Glossary

Acronyms and other terms included in this glossary are relevant to the cancer Biomedical Informatics Grid^® initiative (caBIG^®), the National Cancer Institute (NCI), and/or the software development, clinical trials, or research environments associated with caBIG^®. To provide comments and suggest additions, please send an e-mail to caBIGinfo@cancer.gov.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

Adaptive Clinical Trials: In adaptive trials, data gathered as the trial progresses are used to change some aspect of the trial midstream. The adaptations can be to drop a treatment arm that isn’t effective, alter dose levels, or increase the trial size if a drug proves less responsive than predicted.
API: An Application Programming Interface (API) is a language and message format used by a software program that enables it to interact with other software. It facilitates interaction between different software programs similar to the way the user interface facilitates interaction between humans and computers.

B

Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.
Biomarker: Any biomolecule that is associated with a particular pathological or physiological state. Protein biomarkers may be used to diagnose disease or monitor the response to therapy.
BiomedGT: The Biomedical Grid Terminology (BiomedGT) is an open, collaboratively developed terminology for translational research. BiomedGT builds on the strengths of the NCI Thesaurus, including concept orientation, description logic, and public accessibility.
Biorepositories: A place, room, or container where a large number of biospecimens are stored. Biorepositories vary considerably, ranging from formal organizations to informal collections of materials in an individual researcher's freezer. Well organized biorepositories have a system of quality control standards for the processing and storage of biospecimens, and a system of annotating biospecimens with associated clinical information.
Biospecimens: A quantity of tissue, blood, urine, or other biologically derived material used for clinical diagnosis or research. A biospecimen can include everything from preparations of subcellular structures and biomolecules (such as DNA) to cells, tissue (bone, muscle, connective tissue, and skin), organs (e.g., liver, bladder, heart, kidney), blood, gametes (sperm and ova), and biological waste (urine, feces, sweat, hair and nail clippings, shed epithelial cells, and placenta).
BRIDG: The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort to produce a shared view of the dynamic and static semantics for the domain of protocol-driven research and its associated regulatory artifacts. It engages stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 Regulated Clinical Research Information Management Technical Committee (RCRIM TC), the National Cancer Institute (NCI) and its Cancer Biomedical Informatics Grid (caBIG^®), and the U.S. Food and Drug Administration (FDA). The BRIDG model is an instance of a Domain Analysis Model (DAM).

