Skip NavigationSkip to Content

CTOS Projects

CTSG provides Technical and Operational support for the NCI CBIIT.
The NCI Center for Biomedical Informatics and Information Technology (CBIIT) seeks to accelerate scientific discovery and facilitate translational research and precision medicine. Its principal activities include developing, coordinating, and deploying enterprise-wide biomedical-informatics and scientific-management information-technology (IT) systems, infrastructure, open-source applications, semantics, and data resources in support of the Institute?s research agenda.

Here is a list of projects tha the CTSG team is working on:

CTSG Projects

Project Brief Description
Project: BRIDG BRIDG provides the foundation for biomedical research across our communities. As an activity supported by the FDA, HL7, CDISC and the NCI, it is an important standard that has been formally balloted by HL7 (version 2.x in ~ 2006) and to which the CDISC SDTM safety and efficacy domains have all been mapped. Integration of the BAM and the Life Sciences Domain Analysis Model into BRIDG occurs in FY13/14. LSDAM gives BRIDG a domain for the life sciences. CDISC initiated balloting of BRIDG by ISO.
Project: C3D Tools Production Support and Clinical Connector for C3D This project fulfills two key business needs and requirements1. Production support for NCI – CCR’s installation of C3D tools as well as CDE load, Lab Mapping and Lab Load production processes2. A Grid-service based in-bound and out-bound connectivity with C3D data
Project: caAdapter caAdapter is an open source tool set that provides model mapping services in support of building interoperable applications, and facilitates data mapping and transformation among different kinds of data sources including CSV data, HL7 messages, and CDISC SDTM (Study Data Tabulation Model) datasets.
Project: caAERS-Rave Integration Presently there are over 900 clinical trials being supported by the NCI, with more being created every month. For each clinical trial patient may experience some adverse events (AE) and some serious adverse events (SAE). There are ethical and legal reporting requirements for these adverse events. Today these events are reported through specialized adverse event reporting tools such as Adverse Event Expedited Reporting System (adEERs) and Cancer Adverse Event Reporting System (caAERS). Because these are separate systems from the electronic data capture systems (EDC), it requires duplication of entry and some subjective decisions on the seriousness of the Adverse Event resulting in over- or under-reporting of the Serious Adverse Events.
Project: caArray Microarray-based profiling is now a standard tool set with which to interrogate biological systems. Parallel advances in computing and new array technology provide an opportunity for collaboration and discovery within the scientific community and across traditional boundaries to reach clinicians and ultimately patients. The insistence on open source development provides the community with the greatest opportunity to gain access to the tools they desperately need to execute their respective mission.
Project: caCORE Tools The caCORE (Cancer Common Ontologic Rpresentation Envirinment) SDK (Softwae Development Kit) provides tools that support the creation of semantically integrated caCORE-like systems. The tools support model driven development generation of services and provide common software modules. The primary areas of focus are security, logging, uniform API generation, and generation of services
Project: caGrid legacy support caGrid provides the technology that enables collaborating institutions to share information and analytical resources efficiently and securely, while also allowing investigators to easily contribute to and leverage the resources of a national-scale, multi-institutional environment.
Project: caIntegrator Support for analysis and visualization of genomics, clinical and imaging data for TCGA, Rembrandt, TARGET ALL, the NCI Director’s Challenge Lung Study, ISPY1, ISPY2
Project: caMOD Retrieve information about the making of models, their genetic description, histopathology, derived cell lines, associated images, carcinogenic agents, and therapeutic trials. Links to associated publications and other resources are provided. Animal models recapitulate many aspects of the genesis, progression, and clinical course of human cancers and are valuable resources to cancer researchers engaged in a variety of investigations
Project: caNanoLab The cancer Nanotechnology Laboratory portal (caNanoLab) is a web-based portal designed to facilitate data sharing in the research community to expedite and validate the use of nanomaterials in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro nanomaterial assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.
Project: caTissue ODI Transition The primary focus of the 2.0 release will improve interoperability with other Life Science (LS) products; integrate with assay systems like caArray, Clinical Trial Management System (CTMS), NSI Enterprise Service (NES), and Biospecimen Research Database; improve interoperability by implementing CMB; improve grid compatibility, quality, performance, scalability of the system by refactoring and re-architecting the existing system.
Project: CBIIT and NCI Web Presence The CBIIT/NCIP Web Presence provides an essential technical outreach function for NCI. As an online channel, these websites are primary vehicles for communicating with and developing both IT and informatics stakeholders. It is integrated and aligned with overall strategic program objectives and communications strategies.
