BioYODIE Named Entity Disambiguation (MeSH only)
Bio-YODIE 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. This version of
Bio-YODIE uses only the MeSH (Medical Subject Headings) vocabulary from UMLS version 2018AB.
| 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
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/bio-yodie-mesh