C

C3D: The Cancer Central Clinical Database (C3D) is a clinical trials data management system that collects clinical trial data using standard case report forms (CRFs) based on common data elements (CDEs). As required by FDA regulations, C3D utilizes security procedures to protect patient confidentiality and maintain an audit trail.
C3PR: The Cancer Central Clinical Participant Registry (C3PR) is an open source, Web-based system that enables efficient and streamlined registration of participants into clinical trials. It can be used by an individual site or across multiple institutions. C3PR helps to organize and standardize a template for patient registration.
caBIG^® Application Bundle: A set of interrelated bioinformatics tools or resources designed to be used together to perform within a specific domain. caBIG^® informatics tools are organized into three bundles: the Life Sciences Distribution (LSD); the Clinical Trials Suite; and the Data Sharing and Security Framework (DSSF).
C-DAC: The Center for the Development of Advanced Computing (C-DAC) is the premier R&D organization of the Department of Information Technology (DIT), Ministry of Communications & Information Technology (MCIT) focused on IT, electronics and associated areas.
caAdapter: caAdapter is an open source tool set that provides model mapping services, and facilitates data mapping and transformation among different kinds of data sources including HL7 v2 messages, HL7 v3 messages, and Regulatory Data Sets. caAdapter can be integrated easily with other applications such as caBIG^® Integration Hub, and a web service that exposes caAdapter functions for integration with other caGrid applications.
caAERS: The cancer Adverse Event Reporting System (caAERS) is used to collect, process, and report adverse events that occur during clinical trials. This tool supports regulatory and protocol compliance for adverse event reporting and allows local collection, management, and querying of adverse event data. It also supports service-based integration of data from other clinical trials management systems.
caArray: The cancer Array (caArray) is a microarray data management system that supports annotation and the exchange of array data. It also facilitates integration of array data with diverse data types, including clinical, imaging, tissue, and other functional genomics and connects to caBIG^® analytical tools like geWorkbench and GenePattern.
caB2B: The cancer Bench-to-Bedside (caB2B) is an open-source, secure query tool that permits translational research scientists to search and combine data from virtually any caGrid data service. Specifically, it provides easy search and retrieval of microarray data (from caArray), imaging data (from the National Biomedical Imaging Archive), specimen data (from caTissue), and nanoparticle data (from caNanoLab) across the grid.
caBIG^®: The cancer Biomedical Informatics Grid^® a collaborative initiative of the NCI that is developing standards-based infrastructure, tools, and data sets to support integrative cancer research and promote multidisciplinary scientific collaboration.
caBIG^® Integration Hub (formerly caXchange): The caBIG^® Integration Hub (formerly caXchange) facilitates automatic capture of clinical laboratory data from clinical systems and automatic translation and import to caBIG^®-compatible clinical trials databases. This software supports integrated clinical trials workflows and offers users the flexible interoperability associated with a service-oriented architecture (SOA).
caBIO: The cancer Bioinformatics Infrastructure Objects (caBIO) is a robust resource for accessing biomedical annotations from curated data sources in an integrated view. The caBIO domain model and architecture is an ongoing effort to model the rapidly changing genomics and proteomics domain and to integrate data from numerous sources, providing a holistic view of the human and mouse genomes. The integration of genome annotations with clinical trials, pathway, and literature associations allows researchers to discover associations in the data that were previously unseen in the separate datasets.
caCORE: The cancer Common Ontologic Representation Environment (caCORE) contains tools and Application Programming Interfaces (APIs) that provide the building blocks for the development of interoperable information management systems. Developers use caCORE components to adapt and build applications that are interoperable with other caBIG^® tools.
CAD: Computer-Aided Detection is the use of computers to aid radiologists in detecting potential abnormalities on diagnostic radiology exams. Pattern recognition software identifies suspicious features on the image and brings them to the attention of the radiologist in order to decrease false negative readings.
caDSR: The cancer Data Standards Repository (caDSR) is a database and set of Application Programming Interfaces (APIs) and tools to create, edit, control, deploy, and find common data elements (CDEs) for use by metadata consumers, and information about the Unified Modeling Language (UML) models and Forms containing CDEs for use in software development. Use of CDEs makes it possible to aggregate and manage data sets in order to ask basic questions and obtain meaningful answers.
caELMIR: The cancer Electronic Laboratory Management Information Resource (caELMIR) provides pre-clinical researchers with a managed, secure laboratory information management system that permits integration with legacy animal colony management systems and legacy pathology systems.
caFE: cancer Function Express (caFE) is an electronically batch-loaded tool that annotates probes on microarrays using publicly available biomedical databases and automatically updates these annotations on a regular basis.
caGrid: caGrid is the underlying network architecture and platform that provides the basis for connectivity of caBIG^® tools and between all of the cancer community institutions, allowing research groups to tap into the rich collection of emerging cancer research data. caGrid securely manages and shares information and analytic resources using locally managed access control policies and by using strongly typed data objects in XML format.
caGrid Portal: The caGrid Portal provides caGrid users with a web interface to explore the contents of a Grid. The caGrid Portal provides several ways to find data sets, people, tools, communities, and institutions that participate in caBIG^®.
caGWAS: The cancer Genome-Wide Association Scan (caGWAS) allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response, or other clinical outcomes. caGWAS also allows researchers and bioinformaticians to access and analyze clinical and experimental data across multiple clinical studies.
caIntegrator: caIntegrator allows researchers to create custom web-based integrative data portals to access and analyze clinical and experimental data across multiple studies. The caIntegrator framework provides a mechanism for integrating and aggregating biomedical research data and provides access to a variety of data types (e.g. microarray-based gene expression, SNPs, clinical trials outcomes data etc.) in a cohesive fashion.
caLAB: The cancer Laboratory Analysis Bench (caLAB) is a "light" Laboratory Information Management System (LIMS) designed to capture the workflow in the laboratory. caLAB provides support for the execution of assays and the recording of assay results. caLAB allows for the management of laboratory inventory (samples, aliquots) that is leveraged as input to experiment assays.
caMOD: The cancer Models Database (caMOD) provides information about animal models for human cancer. Users can retrieve information (where available) about the design of models, their genetic descriptions, histopathology, images, microarray data, and therapeutic trials in which the models were used.
