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{multi-excerpt:name=UserProfiles-caBIGandCommunity}EVS has enjoyed wide use and many collaborations within caBIG® and other organizations in the cancer research and biomedical community. The following are included in this profile:


h2. LexEVS Adopter Community

h3. MD Anderson

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.

h3. Emory University

Emory University 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. This is an example of an academic medical center deploying and  extending EVS components.

h3. 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 provided  the code for that extension, which is now available to the community  via the VKC web site. This is an example of NCI open source technology  being bundled into a commercial healthcare product.

h3. Mayo Clinic Health Solutions and Mayo Clinic Global Products and Services

These Mayo Clinic units are in the  process of deploying LexEVS for terminology hosting and management. The  project will eventually migrate to the GE Qualibria platform, which also  uses LexEVS. This is an example of industry partners engaged in the  development and commercialization of NCI open source tooling.

h3. McGill University Health Center, Canada

McGill is connected to the  TRANSFoRm project for European health care reform. LexEVS was chosen as  the terminology server for the project, but a new loader is required in  support of the ATC terminology. The VKC is currently working with them  on the development of the ATC loader, which includes requirements  gathering, coding, testing, and documentation. This represents an  example where a project-specific use case provided by a customer is used  as the basis for collaborative development of an open source  contribution.

h3. Seoul National University, Korea

The 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. The VKC is  currently working with BiKE to finalize an agreement  under which they  would provide to us the source code for a terminology  mapping UI that  was developed as part of their project. 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.

h2. Nanotechnology

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. 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 (see below).

h3. Nanotechnology Working Group

caBIG® has established a Nanotechnology Working Group as part of its Integrative Cancer Research Workspace (ICR Nano WG) with a mission to federate nanotechnology databases.   The Nanotechnology Working Group includes about   60 people representing   approximately 40 agencies, universities and   institutes, a few from   Europe.  One requirement of  this group has been to develop data and  vocabulary standards to  facilitate federation and increase data  accessibility. EVS is  contributing to this effort as 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. 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, preparing  NPO for integration into  the NCI Metathesaurus (NCIm), and planning for  future editing of NPO in  the BiomedGT Wiki collaborative editing  environment.

h3. caNanoLab

The NCI CCNE  office partnered with CBIIT 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.  Funding for additional development was recently lost, but caNanoLab   continues to be heavily used.  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.

h3. 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.

h3. NanoParticle Ontology (NPO)

This terminology is loaded in NCI  Metathesaurus, on LexEVS, and on the NCI Term Browser. NPO curators use  the NCI Protégé curation tool and they use NCI Thesaurus as a  cross-reference and a source for some of their definitions.

h2. caMOD

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.

h2. 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.

h2. 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.

h2. Imaging Standards

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.

h2. Georgetown University

Georgetown uses LexEVS and other EVS resources for its cancer  Bench-to-Bedside (caB2B) project and other activities. Both 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.

h2. Mayo Clinic / Pharmacogenomics Research Network (PGRN) Ontology Network Resource (PHONT)

Mayo Clinic is the primary site for PHONT, a leading user of EVS resources supporting clear annotation and representation of phenotype (disease, adverse event, or clinical and physiological outcomes) to support data integration and cross-database analyses, collaborating with Case Western Reserve University, Harvard Medical School, MD Anderson Cancer Center, Memorial Sloan Kettering Cancer Center, University of Erlangen, and Washington University.

h2. 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.

h2. 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|].)

h2. 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.

h2. 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, MohantryMohanty S, Sioutos N, Warzel DB, etWright LW, alCrowley RS. 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).

h2. Washington University

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.{multi-excerpt}