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
800 free requests / day
Batch processing not available

Use this pipeline

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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