caNanoLab: The caBIG^® Nanotechnology Laboratory (caNanoLab) is a data sharing portal that provides support for the annotation of nanoparticles with characterizations resulting from physical, chemical, and in vitro nanoparticle assays, and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.
Cancer Centers: The National Cancer Institute Cancer Centers Program supports major academic and research institutions throughout the United States to sustain broad based, coordinated, interdisciplinary programs in cancer research. These institutions are characterized by scientific excellence and capability to integrate a diversity of research approaches to focus on the problem of cancer. Today there are 61 Centers across the United States.
caTIES: The cancer Text Information Extraction System (caTIES) enables researchers to query, browse, and acquire annotated tissue data and physical material across a network.
caTissue Suite: caTissue Suite is a tissue-banking tool for biospecimen inventory, tracking, and annotation. caTissue enables researchers to track the collection, storage, annotation, quality assurance, and distribution of specimens, as well as find and request specimens with specific characteristics.
CBIIT: See NCI CBIIT.
CCTS: The caBIG^® Clinical Trials Suite supports the management of study participant information through the clinical trial lifecycle.
CCR: The Continuity of Care Record (CCR) is a standard specification intended to foster and improve continuity of patient care, to reduce medical errors, and to assure at least a minimum standard of health information transportability when a patient is referred or transferred to, or is otherwise seen by, another provider. It is being developed jointly by ASTM International, the Massachusetts Medical Society (MMS), the Health Information Management and Systems Society (HIMSS), the American Academy of Family Physicians (AAFP), and the American Academy of Pediatrics.
CDE(s): Common Data Element(s) (CDE(s)) are annotations collected in a uniform manner across multiple institutions to allow sharing of data in a standardized format.
CDISC: The Clinical Data Interchange Standards Consortium (CDISC) is a non-profit organization that has established standards to support clinical research data. This standard is widely subscribed to by industry and is a competing system to HL7. BRIDG is the mitigating technology that coordinates HL7 and CDISC standards.
CDMS: The Clinical Data Management System (CDMS) is an application that manages the collection of clinical data generated by a clinical trial.
CED: The Clinical Expression Database (CED) stores and retrieves clinical data and gene expression data in a manner which accommodates diverse projects incorporating human disease and gene expression techniques.
CGAP: The Cancer Genome Anatomy Project (CGAP) is an NCI-based research initiative aimed at determining the gene expression profiles of normal, pre-cancer, and cancer cells.
CGEMS: The Cancer GEnetics Markers of Susceptibility (CGEMS) project began in 2005 as a 3-year pilot study to identify inherited genetic susceptibility to prostate and breast cancer. CGEMS has developed into a robust research program involving genome-wide association studies (GWASs) for a number of cancers to identify common genetic variants that affect a person's risk of developing cancer.
CGI: The Cancer Gene Index (CGI) is a project aimed at creating a database of associations between genes and cancer and genes and drug compounds derived from Medline abstracts that involves a mixture of automatic text mining, semi-automatic verification, and manual validation/scoring of results. The database contains a total of 6,609 genes and their associations and can be accessed through caBIO and the CMA portal.
CGWB: Cancer Genome Workbench: an open-source software platform for identification of insertion/deletion polymorphisms and somatic mutations, and genomic data integration. It provides an integrated view of tumor mutation profiles for The Cancer Genome Atlas (TCGA) and other databases
Cloud Computing: Internet-based computing, whereby shared resources, software, and information are provided to computers and other devices on demand.
CMA Portal: The Cancer Molecular Analysis Portal (CMA Portal) is a web-based portal designed to share data acquired through large-scale research initiatives such as The Cancer Genome Anatomy project. CMA provides online access not only to large data sets but also to an array of tools for integrating and analyzing diverse data types.
Compatibility: To aid in the creation of software that will be able to interoperate within the caBIG^® program, a set of compatibility guidelines was developed that spells out requirements for interoperability in areas of Interface Integration; Vocabularies, Terminologies, and Ontologies; Information Models; and Data Elements. Systems that meet these requirements are said to be "caBIG^® Compatible."
Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to aid the study of biological, behavioral, and social systems.
CORE (Clinical Oncology Requirements for the EHR): The CORE project was designed to create a detailed, consensus-driven reference source of oncology requirements for EHRs. CORE brings together the NCI Center for Biomedical Informatics and Information Technology (CBIIT), the American Society of Clinical Oncology (ASCO) and the National Community Cancer Center Program (NCCCP) to identify the EHR needs of practicing oncologists.
CPAS: The Computational Portal and Analysis System (CPAS) is a set of web-based bioinformatics and collaboration tools to help scientists store, analyze, and share data from high-throughput experiments and clinical trials.
CRF: A Case Report Form (CRF) is an electronic document that contains data obtained during a patient's participation in a clinical trial.
CRIX: The Clinical Research Information Exchange (CRIX) is a collaborative effort among government, the biopharmaceutical industry, and academia to implement a common, secure, standards-based electronic infrastructure to support the sharing of clinical research data.
CSM: The Common Security Module (CSM) is a comprehensive set of security tools for authentication, authorization, and user provisioning.
CTCF: The Clinical Trials Compatibility Framework facilitates the management of electronic clinical research data, including study participant information through the clinical-trials lifecycle, and enables the comprehensive sharing and integration of information.
CTMS Workspace: The Clinical Trial Management System Workspace (CTMS Workspace) is developing modular, interoperable, standards-based software tools to help the clinical research and care communities to securely gather, exchange, integrate and reuse data and information.
CTODS: Clinical Trials Object Data System (CTODS) enables the exchange of identified and de-identified clinical trials data across multiple systems while supporting syntactic and semantic interoperability.
CTWG: The Clinical Trials Working Group (CTWG) was designed to advise the National Cancer Advisory Board and its Subcommittee on Clinical Investigations on the development, conduct, infrastructure, and support necessary for the optimal coordination and future progress of the entire range of intramural and extramural clinical research trials supported by the National Cancer Institute (NCI).
CVRG: The Cardio Vascular Research Grid (CVRG) project is aimed at creating an infrastructure for sharing cardiovascular data and data analysis tools. The project, supported by the National Heart, Lung and Blood Institute (NHLBI) is derived from caGrid technology and demonstrates the applicability of caBIG^®-developed technologies beyond cancer.

