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EVS has worked in partnership with and been used by many other organizations in the cancer research and biomedical community. Some noteworthy examples are described briefly in this section as identified in the list that follows. Single-institution efforts are described first, followed by thematic efforts that span multiple institutions. Some projects not covered in this section have put listings on the NCBO BioPortal detail page for NCI Thesaurus
InstitutionalAmerican Association for Cancer Research (AACR)AACR, founded in 1907, fosters research in cancer and related biomedical science, including advances in the understanding of cancer etiology, prevention, diagnosis, and treatment throughout the world. A key recent initiative related to EVS is GENIE. Genomics, Evidence, Neoplasia, Information, Exchange (GENIE)AACR created GENIE
American College of Cardiology (ACC)American College of Cardiology (ACC) and EVS have worked together for several years on a number of projects, some also involving NHLBI, CDISC and Duke University. EVS worked with ACC and CDISC to develop 389 terms for the ACC/CDISC Cardiovascular Disease Therapeutic Area standard, bundled in 30 new codelists as well as a number of existing codelists. ACC made use of 157 existing NCI Thesaurus terms and added 232 new ones, while EVS added 194 ACC concept definitions as NCI preferred definitions. EVS Related References
American Society of Clinical Oncology (ASCO)ASCO brings together more than 40,000 oncology health care professionals in many activities related to EVS, most notably CancerLinQ. Cancer Learning Intelligence Network for Quality (CancerLinQ)ASCO created (CancerLinQ
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Catalogue of Somatic Mutations in Cancer (COSMIC)
EVS Related References
Clinical Genome Resource (ClinGen)
EVS Related References
Duke UniversityDuke University and EVS have collaborated for several years on various projects. As one example, the Research Informatics group of the Duke Clinical Research Institute (DCRI) has used vocabulary services from the EVS LexEVS terminology server in adding standard metadata to the Cardiovascular DAM. Duke and EVS have worked together with other partners such as CDISC, NHLBI, and the American College of Cardiology, in the development of shared terminology and other standards involving clinical trials, case report forms, cardiology, tuberculosis, and other content. EVS Related References
Emory UniversityEmory University has deployed and extended several EVS resources. Emory is using LexEVS to develop and host local ontologies. Uses include terminology support for an analytic data warehouse, which incorporates custom patient classes defined using ICD-9 codes. EVS Related References
European Bioinformatics Institute (EBI)The European Bioinformatics Institute (EBI) Experimental Factor Ontology (EFO
EVS Related References
General Electric (GE)GE is developing a platform called Qualibria, which includes LexEVS as a terminology server. VKC has been working with GE since 2008. As part of the collaboration, GE created an extension to the LexEVS 5.1 API based on the Common Terminology Services specification. GE made the code for that extension available to the community via the VKC web site, and bundled EVS-supported open source technology into GE's commercial healthcare product. Georgetown UniversityGeorgetown uses LexEVS and other EVS resources for its cancer Bench-to-Bedside (caB2B) project and other translational medicine activities. Both a local LexEVS installation and NCI's production LexEVS servers provide terminology support for this project. Jackson LaboratoryThe Jackson Laboratory has been a close partner with NCI – and EVS in particular – for over 10 years. They have been closely involved in the MMHCC and other initiatives described in the NCI Division of Cancer Biology (DCB) section of 11 - User Profiles - NCI. EVS publishes their Adult Mouse Anatomy (MA) on NCI servers and browsers (see NCI Term Browser). As part of the Mouse-Human Anatomy Project (MHAP), anatomy terms in MA and the NCIt human anatomy were compared and harmonized, and a formal mapping was jointly created and validated in 2006; this mapping has been recently updated and published as a mapping accessible through the LexEVS server APIs and NCI Term Browser (see MA to NCIt Mapping). As both anatomical ontologies are being used to annotate different types of research data for mouse and human, respectively, this cross-mapping between the two ontologies facilitates the integration of mouse and human data, and the translation of basic research discoveries into clinical settings. EVS Related References