Project: CBIIT App Support CBIIT and NCIP Application Support is dedicated to helping users obtain maximum benefit from program resources. Application Support exists to help users find what they need, use and re-use software, integrate data and applications, and facilitate the sharing of information and resources.
Project: CBIIT Enterprise Training Training and educational activities help fulfill CBIIT’s commitment to produce products and services that support research activities. In order to use use these products, services, and specifically standards, to their full potential, the community needs to have quality training provided in ways that meet the demands of a diverse set of professionals.
Project: CDMS Training and educational activities help fulfill CBIIT’s commitment to produce products and services that support research activities. In order to use use these products, services, and specifically standards, to their full potential, the community needs to have quality training provided in ways that meet the demands of a diverse set of professionals.
Project: CGAP and Gene Collections Provide research community access to various kinds of molecular data (EST sequencing, chromosomal abnormalities, gene expression, RNAi, pathways) related to cancer subtypes.
Project:CBIIT Technical Project Management (TPM) To support staff salaries, financial/contract administration activities, and maintanence of office operations.
Project: CRADA “Cooperative Research and Development Agreements (CRADAs) serve as useful instruments for public-private research partnerships. They are the only mechanism by which the Federal Government can guarantee a licensing option to outside collaborators and one of the few technology transfer mechanisms by which Federal laboratories can obtain funds. Several months ago, the ICs in collaboration with the Office of Technology Transfer (OTT) formed the CRADA Review Working Group to review all of the language in the current CRADA models and design a new approach that would be an ?individualized? approach, rather than a ?model? one. This ?individualized? concept provides the contract clauses and terms that comport with the specific intent of the research and needs of the parties. A goal of this approach is that it will decrease the negotiation time between NIH and collaborators.Part of the modernization of the CRADA process is to design and develop an online-automated system utilizing Drupal that would allow NIH technology transfer professionals to generate agreements using a series of guided questions to tailor the terms to the specific needs of the collaboration. This system has been named ?CRADA Builder.? It is intended to be a form wizard analogous to online tax preparation software that asks a series of customized questions and, based on the responses, inserts the appropriate information into a form.
Project: CRF Harmonization and Standardization Initiative Project meets the Clinical Trials Working Group (CTWG) initiative requirement that the NCI clinical trials enterprise infrastructure be supported through a library of harmonized collection instruments (Case Report Forms or CRFs) used to collect data for all trials supported by NCI. Resulting data elements will be maintained as standards, with wide reuse supporting interoperability, and ability to aggregate critical clinical trials data. This initiative supports the mandate of CBIIT to identify and support data standards for the NCI community-at-large.
Project: CTEP Support Cooperative Research and Development Agreements (CRADAs) serve as useful instruments for public-private research partnerships. They are the only mechanism by which the Federal Government can guarantee a licensing option to outside collaborators and one of the few technology transfer mechanisms by which Federal laboratories can obtain funds. Several months ago, the ICs in collaboration with the Office of Technology Transfer (OTT) formed the CRADA Review Working Group to review all of the language in the current CRADA models and design a new approach that would be an ?individualized? approach, rather than a ?model? one. This ?individualized? concept provides the contract clauses and terms that comport with the specific intent of the research and needs of the parties. A goal of this approach is that it will decrease the negotiation time between NIH and collaborators.Part of the modernization of the CRADA process is to design and develop an online-automated system utilizing Drupal that would allow NIH technology transfer professionals to generate agreements using a series of guided questions to tailor the terms to the specific needs of the collaboration. This system has been named ?CRADA Builder.? It is intended to be a form wizard analogous to online tax preparation software that asks a series of customized questions and, based on the responses, inserts the appropriate information into a form.
Project: CTR Transition Infrastructure The objectives of this project are to obtain the IT technical expertise needed to support the full transition of the Janus Clinical Trials Repository (CTR) application, which was developed at CBIIT to full production operation at FDA?s White Oak Data Center (WODC). The technical support to be provided will serve as a ?bridge? to enable a transfer of knowledge between the contractors and FDA staff who will be responsible for its operations and maintenance in production. Performance of the effort and service delivery will be secured through subcontractor (s) to provide FDA CDER IT expertise and support to facilitate the transfer of knowledge regarding the CTR functionality and technology stack, database management, and operational procedures and processes required to operate and maintain the CTR as well as continue to load new study data into the system after it has been deployed in an FDA production environment.