D

Data Liquidity: The use of common terminologies to enable the seamless, rapid flow of information among individuals and across institutions.
D&T Workspace: The caBIG^® Documentation and Training (D&T) Workspace facilitates the widespread adoption, dissemination, and use of caBIG^® interoperable tools, standards, and data sets within the larger cancer and biomedical communities through the creation and dissemination of software documentation and other training materials.
DSIC Workspace: The Data Sharing and Intellectual Capital (DSIC) Workspace addresses issues and develops recommendations related to data sharing, patient privacy, intellectual capital, security and other policies related to caGrid as well as other regulatory and proprietary issues.
DSSF: The Data Sharing and Security Framework (DSSF) is designed to facilitate appropriate data sharing between and among organizations by addressing legal, regulatory, policy, ethical, proprietary, contractual, and socio-cultural barriers. The DSSF provides guidelines to help assess the sensitivity of data that may be shared.
DWD: Distance-Weighted Discrimination (DWD) is a tool that performs statistical corrections to reduce systematic biases resulting from different laboratories, RNA sources, batches of microarrays, or microarray platforms.

E

ECCF: The Enterprise Conformance and Compliance Framework (ECCF) stack architecture provides an organizational framework in which inter-related artifacts are sorted by content. This framework identifies, defines, organizes, and relates a set of artifacts that collectively specify the relevant semantics of a software component specification or other system-of-interest.
EHR: An Electronic Health Record (EHR) is a medical record or any other information relating to the past, present or future physical and mental health, or condition of a patient which resides in computers which capture, transmit, receive, store, retrieve, link, and manipulate multimedia data for the primary purpose of providing health care and health-related services. EHR records include patient demographics, progress notes, SOAP notes, problems, medications, vital signs, past medical history, immunizations, laboratory data and radiology reports.
Electrophoresis: The use of an electric current to separate large molecules (such as proteins) from other molecules for analysis.
EMR: An Electronic Medical Record (EMR) facilitates access of patient data by clinical staff at any given location; accurate and complete claims processing by insurance companies; building automated checks for drug and allergy interactions; clinical notes; prescriptions; scheduling; sending to and viewing by labs. The term has become expanded to include systems which keep track of other relevant medical information.
eRx: A type of computer technology whereby physicians use handheld or personal computer devices to review drug and formulary coverage and to transmit prescriptions to a printer or to a local pharmacy. E-prescribing software can be integrated into existing clinical information systems to allow physician access to patient specific information to screen for drug interactions and allergies.
ESN: The Enterprise Support Network (ESN) facilitates the use of caBIG^® by providing comprehensive support for organizations and individuals (including research end-users and IT staff) that want to implement caBIG^® applications, standards, and technology in their labs. This network includes Support Service Providers (SSPs) and Knowledge Centers (KCs), that help expedite and increase the integration of caBIG^® technologies into scientific and clinical workflows at cancer and academic medical research centers and pharmaceutical and biotechnology companies.
EST(s): Expressed Sequence Tag(s) is a short segment of messenger RNA into which an expressed cDNA sequence has been transcribed. ESTs provide a snapshot of gene expression in a given biospecimen and can be used for gene discovery and the determination of gene sequences as well as to elucidate aberrant patterns of gene expression in disease states.
EVS: The Enterprise Vocabulary Services (EVS) project provides controlled terminology and ontology that is the semantic base for caBIG^®. EVS activities encompass terminology development, licensing and publication, software development and licensing, and operations support to address the broad spectrum of terminology needs of NCI and its partners.

F

Family Health History Tool: A collaborative effort between U.S Department of Health and Human Services and the U.S. Surgeon General's Office, the Family Health History Tool is based on caBIG^® technologies and represents a foundational step towards Personalized Medicine. This free, web-based tool assists consumers in capturing and sharing vital health information to help predict, diagnose, and manage disease.
Federated: Denotes computing practices that provide a global infrastructure enabling local access and administration of data, while making that data appear to be centrally located for remote access and analysis.
FGDP: Functional Genomics Data Pipeline (FGDP) is a Java-based microarray data analysis system. The FGDP provides an integrated, extendable analysis environment permitting multiple simultaneous analyses to be automatically performed, and provides a web server and interface for presenting results.
FIReBIRD: The Federal Investigator Registry of Biomedical Information Research Data (FIReBIRD) automates the submission process of FDA Form 1572.

