English BertForTokenClassification Cased model (from bigscience-biomedical)

Description

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

Predicted Entities

medmentions_full_ner:B-T085), pdr_EAE:Theme), bionlp_shared_task_2009_ner:I-Entity), pcr_ner:B-Herb), gnormplus_ner:I-Gene), bionlp_st_2013_cg_EAE:Participant), pubmed_qa_labeled_fold0_CLF:yes), bionlp_st_2013_gro_ner:B-Ribosome), anat_em_ner:O), seth_corpus_RE:Equals), chemprot_RE:CPR:10), medmentions_full_ner:B-T102), medmentions_full_ner:I-T171), medmentions_full_ner:I-T082), bionlp_st_2013_cg_ED:B-Positive_regulation), anat_em_ner:B-Multi-tissue_structure), hprd50_ner:O), bionlp_st_2013_gro_ner:B-OxidativeStress), mlee_ED:I-Transcription), cellfinder_ner:I-GeneProtein), chia_ner:B-Reference_point), medmentions_full_ner:B-T015), ncbi_disease_ner:B-CompositeMention), bionlp_st_2013_gro_ner:I-RNAPolymerase), bionlp_st_2013_gro_ner:B-Virus), bionlp_st_2013_gro_ED:B-Pathway), medmentions_full_ner:B-T025), chebi_nactem_abstr_ann1_ner:B-Metabolite), bio_sim_verb_sts:7), bionlp_st_2013_gro_ED:B-Maintenance), medmentions_full_ner:I-T129), scai_disease_ner:B-DISEASE), chemprot_RE:CPR:9), biorelex_ner:B-chemical), bionlp_st_2013_gro_ED:I-TranscriptionOfGene), bionlp_st_2013_gro_ED:I-BindingOfProteinToProteinBindingSiteOfProtein), bionlp_st_2013_cg_ner:B-Amino_acid), pubmed_qa_labeled_fold0_CLF:maybe), bionlp_st_2013_gro_ner:I-Sequence), pico_extraction_ner:O), bc5cdr_ner:B-Chemical), bionlp_st_2013_pc_ner:B-Simple_chemical), bionlp_st_2011_id_ED:B-Gene_expression), an_em_ner:B-Developing_anatomical_structure), bionlp_st_2019_bb_ner:I-Phenotype), genia_term_corpus_ner:B-DNA_family_or_group), medmentions_st21pv_ner:I-T204), bionlp_st_2013_gro_ner:B-bZIP), bionlp_st_2013_gro_ner:I-Eukaryote), bionlp_st_2013_pc_ner:I-Complex), mlee_ner:I-Cell), bionlp_shared_task_2009_ED:I-Localization), hprd50_ner:I-protein), mantra_gsc_en_patents_ner:B-PHYS), bionlp_st_2013_gro_ED:B-RegulationOfGeneExpression), medmentions_full_ner:B-T020), genia_term_corpus_ner:B-ANDprotein_moleculeprotein_molecule), bionlp_shared_task_2009_EAE:AtLoc), genia_term_corpus_ner:B-protein_molecule), bionlp_st_2013_gro_ner:B-Agonist), mantra_gsc_en_medline_ner:B-PHEN), medmentions_full_ner:B-T030), biorelex_ner:I-RNA-family), medmentions_full_ner:B-T169), ddi_corpus_ner:B-BRAND), medmentions_full_ner:B-T087), genia_term_corpus_ner:I-nucleotide), bionlp_st_2013_gro_ED:I-CellCyclePhaseTransition), mantra_gsc_en_medline_ner:B-DEVI), tmvar_v1_ner:O), bionlp_st_2013_gro_ED:I-CellularComponentOrganizationAndBiogenesis), bioscope_abstracts_ner:B-speculation), ebm_pico_ner:B-Outcome_Adverse-effects), bionlp_shared_task_2009_EAE:Site), mantra_gsc_en_medline_ner:B-PHYS), bionlp_st_2013_gro_ner:I-Lipid), genia_term_corpus_ner:I-ANDprotein_substructureprotein_substructure), medmentions_st21pv_ner:B-T007), bionlp_st_2013_cg_ner:I-Pathological_formation), bionlp_st_2013_gro_ner:B-Organism), bc5cdr_ner:O), bionlp_st_2011_id_EAE:Site), bionlp_st_2013_gro_ner:I-NucleicAcid), medmentions_full_ner:I-T040), bionlp_st_2013_gro_ED:B-BindingOfProteinToProteinBindingSiteOfProtein), mlee_ED:I-Blood_vessel_development), bionlp_st_2013_gro_ner:B-ExpressionProfiling), medmentions_full_ner:I-T044), mantra_gsc_en_emea_ner:I-DEVI), chia_ner:I-Person), ebm_pico_ner:B-Intervention_Pharmacological), scai_disease_ner:O), medmentions_full_ner:I-T121), bionlp_st_2011_epi_ner:I-Entity), mantra_gsc_en_emea_ner:I-ANAT), genia_term_corpus_ner:B-cell_component), bionlp_st_2019_bb_RE:Lives_In), bionlp_st_2013_gro_ED:B-CatabolicPathway), mantra_gsc_en_medline_ner:B-ANAT), medmentions_full_ner:I-T065), bionlp_st_2013_gro_ner:B-TranscriptionCofactor), bionlp_st_2013_gro_ner:B-ProteinBindingSiteOfDNA), pdr_EAE:Cause), anat_em_ner:I-Developing_anatomical_structure), anat_em_ner:B-Cancer), bionlp_st_2013_pc_ED:B-Gene_expression), genia_term_corpus_ner:I-ORDNA_domain_or_regionDNA_domain_or_region), scai_disease_ner:I-ADVERSE), bionlp_st_2013_cg_ED:B-Dephosphorylation), bionlp_st_2013_gro_ED:I-Heterodimerization), mlee_ED:B-Catabolism), biorelex_ner:I-protein-isoform), bionlp_shared_task_2009_COREF:None), bionlp_st_2013_gro_ED:B-RNASplicing), bionlp_st_2013_gro_EAE:hasPatient), mantra_gsc_en_medline_ner:I-ANAT), medmentions_full_ner:I-T015), bionlp_st_2013_pc_EAE:Product), bionlp_st_2013_pc_EAE:AtLoc), bionlp_st_2013_gro_ED:B-ProteinTargeting), cellfinder_ner:B-CellComponent), mantra_gsc_en_medline_ner:I-DISO), bionlp_st_2013_gro_ED:I-Translation), bionlp_st_2013_gro_ner:I-Prokaryote), genia_term_corpus_ner:I-lipid), bionlp_st_2013_pc_ED:B-Deacetylation), biorelex_ner:B-RNA), scai_chemical_ner:B-FAMILY), bionlp_st_2013_gro_ED:I-Pathway), bionlp_st_2013_gro_ner:B-ProteinIdentification), bionlp_st_2011_ge_ner:O), mlee_ner:B-Protein_domain_or_region), bionlp_st_2011_id_ner:B-Organism), bionlp_st_2013_gro_ner:I-ForkheadWingedHelixTF), bionlp_st_2013_gro_ner:I-Chromatin), mlee_ED:I-Binding), mirna_ner:B-Relation_Trigger), bionlp_st_2013_gro_ner:B-Nucleotide), linnaeus_ner:I-species), medmentions_full_ner:I-T024), verspoor_2013_ner:I-body-part), bionlp_st_2011_epi_EAE:Sidechain), bionlp_st_2013_gro_ner:I-ReporterGeneConstruction), bionlp_st_2013_gro_ner:B-DNAFragment), bionlp_st_2013_gro_ner:B-PositiveTranscriptionRegulator), medmentions_full_ner:I-T049), medmentions_full_ner:I-T025), verspoor_2013_ner:I-gene), bionlp_st_2019_bb_RE:Exhibits), bionlp_st_2013_cg_ED:B-Gene_expression), bionlp_st_2013_ge_ner:O), mlee_ner:I-Developing_anatomical_structure), mlee_ED:B-Positive_regulation), bionlp_st_2013_gro_ED:B-FormationOfTranscriptionInitiationComplex), bionlp_st_2011_ge_ner:B-Entity), ddi_corpus_ner:I-GROUP), medmentions_full_ner:I-T017), bionlp_st_2013_gro_ED:I-Mutation), bionlp_st_2011_id_EAE:AtLoc), bionlp_st_2011_ge_ED:B-Regulation), bionlp_st_2011_ge_EAE:Theme), bionlp_st_2013_gro_ner:I-ExperimentalMethod), bionlp_st_2013_gro_ner:B-HMGTF), chemdner_ner:B-Chemical), ehr_rel_sts:1), medmentions_full_ner:I-T196), bioscope_papers_ner:B-negation), bionlp_shared_task_2009_ED:I-Negative_regulation), bionlp_st_2013_pc_ED:B-Phosphorylation), biorelex_RE:bind), bioinfer_ner:B-Protein_complex), scai_chemical_ner:I-TRIVIALVAR), bionlp_shared_task_2009_ED:I-Binding), bionlp_st_2011_rel_ner:I-Entity), anat_em_ner:B-Tissue), bionlp_st_2013_cg_ED:I-Remodeling), bionlp_st_2013_cg_ner:I-Cell), medmentions_full_ner:I-T074), sciq_SEQ:None), mantra_gsc_en_medline_ner:I-PROC), bionlp_st_2011_id_ED:I-Negative_regulation), bionlp_st_2013_gro_ner:I-Agonist), chia_ner:I-Reference_point), medmentions_full_ner:B-T024), bionlp_st_2013_gro_ner:B-Histone), chia_ner:I-Negation), lll_RE:None), ncbi_disease_ner:I-DiseaseClass), bionlp_st_2013_gro_ner:I-Chromosome), scai_disease_ner:B-ADVERSE), medmentions_full_ner:B-T130), bionlp_st_2011_epi_ED:B-Catalysis), bionlp_st_2011_epi_ner:O), mlee_EAE:AtLoc), bionlp_st_2013_gro_ED:B-RegulationOfPathway), genia_term_corpus_ner:I-RNA_family_or_group), biosses_sts:8), bionlp_st_2013_gro_ner:I-MolecularFunction), verspoor_2013_ner:B-gene), an_em_ner:I-Cell), bionlp_st_2011_id_ED:B-Localization), bionlp_st_2011_ge_EAE:Site), bionlp_st_2013_gro_ner:B-ZincCoordinatingDomainTF), bionlp_st_2013_gro_EAE:hasAgent), bionlp_st_2013_gro_ner:B-DNARegion), bionlp_shared_task_2009_ED:O), mlee_EAE:Cause), bionlp_st_2011_epi_ED:B-Ubiquitination), bionlp_st_2013_gro_ED:I-GeneExpression), bionlp_st_2013_gro_ner:I-CatalyticActivity), anat_em_ner:B-Anatomical_system), lll_RE:genic_interaction), bionlp_st_2013_gro_ner:B-Nucleus), bionlp_st_2013_ge_ED:B-Acetylation), ebm_pico_ner:B-Intervention_Educational), medmentions_st21pv_ner:B-T005), mlee_ner:I-Pathological_formation), bionlp_st_2013_gro_ner:B-OrganicChemical), medmentions_full_ner:I-T022), gnormplus_ner:B-FamilyName), bionlp_st_2013_gro_ED:I-NegativeRegulationOfTranscription), bionlp_st_2013_gro_ner:I-ChromosomalDNA), anat_em_ner:B-Cell), bionlp_st_2013_gro_ner:I-TranscriptionCofactor), chia_ner:I-Observation), bioscope_abstracts_ner:I-negation), medmentions_full_ner:I-T089), bionlp_st_2013_gro_ner:B-AP2EREBPRelatedDomain), bionlp_st_2013_gro_ner:I-ComplexMolecularEntity), bionlp_st_2013_gro_ner:B-Lipid), mlee_ED:B-Death), biorelex_ner:I-gene), bionlp_st_2011_id_ED:I-Positive_regulation), medmentions_st21pv_ner:B-T058), bionlp_st_2011_id_ED:O), biorelex_ner:B-protein-region), bionlp_st_2011_id_ED:B-Regulation), verspoor_2013_RE:relatedTo), bionlp_st_2011_id_ED:I-Gene_expression), genia_term_corpus_ner:B-cell_line), bionlp_st_2013_gro_ner:B-UpstreamRegulatorySequence), genia_term_corpus_ner:B-polynucleotide), genia_term_corpus_ner:I-cell_component), medmentions_full_ner:B-T013), bionlp_st_2011_ge_COREF:None), ebm_pico_ner:B-Participant_Sample-size), bionlp_st_2013_gro_ED:B-RNAMetabolism), bionlp_st_2013_gro_ner:I-RNA), ddi_corpus_RE:EFFECT), medmentions_st21pv_ner:B-T031), bionlp_st_2013_cg_ner:I-Immaterial_anatomical_entity), ebm_pico_ner:I-Intervention_Physical), bionlp_st_2013_gro_ner:B-MolecularStructure), bionlp_st_2013_gro_ED:B-GeneExpression), bionlp_st_2013_pc_ner:B-Complex), medmentions_full_ner:I-T090), medmentions_st21pv_ner:I-T005), bionlp_st_2013_gro_ED:B-ProteinTransport), bionlp_st_2013_gro_ner:I-ZincCoordinatingDomainTF), bionlp_st_2013_gro_ner:I-CpGIsland), bionlp_st_2013_gro_ner:B-AminoAcid), bionlp_st_2013_gro_ED:B-SPhase), bionlp_st_2011_epi_COREF:None), bionlp_st_2013_pc_ner:I-Cellular_component), genia_term_corpus_ner:B-ANDDNA_domain_or_regionDNA_domain_or_region), bionlp_st_2013_gro_ner:B-Chromosome), medmentions_full_ner:I-T010), bionlp_st_2013_gro_ner:I-OxidativeStress), bionlp_st_2013_cg_ner:I-Anatomical_system), bionlp_st_2013_gro_ED:B-BindingOfTFToTFBindingSiteOfDNA), medmentions_st21pv_ner:I-T062), medmentions_full_ner:B-T081), scai_chemical_ner:B-PARTIUPAC), bionlp_st_2013_gro_ner:I-RibosomalRNA), verspoor_2013_ner:O), bionlp_st_2011_epi_ED:B-Methylation), bionlp_shared_task_2009_ner:B-Entity), bionlp_st_2013_pc_ED:B-Transport), bio_sim_verb_sts:3), bionlp_st_2013_gro_ED:I-Elongation), medmentions_full_ner:B-T058), biorelex_ner:B-protein), mantra_gsc_en_patents_ner:B-DEVI), bionlp_st_2013_gro_ner:I-BasicDomain), medmentions_full_ner:I-T071), bionlp_st_2013_gro_ED:I-DevelopmentalProcess), bionlp_st_2013_cg_ED:B-Catabolism), mlee_ED:B-Growth), mlee_EAE:Theme), ebm_pico_ner:I-Intervention_Surgical), bionlp_st_2011_ge_ner:I-Entity), an_em_ner:I-Organ), bionlp_st_2013_ge_ED:B-Positive_regulation), iepa_RE:PPI), bionlp_st_2013_gro_ner:B-PhysicalContinuant), chemprot_RE:CPR:4), bionlp_st_2011_id_EAE:Theme), bionlp_st_2013_cg_ED:B-Amino_acid_catabolism), genia_term_corpus_ner:B-other_name), medmentions_full_ner:I-T130), bionlp_st_2011_id_ED:I-Process), mantra_gsc_en_patents_ner:O), bionlp_st_2013_pc_ED:B-Ubiquitination), medmentions_full_ner:B-T018), bionlp_st_2011_id_EAE:ToLoc), bionlp_st_2013_cg_ner:B-Organism), medmentions_full_ner:B-T014), bionlp_st_2013_pc_ED:I-Activation), mlee_ED:I-Death), medmentions_full_ner:I-T047), bionlp_st_2011_ge_EAE:ToLoc), bionlp_st_2013_cg_ED:I-Gene_expression), bionlp_st_2013_gro_ner:B-AntisenseRNA), bionlp_st_2013_gro_ner:B-ProteinCodingDNARegion), bionlp_st_2013_gro_ED:I-BindingOfTFToTFBindingSiteOfDNA), bionlp_st_2013_pc_ED:B-Methylation), bionlp_st_2013_gro_ED:B-GeneMutation), mlee_EAE:None), bionlp_shared_task_2009_EAE:CSite), chebi_nactem_fullpaper_ner:I-Protein), genia_term_corpus_ner:I-multi_cell), bionlp_st_2013_cg_ED:B-Cell_division), ncbi_disease_ner:B-DiseaseClass), bionlp_st_2013_gro_ner:I-Gene), bionlp_st_2013_pc_EAE:FromLoc|ToLoc), ebm_pico_ner:B-Intervention_Surgical), medmentions_full_ner:B-T042), medmentions_full_ner:I-T051), cellfinder_ner:B-GeneProtein), bionlp_st_2011_id_COREF:None), biorelex_ner:I-brand), bionlp_st_2013_gro_ner:B-CatalyticActivity), chebi_nactem_abstr_ann1_ner:I-Biological_Activity), bionlp_st_2013_gro_ED:B-OrganismalProcess), bionlp_st_2013_gro_EAE:hasAgent2), chebi_nactem_abstr_ann1_ner:I-Species), bionlp_st_2013_pc_ED:B-Deubiquitination), bionlp_st_2013_gro_ner:I-GeneProduct), mayosrs_sts:6), anat_em_ner:B-Immaterial_anatomical_entity), bio_sim_verb_sts:1), bionlp_st_2011_epi_ner:B-Entity), medmentions_full_ner:I-T169), bionlp_st_2013_gro_ner:B-bZIPTF), mlee_ner:B-Immaterial_anatomical_entity), an_em_RE:None), verspoor_2013_ner:B-Physiology), sciq_SEQ:answer), cellfinder_ner:I-CellType), mlee_RE:frag), medmentions_st21pv_ner:I-T103), ddi_corpus_RE:None), bionlp_st_2013_gro_ner:I-AntisenseRNA), medmentions_st21pv_ner:I-T091), bionlp_st_2011_epi_EAE:Cause), bionlp_st_2013_gro_ED:I-BindingToRNA), bionlp_st_2013_gro_ED:I-PositiveRegulationOfTranscription), bionlp_st_2013_pc_COREF:coref), medmentions_full_ner:I-T067), medmentions_full_ner:B-T005), bionlp_st_2013_gro_ED:I-CellularMetabolicProcess), bionlp_st_2011_epi_ED:B-Acetylation), osiris_ner:B-variant), ncbi_disease_ner:O), spl_adr_200db_train_ner:I-DrugClass), mantra_gsc_en_patents_ner:I-CHEM), bionlp_st_2013_gro_ED:B-CellHomeostasis), mayosrs_sts:2), mirna_ner:I-Species), bionlp_st_2013_cg_ED:B-Reproduction), medmentions_full_ner:I-T102), medmentions_st21pv_ner:I-T033), medmentions_full_ner:B-T097), bionlp_st_2013_pc_ED:I-Negative_regulation), bionlp_st_2013_gro_ED:B-Dimerization), ebm_pico_ner:I-Participant_Age), medmentions_full_ner:B-T095), bionlp_st_2013_gro_ED:B-RegulationOfProcess), medmentions_full_ner:B-T002), bionlp_st_2013_gro_ED:B-Binding), bionlp_st_2013_gro_ED:B-BindingOfProtein), chemprot_RE:CPR:10|CPR:2), verspoor_2013_ner:I-Concepts_Ideas), bionlp_st_2011_epi_ner:I-Protein), ddi_corpus_ner:O), bionlp_st_2013_gro_ED:I-RNAMetabolism), an_em_ner:I-Multi-tissue_structure), chemprot_RE:CPR:2|CPR:8), medmentions_full_ner:B-T062), genia_term_corpus_ner:I-ANDDNA_family_or_groupDNA_family_or_group), medmentions_full_ner:I-T080), ebm_pico_ner:B-Outcome_Physical), medmentions_st21pv_ner:B-T103), bionlp_st_2013_gro_ner:I-TranscriptionFactor), chia_ner:I-Qualifier), genia_term_corpus_ner:B-protein_domain_or_region), bionlp_st_2013_gro_ED:B-IntraCellularTransport), bionlp_st_2013_gro_ner:I-ThreeDimensionalMolecularStructure), bionlp_st_2013_gro_ner:I-TranscriptionCoactivator), an_em_ner:I-Immaterial_anatomical_entity), chebi_nactem_fullpaper_ner:I-Chemical), mantra_gsc_en_emea_ner:B-PROC), biosses_sts:5), bionlp_st_2013_cg_ner:B-Cancer), genia_term_corpus_ner:B-BUT_NOTother_nameother_name), bionlp_st_2013_gro_ED:I-CellDivision), bionlp_st_2013_gro_ED:I-TranscriptionTermination), bionlp_st_2013_cg_ED:B-Acetylation), mlee_ED:I-Localization), ehr_rel_sts:2), biorelex_ner:I-protein-DNA-complex), bionlp_st_2011_id_COREF:coref), bioinfer_RE:None), nlm_gene_ner:B-Gene), medmentions_full_ner:B-T104), biosses_sts:6), chemprot_RE:CPR:5|CPR:6), bionlp_st_2013_gro_ner:B-ReporterGene), biosses_sts:1), biorelex_ner:I-organism), chia_ner:B-Value), cellfinder_ner:B-Anatomy), bionlp_st_2013_gro_ED:I-RegulatoryProcess), verspoor_2013_ner:B-body-part), bionlp_st_2013_gro_ED:I-Localization), biorelex_ner:B-RNA-family), ebm_pico_ner:B-Intervention_Control), bionlp_st_2013_cg_ED:B-Binding), bionlp_st_2013_gro_ED:B-BindingOfProteinToDNA), bionlp_st_2013_ge_EAE:Cause), chemprot_RE:CPR:3), chia_RE:Has_mood), pico_extraction_ner:I-outcome), medmentions_st21pv_ner:B-T074), bionlp_st_2013_cg_ner:I-Amino_acid), bionlp_st_2013_cg_ED:B-Protein_processing), bionlp_st_2013_cg_ED:B-Regulation), medmentions_full_ner:B-T197), bionlp_st_2013_gro_ED:I-NegativeRegulationOfTranscriptionOfGene), bionlp_st_2013_cg_ED:I-Transcription), bionlp_st_2013_ge_ED:B-Gene_expression), mantra_gsc_en_patents_ner:I-PHYS), bionlp_st_2013_gro_ner:B-NucleicAcid), bionlp_st_2013_gro_ED:B-CellDivision), medmentions_st21pv_ner:I-T017), bionlp_st_2011_id_EAE:CSite), medmentions_full_ner:I-T046), medmentions_full_ner:B-T204), bionlp_st_2013_pc_ED:I-Dissociation), spl_adr_200db_train_ner:B-Negation), bionlp_st_2013_gro_ED:I-MetabolicPathway), bionlp_st_2013_ge_ED:B-Regulation), nlm_gene_ner:B-GENERIF), verspoor_2013_ner:I-Disorder), bionlp_st_2013_gro_ner:I-ReporterGene), bionlp_st_2013_gro_ner:B-Vitamin), bionlp_st_2013_cg_ner:B-Immaterial_anatomical_entity), bionlp_st_2013_pc_ED:B-Acetylation), chia_ner:B-Visit), mantra_gsc_en_medline_ner:I-OBJC), scicite_TEXT:cant_determine|result), mayosrs_sts:8), scicite_TEXT:not_supportive|result), bionlp_st_2013_cg_ner:I-DNA_domain_or_region), osiris_ner:B-gene), bionlp_st_2013_gro_ner:I-TranscriptionRepressor), bionlp_st_2013_cg_ED:I-Regulation), bionlp_st_2013_gro_ner:I-RNAMolecule), bionlp_st_2011_ge_ner:I-Protein), mlee_ED:I-Regulation), mlee_COREF:coref), bionlp_st_2013_cg_ED:B-Metastasis), bionlp_st_2013_gro_ner:I-ForkheadWingedHelix), bioinfer_ner:I-Gene), bionlp_st_2013_gro_ner:B-TranscriptionActivatorActivity), medmentions_full