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
AACR
American Association of Cancer Researchers
AMIA
American Medical Informatics Association
API
Application Programming Interface: a set of routines, protocols, and tools for building software applications.
ASCO
American Society of Clinical Oncology
ASTRO
American Society for Therapeutic Radiology & Oncology
B
Biomarker
A biomarker is 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
Biomedical Grid Terminology: the biomedical ontology under development by the Vocabulary and Data Elements Workspace.
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
Biomedical Research Integrated Domain Group: structured computable protocol representation that supports the entire life-cycle of clinical trials. Stakeholders include caBIG®, NCI, CDISC, FDA, and HL7.
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
C3D
Cancer Central Clinical Database: a Web-based application for managing clinical trial data across multiple cancer clinical trials.
C3PR
Cancer Central Clinical Participant Registry: a Web-based application intended to improve clinical trials activation and execution by providing an efficient Web-based clinical trials information management system available for use by multiple, geographically dispersed cancer research centers.
C-DAC
The Center for the Development of Advanced Computing, India
C-DOCS
Cancer Distributed Ontology Consensus System: a tool designed to facilitate collaborative consensus for new phenotype vocabularies.
caAERS
cancer Adverse Event Reporting System: a data management system that allows local collection, management, and querying of adverse-event data and supports regulatory compliance.
caArray
cancer Array: an open-source database that is MIAME 1.1compliant and developed for the management, annotation, sharing, and publication of microarray data.
caB2B
cancer Bench-to-Bedside: a caGrid client that permits bench scientists, translational researchers, and clinicians to use caBIG® compatible data and analytical services in order to query tissue banks at multiple cancer centers and perform in silico experiments using already-collected data sets. Users are able to specify sites, aggregate data, refine queries based on results, and export data in different formats.
caBIG®
cancer Biomedical Informatics Grid®: a collaborative NCI-based initiative that is developing standards-based infrastructure, tools, and data sets to support integrative cancer research and promote multidisciplinary scientific collaboration.
caBIO
cancer Bioinformatics Infrastructure Objects: a biomedical data system built using a model-driven approach to develop objects, data models middleware, vocabularies, and ontologies for biomedical research.
caCORE
cancer Common Ontologic Representation Environment: open-source software designed to help streamline informatics development throughout the cancer community.
caDSR
cancer Data Standards Repository: a database and tool set designed to create, edit, and deploy common data elements (CDEs).
caELMIR
cancer Electronic Laboratory Management Information Resource: 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: 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 1.2 (released March, 2008)
The underlying service-oriented infrastructure for caBIG®. caGrid's basic technical goals are to enable universal mechanisms for providing interoperable programmatic access to data and analytics in caBIG®; to create an infrastructure wherein the structure and semantics of data can be programmatically determined; and to provide a powerful means by which services available in caBIG® can be programmatically discovered and leveraged.
caGrid Portal
A Web-based gateway to the cancer Biomedical Informatics Grid
caGWAS
cancer Genome-Wide Association Study (Studies): allows researchers to access SNP association findings and population-frequency data as well as data concerning genotype and phenotype. caGWAS also provides the capability of accessing and analyzing clinical and experimental data across multiple studies.
caIntegrator 2
A translational informatics that permits integrative analysis and viewing of molecular, clinical, and imaging data. It also allows researchers and bioinformaticians to access and analyze data across multiple clinical trials.
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. caLAB was based on domain concepts from the cancer
Laboratory Information Management System (caLIMS).
caMOD
cancer MOdels Database: an open-source data management system developed for the management and sharing of data derived from animal models.
caNanoLab
A data portal that allows researchers to share information on nanoparticles, including the composition, functions, characterizations, and protocols of nanoparticle assays.
Cancer
Centers
The Cancer Centers Program of the National Cancer Institute 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, spread widely across the United States.
For more
information about the Cancer Centers program, please visit: http://www3.cancer.gov/cancercenters/
caTIES
cancer Text Information Extraction System: enables researchers to query, browse, and acquire annotated tissue data and physical material across a network.
caTissue Core
caBIG®-developed tissue bank repository tool for biospecimen inventory, tracking, and basic annotation. It permits users to track the collection, storage, quality assurance, and distribution of specimens and also to find and request specimens that can be used in molecular correlative studies.
caTissue Suite
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.
caWorkbench
caWorkbench is a
suite of tools for loading, visualizing and analyzing gene expression data.
caXchange
cancer Clinical Data EXchange System: a configurable hub for exchanging clinical trial information between applications and systems; it also provides a "lab viewer" application that allows users to view and query laboratory data sent to the hub and select subsets of tests to be sent to a clinical trials database.