Mayo ClinicMayo Clinic has partnered with, supported and used EVS resources in a variety of ways for more than 10 years. This has included joint work on analyzing cancer clinical trials vocabulary and informatics needs in the U.S., improving research and clinical data representation and reuse through projects such as PHONT and SHARPn , and development of shared community standards for vocabulary representation and infrastructure including the draft HL7/OMG standard Common Terminology Services Release 2 (CTS 2) specification and the the Mayo Clinic LexEVS terminology server that EVS has supported and uses. Mayo Clinic has a lead role in the ICD-11 revision effort, and Mayo has worked with EVS to leverage NCI Thesaurus cancer content and EVS subject matter experts in supporting revisions to the WHO ICD terminologies (see the WHO section). Pharmacogenomics Research Network (PGRN) Ontology Network Resource (PHONT)Mayo Clinic is the primary site for PHONT, a networked PGRN ontology resource that has been one of the highest-volume users of EVS resources. PHONT supports clear annotation and representation of phenotype (disease, adverse event, or clinical and physiological outcomes) to support data integration and cross-database analyses. PHONT has deployed its own instance of LexEVS, depending in particular on full support of CTS 2 value sets. PHONT is a collaboration with Case Western Reserve University, Harvard Medical School, MD Anderson Cancer Center, Memorial Sloan Kettering Cancer Center, University of Erlangen, and Washington University. Strategic Health IT Advanced Research Projects: Area 4 - Secondary Use of EHR Data (SHARPn)
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MD AndersonMD Anderson is using a wide range of EVS terminology content and technologies as part of its enterprise infrastructure. A LexEVS server and EVS terminology browsers have been deployed locally at MD Anderson. NCIt and other EVS terminology resources are also being used. Memorial Sloan Kettering Cancer CenterThe MSK Cancer Center (MSK) has used NCI Thesaurus (NCIt) in its precision oncology efforts, most notably through the OncoTree tumor type tree used in cBioPortal and its new OncoKB project. OncoKBOncoKB was first released in June 2016 as a precision oncology knowledge base for annotation of somatic mutations in cancer. It contains information about the effects and treatment implications of specific cancer gene alterations. It is developed and maintained by the Knowledge Systems group in the Marie Josée and Henry R. Kravis Center for Molecular Oncology (CMO), which is integrating OncoKB information with cBioPortal. cBioPortalThe cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets including The Cancer Genome Atlas (TCGA). Originally developed by, and still hosted at, MSK, cBioPortal is now developed and maintained by a multi-institutional team. OncoTreeThe OncoTree CMO Tumor Type Tree provides a user-friendly interface to 524 tumor types from 32 tissues, most linked to NCI Thesaurus (NCIt) and NCI Metathesaurus (NCIm) codes. Ohio State University Medical CenterOhio State is using LexEVS, NCIt, and NCIm, notably for its openMDR project. Ohio State University launched openMDR (open metadata repository) in 2009, using local instances of LexEVS, BioPortal, and caDSR. Seoul National University, KoreaThe Biomedical Knowledge Engineering (BiKE) lab adopted the 2005 version of the LexGrid model and over the last several years created an entire terminology-based application suite on that model called LexCare Suite. The VKC facilitated the signing of an agreement between Mayo Clinic and SNU's BiKE to solidify a collaboration under which they will work together on conferences and papers surrounding terminology creation/mapping/use. The BiKE mapping tool is of particular interest for a community tool in this regard. This would be a potentially significant contribution, as it would add a new tool in an area with a known gap in the current functionality of LexEVS. Stanford UniversitySince 2003, EVS has worked closely with the Stanford University Center for Biomedical Informatics Research (BMIR) and the NCBO project to develop shared community tools, standards and resources. Protégé OWL and NCI Protégé have pushed the envelope on open source software for ontology development and production management. NCBO and EVS collaborated on terminology metadata standards, with caBIG and the UK National Cancer Research Institute. NCBO hosts copies of NCI Thesaurus (NCIt), one of its most highly accessed terminologies. NCIt is also used by the NCBO Annotator tool for annotating documents and data with terminology concepts. NCBO and EVS have complementary resources, and share knowledge and expertise. ProtégéEVS has worked closely with BMIR and its predecessor, Stanford Medical Informatics. An early focus was development of Protégé OWL, so that EVS could move from proprietary to open source terminology editing software that used the emerging OWL DL standard; this was followed by support for an NCI specific plug-in that enable NCI terminology production management. Over time, many of these NCI specific changes have been rolled into the main Protégé 3.4 code, so that users worldwide could take advantage of such features as distributed collaborative terminology development. In addition, the NCI specific Protégé configuration, with its additional plug-ins, is available for non-NCI users. EVS editors and staff have been heavy users of Protégé, collaborators on collaborative ontology workflows, and testers of collaborative Protégé, Web Protégé and NCBO tools and services such as concept merging and terminology mapping tools. National Center for Biomedical Ontology (NCBO)
