2013_gro_ner:B-ProteinBindingSiteOfProtein), bionlp_st_2013_pc_NER:B-Deacetylation), meddocan_ner:B-NOMBRE_PERSONAL_SANITARIO), chemprot_RE:CPR:7), chia_ner:I-Value), medmentions_full_ner:I-T048), chemprot_ner:B-GENE-Y), bionlp_st_2013_cg_NER:B-Reproduction), pharmaconer_ner:B-UNCLEAR), bionlp_st_2011_id_ner:I-Regulon-operon), ebm_pico_ner:I-Outcome_Adverse-effects), bioinfer_ner:B-DNA_family_or_group), bionlp_st_2013_gro_ner:I-bZIPTF), mirna_ner:I-GenesProteins), biorelex_ner:I-process), chemdner_TEXT:MESH:D001555), genia_term_corpus_ner:B-DNA_domain_or_region), cellfinder_ner:O), bionlp_st_2013_gro_ner:I-MutatedProtein), bionlp_st_2013_gro_NER:I-CellularComponentOrganizationAndBiogenesis), spl_adr_200db_train_ner:O), medmentions_full_ner:I-T026), chemdner_TEXT:MESH:D013619), bionlp_st_2013_gro_NER:I-BindingToRNA), biorelex_ner:I-drug), bionlp_st_2013_pc_NER:B-Translation), mantra_gsc_en_emea_ner:B-LIVB), mantra_gsc_en_patents_ner:B-PROC), bionlp_st_2013_pc_NER:B-Binding), bionlp_st_2013_gro_NER:B-ModificationOfMolecularEntity), bionlp_st_2013_cg_NER:I-Cell_transformation), scai_chemical_ner:B-TRIVIALVAR), bionlp_st_2013_gro_ner:I-ZincCoordinatingDomain), bionlp_st_2013_gro_NER:I-TranscriptionInitiation), chemdner_TEXT:MESH:D010907), bionlp_st_2013_gro_ner:B-InorganicChemical), bionlp_st_2013_pc_RE:None), chemdner_TEXT:MESH:D002922), chemdner_TEXT:MESH:D010743), bionlp_st_2019_bb_ner:O), medmentions_full_ner:I-T001), chemdner_TEXT:MESH:D001381), bionlp_shared_task_2009_ner:I-Protein), bionlp_st_2013_gro_ner:B-Spliceosome), bionlp_st_2013_gro_ner:I-HMGTF), minimayosrs_sts:3), ddi_corpus_RE:ADVISE), mlee_NER:B-Dissociation), bionlp_st_2013_gro_ner:I-Holoenzyme), chemdner_TEXT:MESH:D001552), bionlp_st_2013_gro_ner:B-bHLH), chemdner_TEXT:MESH:D000109), chemdner_TEXT:MESH:D013449), bionlp_st_2013_gro_ner:I-GeneRegion), medmentions_full_ner:B-T019), scai_chemical_ner:B-TRIVIAL), mlee_ner:B-Gene_or_gene_product), biosses_sts:3), bionlp_st_2013_cg_NER:I-Pathway), bionlp_st_2011_id_ner:I-Organism), bionlp_st_2013_gro_ner:B-tRNA), chemdner_TEXT:MESH:D013109), mlee_ner:I-Immaterial_anatomical_entity), medmentions_full_ner:B-T065), ebm_pico_ner:I-Participant_Sample-size), genia_term_corpus_ner:I-protein_family_or_group), chemdner_TEXT:MESH:D002444), chemdner_TEXT:MESH:D063388), mlee_NER:B-Translation), chemdner_TEXT:MESH:D007052), bionlp_st_2013_gro_ner:B-Gene), chia_ner:B-Scope), bionlp_st_2013_ge_NER:I-Positive_regulation), chemdner_TEXT:MESH:D007785), medmentions_st21pv_ner:I-T097), iepa_RE:None), medmentions_full_ner:B-T001), medmentions_full_ner:I-T194), chemdner_TEXT:MESH:D047309), bionlp_st_2013_gro_ner:B-Substrate), chemdner_TEXT:MESH:D002186), ebm_pico_ner:B-Outcome_Other), bionlp_st_2013_gro_NER:I-OrganismalProcess), bionlp_st_2013_gro_ner:B-Ion), bionlp_st_2013_gro_NER:I-ProteinBiosynthesis), chia_ner:B-Drug), bionlp_st_2013_gro_ner:I-MolecularEntity), cadec_ner:I-Symptom), anat_em_ner:B-Cellular_component), bionlp_st_2013_cg_ner:B-Multi-tissue_structure), medmentions_full_ner:I-T122), an_em_ner:B-Cell), chemdner_TEXT:MESH:D011564), bionlp_st_2013_gro_NER:B-Splicing), bionlp_st_2013_cg_NER:I-Metabolism), bionlp_st_2013_pc_NER:B-Activation), bionlp_st_2013_gro_ner:I-BindingSiteOfProtein), bionlp_st_2011_id_ner:B-Chemical), bionlp_st_2013_gro_ner:I-Ribosome), nlmchem_ner:I-Chemical), mirna_ner:I-Specific_miRNAs), medmentions_full_ner:I-T012), bionlp_st_2013_gro_NER:B-IntraCellularTransport), bionlp_st_2011_id_NER:I-Transcription), mantra_gsc_en_patents_ner:I-ANAT), an_em_ner:B-Immaterial_anatomical_entity), scai_chemical_ner:I-IUPAC), distemist_ner:B-ENFERMEDAD), bionlp_st_2011_epi_NER:B-Deubiquitination), chemdner_TEXT:MESH:D007295), meddocan_ner:I-NOMBRE_SUJETO_ASISTENCIA), bionlp_st_2011_ge_NER:B-Binding), bionlp_st_2013_pc_NER:B-Localization), chia_ner:B-Procedure), medmentions_full_ner:I-T109), chemdner_TEXT:MESH:D002791), mantra_gsc_en_medline_ner:I-CHEM), chebi_nactem_fullpaper_ner:B-Biological_Activity), ncbi_disease_ner:B-SpecificDisease), medmentions_full_ner:B-T063), chemdner_TEXT:MESH:D016595), bionlp_st_2011_id_NER:B-Transcription), bionlp_st_2013_gro_ner:B-DNAMolecule), mlee_NER:B-Protein_processing), biorelex_ner:B-protein-complex), anat_em_ner:I-Cancer), bionlp_st_2013_cg_RE:AtLoc), medmentions_full_ner:I-T072), bio_sim_verb_sts:2), seth_corpus_ner:O), medmentions_full_ner:B-T070), biorelex_ner:I-experiment-tag), chemdner_TEXT:MESH:D020126), biorelex_ner:I-protein-RNA-complex), bionlp_st_2013_pc_NER:I-Phosphorylation), medmentions_st21pv_ner:I-T201), genia_term_corpus_ner:B-protein_complex), medmentions_full_ner:I-T125), bionlp_st_2013_ge_ner:I-Entity), chemdner_TEXT:MESH:D054659), bionlp_st_2013_pc_RE:ToLoc), medmentions_full_ner:B-T099), bionlp_st_2013_gro_NER:B-Binding), medmentions_full_ner:B-T114), spl_adr_200db_train_ner:B-Factor), bionlp_st_2013_gro_ner:B-HMG), bionlp_st_2013_gro_ner:B-Operon), bionlp_st_2013_ge_NER:I-Protein_catabolism), ebm_pico_ner:I-Outcome_Pain), bionlp_st_2013_ge_NER:B-Transcription), chemdner_TEXT:MESH:D000880), ebm_pico_ner:I-Outcome_Physical), bionlp_st_2013_gro_ner:I-ProteinBindingSiteOfDNA), chemdner_TEXT:MESH:D006160), gnormplus_ner:B-DomainMotif), medmentions_full_ner:I-T016), pharmaconer_ner:O), pdr_ner:I-Disease), bionlp_st_2013_gro_NER:B-BindingOfProteinToProteinBindingSiteOfProtein), chemdner_TEXT:MESH:D002264), genia_term_corpus_ner:I-protein_NA), bionlp_shared_task_2009_NER:I-Negative_regulation), medmentions_full_ner:I-T011), bionlp_st_2013_gro_NER:I-CellularMetabolicProcess), mqp_sts:1), an_em_ner:I-Pathological_formation), bionlp_st_2011_epi_NER:B-Deacetylation), bionlp_st_2013_pc_RE:Theme), medmentions_full_ner:I-T103), bionlp_st_2011_epi_NER:B-Methylation), ebm_pico_ner:B-Intervention_Psychological), bionlp_st_2013_gro_ner:B-Stress), genia_term_corpus_ner:B-multi_cell), bionlp_st_2013_cg_NER:B-Positive_regulation), anat_em_ner:I-Cellular_component), spl_adr_200db_train_ner:I-Negation), chemdner_TEXT:MESH:D000605), bionlp_st_2013_gro_ner:B-RegulatoryDNARegion), bionlp_st_2013_gro_ner:I-HomeoboxTF), bionlp_st_2013_gro_NER:I-GeneSilencing), ddi_corpus_ner:I-DRUG), bionlp_st_2013_cg_NER:I-Growth), mantra_gsc_en_medline_ner:B-OBJC), mayosrs_sts:3), bionlp_st_2013_gro_NER:B-RNAProcessing), cellfinder_ner:B-CellType), medmentions_full_ner:B-T007), chemprot_ner:B-GENE-N), biorelex_ner:B-brand), ebm_pico_ner:B-Outcome_Mental), bionlp_st_2013_gro_NER:B-RegulationOfTranscription), bionlp_st_2013_gro_ner:B-EukaryoticCell), genia_term_corpus_ner:I-ANDprotein_subunitprotein_subunit), medmentions_full_ner:I-T184), bionlp_st_2013_gro_NER:B-RegulatoryProcess), bionlp_st_2011