This section outlines the EVS terminology content and tools whose use is described in the subsequent sections of the EVS Use and Collaborations document. The following resources are described.
Controlled Terminology
EVS produces two major reference resources, NCI Thesaurus and NCI Metathesaurus, in collaboration with a range of partners. EVS also produces, licenses, processes and makes available a wide range of other terminology content.
NCI Thesaurus (NCIt)
NCIt is NCI's reference terminology and core biomedical ontology. It covers some 100,000 key biomedical concepts with a rich set of terms, codes, definitions, and over 200,000 inter-concept relationships, and is used to code most NCI and caBIG® metadata and models. About 700 concepts are added each month in response to user requests and the requirements of dependent systems and applications, and much more content is similarly added to existing concepts. Many of these concepts include content created and maintained jointly with NCI's partners, making NCIt a shared coding and semantic infrastructure resources (see Shared Development of Terminology Content).
NCI Metathesaurus (NCIm)
NCIm currently consists of 76 biomedical terminologies whose 3,600,000 terms are mapped to 1,400,000 concepts representing their shared meanings. NCIm is updated approximately six times a year, growing by some 100,000 concepts annually. This growth involves adding new terminologies, and updated versions of existing terminologies, to meet the requirements of EVS users for specific terminologies and for mappings between them. NCIm also provides a rich reference resource for a broad range of users seeking definitions, synonyms, codes, and other information.
Other terminologies
EVS licenses, processes and makes available many other terminologies through standardized application and browser interfaces, and frequently through various data file formats as well. EVS has helped create, harmonize with, and publish several of these terminologies. Currently available are:
- ChEBI: Chemical Entities of Biological Interest
- CTCAE: Common Terminology Criteria for Adverse Events
- GO: Gene Ontology
- HUGO: Human Genome Organization
- ICD-10-CM: International Classification of Diseases, Tenth Revision, Clinical Modification
- ICD-10: International Classification of Diseases, Tenth Revision
- ICD-9-CM: International Classification of Diseases, Ninth Revision, Clinical Modification
- LOINC: Logical Observation Identifiers Names and Codes
- MedDRA: Medical Dictionary for Regulatory Activities Terminology
- MGED Ontology: Microarray Gene Expression Data Ontology
- NDF-RT: National Drug File Reference Terminology Public Inferred Edition
- NPO: NanoParticle Ontology
- OBI: Ontology for Biomedical Investigations
- PDQ: Physician Data Query
- RadLex: Radiology Lexicon
- SNOMED CT: Systematized Nomenclature of Medicine-Clinical Terms
- UMLS SemNet: UMLS Semantic Network
- Zebrafish: Zebrafish Model Organism Database
Terminology Value Sets
Value sets provide a standardized representation of selected values from these terminologies, following the draft Common Terminology Services Release 2 (CTS 2) specification. Some 200 value sets are currently defined in the EVS LexEVS 6 server, covering a range of standards from CDISC, FDA, NCPDP, NDF-RT, NICHD, and others.
Terminology Mappings
Mappings between several supported terminologies have also been published:
- GO to NCIt Mapping
- NCIt to ChEBI Mapping
- PDQ to NCIt Mapping
- SNOMEDCT to ICD9CM
EVS Terminology Tools
LexEVS
LexEVS is a set of software and services to load, publish, and access vocabulary and ontology resources.
EVS has supported and migrated to LexEVS, developed by the Mayo Clinic, as an open source tool that is freely sharable and that is now being deployed at a number of other partner organizations such as MD Anderson, Stanford, Emory, Ohio State University Medical Center, Georgetown University, Washington University, and National Cancer Research Institute (NCRI)/UK CancerGrid, as well as by commercial vendors such as IBM and GE Healthcare.
EVS Terminology Browsers
EVS has developed two cross-linked, user-friendly terminology browsers: NCI Term Browser and NCI Metathesaurus Browser. These browsers are designed to meet NCI's internal and public information needs across the full range of EVS content, and also provide important support for collaborative content and standards development. EVS browsers are heavily used from both NCI servers and non-NCI adopter sites. The browsers are freely available as open source software.
NCI Protégé
EVS editing software has been based on Stanford's open source Protégé tool, widely used for editing biomedical terminology and ontologies. NCI extensively customized Protégé to meet EVS requirements and business rules, contributing its code back to the community to help support Protégé development. The most demanding use is as the editing software for NCIt, but Protégé is also used locally for CTCAE and other editing work, and by NanoParticle Ontology (NPO) (see Nanotechnology section below).
Term Suggestion
EVS Term Suggestion software is used extensively-both standalone and integrated into the EVS terminology browsers-to get community feedback and contributions to both NCI and EVS partner terminology products.
BiomedGT Semantic Media Wiki
This collaborative terminology development environment has been used for NCI terminology such as CTCAE and BiomedGT, as well as partner efforts such as the NanoParticle Ontology (NPO) based at Washington University.
LexWiki
LexWiki was created by the Mayo Clinic, developed further for the BiomedGT wiki, then updated and published as the open source LexWiki tool by the Mayo Clinic, through the Vocabulary Knowledge Center.
EVS Report Writer
EVS Report Writer is standalone software that connects to the LexEVS servers. It is used internally to generate many value sets and other reports, and is available for use by others.