G

GAI: The Genetic Annotation Initiative is an NCI-supported research project aimed at identifying single SNPs from publicly available EST sequencing traces.
GBM: Glioblastoma multiforme (GBM) is the most common and most malignant of the glial tumors. Of the estimated 17,000 primary brain tumors diagnosed in the United States each year, approximately 60% are gliomas. Gliomas comprise a heterogeneous group of neoplasms that differ in location within the central nervous system, in age and sex distribution, in growth potential, in extent of invasiveness, in morphological features, in tendency for progression, and in response to treatments.
Genbank: Genbank is the National Institute of Health's genetic sequence database, an annotated collection of all publicly available DNA sequences.
GenePattern: Developed by researchers at The Broad Institute, GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface, GenePattern provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
Genomics: The study of all or a substantial portion of the genes of an organism as a dynamic system, over time, to determine how those genes interact and influence biological pathways, networks, and physiology.
geWorkbench: geWorkbench is a desktop bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization, and annotation of microarray-based gene expression and sequence data. The platform enables integrated and sophisticated analysis of genomic data through the integration of visualization tools, external databases, and computational services.
GForge: Hosted by CBIIT, the GForge Collaborative Development Environment provides a unified home to all caBIG^® projects and offers many features enabling collaborative development, including message forums, mailing lists, wiki, bug tracking, and connection to the caBIG^® source code management repository.
gridPIR: The grid Protein Information Resource (gridPIR) provides a data resource for genomic and proteomic research containing high-quality annotated information on protein sequences. The resource is supported by UniProt Knowledgebase (UniProtKB) and other databases.
GUI: Graphical User Interface: A visually-oriented interface for computer software and hardware.
GWAS: The Genome-Wide Association Study (Studies) (GWAS) involves rapidly scanning markers across the complete sets of DNA, or genomes, of many people to find genetic variations associated with a particular disease. Once new genetic associations are identified, researchers can use the information to develop better strategies to detect, treat and prevent the disease. Such studies are particularly useful in finding genetic variations that contribute to common, complex diseases, such as asthma, cancer, diabetes, heart disease and mental illnesses.

H

HOW (Health of Women) Study: In December of 2009, the Dr. Susan Love Research Foundation in collaboration with the Beckman Research Institute, City of Hope and the National Cancer Institute's (NCI) Cancer Biomedical Informatics Grid (caBIG^®) launched the Health of Women Study (HOW) of the Army of Women. The HOW Study is the first ever online "cohort" study of an anticipated one million women, and will be looking at breast cancer risk factors in order to understand the cause of the disease and ways to prevent it.
HIPAA: The Health Insurance Portability and Accountability Act (HIPAA) is federal legislation that gives patients greater access to their own medical records and more control over how their personally identifiable health information is used. The regulation also includes privacy standards that protect patients' medical records and other health information.
HL7 Services-Aware Interoperability Framework (SAIF): Services-Aware Interoperability Framework (SAIF) is an architectural framework for making healthcare systems interoperable. SAIF defines a critical sub-framework—the Enterprise Conformance and Compliance Framework (ECCF) — that enables services to be specified from both an operational and interoperability perspective
HL7 V3 Reference Information Model (RIM): The Reference Information Model (RIM) is the cornerstone of the HL7 Version 3 development process. An object model created as part of the Version 3 methodology, the RIM is a large, pictorial representation of the HL7 clinical data (domains) and identifies the life cycle that a message or groups of related messages will carry. It is a shared model between all domains and, as such, is the model from which all domains create their messages.

I

ICR Workspace: The Integrative Cancer Research (ICR) Workspace is producing modular and interoperable tools and interfaces that provide for integration between biomedical informatics applications and data. This workspace develops a spectrum of molecular research technologies including proteomics, genomics, and nanotechnology.
Interoperable: The ability of systems or software tools to link together and access and use data from different sources.
Informatics or Information Science: Informatics is primarily concerned with the structure, creation, management, storage, retrieval, dissemination and transfer of information. Informatics also includes studying the application of information in organizations, on its usage and the interaction between people, organizations and information systems.
in silico: in silico is an expression used to mean "performed on computer or via computer simulation." in silico, or bioinformatics-driven research, represents an opportunity for researchers to test a hypothesis virtually as a precursor to laboratory experiments. Such work is often less costly than traditional methods of investigation and can extend the life of previously gathered data.
in vitro: A phrase referring to processes that occur in an isolated, experimental environment outside of a cell or living organism, such as a test tube.
in vivo: A phrase referring to processes that occur within a living cell or organism.
IO: InterOperability is the ability of systems or tools to both access (syntactic IO) and use (semantic IO) data from a remote data resource.
IPBS: The Inter-SPORE Prostate Biomarker Study (IPBS) is an NCI-supported multicenter prospective trial aimed at validating promising prostate cancer biomarkers using standardized methods, sustainable infrastructure, and optimized design.
IRB: Institutional Review Board is a committee of physicians, statisticians, researchers, community advocates, and others that ensures that a clinical trial is ethical and that the rights of study participants are protected.
I-SPY Trials: The Investigation of Serial Studies to Predict Your (I-SPY) Therapeutic Response with Imaging and Molecular Analysis is a series of national studies supported by CBIIT and selected SPOREs designed to identify biomarkers predictive of response to therapy in women with Stage 3 breast cancer.
ISO: The International Standards Organization (ISO) is the world's largest developer of technical standards.

J

JAR: Java ARchive: a file format used to bundle all components required by a Java applet (a software component that runs within the context of another program).
Java: A high-level, general-purpose programming language with a number of features that make it well suited for use on the World Wide Web.