Terminology MetadataNCBO and EVS have collaborated on standards for terminology metadata with caBIG participants and the UK National Cancer Research Institute (NCRI), to develop and promote standards for annotating the content, structure and use of ontologies and terminologies, based on earlier work of Stanford and a European group on the Ontology Metadata Vocabulary (OMV). This work has fed into the terminology metadata content now embedded in the CTS 2 (Common Terminology Services 2) standard published by HL7 and the OMG (Object Management Group). Tissue Microarray Database (TMAD)
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Swiss Institute of Bioinformatics (SIB)The SIB Computer Analysis and Laboratory Investigation of Proteins of Human Origin (CALIPHO) group develops a number of biocurated resources including neXtProt and the Cellosaurus. Both resources make use of the NCI Thesaurus (NCIt). neXtProtneXtProt maps Catalogue of Somatic Mutations in Cancer (COSMIC) cancer terms to the corresponding terms in NCIt so as to present to its users a standardized vocabulary for the provenance of cancer protein variations extracted from COSMIC. CellosaurusThe Cellosaurus, a cell line thesaurus, uses NCIt to annotate cell lines originating from diseased patients and animals (mainly cancers of human and animal model origins and genetic diseases); as of March 2016, Cellosaurus contains over 25,000 cell lines linking to over 1,000 diseases in NCIt. EVS Related References
University of PittsburghEVS resources, notably NCI Thesaurus (NCIt) and NCI Metathesaurus (NCIm), are now deeply rooted in University of Pittsburgh core informatics applications used by hundreds of basic, translational and clinical researchers, and by many more using those applications at other institutions. University of Pittsburgh uses the NCIt cancer, anatomy, and pathology findings terminologies for their research and informatics projects. Millions of pathology reports have been encoded using NCIm and indexed using NCIt. Collaborations are ongoing, and have resulted in several journal articles published over the last 8 years. Ontology Development Information Extraction (ODIE)
Multiple informatics projects at Pittsburgh build on the ODIE framework. Text Information Extraction System (TIES)
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Washington UniversityWashington 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, supporting both research and clinical enterprise infrastructure. Yale UniversityYale University has used EVS resources in several biomedical research and informatics projects, including some with a special focus on semantic web technologies. EVS Related References
Project and TopicalAnimal Models and MappingsEVS has worked since 1999 on a variety of animal models of cancer and terminology mappings between human and non-human species. In addition to work described earlier involving the NCI Division of Cancer Biology with extensive community outreach (see the detailed profile), and the section above on work with the Jackson Laboratory, EVS has been involved in a number of other community efforts. EVS has extended animal model terminology support to cover rats and zebrafish using two important community standards:
EVS terminology is also being used in community efforts such as those below. Uberon
Ontology Alignment Evaluation Initiative (OAEI)The OAEI
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. In early 2012, EVS provided support for mapping SNOMED concepts used in caTissue with NCIt concepts used in CBM, to facilitate data sharing. eMERGE NetworkThe eMERGE (electronic MEdical Records and GEnomics) Network
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eTOX
Global Alignment of Immunization safety Assessment in pregnancy (GAIA)The Global Alignment of Immunization safety Assessment in pregnancy (GAIA) is a global consortium to develop common standards, guidance, and tools to strengthen programs of immunization in pregnancy, with a specific focus on low and middle income countries. GAIA seeks to improve data and understanding on maternal, pregnancy, fetal, and neonatal health outcome assessment. The National Institute of Child Health and Human Development (NICHD) and EVS have been collaborating with GAIA since 2014 to help develop standard terminology related to Fetal and Neonatal Events, Maternal, and Pregnancy Events and Outcomes. This expands on the Pediatric Terminology joint effort, ongoing since 2009, to establish a core library of harmonized pediatric terms that enable clinical investigators to more readily compare and aggregate data across clinical research portfolios. To this end, terminology data and draft standards were developed as part of the NCI Thesaurus (NCIt) by experts from the NICHD, EVS, and other participants. All NCIt content is freely available without restriction. EVS Related References
Human Studies Database (HSDB)
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International Human Epigenome Consortium (IHEC)
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Imaging StandardsImaging 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. EVS Related References
