Dictionaries, Ontologies, MeSH, Linnaeus, Entrez Gene, Databases, MedLine, PubMed, Genia Ontology, Gene Onotology, UMLS, Medical Wordnet, WordNet, Lexical Resources, Stanford Biomedical Abbreviation Database, ARGH, Galen, FMA

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The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.


The GALEN CORE Model for representation of the Common Reference Model for Procedures contains the building blocks for defining procedures - the anatomy, surgical deeds, diseases, and their modifiers used in the definitions of surgical procedures. This document describes the structure the CORE model and gives a detailed account of its high level schemata followed by a detailed example of the use of the ontology for a portion of the model of the cardiovascular system and diseases.


ARGH: Biomedical Acronym Resolver

This database was constructed in a purely automated manner, using a set of heuristics to identify acronyms/abbreviations and their definitions within MEDLINE records. Currently, it is the world's largest and most comprehensive catalog of biomedical acronyms and abbreviations, containing approximately 257,000 out of an estimated 277,000 unique acronyms within MEDLINE.

Stanford Biomedical Abbreviation Database

What you can do: Search for longer forms of abbreviations in MEDLINE or the context in MEDLINE for biomedical abbreviations.

Highlights: We have scanned 11,447,996 PubMed citations for abbreviations and put them in a database.
The database currently has 2,074,367 abbreviations.

medical abbreviations
abbreviation dictionary
online dictionary
literature study tools
terminology tools
nomenclature tools
Literature & Tutorials:
PubMed Link: Stanford Biomedical Abbreviation Server

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The UMLS integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records.

What is the UMLS?
The UMLS, or Unified Medical Language System, is a set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems.


The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.

Genia Ontology

The GENIA ontology is intended to be a formal model of cell signaling reactions in human. It is to be used as a basis of thesauri and semantic dictionaries for natural language processing applications, e.g.,

Information retrieval (IR) & filtering (IF)
Information extraction (IE)
Document and term classification & categorization
Summarization, etc.

Another use of the GENIA ontology is to provide the basis for integrated view of multiple databases including CSNDB developed at National Institiute of Health Science.


MEDLINE is the U.S. National Library of Medicine's® (NLM) premier bibliographic database that contains over 19 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive feature of MEDLINE is that the records are indexed with NLM Medical Subject Headings (MeSH®).

Entrez Gene Database

Entrez Gene is NCBI's repository for gene-specific information. Access to this information either through the Entrez Gene website or by flat files via NCBI's ftp site can be time consuming and limiting in regards to the number of and what questions you can ask about the data. A better solution for intense data mining is to create a relational database.


MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity.

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