K

KC(s): A Knowledge Center(s) is a primary component of the caBIG^® Enterprise Support Network, KCs are NCI-supported entities focused on the specific domains in which they have expertise. Each Knowledge Center provides a centralized, authoritative repository of knowledge, information, and Web-based support to facilitate the adoption of caBIG^® tools, standards, and infrastructure for that domain.

L

LIMS: The Laboratory Information Management System is a software system used in laboratories for the integration of all laboratory software, instruments, and the management of samples, laboratory users, standards and other laboratory functions such as QA/QC, sample planning, invoicing, plate management, and workflow automation.
LOINC: Logical Observation Identifiers Names and Codes: the standard for laboratory result names.
LSD: The caBIG^® Life Sciences Distribution (LSD) supports a variety of capabilities from tracking and managing biospecimens, to analyzing and integrating microarray data.
LS-DAM: The Life Sciences Domain Analysis Model (LS-DAM) is an ongoing project aimed at developing a structured computable protocol representation for the life sciences similar to the BRIDG model for clinical trials.

M

MAGE-ML: The Microarray And Gene Expression Markup Language is an extensible markup language designed to describe microarray designs, microarray experiment setup, gene expression data, and data analysis results.
MAGE-TAB: The Microarray And Gene Expression-TAB is a simplified, tab-delimited spreadsheet format that can be used to annotate and communicate microarray data in a MIAME-compliant manner.
MedDRA: Medical Dictionary for Regulatory Activities: a resource for medical terminology applying to all phases of drug development and medical devices. The emphasis is on ease of use for data entry, retrieval, and display within the regulatory environment.
Metadata: Contextual information about a data file or the information contained within.
MHAP: Mouse-Human Anatomy Project: provides a mapping and harmonization of human and mouse anatomical descriptors as they are currently used for murine and human models by Mouse Genome Informatics.
MIAME: Minimum Information About a Microarray Experiment (MIAME) according to the MGED Society is the minimum amount of information needed to interpret the results of a microarray experiment and to reproduce the results.
Microarray: A device that measures differences in gene sequence, gene expression or protein expression in biological samples. Microarrays may be used to compare gene or protein expression under different conditions, such as healthy versus diseased tissues or cells found in cancer. In the typical protein array, the capture reagent, such as an antibody, is immobilized on the surface of the array and a liquid phase containing proteins derived from a sample are applied. Binding or interaction of proteins in the liquid phase with the capture reagent is detected using various chemical or radioactive labeling methods.
Molecular Medicine: The diagnosis and treatment of disease based on a detailed knowledge of the interaction and function of genes, proteins and other biomolecules.
Molecular Data: Information such as DNA sequences, levels of genetic expression, biomarkers and protein structure and function that are key to modern cancer research, diagnosis and treatment.
MRI: Magnetic Resonance Imaging is a non-invasive 3-dimensional medical imaging technology based on the interaction between biological material and a strong magnetic field. MRI can provide a picture of living tissue within the body in order to detect abnormalities, such as arterial blockage, lesions, or tumors.

N

NBIA: The National Biomedical Imaging Archive (NBIA) is a searchable national repository of in vivo cancer images that integrates cancer images with clinical and genomic data. NBIA also enables public access to DICOM images, image markup, annotations, and metadata. (Formerly known as the National Cancer Imaging Archive [NCIA])
NCCN: The National Comprehensive Cancer Network (NCCN) is an alliance of 21 of the world's leading cancer centers, working together to develop treatment guidelines for most cancers, and dedicated to research that improves the quality, effectiveness, and efficiency of cancer care. NCCN offers a number of programs to give clinicians access to tools and knowledge that can help guide decision-making in the management of cancer.
NCCCP: The NCI National Community Cancer Centers Program (NCCCP) is a three-year pilot program to test the concept of a national network of community cancer centers to expand cancer research and deliver the latest, most advanced cancer care to a greater number of Americans in the communities in which they live. As part of the pilot program, caBIG^® technologies are being deployed at 16 NCCCP sites.
NCI CBIIT: The NCI Center for Biomedical Informatics and Information Technology (NCI CBIIT) helps speed scientific discovery and facilitates translational research by building tools and resources that enable information to be shared along the continuum from the scientific bench to the clinical bedside and back.
NCIT: The NCI Thesaurus: now decommissioned.
NCRI: The National Cancer Research Institute (U.K.) is a UK-wide partnership between the government, charity and industry which promotes co-operation in cancer research among the 21 member organizations for the benefit of patients, the public and the scientific community.
NHIN: The Nationwide Health Information Network (NHIN) provides a secure, nationwide, interoperable health information infrastructure that connects providers, consumers, and others involved in supporting health and healthcare. This includes enabling health information to follow the consumer, be available for clinical decision making, and support appropriate use of healthcare information beyond direct patient care so as to improve health.