Project: CTRP Clinical Trials Database NCI’s Clinical Trials Reporting Program (CTRP) fulfills a recommendation made by the NCI Clinical Trials Working group to the National Cancer Advisory Board. The purpose of the program is to establish a comprehensive database containing regularly updated information on all NCI-supported clinical trials. NCI will use this information to coordinate research efforts to optimize our nation’s investment in cancer research. CTRP, launched January 2009 in a phased approach focusing initially on registering interventional trials by NCI-designated Cancer Centers. It is anticipated that NCI-designated Cancer Centers complete registration of existing cancer clinical trials in 2011. Trial Amendment(s) and update(s) reporting as well as patient accrual are targeted for 2012. NCI is reviewing requirements for registering non-interventional trials and outcomes reporting.
Project: CTRP DCP Integration Reduces duplicative data entry and the need for manual data entry of study data into CTRP.
Project: DCP Support Provide operational support to DESK and Protocol Information Office (PIO). Integrate the NCI Enterprise Services into DCP operations.
Project: EVS Browser, Reporting, Request and Specialized Software Provides essential tooling and technical support for EVS to create, process and publish controlled terminology resources needed by NCI infrastructure, research, clinical trial and other operations. This project provides application development and resources including, but not limited to, software that allows users to view, search and retrieve data from all biomedical terminologies hosted by EVS, and to create and serve EVS developed terminology resources including NCI Thesaurus and Metathesaurus.
Project: EVS Operations – Content, Production, Maintenance and NCIm Software Produces or provides access to all major terminologies required by NCI and its collaborating partners including the NCI Thesaurus and NCI Metathesaurus, as well as other coding terminologies required for business operations including ICD-9 and 10, the Common Terminology Criteria for Adverse Events (CTCAE), the Medical Dictionary for Regulatory Activities (MedDRA), and many others used in clinical applications, grant coding, information services and research. Manages production, publication, licensing and updates as needed on behalf of the Institute.
Project: EVS Terminology Editing Software NCI Thesaurus and NCI Metathesaurus are produced as part of the Enterprise Vocabulary Services. Software to edit/update, manage, publish and report on the terminology content is required. The current editing environment for NCI Thesaurus is NCI Protege (open source Protege 3.4 with a package of NCI plugins specific to the NCI editing and production process.) The current editing environment for NCI Metathesaurus is MEME (Metathesaurus Editors Management Environment), also used by NLM to edit / manage production of UMLS.
Project: EVS Terminology Server Software NCI Enterprise Vocabulary Services (EVS) provides resources and services to meet NCI needs for controlled terminology, and to facilitate the standardization of terminology and information systems across the Institute and the larger biomedical community.An overview of the EVS program can be found at: https://wiki.nci.nih.gov/display/EVS/EVS+Wiki. The LEXEVS Server plays a critical role in the EVS infrastructure. It provides standard terminologies, value sets, and terminology-to-terminology mappings through a standard web service, a caGrid service, and a Representational State Transfer (REST) interface. Many users make direct use of the NCI LEXEVS servers. LEXEVS is also used 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. Information on users is available at: https://wiki.nci.nih.gov/x/dYf_Ag .
Project: Family Health History FHH system will be an integral part of the NCI Infrastructure. The system will collect information about a family?s health and generates information about health risks. The system should have the capability to be expanded easily to include additional disease states and risk models as needed.
Project: Grants Management “This project implements an electronic workflow and approval process to track an award from the point of inception to delivery of notice of grant award and the measurement of time to process. Design, implementation, operations, maintenance and management ofapplications supporting NCI’s extramural business processes (referred to as “”Workbench””)”
Project: Imaging Middleware It is required by Enterprise Use Case (EUC) of IMAG workspace to provide a middleware to support Imaging Suite integration. This project provides a Centralized Imaging Security Service (CISS) and Annotation and Image Markup (AIM) data services.
Project: Metadata Curation and Harmonization (caDSR) Supports strong and growing need to produce standardized metadata for cancer prevention trials, biomedical imaging, clinical trials, genomic research, population studies and epidemiology, patient-centered outcomes, and quality and evidence-based research indicators. Registry and its content is central of a large number of projects and activities, and supports principles of semantic and syntactic interoperability.