_id_NER:B-Negative_regulation), bionlp_st_2013_cg_NER:I-Development), cellfinder_ner:I-Anatomy), chia_ner:B-Condition), chemdner_TEXT:MESH:D003065), medmentions_full_ner:B-T012), bionlp_st_2011_id_NER:I-Positive_regulation), bionlp_st_2013_gro_ner:I-TranscriptionFactorComplex), bionlp_st_2013_cg_NER:I-Carcinogenesis), medmentions_full_ner:B-T064), medmentions_full_ner:B-T026), nlmchem_ner:B-Chemical), genia_term_corpus_ner:I-RNA_domain_or_region), ebm_pico_ner:I-Intervention_Educational), genia_term_corpus_ner:B-ANDcell_linecell_line), distemist_ner:I-ENFERMEDAD), genia_term_corpus_ner:B-protein_substructure), bionlp_st_2013_gro_NER:I-ProteinTransport), bionlp_st_2013_cg_NER:B-DNA_demethylation), medmentions_full_ner:I-T058), biorelex_ner:B-parameter), chemdner_TEXT:MESH:D013006), mirna_ner:I-Relation_Trigger), bionlp_st_2013_gro_ner:B-PrimaryStructure), bionlp_st_2013_gro_NER:I-Phosphorylation), chemdner_TEXT:MESH:D003911), pico_extraction_ner:I-participant), chemdner_TEXT:MESH:D010938), chia_ner:B-Person), an_em_ner:B-Tissue), medmentions_st21pv_ner:B-T170), chemdner_TEXT:MESH:D013936), chemdner_TEXT:MESH:D001080), mlee_RE:None), chemdner_TEXT:MESH:D013669), chemdner_TEXT:MESH:D009943), spl_adr_200db_train_ner:I-Factor), chemdner_TEXT:MESH:D044004), ebm_pico_ner:I-Participant_Sex), chemdner_TEXT:MESH:D000409), bionlp_st_2013_cg_NER:B-Cell_division), medmentions_st21pv_ner:B-T033), pcr_ner:I-Herb), chemdner_TEXT:MESH:D020112), bionlp_st_2013_pc_NER:B-Gene_expression), bionlp_st_2011_rel_ner:O), chemdner_TEXT:MESH:D008610), bionlp_st_2013_gro_NER:B-BindingOfDNABindingDomainOfProteinToDNA), bionlp_st_2013_gro_ner:I-Cell), medmentions_full_ner:I-T055), bionlp_st_2013_pc_NER:I-Negative_regulation), chia_RE:Has_value), tmvar_v1_ner:I-SNP), biorelex_ner:I-experimental-construct), genia_term_corpus_ner:B-), chemdner_TEXT:MESH:D053978), bionlp_st_2013_gro_ner:I-Stress), mlee_ner:B-Pathological_formation), bionlp_st_2013_cg_ner:O), chemdner_TEXT:MESH:D007631), chemdner_TEXT:MESH:D011084), medmentions_full_ner:B-T080), bionlp_st_2013_gro_NER:I-PositiveRegulationOfTranscription), bionlp_st_2013_gro_ner:B-TranscriptionCorepressor), ehr_rel_sts:4), mlee_ner:I-Gene_or_gene_product), chemdner_TEXT:MESH:D003474), medmentions_full_ner:B-T098), scicite_TEXT:method), medmentions_full_ner:B-T100), chemdner_TEXT:MESH:D011849), medmentions_full_ner:I-T039), anat_em_ner:B-Organism_subdivision), bionlp_st_2013_gro_ner:I-Nucleus), mlee_NER:I-Regulation), bionlp_st_2013_gro_ner:I-NuclearReceptor), bionlp_st_2013_ge_RE:None), chemdner_TEXT:MESH:D019483), bionlp_st_2013_cg_ner:B-Cell), bionlp_st_2013_gro_ner:B-Holoenzyme), bionlp_st_2011_epi_NER:I-Methylation), bionlp_shared_task_2009_ner:B-Protein), medmentions_st21pv_ner:I-T038), bionlp_st_2013_gro_ner:I-DNARegion), bionlp_st_2013_gro_NER:I-CellCyclePhase), bionlp_st_2013_gro_ner:I-tRNA), mlee_ner:I-Multi-tissue_structure), chemprot_ner:O), medmentions_full_ner:B-T094), bionlp_st_2013_gro_RE:fromSpecies), bionlp_st_2013_gro_NER:O), bionlp_st_2013_gro_NER:B-Acetylation), bioinfer_ner:I-Protein_family_or_group), medmentions_st21pv_ner:I-T098), pdr_ner:B-Disease), chemdner_ner:I-Chemical), bionlp_st_2013_cg_NER:B-Negative_regulation), chebi_nactem_fullpaper_ner:B-Chemical_Structure), bionlp_st_2011_ge_NER:I-Negative_regulation), sciq_CLF:no), diann_iber_eval_en_ner:O), bionlp_shared_task_2009_NER:I-Binding), mlee_NER:I-Cell_proliferation), chebi_nactem_fullpaper_ner:B-Protein), bionlp_st_2013_gro_NER:B-Phosphorylation), bionlp_st_2011_epi_COREF:coref), medmentions_full_ner:B-T200), bionlp_st_2013_cg_ner:B-Tissue), chemdner_TEXT:MESH:D000082), chemdner_TEXT:MESH:D037201), bionlp_st_2013_gro_ner:B-ComplexMolecularEntity), 