O

OCTRI: The Oregon Clinical and Translational Research Institute (OCTRI) is a collaboration between Oregon Health & Science University and the Kaiser Permanente Center for Health Research. With major funding from the National Institutes of Health through the Clinical and Translational Science Awards (CTSA), and significant institutional commitment from OHSU and Kaiser Permanente, OCTRI's mission is to improve human health by enhancing clinical and translational research.
Ontology: A controlled vocabulary that describes objects and the relations between them in a formal way; used to make queries and assertions.
Open access (noun phrase); Open-access (adjective phrase): Web-accessible information that has been made available through interoperable repositories for the purposes of sharing data, publishing data, and archiving metadata.
Open source (noun phrase); Open-source (adjective phrase): Software that provides the fundamental code for review or implementation without a licensing fee.
OWL: The Web Ontology Language (OWL) is intended to be used when the information contained in documents needs to be processed by applications, as opposed to situations where the content only needs to be presented to humans. OWL can be used to explicitly represent the meaning of terms in vocabularies and the relationships between those terms.

P

Patient Outcomes Data Service (PODS): The Patient Outcomes Data Service (PODS) provides user access to a data repository containing de-identified patient outcome data for cancer patients. Patient outcome records can contain de-identified demographic, diagnosis, treatment, and outcome data.
Personalized Medicine: Personalized medicine is a medical model emphasizing the systematic use of information about an individual patient to select or optimize that patient's preventative and therapeutic care. Personalized medicine can broadly be defined as products and services that leverage the science of genomics and proteomics (directly or indirectly) to enable tailored approaches to prevention and care.
PET: A Positron Emission Tomography (PET) is a non-invasive 3-dimensional medical imaging technology that detects the presence of a metabolically active chemical that has been modified to contain a short-lived radioactive tracer isotope that emits a positron.
PHIT: The Personal Health Information Technology (PHIT) enables the documentation of an individual's complete, lifelong health and medical history into a private, secure and standardized format that he or she owns and controls, but yet is accessible to legitimate providers day or night from any location.
PID: The Pathway Interaction Database is a highly structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways; users can query the database by pathway name and by molecule name or accession number.
Proteomics: The field of study that seeks to understand the entire protein component of an organism or a large subset of that component. One of the goals of proteomic discovery is the development of suitable biomarkers for disease diagnosis, treatment and monitoring.
PSC: The Patient Study Calendar is an open-source, standards-compliant Web-based software application designed to manage patients on clinical trials. It provides the ability to create and edit study calendar templates, generate and view prospective calendars of patient activities, track activities as they occur, and manage patient calendars as they change during a study.

Q

R

Rapid Learning Healthcare System: In 2007, the Institute of Medicine published a landmark report describing a new approach called the Rapid Learning Healthcare System, in which data of all types is contributed, analyzed, and disseminated in a continuous feedback loop that integrates research and care. Such a system provides the gateway to 21^st century medicine —personalized, predictive, preemptive, and participatory—where the patient and his/her particular genetic and clinical characteristics are at the center of all activity, playing a key role in both research and self-management of health.
REMBRANDT: The REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) provides a bioinformatics framework and Web portal that allows researchers to integrate clinical and functional genomics data from clinical trials involving patients suffering from Gliomas.

S

SDK: A Software Development Kit (SDK) is a programming package that enables a programmer to develop applications for a specific platform.
Semantic Connector: A component of the caCORE SDK that assists with semantic integration with the EVS.
sSOA: Semantic Service Oriented Architecture (sSOA) is a computer architecture that allows for scalable and controlled Enterprise Application Integration solutions. sSOA describes a sophisticated approach to enterprise-scale IT infrastructure. It leverages rich, machine-interpretable descriptions of data, services, and processes to enable software agents to autonomously interact to perform critical mission functions.
SOA: Service-Oriented Architecture (SOA) is a set of design principles. A system based on a SOA architecture will provide a loosely-coupled suite of services that can be used within multiple separate systems from several business domains.
SNP(s): Single Nucleotide Polymorphism(s) (SNPs) are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered.
SaaS: Software As A Service (SaaS) refers to software that is deployed over the internet and/or is deployed to run behind a firewall on a local area network or personal computer. This approach to application delivery is part of the utility computing model where all of the technology is in the "cloud" and accessed over the Internet as a service.
SPORE: The Specialized Program Of Research Excellence (SPORE) is an NCI-funded grant to centers aimed at promoting interdisciplinary cancer research and rapidly moving basic research findings from the laboratory into the clinic.
SQL: Structured Query Language (SQL) is a standardized query language used to request information from a relational database.
SSP(s): Support Service Provider(s) (SSP(s)) is a primary component of the caBIG^® Enterprise Support Network. SSPs are third-party organizations that provide comprehensive technical and end-user support.
Systems Biology: A combination of biochemistry, proteomics, genomics, metabolomics and bioinformatics used to better understand the contribution of each element of the system to the whole. In proteomics and cancer, perturbations in the protein component of signal transduction systems, for example, can lead to cell and tissue changes that promote tumorigenesis.