Project: Metadata Software Engineering caDSR “see: https://wiki.nci.nih.gov/display/caDSR/caDSR+-+Overview+of+Use+and+Collaborations for detail of usage and collaborations. This project supports describing, sharing and reusing human and computer readable descriptions of data, thus preserving them for use in building case report forms (CRFs), creating new applications to validate and store data, and for apps to support secondary uses of data. Business processes supported: 24/7 Data Management and App Development. Using a standard framework conforming to ISO/IEC 11179 Metadata Registry (MDR) it ensures broad acceptability. It supports stakeholders within CBIIT, NCI, caBIG and BIG Health communities, including those charged with creating and distributing data standards and building applications to integrate data for clinical research, clinical care, life sciences, translational research, regulatory bodies and standards development organizations. It supports the data mngt processes of creating/editing/reviewing/querying/preserving data documentation, it allows application developers to reuse descriptions to provision web services and clinical trials applications with common data descriptions and discover the meaning of data held in application databases. The descriptions can queried and downloaded publically using web browsers or accessed programmatically to use to customize new CRFs by importing the descriptions into commercially available software including MediData, Velos and REDCap.Supports NCI and caBIGĀ® initiatives: NCI Cooperative Groups, C3D, CTEP, DCP CCR SPOREs caTissue, Ntl Marrow Donor Program(NMDP), caIntegrator, caB2B, TCGA, NAACCR, DCCPS/caSEER program, In Vivo Imaging Workgroup, DICOM, ACRIN, CTSA, Health Ontology Mapper, caGrid 1.0-OSU, MDACC-A Growable Network Information System(AGNIS)Supports NIH: NHLBI, NIDCR, NICHD, NINDSExternal:Winthrop P. Rockefeller Cancer Institute- Univ of Arkansas Medical Sciences(Breast Mammography)Union of Light Ion Centers in Europe(ULICE”
Project: NBIA “NBIA is a mature product that is adopted by various end users in conducting their clinical trials, public educations, and life science research. It is required by the Enterprise Use Case (EUC) to support business cases for QIN and Imaging Radiation Oncology (RadOnc) Clinical Trial. In fact, demands for NBIA is growing across workspaces when it comes to viewing images. NBIA plays a majr role in Imaging repository to support various business process and domains.supports”
Project: NCI Business Application Development and Support “This project involves development, support and maintenance for a suite of applications supporting a range of NCI business processes. These include applications for CBIIT (NCI Computer Services Support System (NCS3), NCI Central Receiving Applications (CR Waiver), Government Furnished Equipment Tracking Tool (GFET), Engineer On-Call application (ONCALL), Mac Laptops Encryption Application) as well as other NCI organizations (Privacy Impact Assessment (PIA) tracking system (OD/OM), Paper Reduction Act for OMB Clearance (OD/OM), Ethics Sponsored Travel Reporting System (OD/OM), Advocacy Recruitment (OAR), NCI Telework Electronic System, Emergency Tier Designation, Orientation signup, HCIP, ICRC, CIP (OD/OWD), as well as conference sites such as SPORE”
Project: NCI Match The NCI-MATCH (Molecular Analysis for Therapy Choice) will pursue the therapeutic approach in a comprehensive fashion by screening for molecular features that may predict response to a targeted agent with a specific mechanism of action. The study will serve as an umbrella for multiple, single-arm phase 2 trials. To support this study, CBIIT will undertake the development and deployment of an integrated informatics environment for genomics-based cancer screening that will support the assignment of patients to specified arms on the NCI-MATCH trial based on the underlying genetic defects identified as present in their tumor and a series of clinical business rules that define patient segregation based on specific scientific criteria defined for that genomic variant and disease set.
Project: Next Generation Data Collection Tool (eDCT) A critical component of the NCI CBIIT program is the development of a data collection and data exchange infrastructure where disparate systems, and research data in different formats can be collected, mined and made available to researchers in a seamless manner. This project supports the process of creating forms from standard components, using those forms to crete a data collection system, data collectiong/validation and analysis.
Project: Next Generation Data Collection Tool (eDCT) A critical component of the NCI CBIIT program is the development of a data collection and data exchange infrastructure where disparate systems, and research data in different formats can be collected, mined and made available to researchers in a seamless manner. This project supports the process of creating forms from standard components, using those forms to crete a data collection system, data collectiong/validation and analysis.
Project: OSDI Migration This project is a restart of the migration of all the code from the internal subversion repositories to GitHub Repositories. We now need to move the active repositories (~40) from the NCIP channel to the CBIIT channel. For all inactive projects (~120 repositories) we need to lock down edits and admin priveledges to the NCI admin teams.
Project: Pathway Interaction Database Provides curated, high quality biological pathway data to the research community. The cancer research community uses this data to aggregate and interpret high-throughput molecular data.
Project: Rave CRF Curation Support Supports usage of caDSR and NCI standard CRFs as per the Rave EULA and standards policy.
Project: Rembrandt Data Portal Support for the NCI Glioma Molecular Diagnostic Initiative data sharing and analysis. We have about 800 registered users for Rembrandt.
Project: TARGET (Portal and Data Coordination) Identify valid therapeutic targets in childhood cancers so that new, more effective treatments can be rapidly developed.
Project: TCGA Data Coordination Center and Portal Accelerate understanding of the genetics of cancer.
Project: Wiki Development and Maintenance This project provides ongoing support to technical documentation to create and maintain Wiki for each project