BioYODIE Named Entity Disambiguation

BioYODIE is a named entity recognition and disambiguation system that identifies various types of biomedical named entities in text and attempts to link them to the most appropriate concept label in the UMLS.

Default annotations
Bio:Drug Named entity mentions grouped into broad types, with class and inst features where available.
Bio:Disease
Bio:Anatomy
Bio:Investigation
Bio:Care
Bio:Observation
Additional annotations available if selected
Bio:Mention Any named entity annotation with UMLS class and inst features
Bio:Body_Location_or_Region Specific types of entities corresponding to the top-level TUI classifications in UMLS. Every instance of one of these types will correspond to a Mention but there may be other mentions that are not under these TUIs.
Bio:Body_Part_Organ_or_Organ_Component
Bio:Body_Space_or_Junction
Bio:Body_System
Bio:Tissue
Bio:Anatomical_Abnormality
Bio:Acquired_Abnormality
Bio:Congenital_Abnormality
Bio:Finding
Bio:Injury_or_Poisoning
Bio:Pathologic_Function
Bio:Disease_or_Syndrome
Bio:Mental_or_Behavioral_Dysfunction
Bio:Mental_Process
Bio:Cell_or_Molecular_Dysfunction
Bio:Experimental_Model_of_Disease
Bio:Sign_or_Symptom
Bio:Neoplastic_Process
Bio:Diagnostic_Procedure
Bio:Laboratory_Procedure
Bio:Laboratory_or_Test_Result
Bio:Research_Activity
Bio:Molecular_Biology_Research_Technique
Bio:Clinical_Drug
Bio:Pharmacologic_Substance
Bio:Antibiotic

This version of Bio-YODIE includes terms from the following UMLS vocabularies:

  • AI/RHEUM
  • Alcohol and Other Drug Thesaurus
  • Alternative Billing Concepts
  • Anatomical Therapeutic Chemical Classification System
  • Authorized Osteopathic Thesaurus
  • Beth Israel Problem List
  • BioCarta online maps of molecular pathways, adapted for NCI use
  • Biomedical Research Integrated Domain Group Model
  • Cancer Research Center of Hawaii Nutrition Terminology
  • Cancer Therapy Evaluation Program - Simple Disease Classification
  • CDISC Glossary Terminology
  • Clinical Care Classification
  • Clinical Classifications Software
  • Clinical Classifications Software 10
  • Clinical Concepts by R A Miller
  • Clinical Data Interchange Standards Consortium
  • Clinical Problem Statements
  • Clinical Trials Reporting Program
  • Common Terminology Criteria for Adverse Events
  • Common Terminology Criteria for Adverse Events 3.0
  • Common Terminology Criteria for Adverse Events 5.0
  • Congenital Mental Retardation Syndromes
  • Consumer Health Vocabulary
  • Content Archive Resource Exchange Lexicon
  • COSTAR
  • COSTART
  • CPT in HCPCS
  • CRISP Thesaurus
  • Current Dental Terminology
  • Current Dental Terminology in HCPCS
  • Current Procedural Terminology
  • Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition
  • Digital Anatomist
  • Digital Imaging Communications in Medicine
  • Diseases Database
  • DrugBank
  • DXplain
  • FDA Structured Product Labels
  • FDB MedKnowledge
  • Foundational Model of Anatomy
  • Gene Ontology
  • Geopolitical Entities, Names, and Codes (GENC) Standard Edition 1
  • lobal Alignment of Immunization Safety Assessment in pregnancy
  • Glossary of Clinical Epidemiologic Terms
  • Gold Standard Drug Database
  • HCPCS Hierarchical Terms (UMLS)
  • Healthcare Common Procedure Coding System
  • HL7 Version 2.5
  • HL7 Version 3.0
  • HUGO Gene Nomenclature Committee
  • Human Phenotype Ontology
  • ICD-10 Procedure Coding System
  • ICD-10, American English Equivalents
  • ICD-10, Australian Modification
  • ICD-10, Australian Modification, Americanized English Equivalents
  • ICD-9-CM Entry Terms
  • ICPC-2 PLUS
  • ICPC2-ICD10 Thesaurus
  • ICPC2E American English Equivalents
  • ICPC2E-ICD10 Thesaurus, American English Equivalents
  • International Classification for Nursing Practice
  • International Classification of Diseases and Related Health Problems, Tenth Revision
  • International Classification of Diseases, Ninth Revision, Clinical Modification
  • International Classification of Diseases, Tenth Revision, Clinical Modification
  • International Classification of Functioning, Disability and Health
  • International Classification of Functioning, Disability and Health for Children and Youth
  • International Classification of Primary Care
  • International Classification of Primary Care, 2nd Edition, Electronic
  • International Conference on Harmonization
  • Jackson Laboratories Mouse Terminology, adapted for NCI use
  • KEGG Pathway Database
  • Library of Congress Subject Headings
  • Library of Congress Subject Headings, Northwestern University subset
  • LOINC
  • Manufacturers of Vaccines
  • MEDCIN
  • MedDRA
  • Medical Entities Dictionary
  • Medication Reference Terminology
  • MedlinePlus Health Topics
  • MeSH
  • Metathesaurus CMS Formulary Reference File
  • Metathesaurus Names
  • Micromedex
  • Minimal Standard Terminology (UMLS)
  • Multum
  • NANDA-I Taxonomy
  • National Cancer Institute Nature Pathway Interaction Database
  • National Council for Prescription Drug Programs
  • National Drug File
  • National Drug File - FDASPL
  • National Drug File - FMTSME
  • National Drug File - Reference Terminology
  • National Institute of Child Health and Human Development
  • National Uniform Claim Committee - Health Care Provider Taxonomy
  • NCBI
  • NCI Developmental Therapeutics Program
  • NCI Dictionary of Cancer Terms
  • NCI Division of Cancer Prevention Program
  • NCI Health Level 7
  • NCI HUGO Gene Nomenclature
  • NCI SEER ICD Mappings
  • NCI Thesaurus
  • Neuronames Brain Hierarchy
  • Nursing Interventions Classification
  • Nursing Outcomes Classification
  • Omaha System
  • Online Mendelian Inheritance in Man
  • Patient Care Data Set
  • Perioperative Nursing Data Set
  • Pharmacy Practice Activity Classification
  • Physician Data Query
  • Prostate Imaging Reporting and Data System
  • Psychological Index Terms
  • Quick Medical Reference
  • Read Codes
  • Read Codes Am Engl
  • Read Codes Am Synth
  • Read Codes Synth
  • Registry Nomenclature Information System
  • RXNORM
  • SNOMED 1982
  • SNOMED Intl 1998
  • Source of Payment Typology
  • Source Terminology Names (UMLS)
  • Standard Product Nomenclature
  • U.S. Centers for Disease Control and Prevention
  • U.S. Food and Drug Administration
  • UltraSTAR
  • Unified Code for Units of Measure
  • Universal Medical Device Nomenclature System
  • US Edition of SNOMED CT
  • USP Compendial Nomenclature
  • USP Model Guidelines
  • Vaccines Administered
  • Veterinary Extension to SNOMED CT
  • WHOART
  • Zebrafish Model Organism Database
800 free requests / day
Batch processing not available

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Single documents

You can process up to 800 documents per day free of charge using the REST API, at an average rate of 2 documents/sec. Higher quotas are available for research users by arrangement, contact us for details.

The API endpoint for this pipeline is:

https://cloud-api.gate.ac.uk/process-document/bio-yodie

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