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bionlp_st_2013_pc_ner:B-Cellular_component), bionlp_st_2011_id_ner:I-Chemical), chemdner_TEXT:MESH:D013831), biorelex_COREF:None), chemdner_TEXT:MESH:D005609), bionlp_st_2013_gro_ner:B-TranscriptionFactor), mlee_NER:B-Regulation), chemdner_TEXT:MESH:D059808), bionlp_st_2013_gro_ner:I-bHLHTF), chemdner_TEXT:MESH:D010121), chemdner_TEXT:MESH:D017608), chemdner_TEXT:MESH:D007455), mlee_NER:B-Blood_vessel_development), bionlp_st_2013_gro_ner:B-TranscriptionFactorComplex), biorelex_ner:B-disease), bionlp_st_2013_cg_NER:B-Cell_differentiation), medmentions_st21pv_ner:I-T092), chemdner_TEXT:MESH:D007477), medmentions_full_ner:B-T168), pcr_ner:I-Chemical), chemdner_TEXT:MESH:D009636), chemdner_TEXT:MESH:D008051), pharmaconer_ner:I-UNCLEAR), bionlp_shared_task_2009_NER:I-Gene_expression), chemprot_ner:I-GENE-N), biorelex_ner:B-reagent), chemdner_TEXT:MESH:D020123), nlmchem_ner:O), ebm_pico_ner:I-Outcome_Mental), chemdner_TEXT:MESH:D004040), chemdner_TEXT:MESH:D000450), 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chemdner_TEXT:MESH:D004164), chemdner_TEXT:MESH:D015032), chemdner_TEXT:MESH:D014255), ebm_pico_ner:B-Outcome_Pain), bionlp_st_2013_gro_ner:I-UpstreamRegulatorySequence), meddocan_ner:I-CALLE), bionlp_st_2013_pc_NER:I-Positive_regulation), bionlp_st_2013_cg_NER:I-Regulation), chemdner_TEXT:MESH:D001151), medmentions_full_ner:I-T077), chemdner_TEXT:MESH:D000081), bionlp_st_2013_gro_NER:B-Stabilization), mayosrs_sts:1), biorelex_ner:B-mutation), chemdner_TEXT:MESH:D000241), chemdner_TEXT:MESH:D007930), bionlp_st_2013_gro_NER:B-MetabolicPathway), chemdner_TEXT:MESH:D013629), chemdner_TEXT:MESH:D016202), tmvar_v1_ner:I-DNAMutation), chemdner_TEXT:MESH:D012502), chemdner_TEXT:MESH:D044945), bionlp_st_2013_cg_ner:I-Cellular_component), mlee_ner:B-Developing_anatomical_structure), bionlp_st_2013_gro_ner:I-AP2EREBPRelatedDomain), chemdner_TEXT:MESH:D002338), mayosrs_sts:5), bionlp_st_2013_gro_ner:B-Intron), genia_term_corpus_ner:I-DNA_domain_or_region), 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chemdner_TEXT:MESH:D011092), chemdner_TEXT:MESH:D015283), chemdner_TEXT:MESH:D018698), cadec_ner:I-Finding), chemdner_TEXT:MESH:D009569), muchmore_en_ner:I-umlsterm), bionlp_st_2013_cg_NER:B-Death), nlm_gene_ner:I-Other), medmentions_full_ner:B-T109), osiris_ner:I-variant), ehr_rel_sts:6), chemdner_TEXT:MESH:D001120), mlee_ner:I-Protein_domain_or_region), bionlp_st_2013_pc_NER:B-Dissociation), bionlp_st_2013_cg_NER:B-Metastasis), chemdner_TEXT:MESH:D014204), chemdner_TEXT:MESH:D005857), medmentions_full_ner:I-T030), chemdner_TEXT:MESH:D019256), bionlp_st_2013_gro_ner:B-Polymerase), chia_ner:B-Negation), bionlp_st_2013_gro_NER:B-CellularMetabolicProcess), bionlp_st_2013_gro_NER:B-CellDifferentiation), biorelex_ner:I-protein-motif), medmentions_full_ner:I-T093), chemdner_TEXT:MESH:D019820), anat_em_ner:B-Pathological_formation), meddocan_ner:I-PROFESION), bionlp_shared_task_2009_NER:B-Localization), genia_term_corpus_ner:B-RNA_domain_or_region), chemdner_TEXT:MESH:D014668), bionlp_st_2013_pc_ner:I-Gene_or_gene_product), chemdner_TEXT:MESH:D019207), bionlp_st_2013_gro_NER:B-BindingOfProteinToProteinBindingSiteOfDNA), medmentions_full_ner:B-T059), bionlp_st_2013_gro_ner:B-Ligand), bio_sim_verb_sts:6), biorelex_ner:B-experimental-construct), bionlp_st_2013_gro_ner:I-DNA), pdr_NER:O), chemdner_TEXT:MESH:D008670), bionlp_st_2011_ge_RE:Cause), meddocan_ner:B-CALLE), chemdner_TEXT:MESH:D015232), bionlp_st_2013_pc_NER:O), bionlp_st_2013_gro_NER:B-FormationOfProteinDNAComplex), medmentions_full_ner:B-T121), bionlp_shared_task_2009_NER:B-Regulation), chemdner_TEXT:MESH:D009534), chemdner_TEXT:MESH:D014451), bionlp_st_2011_id_RE:AtLoc), chemdner_TEXT:MESH:D011799), medmentions_st21pv_ner:B-T204), genia_term_corpus_ner:I-protein_subunit), biorelex_ner:I-assay), chemdner_TEXT:MESH:D005680), an_em_ner:I-Organism_substance), chemdner_TEXT:MESH:D010368), chemdner_TEXT:MESH:D000872), bionlp_st_2011_id_NER:I-Gene_expression), bionlp_st_2013_cg_NER:B-Regulation), mlee_ner:I-DNA_domain_or_region), chemdner_TEXT:MESH:D001393), medmentions_full_ner:I-T038), chemdner_TEXT:MESH:D047311), chemdner_TEXT:MESH:D011453), chemdner_TEXT:MESH:D020106), chemdner_TEXT:MESH:D019257), bionlp_st_2013_gro_ner:B-NuclearReceptor), chemdner_TEXT:MESH:D002117), genia_term_corpus_ner:B-lipid), bionlp_st_2013_gro_ner:B-SmallInterferingRNA), chemdner_TEXT:MESH:D011205), chemdner_TEXT:MESH:D002686), bionlp_st_2013_gro_NER:B-Translation), ebm_pico_ner:I-Intervention_Psychological), mlee_ner:I-Drug_or_compound), bionlp_st_2013_gro_ner:I-TranscriptionFactorBindingSiteOfDNA), chemdner_TEXT:MESH:D000688), bionlp_st_2011_ge_RE:None), bionlp_st_2013_gro_ner:B-ProteinSubunit), genia_term_corpus_ner:I-ANDother_nameother_name), bionlp_st_2013_gro_NER:I-Heterodimerization), pico_extraction_ner:B-intervention), bionlp_st_2013_cg_ner:I-Organism), bionlp_st_2013_gro_ner:I-ProteinDomain), bionlp_st_2013_gro_NER:I-BindingToProtein), scai_chemical_ner:I-), biorelex_ner:B-experiment-tag), ebm_pico_ner:B-Intervention_Physical), bionlp_st_2013_cg_RE:ToLoc), bionlp_st_2013_gro_NER:B-FormationOfTranscriptionFactorComplex), linnaeus_ner:B-species), medmentions_full_ner:I-T062), chemdner_TEXT:MESH:D014640), mlee_NER:B-Gene_expression), chemdner_TEXT:MESH:D008701), mlee_NER:O), chemdner_TEXT:MESH:D014302), genia_term_corpus_ner:B-RNA_family_or_group), medmentions_full_ner:I-T091), medmentions_full_ner:B-T022), medmentions_full_ner:B-T074), bionlp_st_2013_gro_NER:B-ProteinCatabolism), chemdner_TEXT:MESH:D011388), bionlp_st_2013_ge_NER:I-Phosphorylation), bionlp_st_2013_gro_NER:I-CellAdhesion), anat_em_ner:I-Organ), medmentions_full_ner:B-T045), chemdner_TEXT:MESH:D008727), chebi_nactem_abstr_ann1_ner:B-Species), bionlp_st_2013_gro_ner:I-RNAPolymeraseII), nlm_gene_ner:B-STARGENE), mantra_gsc_en_emea_ner:B-OBJC), meddocan_ner:B-PROFESION), bionlp_st_2013_gro_ner:B-DNABindingDomainOfProtein), chemdner_TEXT:MESH:D010636), chemdner_TEXT:MESH:D004061), mlee_NER:I-Binding), medmentions_full_ner:B-T075), medmentions_full_ner:B-UnknownType), chemdner_TEXT:MESH:D019081), bionlp_st_2013_gro_NER:I-Binding), medmentions_full_ner:I-T005), chemdner_TEXT:MESH:D009821)

