CTCAE is designed to integrate into information networks for safety data exchange, and is expected to have a significant impact in data management for AE data collection, analysis, and patient outcomes associated with cancer research and care. EVS played a central role in designing and managing this effort, working closely with CTEP, DCP, VCDE, the Vocabulary Knowledge Center, and many participants from the broader community. The revision was developed and deployed using various EVS tools including the BiomedGT Wiki, Protégé editing tools, LexEVS terminology server, NCI Term Browser, and the EVS ftp site .
This database, which predates caBIG®, provides curated information for animal models of human cancers. caMOD annotates information with NCIt terminology, and uses the LexEVS API directly to generate anatomy and diagnosis tree hierarchies. 400 concepts were added or updated for caMOD in the past six months.
ICR (Integrative Cancer Research) Nanotechnology Working Group
caNanoLab has a goal of semantic interoperability across centers performing nanoparticle characterization studies. caNanoLab is based on an information model representing nanoparticles and their physical and in vitro characterization.
EVS provides assistance in curating concept definitions with the community, making them available in NCIt; a glossary of these terms also is provided within the caNanoLab application. (Funding for additional development was recently lost, but caNanoLab continues to be used.) The Nanotechnology Working Group includes about 60 people representing approximately 40 agencies, universities and institutes, a few from Europe. caNanolab is heavily used, representing substantial use of EVS effort. It currently contains 886 samples, 72 sample sources, 3,329 characterizations, and 41 protocols, and identifies 1,073 publications. The caNanoLab homepage shows 141,668 visitors since June 3, 2010. (See also additional nanotechnology-related detail below.)
Georgetown uses LexEVS and other EVS resources for its cancer Bench-to-Bedside (caB2B) project and other activities. A local LexEVS installation, and NCI's production LexEVS servers, provide terminology support for this project. This is an example of how terminology services are being incorporated into other tools as primary components in support of translational medicine.
Washington University uses LexEVS and EVS terminology content in its clinical data warehouse project (CIDER). Washington University deployed LexEVS in 2008 as the terminology server for CIDER. The terminologies are used to code data and for information retrieval. This is an example of an academic medical center adopting NCI EVS technology to support research and clinical enterprise infrastructure.
Ohio State University Medical Center
Ohio State is using LexEVS, NCIt, and NCIm, notably for openMDR. Ohio State University launched openMDR (open metadata repository) in 2009, using local instances of LexEVS, BioPortal, and caDSR. This is an example of an academic research group adopting several open source components of NCI's EVS and semantic infrastructure, and integrating them to create a novel tool for metadata management.
University of Pittsburgh
Pittsburgh uses the NCI Thesaurus cancer, anatomy, and pathology findings terminologies for their research and informatics projects. The ODIE project is used by the University of Pittsburgh, University of California, San Diego, and Children's Hospital, Boston. This collaboration has resulted in the publication of two papers in peer-reviewed journals so far:
- Tobias J, Chilukuri R, Komatsoulis GA, Mohantry S, Sioutos N, et al: The CAP Cancer Protocols-A Case Study of caCORE Based Data Standards Implementation to Integrate with the Cancer Biomedical Informatics Grid. BMC Medical Informatics Decision Making, 20; 6:25, 2006.
- Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS:Effectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents. Methods Inf Med. 2010: 8;49(6).
Human Studies Database (HSDB) Consortium
HSDB is using LexEVS as a core component of its collaborative, distributed, clinical research systems. The OCRe Terminology is served through an NCBO site, which uses LexEVS. This is an example of a consortium of institutions leveraging LexEVS terminology services at the core of a new workflow for the collection of human studies data.
Common Biorepository Model (CBM)
EVS has provided about 1,300 concepts for this model through support for caDSR. CBM is used in many domains including clinical trials management, ICR, in vivo imaging, and tissue banks and pathology tools.
National Library of Medicine (NLM)
Since its inception, EVS has worked with NLM on a variety of terminology content and technology efforts. EVS licenses content from and harmonizes with NLM's Unified Medical Language System (UMLS), building NCIm by modifying and extending a subset of the UMLS Metathesaurus and using NLM editing software.
NLM's DailyMed gets over 10 million hits each month, and each of the SPL files in DailyMed uses terminology that is maintained by NCI. There are over 27,000 SPL files on DailyMed, and another 5,000 SPL files that are not on DailyMed. Each of these SPL files requires NCIt codes.