_ner:I-T131), genia_term_corpus_ner:B-protein_family_or_group), linnaeus_filtered_ner:I-species), medmentions_st21pv_ner:I-T168), medmentions_full_ner:B-T123), genia_term_corpus_ner:B-cell_type), chemprot_RE:CPR:2|CPR:5), chebi_nactem_fullpaper_ner:B-Chemical), ddi_corpus_ner:I-DRUG_N), scai_chemical_ner:I-FAMILY), bionlp_st_2013_gro_ner:I-Locus), biorelex_ner:B-DNA), mlee_EAE:FromLoc), mlee_ED:B-Synthesis), bionlp_st_2013_pc_ED:I-Inactivation), bionlp_st_2013_gro_EAE:hasPatient2), bionlp_st_2013_gro_ner:B-Transcript), anat_em_ner:B-Organ), chebi_nactem_abstr_ann1_ner:I-Spectral_Data), anat_em_ner:I-Organism_substance), spl_adr_200db_train_ner:B-DrugClass), bionlp_st_2013_gro_ED:I-Splicing), bionlp_st_2013_pc_ED:B-Positive_regulation), bionlp_st_2013_gro_ner:I-ProteinSubunit), bionlp_st_2013_gro_ED:B-ResponseToChemicalStimulus), bionlp_st_2013_gro_ner:B-MutantGene), bionlp_st_2013_pc_ED:B-Binding), bionlp_st_2019_bb_ner:B-Phenotype), bionlp_st_2013_gro_ED:B-CellMotility), diann_iber_eval_en_ner:I-Neg), mantra_gsc_en_medline_ner:B-DISO), mlee_ED:I-Growth), ddi_corpus_ner:B-DRUG_N), biorelex_ner:B-protein-domain), bionlp_st_2013_gro_ner:B-Eukaryote), ncbi_disease_ner:I-CompositeMention), chebi_nactem_fullpaper_ner:I-Spectral_Data), seth_corpus_ner:I-SNP), bionlp_st_2013_gro_ED:B-Elongation), bionlp_st_2013_cg_ner:B-Organ), hprd50_ner:B-protein), biorelex_ner:I-DNA), bionlp_st_2013_gro_ED:I-CellDeath), bionlp_st_2013_cg_ner:I-Organism_subdivision), bionlp_st_2013_cg_ED:B-Planned_process), bionlp_st_2013_cg_ner:B-Cellular_component), chemprot_RE:CPR:2|CPR:9), bionlp_st_2013_pc_ner:B-Cellular_component), bionlp_st_2019_bb_ner:B-Microorganism), ddi_corpus_RE:INT), medmentions_st21pv_ner:B-T038), cellfinder_ner:B-CellLine), bioinfer_ner:I-GeneproteinRNA), bionlp_shared_task_2009_EAE:None), bionlp_st_2011_id_ner:I-Chemical), bionlp_st_2013_gro_ED:B-BindingOfTranscriptionFactorToDNA), bionlp_st_2011_id_ED:B-Protein_catabolism), bionlp_st_2013_cg_ED:B-Cell_differentiation), bionlp_shared_task_2009_ED:B-Negative_regulation), bionlp_st_2013_cg_ED:B-Ubiquitination), nlm_gene_ner:O), bionlp_st_2013_pc_ED:I-Regulation), bionlp_st_2013_gro_ED:I-CellFateDetermination), biorelex_ner:I-mutation), bionlp_st_2013_gro_ner:B-TranscriptionFactorBindingSiteOfDNA), mantra_gsc_en_emea_ner:I-LIVB), biorelex_COREF:None), bionlp_st_2013_gro_ED:I-CellHomeostasis), bionlp_st_2013_gro_ner:B-PhysicalContact), bionlp_st_2013_gro_ner:B-TranscriptionFactor), medmentions_full_ner:B-T167), medmentions_st21pv_ner:B-T091), seth_corpus_ner:I-Gene), bionlp_st_2013_gro_ED:I-ProteinCatabolism), ebm_pico_ner:O), bionlp_st_2011_ge_COREF:coref), bionlp_st_2013_gro_ner:I-bHLHTF), mlee_ner:B-Organ), bionlp_st_2013_gro_ED:B-BindingToMolecularEntity), pdr_ED:I-Cause_of_disease), bionlp_st_2011_epi_ED:B-Glycosylation), medmentions_full_ner:B-T031), bionlp_st_2013_gro_ner:B-TranscriptionFactorComplex), biorelex_ner:B-disease), chebi_nactem_fullpaper_ner:I-Biological_Activity), medmentions_st21pv_ner:I-T092), bionlp_st_2013_cg_COREF:coref), medmentions_full_ner:B-T168), pcr_ner:I-Chemical), mlee_ED:B-Dissociation), genia_relation_corpus_RE:None), medmentions_full_ner:B-T092), genia_term_corpus_ner:I-ANDDNA_domain_or_regionDNA_domain_or_region), bionlp_st_2013_gro_ED:I-FormationOfProteinDNAComplex), mlee_ED:B-Development), medmentions_full_ner:I-T032), bionlp_st_2013_gro_ED:I-RNASplicing), medmentions_full_ner:I-T167), genia_term_corpus_ner:B-protein_NA), bionlp_st_2013_gro_ner:I-TranscriptionActivator), bionlp_st_2013_ge_ner:B-Entity), chemprot_RE:CPR:5), bionlp_shared_task_2009_ED:I-Transcription), an_em_ner:B-Multi-tissue_structure), minimayosrs_sts:2), chia_ner:I-Measurement), chia_RE:Has_temporal), bionlp_shared_task_2009_EAE:Cause), bionlp_st_2013_gro_ED:B-RegulationOfTranscription), biorelex_ner:B-protein-DNA-complex), cellfinder_ner:I-CellComponent), bionlp_st_2013_gro_ED:B-MolecularInteraction), bionlp_st_2013_cg_ED:B-Transcription), medmentions_full_ner:I-UnknownType), mlee_EAE:Site), bionlp_st_2013_gro_ED:I-Homodimerization), bionlp_st_2013_gro_ner:I-Phenotype), chemprot_ner:I-GENE-N), nlm_gene_ner:B-Other), biorelex_ner:B-reagent), genia_term_corpus_ner:B-ANDDNA_family_or_groupDNA_family_or_group), medmentions_full_ner:I-T019), bionlp_st_2013_gro_ner:B-DNABindingSite), nlmchem_ner:O), biorelex_ner:B-organism), chebi_nactem_abstr_ann1_ner:B-Spectral_Data), bionlp_st_2013_cg_ner:I-Multi-tissue_structure), ebm_pico_ner:I-Outcome_Mental), medmentions_full_ner:B-T010), scai_disease_ner:I-DISEASE), mantra_gsc_en_medline_ner:I-GEOG), scai_chemical_ner:B-IUPAC), bionlp_st_2013_gro_ner:I-ProteinBindingSiteOfProtein), chebi_nactem_fullpaper_ner:O), verspoor_2013_ner:B-mutation), biorelex_ner:B-protein-isoform), chemprot_ner:I-GENE-Y), bionlp_st_2013_cg_EAE:CSite), medmentions_full_ner:I-T095), bionlp_st_2013_gro_ED:B-ResponseProcess), mirna_ner:I-Diseases), bionlp_st_2013_gro_ner:I-DNABindingSite), an_em_ner:O), biorelex_ner:O), seth_corpus_RE:AssociatedTo), mlee_EAE:Participant), mlee_ED:B-Negative_regulation), bioscope_abstracts_ner:B-negation), chebi_nactem_fullpaper_ner:I-Metabolite), bionlp_st_2011_epi_ED:B-Demethylation), bionlp_st_2013_gro_ner:I-TranscriptionRepressorActivity), bionlp_shared_task_2009_ner:O), bionlp_shared_task_2009_EAE:Theme), mlee_ED:B-Protein_processing), medmentions_full_ner:B-T029), medmentions_st21pv_ner:I-T058), bionlp_st_2011_ge_ner:B-Protein), chemprot_RE:CPR:2|CPR:4), bionlp_st_2013_ge_ner:B-Protein), scicite_TEXT:background), medmentions_full_ner:I-T029), bionlp_st_2013_ge_ED:B-Negative_regulation), genia_term_corpus_ner:B-ANDcell_typecell_type), bionlp_st_2013_gro_ner:I-Tissue), genia_term_corpus_ner:I-protein_substructure), bionlp_st_2013_gro_ner:I-TranslationFactor), scai_chemical_ner:B-SUM), bionlp_st_2011_ge_ED:I-Gene_expression), minimayosrs_sts:5), medmentions_full_ner:B-T082), bionlp_st_2011_epi_ED:B-Dehydroxylation), genia_term_corpus_ner:B-mono_cell), bionlp_st_2013_gro_ner:B-DNA), medmentions_full_ner:I-T200), medmentions_full_ner:I-T114), ncbi_disease_ner:I-Modifier), bionlp_st_2013_cg_EAE:Theme), medmentions_full_ner:B-T079), bionlp_st_2013_gro_ner:B-ComplexOfProteinAndRNA), genetaggold_ner:B-NEWGENE), bionlp_st_2013_ge_EAE:Cause|Theme), mlee_ner:I-Organism_subdivision), bionlp_st_2013_gro_ED:B-PositiveRegulation), medmentions_full_ner:B-T196), bio_sim_verb_sts:4), bionlp_st_2013_gro_ner:B-Microorganism), bionlp_st_2013_pc_ED:I-Binding), biorelex_ner:B-process), bionlp_st_2013_gro_RE:encodes), biorelex_ner:B-fusion-protein), mirna_ner:I-Non-Specific_miRNAs), biorelex_ner:B-amino-acid), bionlp_st_2013_ge_ED:I-Protein_catabolism), bioinfer_ner:I-DNA_family_or_group), mlee_COREF:None), bionlp_st_2013_cg_ED:I-Positive_regulation), mlee_ED:B-DNA_methylation), bionlp_st_2013_gro_ner:I-Chemical), bionlp_st_2013_gro_ner:B-ProteinBindingSiteOfProtein), mantra_gsc_en_patents_ner:I-DEVI), bionlp_st_2013_gro_ED:B-CellGrowth), mantra_gsc_en_medline_ner:O), medmentions_full_ner:B-T043), chemprot_RE:CPR:7), bionlp_st_2013_gro_ED:B-Heterodimerization), chia_ner:I-Value), medmentions_full_ner:B-T046), medmentions_full_ner:I-T048), bionlp_st_2013_cg_EAE:Site), gnormplus_ner:O), chemprot_ner:B-GENE-Y), bionlp_st_2013_gro_ED:I-SignalingPathway), scicite_TEXT:result), bionlp_st_2011_id_ner:I-Regulon-operon), bionlp_st_2013_gro_ED:B-BindingOfDNABindingDomainOfProteinToDNA), cellfinder_ner:I-CellLine), ebm_pico_ner:I-Outcome_Adverse-effects), medmentions_full_ner:I-T116), bionlp_st_2013_gro_ner:I-DNABindingDomainOfProtein), genia_term_corpus_ner:I-protein_domain_or_region), bionlp_st_2013_gro_ner:B-Nucleosome), medmentions_st21pv_ner:B-T168), chemprot_ner:B-CHEMICAL), bionlp_st_2013_gro_ED:I-CatabolicPathway), bioinfer_ner:B-DNA_family_or_group), bionlp_st_2013_gro_ner:I-bZIPTF), genia_term_corpus_ner:B-body_part), mirna_ner:I-GenesProteins), chebi_nactem_abstr_ann1_ner:B-Protein), an_em_ner:B-Organ), bionlp_st_2013_ge_ED:I-Negative_regulation), genia_term_corpus_ner:B-ANDprotein_family_or_groupprotein_family_or_group), biorelex_ner:I-process), mlee_ner:B-Tissue), medmentions_full_ner:B-T041), mlee_ner:I-Tissue), bionlp_st_2013_gro_RE:hasFunction), bionlp_st_2013_gro_ner:I-TranscriptionFactorActivity), bionlp_st_2011_ge_ED:B-Negative_regulation), biorelex_ner:B-protein-family), bionlp_st_2011_epi_ED:I-Deacetylation), ebm_pico_ner:I-Participant_Condition), genia_term_corpus_ner:B-DNA_domain_or_region), medmentions_full_ner:B-T125), bionlp_st_2013_gro_ED:B-DevelopmentalProcess), bionlp_st_2013_ge_ED:I-Ubiquitination), bionlp_st_2013_gro_ED:B-Cleavage), bionlp_st_2013_gro_ner:I-TATAbox), bionlp_st_2013_cg_ner:B-Gene_or_gene_product), cellfinder_ner:O), bionlp_st_2013_gro_ED:B-CellularComponentOrganizationAndBiogenesis), bionlp_st_2013_ge_ED:I-Regulation), bionlp_st_2013_gro_ner:I-MutatedProtein), bionlp_st_2013_gro_ner:I-bZIP), spl_adr_200db_train_ner:O), bionlp_st_2013_gro_ner:B-LivingEntity), bionlp_st_2011_ge_ED:B-Protein_catabolism), bionlp_st_2013_pc_ED:B-Conversion), mantra_gsc_en_medline_ner:B-CHEM), medmentions_full_ner:I-T026), chebi_nactem_abstr_ann1_ner:I-Protein), medmentions_full_ner:I-T085), bionlp_st_2013_cg_ner:I-Organism_substance), medmentions_full_ner:I-T045), medmentions_full_ner:B-T067), tmvar_v1_ner:B-SNP), biorelex_ner:I-drug), bionlp_st_2013_gro_ner:B-ExperimentalMethod), bionlp_st_2013_cg_ED:I-Cell_death), bionlp_st_2013_pc_ED:B-Hydroxylation), bionlp_st_2013_gro_ner:B-ReporterGeneConstruction), bionlp_st_2013_gro_ED:B-CellularDevelopmentalProcess), bionlp_st_2013_gro_ner:B-TranscriptionActivator), bionlp_st_2013_gro_ED:I-CellCycle), mantra_gsc_en_emea_ner:B-LIVB), verspoor_2013_ner:B-disease), mantra_gsc_en_patents_ner:B-PROC), bc5cdr_ner:I-Chemical), medmentions_full_ner:I-T056), nlm_gene_ner:I-STARGENE), medmentions_full_ner:B-T050), scai_chemical_ner:B-TRIVIALVAR), bionlp_st_2013_gro_ner:B-MolecularFunction), medmentions_full_ner:B-T090), bionlp_st_2013_pc_EAE:Theme), bionlp_st_2013_gro_ED:B-CellCyclePhaseTransition), chebi_nactem_fullpaper_ner:I-Species), medmentions_full_ner:B-T170), bionlp_st_2013_gro_ner:I-ZincCoordinatingDomain), medmentions_full_ner:B-T060), mlee_ED:I-Development), medmentions_full_ner:I-T060), bionlp_st_2013_gro_ner:B-Cell), medmentions_full_ner:I-T037), bionlp_st_2013_gro_ED:B-CellDeath), bionlp_st_2013_gro_ner:B-ForkheadWingedHelix), bionlp_st_2013_gro_ner:B-InorganicChemical), medmentions_full_ner:B-T037), bionlp_st_2013_cg_ner:B-Organism_subdivision), genia_term_corpus_ner:B-RNA_NA), bionlp_st_2013_cg_ED:B-Blood_vessel_development), bionlp_st_2013_gro_ED:B-CellDifferentiation), genia_term_corpus_ner:I-DNA_molecule), bionlp_st_2013_gro_ED:B-IntraCellularProcess), bionlp_st_2013_gro_ner:I-MessengerRNA), bionlp_st_2013_pc_ED:B-Pathway), medmentions_full_ner:I-T086), bionlp_st_2013_ge_ED:I-Transcription), bionlp_st_2019_bb_ner:O), medmentions_full_ner:I-T001), minimayosrs_sts:6), medmentions_full_ner:I-T020), an_em_RE:Part-of), bionlp_shared_task_2009_ner:I-Protein), an_em_ner:B-Pathological_formation), bionlp_st_2013_gro_ner:B-Spliceosome), chebi_nactem_fullpaper_ner:B-Species), mirna_ner:O), bioinfer_RE:PPI), bionlp_st_2013_cg_ner:B-Protein_domain_or_region), anat_em_ner:B-Organism_substance), bionlp_st_2013_gro_ED:I-IntraCellularProcess), bioscope_papers_ner:I-speculation), ddi_corpus_ner:B-DRUG), medmentions_full_ner:I-T078), bionlp_st_2013_gro_ner:I-HMGTF), medmentions_full_ner:B-T053), bionlp_st_2013_gro_ner:B-HomeoBox), minimayosrs_sts:3), mlee_ner:B-Multi-tissue_structure), biosses_sts:4), mlee_ED:I-Gene_expression), medmentions_full_ner:B-T004), chia_ner:I-Drug), bionlp_st_2013_gro_ner:B-FusionOfGeneWithReporterGene), genia_term_corpus_ner:I-cell_line), ddi_corpus_RE:ADVISE), bioscope_abstracts_ner:I-speculation), chebi_nactem_abstr_ann1_ner:I-Metabolite), bionlp_st_2013_gro_ner:I-ExpressionProfiling), medmentions_full_ner:B-T016), bionlp_st_2013_gro_ner:I-Holoenzyme), bionlp_st_2013_gro_ED:B-TranscriptionTermination), bionlp_st_2013_cg_ner:I-Organ), tmvar_v1_ner:B-DNAMutation), bionlp_st_2013_ge_EAE:CSite), genia_term_corpus_ner:B-RNA_substructure), medmentions_full_ner:I-T170), medmentions_full_ner:B-T093), genia_term_corpus_ner:I-inorganic), bionlp_st_2013_gro_ner:B-bHLH), mlee_ED:B-Cell_proliferation), bionlp_st_2013_gro_RE:hasPart), bionlp_st_2013_cg_ED:B-Pathway), bionlp_st_2013_gro_ner:B-BasicDomain), bionlp_st_2013_gro_ED:I-PositiveRegulationOfGeneExpression), mayosrs_sts:4), medmentions_st21pv_ner:B-T037), an_em_ner:B-Anatomical_system), bionlp_st_2013_gro_ner:B-Conformation), bionlp_st_2013_gro_ner:I-GeneRegion), bionlp_st_2013_gro_ED:I-PosttranslationalModification), genia_term_corpus_ner:I-RNA_NA), bionlp_st_2011_ge_EAE:Cause), medmentions_full_ner:B-T019), medmentions_full_ner:I-T069), scai_chemical_ner:B-TRIVIAL), bionlp_st_2013_ge_ED:I-Protein_modification), bionlp_st_2013_pc_ED:B-Degradation), mlee_ner:B-Gene_or_gene_product), bionlp_st_2013_gro_ED:I-Phosphorylation), biosses_sts:3), mlee_ED:B-Acetylation), mlee_ED:I-Negative_regulation), bionlp_st_2013_ge_ED:B-Protein_catabolism), chia_RE:Has_value|Subsumes), bionlp_st_2013_gro_ner:B-Promoter), bionlp_shared_task_2009_ED:I-Phosphorylation), medmentions_full_ner:B-T195), bionlp_st_2013_cg_ED:I-Binding), bionlp_st_2011_id_ner:I-Organism), medmentions_full_ner:I-T073), bionlp_st_2013_gro_ner:I-OrganicChemical), ebm_pico_ner:B-Participant_Age), verspoor_2013_ner:B-Concepts_Ideas), biosses_sts:2), bionlp_st_2013_cg_ED:B-Remodeling), bionlp_st_2013_gro_ner:B-tRNA), medmentions_full_ner:I-T043), an_em_COREF:None), bionlp_st_2011_epi_ED:B-Hydroxylation), mlee_ner:I-Immaterial_anatomical_entity), bionlp_st_2013_ge_ED:B-Ubiquitination), medmentions_full_ner:B-T065), bionlp_st_2019_bb_RE:None), bionlp_st_2013_gro_ED:B-CellAging), mlee_ED:B-Phosphorylation), bionlp_st_2013_gro_ED:I-PositiveRegulationOfTranscriptionOfGene), ebm_pico_ner:I-Participant_Sample-size), biorelex_COREF:coref), bionlp_shared_task_2009_ED:I-Protein_catabolism), bionlp_st_2013_gro_ner:I-DNAMolecule), bionlp_st_2013_gro_ner:I-Enzyme), genia_term_corpus_ner:I-protein_family_or_group), genia_term_corpus_ner:I-ANDprotein_moleculeprotein_molecule), biorelex_ner:B-gene), bionlp_st_2013_gro_ED:I-ProteinTransport), bionlp_st_2013_gro_ED:B-MolecularProcess), chebi_nactem_abstr_ann1_ner:O), bionlp_st_2013_gro_ED:B-BindingOfProteinToProteinBindingSiteOfDNA), chemprot_RE:None), bionlp_st_2013_pc_ner:O), mayosrs_sts:7), bionlp_st_2013_pc_ED:B-Negative_regulation), bionlp_st_2013_gro_ner:B-Sequence), medmentions_full_ner:B-T103), bionlp_st_2013_gro_ner:B-Gene), chia_ner:B-Observation), chia_ner:B-Scope), an_em_COREF:coref), ebm_pico_ner:B-Participant_Sex), mlee_ED:B-Regulation), bionlp_st_2013_gro_ner:B-ComplexOfProteinAndDNA), bionlp_st_2013_gro_ner:B-Phenotype), verspoor_2013_ner:I-age), medmentions_full_ner:B-T120), bionlp_st_2011_epi_ED:B-Deacetylation), bionlp_st_2013_gro_ner:B-Tissue), bionlp_st_2013_gro_ner:B-MolecularEntity), bionlp_st_2013_ge_ED:I-Binding), biorelex_ner:I-peptide), medmentions_st21pv_ner:I-T097), iepa_RE:None), medmentions_full_ner:B-T001), bionlp_shared_task_2009_ED:I-Regulation), bionlp_st_2013_gro_ner:B-FusionProtein), medmentions_full_ner:I-T194), biorelex_ner:B-cell), medmentions_full_ner:I-T096), chebi_nactem_fullpaper_ner:I-Chemical_Structure), medmentions_full_ner:I-T018), medmentions_full_ner:B-T201), chia_RE:None), medmentions_full_ner:B-T054), biorelex_RE:None), ebm_pico_ner:I-Intervention_Pharmacological), bionlp_st_2013_gro_ED:I-CellDifferentiation), bionlp_st_2013_cg_ED:I-Cell_proliferation), bionlp_st_2013_gro_EAE:hasPatient4), bionlp_st_2011_id_EAE:Participant), bionlp_st_2013_gro_ner:B-Substrate), bionlp_st_2011_ge_ED:B-Transcription), verspoor_2013_ner:B-cohort-patient), ebm_pico_ner:B-Outcome_Other), biorelex_ner:B-protein-motif), bionlp_st_2013_gro_ner:B-Ion), mlee_ED:B-Translation), bionlp_st_2013_gro_ner:B-ZincCoordinatingDomain), ebm_pico_ner:B-Participant_Condition), bionlp_st_2011_ge_ED:B-Phosphorylation), nlm_gene_ner:I-Gene), bionlp_st_2013_gro_ner:B-Locus), bionlp_st_2013_gro_ner:B-SecondMessenger), bionlp_st_2013_cg_ED:B-Infection), bionlp_st_2011_epi_EAE:Contextgene), chia_ner:B-Drug), bionlp_st_2019_bb_ner:I-Habitat), bionlp_shared_task_2009_COREF:coref), bionlp_st_2013_gro_ner:I-MolecularEntity), mlee_ner:B-Cellular_component), genia_term_corpus_ner:B-other_organic_compound), bionlp_st_2013_gro_ED:I-CellAdhesion), anat_em_ner:B-Cellular_component), bionlp_st_2013_gro_ED:B-ProteinMetabolism), seth_corpus_ner:B-SNP), pcr_ner:O), bionlp_st_2013_gro_ED:I-CellCyclePhase), mlee_ner:B-DNA_domain_or_region), mantra_gsc_en_emea_ner:B-PHYS), bionlp_st_2013_cg_ner:B-Multi-tissue_structure), genia_term_corpus_ner:I-virus), bionlp_shared_task_2009_ED:I-Positive_regulation), medmentions_full_ner:I-T122), mantra_gsc_en_patents_ner:B-DISO), bionlp_st_2013_gro_ner:B-Heterochromatin), genia_term_corpus_ner:O), mlee_ED:I-Positive_regulation), an_em_ner:B-Cell), bionlp_st_2013_cg_ner:B-Simple_chemical), bionlp_st_2013_gro_ner:I-Peptide), chemprot_RE:CPR:6), chebi_nactem_abstr_ann1_ner:B-Chemical), genia_term_corpus_ner:I-cell_type), genia_term_corpus_ner:I-other_name), bionlp_st_2013_cg_EAE:FromLoc), bionlp_st_2013_gro_ner:B-RNAMolecule), bionlp_st_2013_gro_ner:B-SequenceHomologyAnalysis), medmentions_full_ner:I-T042), tmvar_v1_ner:B-ProteinMutation), pdr_ner:O), bionlp_st_2013_gro_ED:B-MetabolicPathway), medmentions_full_ner:I-T057), bionlp_st_2011_ge_EAE:CSite), bionlp_st_2013_gro_ED:B-BindingToProtein), verspoor_2013_ner:B-size), mlee_ED:B-Transcription), bionlp_st_2013_gro_ner:I-BindingSiteOfProtein), bionlp_st_2011_id_ner:B-Chemical), bionlp_st_2013_gro_ner:I-Ribosome), verspoor_2013_ner:B-Phenomena), medmentions_st21pv_ner:B-T017), medmentions_full_ner:B-T028), chia_ner:B-Temporal), chia_ner:I-Temporal), biorelex_ner:B-assay), bionlp_st_2013_cg_ED:I-Pathway), genia_term_corpus_ner:B-tissue), nlmchem_ner:I-Chemical), mirna_ner:I-Specific_miRNAs), bionlp_st_2013_cg_ED:B-Negative_regulation), medmentions_full_ner:I-T012), mlee_ner:B-Organism_substance), bionlp_st_2013_gro_ner:B-TranscriptionCoactivator), genia_term_corpus_ner:I-tissue), genia_term_corpus_ner:B-amino_acid_monomer), mantra_gsc_en_patents_ner:I-ANAT), medmentions_st21pv_ner:I-T082), mantra_gsc_en_emea_ner:B-DEVI), bionlp_st_2013_gro_RE:None), medmentions_full_ner:I-T052), bionlp_st_2011_ge_ED:I-Phosphorylation), mqp_sts:3), bionlp_st_2013_cg_ED:B-Glycosylation), an_em_ner:B-Immaterial_anatomical_entity), bionlp_st_2013_gro_ner:B-Chemical), bionlp_st_2013_gro_ED:B-GeneSilencing), bionlp_shared_task_2009_ED:B-Transcription), genia_term_corpus_ner:B-other_artificial_source), medmentions_full_ner:B-T072), mantra_gsc_en_medline_ner:B-GEOG), mirna_ner:B-Specific_miRNAs), medmentions_full_ner:B-T190), medmentions_full_ner:I-T031), bionlp_st_2013_gro_ED:B-TranscriptionInitiation), bionlp_st_2013_gro_ner:I-DoubleStrandDNA), bionlp_st_2013_gro_ED:B-Translation), scai_chemical_ner:I-IUPAC), chemdner_ner:O), bionlp_st_2013_gro_ED:B-G1Phase), genia_term_corpus_ner:B-peptide), bionlp_st_2013_gro_ED:B-PosttranslationalModification), bionlp_st_2011_epi_EAE:Site), an_em_ner:I-Organism_subdivision), bionlp_st_2013_cg_ner:B-Developing_anatomical_structure), bionlp_st_2013_gro_EAE:hasPatient3), bionlp_st_2013_gro_ner:B-MessengerRNA), medmentions_full_ner:B-T171), bionlp_st_2013_ge_EAE:Theme2), bionlp_st_2013_gro_ner:B-RNA), chemprot_RE:CPR:4|CPR:9), genia_term_corpus_ner:I-amino_acid_monomer), an_em_ner:B-Organism_substance), bionlp_st_2013_gro_ED:I-RNAProcessing), genia_term_corpus_ner:I-body_part), medmentions_full_ner:B-T052), chia_ner:B-Procedure), bionlp_st_2013_gro_ner:B-Prokaryote), bionlp_st_2011_ge_ED:I-Positive_regulation), medmentions_full_ner:I-T061), genia_term_corpus_ner:B-ANDprotein_subunitprotein_subunit), medmentions_full_ner:B-T096), bionlp_st_2013_cg_ED:B-DNA_demethylation), bionlp_st_2011_epi_ED:B-Deubiquitination), medmentions_full_ner:B-T038), medmentions_full_ner:I-T109), bionlp_st_2013_gro_ED:I-SPhase), bionlp_st_2013_gro_ner:I-EukaryoticCell), pdr_ner:I-Plant), bionlp_st_2013_gro_ED:I-Binding), medmentions_full_ner:I-T092), mantra_gsc_en_medline_ner:I-CHEM), bionlp_st_2011_id_ED:B-Phosphorylation), bionlp_st_2013_cg_ED:I-Metabolism), bionlp_st_2013_gro_ED:B-PositiveRegulationOfGeneExpression), chebi_nactem_fullpaper_ner:B-Biological_Activity), ncbi_disease_ner:B-SpecificDisease), mlee_ner:B-Organism), medmentions_full_ner:B-T063), bionlp_st_2013_cg_ED:B-Glycolysis), medmentions_full_ner:I-T168), medmentions_full_ner:I-T064), bionlp_st_2013_gro_ner:B-DNAMolecule), mlee_ED:B-Binding), bioscope_abstracts_ner:O), biorelex_ner:B-protein-complex), bionlp_st_2013_gro_EAE:None), mantra_gsc_en_medline_ner:I-PHEN), bionlp_st_2013_cg_ner:B-Pathological_formation), mlee_ED:I-Cell_proliferation), bionlp_st_2013_pc_ner:I-Simple_chemical), anat_em_ner:I-Cancer), an_em_ner:I-Anatomical_system), medmentions_full_ner:I-T072), bionlp_st_2013_gro_ner:B-ProteinComplex), bionlp_st_2013_gro_ED:I-NegativeRegulationOfGeneExpression), bio_sim_verb_sts:2), bionlp_st_2013_gro_ner:B-DoubleStrandDNA), medmentions_full_ner:I-T066), pdr_ED:B-Treatment_of_disease), seth_corpus_ner:O), bionlp_st_2013_ge_EAE:ToLoc), bionlp_st_2013_gro_ED:B-Localization), bionlp_st_2013_gro_ner:I-Exon), medmentions_full_ner:B-T070), biorelex_ner:I-experiment-tag), medmentions_full_ner:B-T068), medmentions_full_ner:I-T034), cellfinder_ner:B-Species), biorelex_ner:I-protein-RNA-complex), medmentions_st21pv_ner:I-T201), biosses_sts:0), bionlp_st_2013_cg_ner:B-Organism_substance), bionlp_st_2013_gro_ner:I-FusionGene), genia_term_corpus_ner:B-protein_complex), mantra_gsc_en_emea_ner:B-DISO), bionlp_st_2013_gro_ED:I-RegulationOfGeneExpression), medmentions_full_ner:I-T125), bionlp_st_2013_ge_ner:I-Entity), bionlp_st_2011_rel_ner:B-Entity), medmentions_st21pv_ner:I-T031), medmentions_full_ner:B-T099), bionlp_st_2013_gro_ner:B-TATAbox), bionlp_st_2013_gro_ner:I-BindingAssay), bionlp_st_2019_bb_ner:I-Microorganism), medmentions_full_ner:I-T059), medmentions_full_ner:B-T114), medmentions_st21pv_ner:I-T022), bionlp_st_2013_pc_ED:B-Inactivation), spl_adr_200db_train_ner:B-Factor), bionlp_st_2013_gro_ner:B-Function), bionlp_st_2013_gro_ner:B-GeneRegion), medmentions_full_ner:I-T033), bionlp_st_2013_cg_COREF:None), bionlp_st_2013_gro_ner:B-HMG), bionlp_shared_task_2009_ED:B-Binding), bionlp_st_2013_gro_ner:B-Operon), chemprot_ner:I-CHEMICAL), ebm_pico_ner:I-Outcome_Pain), medmentions_full_ner:I-T053), bionlp_st_2013_gro_ner:B-Protein), ebm_pico_ner:I-Outcome_Physical), biorelex_ner:I-organelle), verspoor_2013_ner:I-cohort-patient), genia_term_corpus_ner:I-ANDprotein_family_or_groupprotein_family_or_group), genia_term_corpus_ner:I-DNA_family_or_group), bionlp_st_2013_gro_ner:I-ProteinBindingSiteOfDNA), bionlp_st_2013_ge_ED:B-Protein_modification), bionlp_st_2011_epi_ED:B-Dephosphorylation), bionlp_st_2013_gro_ner:B-RNAPolymerase), an_em_ner:I-Developing_anatomical_structure), bionlp_st_2013_gro_ner:B-CellComponent), biorelex_ner:I-chemical), bionlp_st_2013_gro_ED:B-Mutation), gnormplus_ner:B-DomainMotif), bionlp_st_2013_gro_ner:B-Peptide), bionlp_st_2013_pc_ED:B-Translation), biorelex_ner:B-tissue), bionlp_st_2011_ge_EAE:AtLoc), biorelex_ner:I-RNA), bionlp_st_2013_pc_ED:B-Regulation), pico_extraction_ner:B-participant), chia_RE:Has_qualifier), chia_ner:I-Visit), medmentions_full_ner:I-T008), bionlp_st_2013_ge_ED:B-Phosphorylation), medmentions_full_ner:I-T016), pdr_ner:I-Disease), pdr_ED:B-Cause_of_disease), verspoor_2013_RE:has), verspoor_2013_ner:I-ethnicity), bionlp_st_2013_pc_EAE:Participant), genia_term_corpus_ner:I-protein_NA), ehr_rel_sts:7), medmentions_full_ner:I-T079), bionlp_st_2013_gro_ner:I-SmallInterferingRNA), bionlp_st_2013_cg_ED:O), pico_extraction_ner:I-intervention), biorelex_ner:I-protein-domain), chebi_nactem_abstr_ann1_ner:I-Chemical), medmentions_full_ner:I-T011), bionlp_st_2013_gro_ED:B-RegulationOfFunction), mlee_ner:O), mqp_sts:1), bioscope_papers_ner:O), chia_RE:Has_scope), an_em_ner:I-Pathological_formation), bc5cdr_ner:B-Disease), gnormplus_ner:I-DomainMotif), bionlp_st_2013_gro_ner:I-OpenReadingFrame), mlee_ner:I-Cellular_component), medmentions_full_ner:I-T195), chemprot_RE:CPR:2|CPR:6), spl_adr_200db_train_ner:B-AdverseReaction), bionlp_st_2011_ge_ED:B-Positive_regulation), muchmore_en_ner:O), bionlp_st_2013_gro_ner:I-Promoter), bionlp_st_2013_gro_EAE:hasPatient5), bionlp_st_2013_gro_ner:I-RegulatoryDNARegion), bionlp_st_2013_gro_ner:I-RuntLikeDomain), bionlp_st_2013_cg_ED:B-Carcinogenesis), medmentions_full_ner:B-T040), medmentions_full_ner:I-T103), medmentions_st21pv_ner:I-T037), mlee_EAE:ToLoc), mlee_EAE:Instrument), medmentions_full_ner:B-T008), ebm_pico_ner:B-Intervention_Psychological), bionlp_st_2013_gro_ner:B-Stress), biorelex_ner:B-protein-RNA-complex), bionlp_st_2013_gro_ED:B-RNAProcessing), bionlp_st_2013_gro_ED:B-SignalingPathway), genia_term_corpus_ner:B-multi_cell), bionlp_st_2013_gro_ner:B-ChromosomalDNA), anat_em_ner:I-Cellular_component), spl_adr_200db_train_ner:I-Negation), medmentions_full_ner:I-T087), bionlp_st_2013_ge_ED:B-Deacetylation), bionlp_st_2013_gro_ner:B-RegulatoryDNARegion), ebm_pico_ner:B-Outcome_Pain), bionlp_st_2011_ge_EAE:None), bionlp_st_2013_gro_ED:I-RNABiosynthesis), bionlp_st_2013_gro_ner:I-HomeoboxTF), mantra_gsc_en_patents_ner:I-LIVB), bionlp_st_2013_gro_ner:I-UpstreamRegulatorySequence), ddi_corpus_ner:I-DRUG), bionlp_st_2011_ge_ED:O), mantra_gsc_en_medline_ner:B-OBJC), bionlp_st_2013_gro_ED:I-ProteinBiosynthesis), mayosrs_sts:3), linnaeus_filtered_ner:O), chia_RE:Has_multiplier), bionlp_st_2011_ge_ED:B-Localization), medmentions_full_ner:B-T116), bionlp_st_2013_cg_EAE:ToLoc), cellfinder_ner:B-CellType), medmentions_full_ner:B-T007), ehr_rel_sts:3), anat_em_ner:B-Developing_anatomical_structure), bionlp_st_2013_gro_ner:I-MutantProtein), bionlp_st_2013_gro_ED:B-NegativeRegulationOfGeneExpression), chemprot_ner:B-GENE-N), mlee_ED:B-Blood_vessel_development), medmentions_full_ner:I-T077), bionlp_st_2013_gro_ner:B-TranscriptionRepressorActivity), biorelex_ner:B-brand), medmentions_full_ner:B-T091), bionlp_st_2013_pc_EAE:Cause|Theme), bionlp_st_2011_id_ED:B-Positive_regulation), ebm_pico_ner:B-Outcome_Mental), bionlp_st_2013_gro_ner:B-EukaryoticCell), bionlp_st_2013_pc_ED:I-Positive_regulation), genia_term_corpus_ner:I-ANDprotein_subunitprotein_subunit), medmentions_full_ner:I-T184), bionlp_st_2011_id_ner:B-Protein), mayosrs_sts:1), mantra_gsc_en_patents_ner:B-CHEM), mlee_ED:B-Ubiquitination), biorelex_ner:B-mutation), mantra_gsc_en_medline_ner:I-DEVI), bionlp_st_2013_ge_ED:I-Positive_regulation), linnaeus_ner:O), bionlp_st_2013_gro_ner:B-Enzyme), medmentions_st21pv_ner:B-T201), medmentions_full_ner:B-T056), bionlp_st_2011_id_EAE:Cause), bionlp_st_2013_gro_ED:B-BindingToRNA), verspoor_2013_ner:B-Disorder), tmvar_v1_ner:I-DNAMutation), mantra_gsc_en_patents_ner:B-OBJC), medmentions_full_ner:B-T073), bionlp_st_2013_gro_ED:I-CellularProcess), bionlp_st_2013_gro_ED:I-NegativeRegulation), anat_em_ner:I-Tissue), bioinfer_ner:I-Individual_protein), medmentions_full_ner:B-T191), cellfinder_ner:I-Anatomy), chia_ner:I-Scope), ncbi_disease_ner:B-Modifier), bionlp_st_2013_cg_ED:I-Growth), medmentions_st21pv_ner:B-T082), bionlp_st_2013_gro_ED:I-GeneSilencing), mlee_ED:B-Pathway), bionlp_st_2013_cg_ner:I-Cellular_component), medmentions_full_ner:I-T054), chia_ner:B-Condition), verspoor_2013_ner:B-ethnicity), genia_term_corpus_ner:I-carbohydrate), mlee_ner:B-Developing_anatomical_structure), medmentions_full_ner:B-T012), bionlp_st_2013_gro_ner:I-AP2EREBPRelatedDomain), bionlp_st_2013_gro_ED:B-Silencing), mayosrs_sts:5), bionlp_st_2013_gro_ner:I-TranscriptionFactorComplex), genia_term_corpus_ner:B-ANDprotein_substructureprotein_substructure), bionlp_shared_task_2009_ED:B-Regulation), medmentions_full_ner:B-T064), bionlp_st_2013_cg_ner:I-Tissue), bionlp_st_2013_gro_ner:B-Intron), bionlp_st_2013_cg_ED:I-Catabolism), mlee_ED:B-Localization), genia_term_corpus_ner:I-DNA_domain_or_region), chia_ner:B-Device), medmentions_full_ner:B-T026), genia_term_corpus_ner:B-carbohydrate), nlmchem_ner:B-Chemical), bionlp_st_2013_gro_ED:B-Disease), anat_em_ner:I-Immaterial_anatomical_entity), genia_term_corpus_ner:B-DNA_molecule), medmentions_full_ner:I-T007), bionlp_st_2013_gro_ner:I-DNAFragment), genia_term_corpus_ner:I-RNA_domain_or_region), bionlp_st_2013_gro_ner:B-MutatedProtein), ebm_pico_ner:I-Outcome_Mortality), bionlp_st_2013_gro_ner:B-ProteinCodingRegion), ebm_pico_ner:I-Intervention_Educational), genia_term_corpus_ner:B-ANDcell_linecell_line), spl_adr_200db_train_ner:I-AdverseReaction), bionlp_st_2013_ge_EAE:Site), bionlp_st_2013_cg_ED:I-Cell_transformation), genia_term_corpus_ner:B-protein_substructure), chia_ner:B-Mood), bionlp_st_2013_gro_ED:I-Transport), bionlp_st_2011_ge_ED:I-Negative_regulation), medmentions_full_ner:I-T058), biorelex_ner:B-parameter), medmentions_st21pv_ner:O), bionlp_st_2013_ge_ED:O), bionlp_st_2013_pc_EAE:ToLoc), cellfinder_ner:I-Species), medmentions_full_ner:B-T069), bionlp_st_2013_gro_ED:B-TranscriptionOfGene), chia_ner:I-Condition), mirna_ner:I-Relation_Trigger), bionlp_st_2013_gro_ED:B-FormationOfProteinDNAComplex), bionlp_st_2013_gro_ner:I-InorganicChemical), bionlp_st_2011_id_ner:B-Entity), bionlp_st_2013_gro_ner:B-PrimaryStructure), an_em_ner:I-Cellular_component), medmentions_full_ner:B-T021), mlee_ner:B-Anatomical_system), bionlp_st_2013_pc_ED:B-Localization), chebi_nactem_fullpaper_ner:B-Spectral_Data), mlee_EAE:CSite), bionlp_st_2013_cg_ED:I-Negative_regulation), mlee_ED:I-Breakdown), bionlp_shared_task_2009_ED:B-Localization), bionlp_shared_task_2009_ED:B-Phosphorylation), medmentions_st21pv_ner:I-T170), pico_extraction_ner:I-participant), bionlp_st_2013_cg_ED:B-Breakdown), bionlp_st_2013_gro_ner:I-Nucleotide), chia_ner:B-Person), medmentions_full_ner:B-T194), chia_RE:Subsumes), mlee_ED:B-Metabolism), medmentions_full_ner:I-T099), bionlp_st_2013_gro_ner:I-Protein), an_em_ner:B-Tissue), bioscope_papers_ner:B-speculation), medmentions_st21pv_ner:B-T170), bionlp_st_2013_gro_ED:B-ExperimentalIntervention), bionlp_st_2011_epi_ED:I-Glycosylation), mlee_ED:B-Gene_expression), bionlp_st_2013_gro_ner:B-TranscriptionFactorActivity), bionlp_st_2011_epi_ED:B-Phosphorylation), mlee_ED:B-Breakdown), mlee_RE:None), bionlp_st_2013_pc_ED:B-Dephosphorylation), mlee_ner:B-Organism_subdivision), bionlp_st_2013_cg_EAE:Cause), bionlp_st_2013_gro_ner:B-RNAPolymeraseII), medmentions_st21pv_ner:B-T098), bionlp_st_2013_ge_ED:I-Phosphorylation), chia_RE:Has_negation), spl_adr_200db_train_ner:I-Factor), bionlp_st_2013_gro_ED:I-OrganismalProcess), bionlp_shared_task_2009_ED:B-Protein_catabolism), verspoor_2013_ner:I-mutation), bionlp_st_2013_gro_ED:B-Phosphorylation), bionlp_st_2013_ge_EAE:Site2), medmentions_full_ner:B-T129), seth_corpus_ner:B-RS), ebm_pico_ner:I-Participant_Sex), genia_term_corpus_ner:I-protein_molecule), medmentions_full_ner:B-T192), bionlp_st_2013_pc_EAE:None), medmentions_full_ner:I-T094), bionlp_st_2013_ge_ED:I-Gene_expression), bionlp_st_2013_cg_ED:B-Mutation), medmentions_st21pv_ner:B-T033), mlee_ner:B-Drug_or_compound), medmentions_full_ner:B-T061), pcr_ner:I-Herb), bionlp_st_2013_gro_ner:I-MolecularStructure), bionlp_st_2013_cg_ED:I-Development), medmentions_full_ner:B-T032), bionlp_st_2013_pc_ED:B-Dissociation), bionlp_st_2013_pc_ED:I-Localization), genia_term_corpus_ner:B-nucleotide), ebm_pico_ner:B-Outcome_Mortality), bionlp_st_2011_rel_ner:O), bionlp_st_2013_gro_ner:I-Cell), medmentions_full_ner:I-T014), mantra_gsc_en_emea_ner:B-ANAT), medmentions_full_ner:I-T055), medmentions_full_ner:B-T101), bionlp_st_2013_gro_ED:I-RegulationOfTranscription), bionlp_st_2013_gro_ner:B-TranscriptionRepressor), bionlp_st_2013_gro_ED:B-ProteinBiosynthesis), biorelex_ner:I-cell), verspoor_2013_RE:None), bionlp_st_2013_cg_ED:I-Blood_vessel_development), genia_term_corpus_ner:I-ANDcell_linecell_line), bionlp_st_2011_id_ED:B-Transcription), medmentions_full_ner:I-T204), tmvar_v1_ner:I-SNP), chia_RE:Has_value), biorelex_ner:I-protein-family), bionlp_st_2013_cg_ED:B-Death), biorelex_ner:I-experimental-construct), mantra_gsc_en_medline_ner:I-PHYS), genia_term_corpus_ner:B-), bionlp_st_2011_ge_EAE:Cause|Theme), medmentions_full_ner:I-T203), bionlp_st_2013_gro_ED:B-CellAdhesion), bionlp_st_2013_gro_ner:B-TranslationFactor), ebm_pico_ner:I-Intervention_Control), bionlp_st_2011_ge_ED:I-Protein_catabolism), bionlp_st_2013_gro_ner:B-BetaScaffoldDomain_WithMinorGrooveContacts), bionlp_st_2013_gro_ED:I-BindingOfTFToTFBindingSiteOfProtein), genia_term_corpus_ner:I-atom), scai_chemical_ner:B-), bionlp_st_2013_gro_ner:I-Stress), bionlp_st_2013_pc_ED:I-Pathway), bionlp_st_2011_epi_ED:I-Catalysis), mlee_ner:B-Pathological_formation), bionlp_st_2013_gro_ner:B-Exon), medmentions_full_ner:I-T083), bionlp_st_2013_cg_ED:B-Translation), chia_ner:B-Measurement), bionlp_st_2011_id_ner:B-Regulon-operon), pdr_ED:I-Treatment_of_disease), bionlp_st_2013_gro_ner:I-TranscriptionActivatorActivity), bionlp_st_2011_epi_ED:I-DNA_methylation), osiris_ner:I-gene), bionlp_st_2013_cg_ner:O), pdr_ner:B-Plant), bionlp_st_2013_gro_ED:B-PositiveRegulationOfTranscription), mantra_gsc_en_patents_ner:B-ANAT), medmentions_full_ner:I-T101), ncbi_disease_ner:I-SpecificDisease), medmentions_full_ner:B-T034), linnaeus_