Glossary

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

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.

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).

C

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/

caArray
Cancer Array Informatics; an open source database developed for the management, sharing and publication of microarray data.

caBIO
Cancer Bioinformatics Infrastructure Objects; a biomedical data system built using a model-driven approach. caBIO employs industry-standard software engineering methodologies to develop objects, data models middleware, vocabularies and ontologies for biomedical research.

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 related to animal models.

caWorkbench
caWorkbench is a suite of tools for loading, visualizing and analyzing gene expression data.

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.

E

Electrophoresis
The use of an electric current to separate large molecules (such as proteins) from other molecules for analysis.

G

GenePattern
An analysis workflow platform that supports multidisciplinary genomic research and the integration of new technologies and analytical tools used in genomic and proteomic research. An adapter to GenePattern will be created to allow the application to read data directly from caBIO/caArray.

Genbank
Genbank is the National Institute of Health’s genetic sequence database, an annotated collection of all publicly available DNA sequences.

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.

I

Interoperable
The ability of systems or software tools to link together and access and use data from different sources.

in vivo
A scientific Latin phrase referring to processes that occur within a living cell or organism.

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.

J
K

L

Lesion
An area of abnormal tissue.

M

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

Node
A point of connection on a network of computers.

O

Ontologies
Controlled, standardized vocabulary that describes objects and the relations between them in a formal way; used to make queries and assertions.

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.

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.

Q

R

S

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

Translational Research
The process of applying ideas, insights, and discoveries generated through basic scientific inquiry to the diagnosis, prevention or treatment of human disease.

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.

U

V

W

Workspaces
Areas of focus within the caBIG^® initiative that are developing specific software applications, policy documents, and other products.