LexEVS Adopter CommunityMany other organizations have adopted the LexEVS terminology server and related tools. Key examples described in the institutional portion of this section are:
For literature references, see the LexEVS section of Bibliography on EVS and Its Use. NanotechnologyNanotechnology, and more specifically nanomedicine, has become important in the development of reagents for cancer detection, diagnosis and treatment. NCI established Cancer Centers of Nanotechnology Excellence (CCNE) to support translational nanomedical research, and collaborative efforts are supported by NHLBI, NHGRI, FDA and others. EVS provides a range of content and technical support to the nanotechnology community, including working with the community in curating specialized concepts and definitions, and making those concepts available in NCI Thesaurus (NCIt) and the NanoParticle Ontology (NPO) hosted on EVS systems and integrated into NCI Metathesaurus (NCIm); a glossary of nanotechnology terms also is provided within the caNanoLab application (see below). Nanotechnology Working GroupThe NCIP Nanotechnology Working Group was started as part of the caBIG® Integrative Cancer Research Workspace (ICR Nano WG), with participation of approximately 40 agencies, universities and institutes working to federate nanotechnology databases. One requirement has been to develop data and vocabulary standards to facilitate federation and increase data accessibility. EVS has been an active participant in the working group. Part of the working group effort is the continuing development of the NanoParticle Ontology (NPO), from Washington University in St. Louis, and the development of the ISA-TAB-Nano data sharing format. EVS has supported this effort in several areas: giving feedback on ontology structure and terminology best practices, supporting NPO curation using the NCI Protégé platform, loading and hosting NPO on LexEVS, and preparing NPO for integration into the NCI Metathesaurus (NCIm). caNanoLabThe NCI Office of Cancer Nanotechnology Research (OCNR) partnered with CBIIT and the NCI Nanotechnology Characterization Laboratory (NCL) in 2006 to develop a data sharing platform called caNanoLab. 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. NCI Thesaurus (NCIt) has been supporting concept curation for development of caNanoLab since its inception. NCIt editors have worked with the developers and users of caNanoLab from the CCNEs and other academic institutions to define concepts for data curation and to expand the object model to include data submission for both characterizations of experimental nanomaterials and translational research studies. The infrastructure available for further development of caNanoLab has been decreased over the last several years, but caNanoLab continues to be maintained and is heavily used. As of February 21, 2014, it contains 1,027 samples, 95 sample sources, 4,025 characterizations, and 46 protocols, and identifies 1,894 publications, while the caNanoLab home page shows 420,937 visitors since June 3, 2010. For more information about caNanoLab, visit the wiki home page. ISA-TAB-NanoISA-TAB-Nano is being developed by a subset of participants of the NCIP Nanotechnology Working Group, which includes members representing CBIIT, Oregon State University, PNNL, Washington University St. Louis, Stanford, Jackson Labs, Pennsylvania BioNano Systems, NIOSH, NCI Frederick NCL, and Emory/Georgia Tech. ISA-TAB-Nano is a data representation format that is designed to facilitate sharing research related to the in vivo and in vitro characterization of nanomaterials and any associated small molecules or biological specimens. This format is compatible with spreadsheets or tab-delimited files. ISA-TAB-Nano is based on the existing specification developed by the ISA community, the investigation/study/assay (ISA-TAB) format specification. ISA-TAB was designed to assist in recording and sharing of both data and metadata associated with the large volume of data generated by the numerous assays and technology types used in the “omics” communities. The ISA-TAB file structure relies on three primary files: investigation, study, and assay (ISA) files. The ISA-TAB-Nano specification adds additional fields to the ISA-TAB files and an additional material file to record nanomaterial and small molecule structural and functional characteristics. ISA-TAB-Nano has been reviewed as an ASTM standard (WK28974). Further development for this data sharing format is focused on training users, improving the usability of the format and increasing the compatibility between ISA-TAB-Nano and the ISA community curation and validation tool sets. See the ISA-TAB-Nano Specification for more information. NanoParticle Ontology (NPO)The NanoParticle Ontology (NPO
EVS Related References
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 community use. (For more information, visit the OBO Foundry website
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PhenX
Translational Research and Patient Safety in Europe (TRANSFoRm)The TRANSFoRm
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