filtered_ner:B-species), bionlp_st_2011_ge_ED:B-Binding), bionlp_st_2013_gro_EAE:hasAgent|hasPatient), bionlp_st_2013_gro_ner:I-Histone), bionlp_st_2013_cg_ED:I-Carcinogenesis), medmentions_full_ner:I-T192), medmentions_full_ner:B-T080), bionlp_st_2013_ge_EAE:None), bionlp_st_2013_gro_ner:B-BindingSiteOfProtein), bionlp_st_2013_gro_ner:B-TranscriptionCorepressor), ehr_rel_sts:4), chemprot_RE:CPR:3|CPR:9), mlee_ner:I-Gene_or_gene_product), ddi_corpus_RE:MECHANISM), bionlp_st_2011_ge_ED:I-Localization), bionlp_st_2013_gro_ED:I-CellularDevelopmentalProcess), medmentions_full_ner:B-T098), genia_term_corpus_ner:B-protein_subunit), mantra_gsc_en_emea_ner:I-PROC), bionlp_st_2013_gro_ner:I-ProteinCodingDNARegion), scicite_TEXT:method), bionlp_st_2013_gro_ner:I-CellComponent), genia_term_corpus_ner:I-peptide), medmentions_full_ner:B-T100), bionlp_st_2013_pc_EAE:Cause), medmentions_full_ner:B-T049), bionlp_st_2013_gro_ED:B-Transport), scai_chemical_ner:O), medmentions_full_ner:B-T083), diann_iber_eval_en_ner:I-Disability), bionlp_st_2013_pc_ED:I-Translation), medmentions_full_ner:I-T039), anat_em_ner:B-Organism_subdivision), bionlp_st_2013_gro_ner:I-Ligand), bionlp_st_2013_cg_ED:B-Metabolism), bionlp_st_2013_pc_ED:I-Phosphorylation), bionlp_st_2011_id_ner:O), mantra_gsc_en_patents_ner:B-PHEN), bionlp_st_2013_gro_ner:I-Nucleus), biorelex_ner:I-fusion-protein), bionlp_st_2013_gro_ED:B-Affecting), bionlp_st_2013_gro_ner:I-ComplexOfProteinAndRNA), bionlp_st_2013_gro_ED:B-Methylation), bionlp_st_2013_gro_ner:I-NuclearReceptor), bionlp_st_2013_gro_ED:B-Mitosis), bionlp_st_2013_gro_ED:I-PositiveRegulation), bionlp_st_2013_gro_ED:B-ModificationOfMolecularEntity), pdr_ED:O), bionlp_st_2013_cg_ner:B-Cell), chia_RE:OR), bionlp_st_2013_cg_ner:I-Gene_or_gene_product), bionlp_st_2013_gro_ner:B-Holoenzyme), bionlp_shared_task_2009_EAE:ToLoc), verspoor_2013_ner:I-disease), biorelex_ner:I-tissue), muchmore_en_ner:B-umlsterm), bionlp_st_2013_gro_ED:B-NegativeRegulationOfTranscriptionByTranscriptionRepressor), ehr_rel_sts:5), bionlp_shared_task_2009_ner:B-Protein), mantra_gsc_en_patents_ner:B-LIVB), medmentions_st21pv_ner:I-T038), bionlp_st_2013_gro_ner:B-TranscriptionRegulator), medmentions_full_ner:O), medmentions_full_ner:I-T002), bionlp_st_2013_gro_ner:I-DNARegion), chemprot_RE:CPR:2|CPR:3), medmentions_full_ner:B-T089), bionlp_st_2013_gro_ED:I-BindingToProtein), bionlp_st_2013_cg_EAE:AtLoc), medmentions_full_ner:B-T077), mirna_ner:B-Species), bionlp_st_2013_gro_ner:I-TranscriptionRegulator), bionlp_st_2013_gro_ner:I-tRNA), bionlp_st_2013_gro_ner:I-Operon), bionlp_st_2011_epi_ED:B-Deglycosylation), chemprot_ner:O), mlee_ner:I-Multi-tissue_structure), genia_term_corpus_ner:B-AND_NOTcell_typecell_type), medmentions_full_ner:I-T023), medmentions_full_ner:B-T094), chemprot_RE:CPR:1), mlee_ED:B-Planned_process), scai_chemical_ner:B-ABBREVIATION), bionlp_st_2013_gro_ner:B-HomeoboxTF), bionlp_st_2011_id_ED:B-Process), bionlp_st_2013_gro_ner:I-Virus), genia_term_corpus_ner:B-atom), chemprot_RE:CPR:3|CPR:4), bionlp_st_2013_gro_RE:fromSpecies), bionlp_st_2011_id_ED:B-Binding), bionlp_st_2011_id_EAE:None), medmentions_full_ner:B-T203), bionlp_st_2013_gro_ner:B-ThreeDimensionalMolecularStructure), muchmore_en_ner:I-umlsterm), bionlp_st_2013_cg_ner:I-Developing_anatomical_structure), bionlp_st_2013_pc_EAE:FromLoc), genetaggold_ner:I-NEWGENE), bionlp_st_2013_ge_EAE:Theme), bionlp_st_2013_gro_ner:I-Attenuator), nlm_gene_ner:I-Other), medmentions_full_ner:B-T109), osiris_ner:I-variant), chia_ner:I-Mood), medmentions_full_ner:I-T068), minimayosrs_sts:4), bionlp_st_2013_gro_ED:B-CellCyclePhase), bionlp_st_2019_bb_ner:B-Habitat), medmentions_full_ner:I-T097), ehr_rel_sts:6), bionlp_st_2011_epi_ED:I-Methylation), bioinfer_ner:I-Protein_family_or_group), medmentions_st21pv_ner:I-T098), bionlp_st_2013_gro_ner:I-BetaScaffoldDomain_WithMinorGrooveContacts), medmentions_full_ner:B-T047), mlee_ED:B-Dephosphorylation), mantra_gsc_en_emea_ner:I-PHYS), pdr_ner:B-Disease), genia_term_corpus_ner:I-), chemdner_ner:I-Chemical), bionlp_st_2013_gro_ED:B-PositiveRegulationOfTranscriptionOfGene), mlee_ner:I-Protein_domain_or_region), medmentions_full_ner:I-T104), medmentions_full_ner:B-T039), bio_sim_verb_sts:5), chebi_nactem_abstr_ann1_ner:B-Biological_Activity), bionlp_st_2011_epi_ED:I-DNA_demethylation), nlm_gene_ner:I-GENERIF), bionlp_st_2013_gro_ED:B-NegativeRegulationOfTranscription), mantra_gsc_en_emea_ner:I-PHEN), chebi_nactem_fullpaper_ner:B-Chemical_Structure), genia_term_corpus_ner:B-RNA_molecule), mlee_ner:B-Cell), chia_ner:B-Qualifier), bionlp_shared_task_2009_ED:B-Gene_expression), bionlp_st_2013_gro_ner:I-Vitamin), medmentions_full_ner:I-T013), ehr_rel_sts:8), medmentions_full_ner:I-T030), diann_iber_eval_en_ner:O), an_em_RE:frag), genia_term_corpus_ner:I-DNA_substructure), bionlp_st_2013_pc_EAE:Site), genia_term_corpus_ner:I-ANDprotein_complexprotein_complex), bionlp_st_2013_gro_ED:I-TranscriptionInitiation), bionlp_st_2013_gro_ner:B-Polymerase), medmentions_full_ner:I-T004), bionlp_st_2013_gro_ED:B-NegativeRegulationOfTranscriptionOfGene), bionlp_st_2013_gro_ner:B-FusionGene), bionlp_st_2011_ge_ED:I-Binding), bionlp_st_2013_cg_ner:B-DNA_domain_or_region), chia_ner:B-Negation), bionlp_st_2013_gro_ner:I-FusionProtein), minimayosrs_sts:8), chebi_nactem_fullpaper_ner:B-Protein), bionlp_st_2013_gro_ner:B-Enhancer), bionlp_st_2013_gro_ED:B-NegativeRegulation), medmentions_full_ner:I-T041), mantra_gsc_en_emea_ner:O), biorelex_ner:I-protein-motif), bionlp_st_2011_epi_COREF:coref), medmentions_full_ner:I-T093), medmentions_full_ner:B-T200), bionlp_st_2013_gro_ner:B-OpenReadingFrame), bionlp_st_2013_cg_ED:I-Localization), bionlp_st_2013_cg_ner:B-Tissue), bionlp_st_2013_pc_COREF:None), medmentions_full_ner:I-T123), mlee_ED:O), bionlp_st_2013_gro_ner:O), bionlp_st_2013_gro_ner:B-ComplexMolecularEntity), bionlp_st_2013_pc_ED:B-Transcription), anat_em_ner:B-Pathological_formation), diann_iber_eval_en_ner:B-Neg), bionlp_st_2013_ge_ner:I-Protein), scai_chemical_ner:I-TRIVIAL), bionlp_st_2013_gro_ner:B-RibosomalRNA), an_em_ner:B-Organism_subdivision), mlee_ED:I-Remodeling), genia_term_corpus_ner:B-RNA_domain_or_region), bionlp_st_2013_gro_ner:B-BindingAssay), medmentions_full_ner:B-T017), mlee_ED:I-Translation), bionlp_st_2013_gro_ner:B-CpGIsland), bionlp_st_2013_pc_ner:I-Gene_or_gene_product), bionlp_st_2013_gro_ner:I-HMG), bionlp_st_2013_gro_ED:B-FormationOfTranscriptionFactorComplex), mlee_ner:I-Organism_substance), medmentions_full_ner:I-T075), nlm_gene_ner:B-Domain), anat_em_ner:I-Anatomical_system), medmentions_full_ner:B-T057), bionlp_st_2013_gro_ner:I-SecondMessenger), bionlp_st_2013_gro_ner:B-GeneProduct), ebm_pico_ner:I-Outcome_Other), bionlp_st_2013_gro_ED:B-ProteinModification), bionlp_st_2013_gro_ED:B-Modification), bioinfer_ner:B-Protein_family_or_group), medmentions_full_ner:B-T059), bionlp_st_2013_gro_ner:B-Ligand), gnormplus_ner:I-FamilyName), mantra_gsc_en_emea_ner:B-CHEM), bionlp_st_2013_gro_ED:I-CellGrowth), genia_term_corpus_ner:B-DNA_NA), mantra_gsc_en_medline_ner:B-LIVB), verspoor_2013_ner:B-gender), bio_sim_verb_sts:6), spl_adr_200db_train_ner:B-Severity), bionlp_st_2013_cg_ED:I-Breakdown), ddi_corpus_ner:I-BRAND), medmentions_st21pv_ner:B-T097), biorelex_ner:B-experimental-construct), bionlp_st_2013_ge_ED:B-Transcription), chia_ner:I-Multiplier), bionlp_st_2013_gro_ner:I-DNA), geokhoj_v1_TEXT:0), bionlp_st_2013_gro_RE:locatedIn), genia_term_corpus_ner:B-virus), bionlp_st_2013_gro_ner:I-SequenceHomologyAnalysis), bionlp_st_2013_gro_ED:B-RegulatoryProcess), bionlp_st_2013_pc_ED:B-Activation), anat_em_ner:I-Organism_subdivision), bionlp_st_2013_gro_ner:B-RuntLikeDomain), bioinfer_ner:I-Protein_complex), bionlp_st_2013_gro_ED:I-Increase), anat_em_ner:I-Cell), medmentions_full_ner:B-T131), bionlp_st_2013_gro_ner:B-ProteinDomain), bionlp_st_2013_gro_ner:I-ProteinCodingRegion), bionlp_st_2013_gro_ner:I-PrimaryStructure), seth_corpus_RE:None), genia_term_corpus_ner:I-mono_cell), bioscope_papers_ner:I-negation), chemprot_RE:CPR:4|CPR:6), genia_term_corpus_ner:I-other_artificial_source), medmentions_full_ner:I-T098), bionlp_st_2013_gro_ner:I-Enhancer), bionlp_st_2013_gro_ner:I-PositiveTranscriptionRegulator), genia_term_corpus_ner:I-polynucleotide), bionlp_st_2011_ge_ED:B-Gene_expression), medmentions_full_ner:B-T121), bionlp_st_2