CCTS
caBIG® Clinical Trials Suite: supports the management of study participant information through the clinical trial lifecycle.
CDE(s)
Common Data Element(s): 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: a non-profit organization that has established standards to support clinical research data (http://www.cdics.org/about/index.html). 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
Clinical Data Management System: an application that manages the collection of clinical data generated by a clinical trial.
CED
Clinical Expression Database: a database that 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: an NCI-based research initiative aimed at determining the gene expression profiles of normal, precancer, and cancer cells.
CGEMS
The Cancer GEnetics Markers of Susceptibility program: an NCI-based research initiative aimed at identifying genetic alterations that confer susceptibility to breast or prostate cancer.
CGI
Cancer Gene Index: 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
CMA Portal
The Cancer Molecular Analysis Portal: 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. The first data set available through the portal is derived from the TCGA's pilot study of the GBM genome, which identified a gene that may contribute to GBM resistance to temozolomide.
CMAP
The Cancer Molecular Analysis Project: a web-based prototype application that provides information about molecular targets, molecular profiles, agents, pathways, and therapeutic clinical trials.
Common Rule
The "Common
Rule" refers to 45-CFR-46, the code of federal regulations governing patient
protection for research conducted with federal funds or sites supported with
such funds.
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."
CPAS
Computational Portal and Analysis System: 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
Case Report Form: an electronic document that contains data obtained during a patient's participation in a clinical trial.
CRIX
Clinical Research Information EXchange: 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.
CSA
Custom Sequencing Analysis: provides print and electronic research databases of citations and full texts in the sciences.
CSM
Common Security Module: 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
The Clinical Trials Management System: the caBIG® CTMS Workspace is developing modular, interoperable, standards-based software tools to deliver to the clinical research and care communities the ability to securely father, exchange, integrate and reuse data and information. Tools under development include an adverse event reporting module, a clinical trials participant registry, a patient study calendar, and a clinical data information exchange module.
CTMS Workspace
The Clinical Trial Management System Workspace: a caBIG® workspace that is developing a comprehensive set of modular, interoperable, and standards-based tools designed to meet the diverse clinical trials management needs of the Cancer Center community.
CTODS
Clinical Trials Object Data System: enables the exchange of identified and de-identified clinical trials data across multiple systems while supporting syntactic and semantic interoperability.
CVRG
The Cardio Vascular Research Grid: a project supported by the National Heart, Lung and Blood Institute (NHLBI), NIH that is based on the same technology as caGrid, demonstrating the applicability of caBIG®-developed technologies beyond cancer.
D
D&T
Documentation and Training: the caBIG® Documentation and Training 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 Workspace: a caBIG® workspace that addresses issues related to data sharing and intellectual capital associated with caBIG®.
DSSF
The caBIG® Data Sharing and Security Framework: provides organizations with a conceptual framework and implementation tools to facilitate the evaluation of the level of data sensitivity and levels of access controls that such organizations will require to share data sets.
DWD
Distance-Weighted Discrimination: a tool that performs statistical corrections to reduce systematic biases resulting from different laboratories, RNA sources, batches of microarrays, or microarray platforms.
E
EHR
Electronic Health Record: the electronic documentation of an individual's overall health history and status.
Electrophoresis
The use
of an electric current to separate large molecules (such as proteins) from other
molecules for analysis.
ESN
The Enterprise Support Network: a network of Support Service Providers (SSPs) and Knowledge Centers (KCs), that will 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): a short segment of messenger RNA into which an expressed cDNA sequence has been transcribed. ESTs thus 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
Enterprise Vocabulary Services: a set of services and resources designed to address NCI's needs for a controlled vocabulary.
F
Family Health History Tool
A collaborative effort between HHS and the U.S. Surgeon General's Office, the Family Health History Tool is based caBIG® technologies and represents a foundational step towards Personalized Medicine.
FDA
The U.S. Food and Drug Administration
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: a Java-based microarray data analysis system.
FIReBIRD
Federal Investigator Registry of Biomedical Information Research Data: automates the FDA Form 1572 submission process.
G
GAI
The Genetic Annotation Initiative: an NCI-supported research project aimed at identifying single SNPs from publicly available EST sequencing traces.
GBM
Glioblastoma multiforme: The most common and most aggressive type of primary brain tumors in humans.
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 comprises an application interface that gives a broad audience access to a growing repository of analytic tools. It has been designed to support multidisciplinary genomic research programs and to encourage rapid integration of new techniques. Gene Pattern is now available through caBIG®, which supports its continued development and dissemination throughout the biomedical research community.
Genomics
The study of genes and their function;
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
Proves an integrated view of genomics data—gene expression, sequence, pathways—and integrates genomic data with visualization tools, external databases, and computational services.
GForge (gforge.nci.nih.gov)
Hosted by CBIIT, the GForge Collaborative Development Environment is an implementation of the SourceForge model. It 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
grid Protein Information Resource: 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
Genome-Wide Association Study (Studies); see caGWAS.
H
HIMSS
Healthcare Information and Management Systems Society
HIPAA
The Health Insurance Portability and Accountability Act: 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
Health Level 7: a standards development organization whose messaging standard is currently the selected standard for the interfacing of clinical data in most institutions.
HTTP
HyperText Transfer Protocol: the underlying protocol used in the World Wide Web.
I
ICR Workspace
Integrative Cancer Research Workspace: a caBIG® workspace that is producing modular and interoperable tools and interfaces that provide for integration between biomedical informatics applications and data.
Interoperable
The ability of systems or software tools to link together and access and use
data from different sources.
in vitro
A scientific Latin 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 scientific Latin phrase referring to processes that
occur within a living cell or organism.
IO
InterOperability: 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: 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: 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.
ISBER
International Society for Biological and Environmental Repositories.
ISBRA
International Symposium on Bioinformatics Research and Applications.
I-SPY Trials
Investigation of Serial Studies to Predict Your Therapeutic Response with Imaging and Molecular Analysis: 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
International Standards Organization: the world's largest developer of primarily 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)
Knowledge Center(s): a primary component of the caBIG® Enterprise Support Network, KCs are NCI-supported entities focusing 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
Lesion
An area of
abnormal tissue.
LIMS
Laboratory Information Management System
LOINC
Logical Observation Identifiers Names and Codes: the standard for laboratory result names.
LSD
The Life Sciences Distribution: supports a variety of capabilities from tracking and managing biospecimens, to analyzing and integrating microarray data.
LS-DAM
Life Sciences Domain Analysis Model: 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
Microarray And Gene Expression Markup Language: an XML designed to describe microarray designs, microarray experiment setup, gene expression data, and data analysis results.
MAGE-TAB
Microarray And Gene Expression-TAB: 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.
MGED Society
Microarray and Gene Expression Data Society
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: according to the MGED Society, 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; a commonly used 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: a searchable national repository of in vivo cancer images that integrates cancer images with clinical and genomic data. 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: a not-for-profit alliance of 21 leading cancer centers whose main activity is the development of evidence-based oncology practice guidelines. For more information, visit http://www.nccn.org/.
NCCCP
The NCI National Community Cancer Centers Program: 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: the successor to the NCI Center for Bioinformatics (NCICB), CBIIT is responsible not only for overseeing the caBIG® initiative but also for centralizing NCI's development, acquisition, and use of intramural informatics and IT assets. CBIIT also aids the Institute's leaders in formulating strategic plans relevant to its bioinformatics and IT initiatives.
NCIT
The NCI Thesaurus: now decommissioned.
NCRI
The National Cancer Research Institute (U.K.): the lead organization for a U.K.-wide partnership among government, charity, and industry that promotes cooperation in cancer research. See http://www.ncri.org.uk/.
NHIN
The Nationwide Health Information Network: Overseen by the Office of the National Coordinator for Health Information Technology (ONC) in the U.S. Department of Health and Human Services, the primary goal of the NHIN to provide every American with an electronic health record.
Node
A
point of connection on a network of computers.
O
OCTRI
Oregon Clinical and Translational Research Institute
OIL
Ontology Inference Layer: a joint standard for ontologies.
