UMLS Semantic Network
paper - Lists of 133 semantic types and 54 semantic relationships covering biomedical concepts and vocabulary. Is the Metathesaurus too complex for your needs? Try this. Does not require UTS account to download.
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- Biomedical Information Extraction
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- 2026-10-10
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UMLS Metathesaurus nlm.nih.gov
paper - Mappings between >3.8 million concepts, 14 million concept names, and >200 sources of biomedical vocabulary and identifiers. It's big. It may help to prepare a subset of the Metathesaurus with the MetamorphoSys installation tool but we're still talking about ~30 Gb of…
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Disease Ontology disease-ontology.org
paper - An ontology of human diseases. Has cross-links to MeSH, ICD, NCI Thesaurus, SNOMED, and OMIM. Public domain. Available on GitHub and on the OBO Foundry.
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UMLS Knowledge Sources nlm.nih.gov
reference manual - A large and comprehensive collection of biomedical terminology and identifiers, as well as accompanying tools and scripts. Depending on your purposes, the single file MRCONSO.RRF may be sufficient, as this file contains unique identifiers and names for all…
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NCBI Disease Corpus ncbi.nlm.nih.gov
paper - A corpus of 793 biomedical abstracts annotated with names of diseases and related concepts from MeSH and OMIM.
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BioUML wiki.biouml.org
paper - An architecture for biomedical data analysis, integration, and visualization. Conceptually based on the visual modeling language UML.
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Structured information extraction from scientific text with large language models nature.com
Nature Communications, 2024. [All Versions]. This paper presents a simple approach to joint named entity recognition and relation extraction and demonstrate how pretrained large language models can be fine-tuned to extract useful records of complex scientific knowledge. The…
Biomedical Information Extraction › Ontologies and Controlled Vocabularies: “paper - Lists of 133 semantic types and 54 semantic relationships covering biomedical concepts and vocabulary. Is the Metathesaurus too complex for your needs? Try this. Does not require UTS account to download.”