011_id_ED:I-Transcription), biorelex_ner:I-protein-region), chebi_nactem_fullpaper_ner:B-Metabolite), diann_iber_eval_en_ner:B-Disability), bionlp_st_2013_cg_ED:B-Dissociation), medmentions_st21pv_ner:B-T204), genia_term_corpus_ner:I-protein_subunit), medmentions_full_ner:B-T023), bionlp_st_2013_gro_ED:B-Splicing), bionlp_st_2013_gro_ED:I-Silencing), biorelex_ner:B-peptide), bionlp_st_2013_gro_ED:B-BindingOfTFToTFBindingSiteOfProtein), biorelex_ner:I-assay), medmentions_full_ner:B-T048), an_em_ner:I-Organism_substance), bionlp_st_2013_gro_ner:I-Function), spl_adr_200db_train_ner:B-Animal), genia_term_corpus_ner:I-DNA_NA), medmentions_full_ner:I-T070), mlee_ner:I-Anatomical_system), bioinfer_ner:B-Individual_protein), biorelex_ner:B-organelle), verspoor_2013_ner:I-Physiology), bionlp_st_2013_gro_ner:I-ProteinComplex), genia_term_corpus_ner:I-RNA_molecule), mlee_ner:I-DNA_domain_or_region), mlee_ED:I-Pathway), bionlp_st_2013_gro_ED:B-ActivationOfProcess), pico_extraction_ner:B-outcome), minimayosrs_sts:7), medmentions_full_ner:I-T038), verspoor_2013_ner:I-size), ebm_pico_ner:B-Intervention_Other), bionlp_st_2013_gro_ED:B-RNABiosynthesis), bionlp_st_2013_cg_ner:I-Simple_chemical), mantra_gsc_en_medline_ner:I-LIVB), seth_corpus_ner:B-Gene), biorelex_ner:I-reagent), bionlp_st_2013_cg_ED:B-Phosphorylation), bionlp_st_2013_gro_ner:B-Attenuator), pdr_EAE:None), bionlp_st_2011_epi_ED:B-DNA_methylation), bionlp_st_2013_cg_ED:I-Translation), bionlp_st_2013_gro_ED:B-Transcription), medmentions_st21pv_ner:I-T074), bionlp_st_2013_gro_ED:B-ProteinCatabolism), bionlp_st_2013_gro_ED:B-Growth), chia_RE:AND), bionlp_st_2013_pc_ED:I-Transcription), medmentions_full_ner:I-T191), medmentions_full_ner:I-T028), bionlp_st_2013_cg_ED:I-Glycolysis), bionlp_st_2013_ge_ED:B-Localization), mlee_ner:I-Organ), medmentions_full_ner:B-T033), ebm_pico_ner:I-Intervention_Other), bionlp_st_2013_gro_ner:B-NuclearReceptor), genia_term_corpus_ner:B-ANDprotein_complexprotein_complex), an_em_ner:B-Cellular_component), medmentions_full_ner:I-T100), geokhoj_v1_TEXT:1), genia_term_corpus_ner:I-BUT_NOTother_nameother_name), bionlp_st_2013_cg_ED:B-Cell_death), gnormplus_ner:B-Gene), genia_term_corpus_ner:I-RNA_substructure), medmentions_full_ner:I-T190), bionlp_st_2013_gro_ED:B-Homodimerization), medmentions_full_ner:B-T051), genia_term_corpus_ner:B-lipid), bioinfer_ner:B-GeneproteinRNA), bioinfer_ner:B-Gene), medmentions_full_ner:B-T184), anat_em_ner:I-Pathological_formation), bionlp_st_2013_gro_ner:B-ForkheadWingedHelixTF), bionlp_st_2013_cg_ner:I-Protein_domain_or_region), genia_term_corpus_ner:I-other_organic_compound), bionlp_st_2013_gro_ner:B-SmallInterferingRNA), bionlp_st_2013_cg_ED:B-Growth), bionlp_st_2013_cg_ED:B-Synthesis), chia_RE:Has_index), chia_ner:I-Device), ddi_corpus_ner:B-GROUP), bionlp_shared_task_2009_ED:I-Gene_expression), bionlp_st_2013_gro_ner:B-MutantProtein), genia_term_corpus_ner:B-DNA_substructure), biorelex_ner:I-disease), biorelex_ner:I-amino-acid), medmentions_full_ner:B-T127), ebm_pico_ner:I-Intervention_Psychological), mlee_ED:I-Planned_process), pubmed_qa_labeled_fold0_CLF:no), mlee_ner:I-Drug_or_compound), medmentions_full_ner:I-T185), minimayosrs_sts:1), bionlp_st_2011_epi_ED:B-DNA_demethylation), bionlp_st_2013_gro_ner:I-TranscriptionFactorBindingSiteOfDNA), bionlp_st_2013_gro_ED:I-ResponseProcess), medmentions_full_ner:I-T201), bionlp_st_2011_ge_ED:I-Transcription), bionlp_st_2013_cg_ED:I-Mutation), tmvar_v1_ner:I-ProteinMutation), medmentions_full_ner:I-T063), verspoor_2013_ner:I-Phenomena), bionlp_st_2011_id_ED:B-Negative_regulation), chemprot_RE:CPR:2), bionlp_st_2013_gro_ner:B-ProteinSubunit), medmentions_full_ner:B-T011), genia_term_corpus_ner:I-ANDother_nameother_name), an_em_ner:I-Tissue), bionlp_st_2013_gro_ner:B-bHLHTF), pico_extraction_ner:B-intervention), bionlp_st_2013_gro_ED:B-Increase), mlee_ner:I-Organism), mantra_gsc_en_emea_ner:I-CHEM), bionlp_st_2013_cg_ner:I-Organism), bionlp_st_2013_gro_ner:I-ProteinDomain), medmentions_full_ner:B-T185), mantra_gsc_en_patents_ner:I-PROC), medmentions_full_ner:I-T120), bionlp_st_2013_gro_ED:B-CellularMetabolicProcess), scai_chemical_ner:I-ABBREVIATION), bionlp_st_2013_cg_ED:I-Planned_process), bionlp_st_2013_cg_ner:B-Anatomical_system), chia_ner:I-Procedure), genia_term_corpus_ner:I-ANDcell_typecell_type), scai_chemical_ner:I-), biorelex_ner:B-experiment-tag), genia_term_corpus_ner:B-ORDNA_domain_or_regionDNA_domain_or_region), medmentions_full_ner:B-T044), mirna_ner:B-Non-Specific_miRNAs), mlee_ED:B-Cell_division), bionlp_st_2011_id_ner:I-Entity), bionlp_st_2013_cg_ED:B-Cell_proliferation), bionlp_st_2011_epi_EAE:None), bionlp_st_2013_cg_ED:B-DNA_methylation), bionlp_st_2013_gro_ED:O), bionlp_st_2013_gro_ED:B-Producing), bionlp_st_2013_cg_EAE:Instrument), bionlp_st_2013_gro_ED:B-Stabilization), pcr_ner:B-Chemical), bionlp_st_2013_cg_ED:B-Development), ebm_pico_ner:B-Intervention_Physical), bionlp_st_2011_ge_ED:I-Regulation), bionlp_st_2013_pc_ED:B-Demethylation), bionlp_st_2011_epi_ner:B-Protein), chemprot_RE:CPR:0), medmentions_full_ner:B-T055), bionlp_st_2013_gro_ED:B-Decrease), spl_adr_200db_train_ner:I-Severity), bionlp_st_2013_gro_ner:I-Ion), bionlp_st_2013_pc_ner:B-Gene_or_gene_product), genia_term_corpus_ner:B-inorganic), chia_ner:O), linnaeus_ner:B-species), biorelex_ner:I-protein), mantra_gsc_en_medline_ner:B-PROC), medmentions_full_ner:B-T078), medmentions_full_ner:I-T062), medmentions_full_ner:I-T081), mantra_gsc_en_emea_ner:B-PHEN), medmentions_st21pv_ner:B-T022), bc5cdr_ner:I-Disease), chia_ner:B-Multiplier), bionlp_st_2013_gro_ner:I-bHLH), bionlp_st_2013_gro_ED:B-CellularProcess), bionlp_st_2013_gro_ED:B-Acetylation), scicite_TEXT:result|supportive), genia_term_corpus_ner:B-RNA_family_or_group), bionlp_st_2013_gro_ED:I-IntraCellularTransport), bionlp_st_2013_gro_ner:B-Chromatin), bionlp_st_2013_ge_ED:B-Binding), bionlp_st_2013_gro_ner:I-AminoAcid), bionlp_st_2013_gro_ED:B-CellFateDetermination), medmentions_full_ner:I-T091), medmentions_full_ner:B-T066), medmentions_full_ner:B-T022), genetaggold_ner:O), medmentions_full_ner:B-T074), bionlp_st_2013_pc_ED:I-Gene_expression), bionlp_st_2013_gro_ED:I-Disease), biosses_sts:7), medmentions_full_ner:B-T071), medmentions_full_ner:B-T086), biorelex_ner:I-protein-complex), mlee_ED:B-Remodeling), medmentions_st21pv_ner:I-T007), bionlp_st_2011_id_ED:I-Regulation), biorelex_ner:B-drug), bionlp_st_2013_gro_ED:I-Transcription), bionlp_st_2011_epi_EAE:Theme), mantra_gsc_en_patents_ner:I-DISO), anat_em_ner:I-Organ), scai_chemical_ner:I-PARTIUPAC), bionlp_st_2013_cg_ED:I-Metastasis), medmentions_full_ner:I-T197), bionlp_st_2013_pc_ED:O), medmentions_st21pv_ner:B-T092), bionlp_shared_task_2009_ED:B-Positive_regulation), medmentions_full_ner:B-T045), chemprot_RE:CPR:8), bionlp_st_2013_cg_ED:B-Localization), nlm_gene_ner:I-Domain), verspoor_2013_ner:B-age), bionlp_st_2011_epi_ED:O), chebi_nactem_abstr_ann1_ner:B-Species), medmentions_full_ner:B-T122), bionlp_st_2011_id_ner:I-Protein), bionlp_st_2013_gro_ED:I-BindingOfProteinToDNA), bionlp_st_2013_gro_ner:I-RNAPolymeraseII), medmentions_full_ner:I-T050), genia_term_corpus_ner:B-ANDother_nameother_name), nlm_gene_ner:B-STARGENE), bionlp_st_2013_gro_ED:B-BindingOfMolecularEntity), mirna_ner:B-GenesProteins), scai_chemical_ner:B-MODIFIER), mantra_gsc_en_emea_ner:B-OBJC), mirna_ner:B-Diseases), bionlp_st_2013_cg_ED:I-Death), mantra_gsc_en_emea_ner:I-DISO), bionlp_st_2013_gro_ED:I-Decrease), bionlp_st_2013_gro_ner:B-DNABindingDomainOfProtein), bioinfer_ner:O), anat_em_ner:I-Multi-tissue_structure), osiris_ner:O), bionlp_st_2013_cg_EAE:None), medmentions_st21pv_ner:B-T062), medmentions_full_ner:B-T075), genia_term_corpus_ner:I-AND_NOTcell_typecell_type), bionlp_st_2013_gro_ED:B-CellCycle), medmentions_full_ner:B-UnknownType), bionlp_st_2013_cg_ner:I-Cancer), medmentions_full_ner:I-T005), genia_term_corpus_ner:I-protein_complex), bionlp_st_2013_cg_ED:B-Cell_transformation)

Live Demo Open in Colab Download Copy S3 URI

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_bigbio_mtl","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_bigbio_mtl","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.by_bigscience_biomedical").predict("""PUT YOUR STRING HERE""")

Model Information

References

• https://huggingface.co/bigscience-biomedical/bigbio-mtl