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How to use

documentAssembler = DocumentAssembler() \
        .setInputCol("text") \
        .setOutputCol("document")

sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl", "xx")\
       .setInputCols(["document"])\
       .setOutputCol("sentence")

tokenizer = Tokenizer() \
    .setInputCols("sentence") \
    .setOutputCol("token")

tokenClassifier = BertForTokenClassification.pretrained("bert_ner_bunsen_base_best","en") \
    .setInputCols(["sentence", "token"]) \
    .setOutputCol("ner")

pipeline = Pipeline(stages=[documentAssembler, sentenceDetector, tokenizer, tokenClassifier])

data = spark.createDataFrame([["PUT YOUR STRING HERE"]]).toDF("text")

result = pipeline.fit(data).transform(data)

val documentAssembler = new DocumentAssembler() 
          .setInputCol("text") 
          .setOutputCol("document")

val sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl", "xx")
       .setInputCols(Array("document"))
       .setOutputCol("sentence")

val tokenizer = new Tokenizer() 
    .setInputCols(Array("sentence"))
    .setOutputCol("token")

val tokenClassifier = BertForTokenClassification.pretrained("bert_ner_bunsen_base_best","en") 
    .setInputCols(Array("sentence", "token")) 
    .setOutputCol("ner")

val pipeline = new Pipeline().setStages(Array(documentAssembler,sentenceDetector, tokenizer, tokenClassifier))

val data = Seq("PUT YOUR STRING HERE").toDF("text")

val result = pipeline.fit(data).transform(data)

import nlu
nlu.load("en.ner.bert.base.by_leonweber").predict("""PUT YOUR STRING HERE""")

Model Information

Model Name: bert_ner_bunsen_base_best
Compatibility: Spark NLP 5.2.0+
License: Open Source
Edition: Official
Input Labels: [document, token]
Output Labels: [ner]
Language: en
Size: 420.5 MB
Case sensitive: true
Max sentence length: 128

References

References

  • https://huggingface.co/leonweber/bunsen_base_best