NCI and National Human Genome Research Institute (NHGRI)
The Cancer Genome Atlas (TCGA) is a joint effort between NCI and NHGRI, developing a database of the changes that occur in the genome, associated with a specific cancer type. TCGA creates a national network of research and technology teams, and provides a mechanism for pooling results; data are publically available. 25 Studies are associated with this data, and data are being actively submitted or used by 16 academic and research organizations, 27 commercial organizations, and 17 non-profit organizations. EVS supports terminology for annotating the CDEs for tagging information and samples, mainly cell and specimen type, with information about tumor size, anatomic location, sample preparation, and patient demographics.
National Heart, Lung, and Blood Institute (NHLBI)
Since 2005, NHLBI and EVS have jointly developed terminology in NCIt for various projects including bone marrow transplant clinical trials and the Family Blood Pressure Program. Duke, through an NIH Roadmap project, the American College of Cardiology, and CDISC, have also collaborated with EVS to produce several cardiovascular data standard sets now in use at NHLBI, with a portion incorporated into CDISC SDTM.
National Institute of Child Health and Human Development (NICHD)
Since 2009, NICHD and EVS have jointly developed terminology in NCIt for pediatric terminology, including standardizing data for newborn screening forms, through the Pediatric Terminology Harmonization Initiative, developed to assist Pediatric clinical researchers. This is associated with 848 NICHD Clinical Trials, and is being used by 52 different academic and research organizations.
National Institute of Dental and Craniofacial Research (NIDCR)_*
Since 2008, NIDCR and EVS have jointly developed terminology in NCIt for dental treatments and medical procedures.
NIH Biomedical Translational Research Information System (BTRIS)
Collaboration includes planned EVS publication of the BTRIS Research Entities Dictionary (RED) in support of NIH researchers' coding, retrieval, and analysis of clinical research data stored in BTRIS. RED began with NCIt as a foundation.
NCIt is one of four NIH-approved terminologies for grant coding, and EVS has helped develop the Research, Condition and Disease Categorization (RCDC) grant coding system.
EVS Partnerships and External Adoption
NCI EVS has extensive external partnerships to develop terminology standards, content, technology, and operational support, greatly broadening the base of adoption and having a major impact on the wider biomedical community.
U.S. Food and Drug Administration (FDA)
FDA has worked with EVS since 2001, with formal Memoranda of Understanding starting in 2004, to develop and harmonize terminology content, standards and systems in areas of mutual interest such as drugs, devices, patient safety, and clinical trials. FDA has chosen EVS and NCIt for developing and publishing many important terminology sets; some 15,000 FDA terms in over 20 defined subsets are now maintained in NCIt and required for regulatory reporting and other purposes. These include:
(For more information, visit the NCI website.
Clinical Data Interchange Standards Consortium (CDISC)
All CDISC controlled terminology – more than 9,800 terms – is maintained and published as NCIt subsets, as part of a partnership started in 2002 to develop and support global data standards for medical research. This includes four main terminology efforts:
The CDISC Shared Health and Research Electronic Library (SHARE) project is also building a collaborative authoring platform for harmonizing data elements from multiple organizations, using LexWiki for its initial prototype. CDISC has created a data element curation process, including terminology linking, using the LexWiki and LexGrid technologies; this process provides a collaborative framework and platform for representation and harmonization of clinical study data elements. CDISC will use open tools created by NCI as the basis for developing SHARE.
National Council of Prescription Drug Providers (NCPDP)
NCPDP is a not-for-profit, ANSI-accredited, Standards Development Organization with over 1,600 members representing virtually every sector of the pharmacy services industry. NCPDP creates and promotes the transfer of data related to medications, supplies, and services within the healthcare system through the development of standards and industry guidance. In 2009, NCPDP decided to partner with EVS to use NCIt subsets to support two of those standards, employed by some 200 vendors serving approximately 15,000 pharmacies nationwide:
(For more information, visit the NCI website.)
Federal Medication Terminologies (FMT)
Work started in 2002 as an interagency collaboration between NCI EVS, FDA, VHA, and NLM – joined later by AHRQ, CMS, DoD, and EPA – to improve the exchange and public availability of medication information with coordinated development of terminology standards. The initial FMT terminology set has been endorsed by U.S. Federal standards efforts including the National Committee on Vital and Health Statistics (NCVHS), Consolidated Health Informatics (CHI), the Healthcare Information Technology Standards Panel (HITSP), and the Office of the National Coordinator for Health Information Technology (ONC) within the Department of Health and Human Services (HHS). (For more information, visit the NCI website.)
Veterans Health Administration (VHA)
VHA has worked closely with EVS since 2002. Under an ongoing Memorandum of Understanding, VHA works with EVS on collaborative terminology policy and products, including content collaboration and publication of the VA's National Drug File Reference Terminology (NDF-RT), used by both agencies as a drug information reference resource.