T

TARGET: The National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatments (TARGET), led by CBIIT in collaboration with the Children's Oncology Group, is designed to identify potential therapeutic targets in childhood cancers through genome-wide sequencing and other high-throughput technologies. The organizations collaborating in the initiative work together to enroll children in coordinated clinical studies, exchange massive data sets, and build a collection of clinically annotated, high-quality tissue samples—all activities enabled by caBIG^®.
Taverna Workbench: Taverna allows users to construct complex research workflows that can consist of multiple types of components, which may be located on different machines. Their execution is orchestrated by Taverna Engine (run from the workbench), and the results are gathered and shown in the workbench. Taverna has been downloaded nearly 6000 times and is known to be used in more than 350 different organizations and companies throughout the world.
TBPT Workspace: The Tissue Banks and Pathology Tools (TBPT) Workspace is responsible for the development of tools that inventory, track, mine, and visualize biospecimens and related annotations from geographically dispersed repositories.
TCGA: The Cancer Genome Atlas (TCGA) is a research project jointly supported by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) that is intended to test the feasibility of systematically using large-scale genome analysis technologies to identify important genetic changes involved in cancer.
TRANSCEND: The TRANSlational Informatics System to Coordinate Emerging iomarkers, Novel Agents, and Clinical Data (TRANSCEND) project extends the work of I-SPY 1 to further enhance the clinical trial data collection infrastructure. TRANSCEND uses Web-based case report forms (CRFs) to simplify data collection at two I-SPY trial sites and to demonstrate integration of an electronic health record system with the bioinformatics infrastructure in place for the I-SPY 1 trial.
Transcriptional Factors: Proteins and enzymes that bind to DNA and help control and execute gene expression. Transcriptional factors may regulate the level of gene expression by turning a gene "on" or "off," or they may help synthesize messenger RNA (mRNA) as directed by the DNA template. Messenger RNA serves in turn as the template for protein synthesis.
Translational Research: The process of applying ideas, insights, and discoveries generated through basic scientific inquiry to the diagnosis, prevention or treatment of human disease.
TrAPSS: The Transcript Annotation Prioritization and Screening System (TrAPSS) is designed to predict whether gene sub-sequences have the potential to contain disease-causing mutations, to utilize annotation to prioritize focused regions of a gene during mutation screening, and to aid scientists searching for the genetic mutation or mutations linked to the expression of a disease phenotype.

U

UML: Unified Modeling Language (UML) is a general-purpose notational language for specifying and visualizing complex software, especially software supporting large, object-oriented projects.
URL: Uniform Resource Locator (URL) is the global address of documents and other resources on the World Wide Web.

V

VASARI: The Visually AccesSAble Rembrandt Images (VASARI) is an extension of the original REMBRANDT trial. The VASARI study seeks to validate the use of medical images as predictive biomarkers for cancer diagnosis. More specifically, the goal of VASARI is to develop reproducible methods to classify Magnetic Resonance Images (MRIs) of glioma tumors and provide linkages between those images, histology, and genetic data obtained from brain cancer specimens.
VCDE Workspace: The Vocabulary and Common Data Elements (VCDE) Workspace evaluates and integrates systems and standards for vocabularies and common data elements and ontology content development, as well as software systems for content delivery. This workspace also defines semantic interoperability, trains and provides mentors, and provides guidelines for the adoption of standards and CDE harmonization.
VISDA: The VIsual and Statistical Data Analyzer (VISDA) is an analytical tool for cluster modeling, visualization, and discovery. VISDA exploits the human gift for pattern recognition and allows users to discover hidden clustered data structure within high dimensional and complex biomedical data sets. VISDA allows users across the cancer research community to analyze their genomic/proteomic data to define new cancer subtypes based on the gene expression patterns, construct hierarchical trees of multiclass cancer phenotypic composites, or to discover the correlation between cancer statistics and risk factors.
Visualization: Techniques for turning data into information by using the high capacity of the human brain to visually recognize patterns and trends.

W

Workspaces: Workspaces are areas of focus within the caBIG^® initiative that are developing applications, policy documents, and other products.
WSDL: The Web Services Description Language (WSDL) is an XML-formatted language used to describe a Web service's capabilities as a collection of communication endpoints capable of exchanging messages.

X

XIP: The EXtensible Imaging Platform (XIP) is a project designed to facilitate image collaboration, display and review in research.
XMI: XML Metadata Interchange (XMI) is an extensible markup language (XML) application that facilitates the standardized interchange of object models and metadata over the Internet among groups working in team development environments and using tools and applications from multiple vendors.
XML: EXtensible Markup Language (XML) is a flexible way to create common information formats and share both the format and the data on the World Wide Web, intranets, and elsewhere. XML can be used by any individual or group of individuals or companies that would like to share information in a consistent way. XML describes the content in terms of what data is being described. An XML file can be processed purely as data by a program, stored with similar data on another computer, or displayed (like an HTML file).