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
Web Ontology Language: a computer language intended to be used when the information in documents must be processed by applications rather than humans.
P
PET
Positron Emission Tomography; 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. PET presents a detailed view of a metabolic function within the body,
and may be used for the detection of metastasized tumors.
PID
Pathway Interaction Database: 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. PID is the product of collaboration between CBIIT and the Nature Publishing Group.
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
Patient Study Calendar: 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
RDBMS
Relational DataBase Management System: a type of database management system that stores data in the form of related tables.
REMBRANDT
REpository for Molecular BRAin Neoplasia DaTa: a bioinformatics knowledgebase framework that leverages data warehousing technology to host and integrate clinical and functional genomics data from various cancer clinical and molecular trials. It currently houses two sets of data: the first comes from the NCI-sponsored Glioma Molecular Diagnostic Initiative, the largest genetic/clinical corollary study ever conducted on gliomas; the second comprises a wide array of molecular and genetic data regarding all types of primary brain tumors.
RSNA
The Radiological Society of North America
S
SDK
Software Development Kit: 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.
SNP(s)
Single Nucleotide Polymorphism(s): a change in one nucleotide in the DNA molecule.
SPORE
Specialized Program Of Research Excellence: 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: a standardized query language used to request information from a relational database.
SSP(s)
Support Service Provider(s): a primary component of caBIG®'s Enterprise Support Network, SSPs are third-party organizations that provide comprehensive technical and end-user support.
Systems Biology
The field of biology that examines biological processes in the context of an
entire system of processes within a cell or organism. Systems biology utilizes a
combination of biochemistry, proteomics, genomics, metabolomics and
bioinformatics 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. Therefore understanding the entire
signal transduction system, with its various intersecting molecular pathways,
can often reveal drug targets that would otherwise have been overlooked.
T
TARGET
The NCI Therapeutically Applicable Research to Generate Effective Treatments: led by CBIIT in collaboration with the Children's Oncology Group, TARGET is designed to identify potential therapeutic targets in childhood cancers through genome-wide sequencing and other high-throughput technologies. To this end, 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®—developed grid, clinical trials management, and analytical technologies.
TBPT Workspace
Tissue Banks and Pathology Tools Workspace: a caBIG® workspace that is providing for the integration, development, and implementation of tissue and pathology tools.
TCGA
The Cancer Genome Atlas: a research project jointly supported by 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 Among the first TCGA findings to be reported are the identification of many gene mutations involved in glioblastoma multiforme (GBM), including the discovery of a potential genetic mechanism that may be involved in GBM resistance to temozolomide.
TRANSCEND
TRANSlational Informatics System to Coordinate Emerging Biomarkers, Novel Agents, and Clinical Data: this project extends the work of I-SPY to further enhance the clinical trial data collection infrastructure.
Transcriptional
Factors
Proteins and enzymes that bind to DNA and help control and
execute gene expression. Trancriptional 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
Transcript Annotation Prioritization and Screening System: a system 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
UI
User Interface: the means for a user to interact with a computer program.
UML
Unified Modeling Language: a general-purpose notational language for specifying and visualizing complex software, especially software supporting large, object-oriented projects.
URL
Uniform Resource Locator: the global address of documents and other resources on the World Wide Web.
V
VASARI
Visually AccesSAble Rembrandt Images: an assembly of clinical MRI images obtained at the time of diagnosis on the same samples used in the REMBRANDT program. The goal of VASARI is to develop reproducible methods to classify MRI images 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 Workspace: a caBIG® workspace that is responsible for evaluating and integrating systems for vocabulary and ontology content development, as well as software systems for content delivery.
VISDA
VIsual and Statistical Data Analyzer: a tool for multivariate cluster modeling, discovery, and visualization, particularly for data sets in high-dimensional space.
W
Workspaces
Areas of focus within the caBIG® initiative that are developing applications, policy documents, and other products.
WSDL
Web Services Description Language: an XML-formatted language used to describe a Web service's capabilities as a collection of communication endpoints capable of exchanging messages.
X
XIP
EXtensible Imaging Platform: a project designed to facilitate image collaboration, display and review in research.
XMI
XML Metadata Interchange: 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: a specification designed especially for Web documents enabling the definition, transmission, validation, and interpretation of data between applications and between organizations.