The VHA also performed a thorough comparison of the functional capabilities of LexEVS to those of other terminology servers. The VA provided the results to the VKC, which transformed the matrix into a document that can be used by potential adopters of LexEVS as they evaluate the capabilities of the system. This is an example of a valuable contribution from the community that is not code-based; in an open source model, contributions of documentation can be as important as contributions of code.
Health Level 7 (HL7)
EVS supports terminology content for the Regulated Clinical Research Information Management (RCRIM) committee of HL7, and for other committees as appropriate including Patient Safety, Pharmacy, Clinical Genomics, and the Clinical Interoperability Council.
World Health Organization (WHO)
WHO requested in June, 2009, a Classification Markup Language (ClaML) LexEVS data processing program that could be used to render ICD-10 in preparation for, and as the foundation of, ICD-11. This is an example of an international standards organization using NCI's open source tooling to support the development of a new version of a major international terminology standard.
WHO work on ICD-11 is also using NCI Thesaurus as an important source of cancer terminology and definitions.
Stanford/National Center for Biomedical Ontology (NCBO)
NCBO bases its BioPortal terminology services on LexEVS. NCIt is generally at or near the top of the NCBO ontology use chart (see section 3 above). NCBO and EVS maintain ongoing coordination and harmonization efforts through both caBIG® and other channels. For example, NCBO participates in the VCDE working group on Representing Terminology Metadata, which is adapting work begun by NCBO in this area for use by NCI and NCRI. NCBO also makes its terminologies available through caGrid.
NCBO built its NCBO BioPortal ontology services on top of LexEVS, supporting a very wide collection of ontologies that are actively used in biomedicine. This is an example of how two federally-funded groups are working together on the development of resources that will benefit the biomedical terminology community.
Open Biomedical Ontologies (OBO)
EVS has worked with the OBO Foundry group since around 2005 to develop shared principles for open ontologies. NCI Thesaurus is designated as an Application ontology, since it uses and references domain ontologies within the OBO Foundry group. EVS makes several of the OBO Foundry ontologies available through LexEVS for caBIG® use. (For more information, visit the OBO Foundry website.)
The Taiwan Cancer Registry
The Taiwan Cancer Registry, a population-based cancer registry founded in 1979, uses NCI Thesaurus terminology. Hospitals with greater than 50-bed capacity that provide outpatient and hospitalized cancer care are recruited to participate in reporting all newly diagnosed malignant neoplasms to this registry.
Other Sample Case Studies
Nanotechnology, and more specifically nanomedicine, has become important in the development of reagents for cancer detection and treatment. NCI established Cancer Centers of Nanotechnology Excellence (CCNE) to support translational nanomedical research. The NCI CCNE office became a partner with CBIIT in 2006 to develop a data sharing platform called caNanoLab.
NanoTAB: Developed by CBIIT, Oregon State University, PNNL, Washington University St. Louis, Stanford, Jackson Labs, Pennsylvania BioNano Systems, NIOSH, NCI Frederick NCL, Emory/Georgia Tech. This tool is used by all members of the ICR Nano Working Group. Despite recent loss of caNanoLab funding, NanoTAB continues to be used heavily.
Imaging standards development requires the support of multiple products made available through EVS, including publication of Radlex terminology, developed through a collaboration of the Radiological Society of North America (RSNA), which convened experts in imaging informatics and radiological subspecialties to create this resource, now made freely available. RadLex has developed into a rich, structured radiology-specific ontology, which currently includes more than 30,000 terms and to which EVS provides content as well as publication support. EVS incorporates RadLex into the NCI Metathesaurus, and also supports imaging terminology in the NCI Thesaurus as needed by the imaging community.
MedDRA (Medical Dictionary for Regulatory Activities) is an ICH standard for regulatory reporting. EVS contributes to updates of the cancer domain for this widely employed international terminology. The NCI Thesaurus is used as the basis to update MedDRA neoplastic terminology. MedDRA is translated into 11 languages, with approximately 3,000 institutional subscribers from 60 countries.
Use of LexEVS
MD Anderson is using a local LexEVS server as part of their enterprise infrastructure. Special resources were dedicated to resolving initial software compatibility and other issues, ensuring a successful deployment. NCI EVS terminology browsers have also been deployed, as have NCIt and other EVS terminology resources. This is an example of leveraging a wide range of EVS resources and services in support of the research and clinical enterprise infrastructure of a leading cancer center.