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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  

A

Accident. Any occurrence that deviates from SOPs or applicable government laws and regulations during specimen retrieval, processing, labeling, storage, or distribution that may affect subsequent use of those specimens (ISBER 2005).

Adverse outcome. An undesirable effect or untoward complication consequent to or reasonably related to specimen integrity (ISBER 2005).

Aliquot. A portion of a specimen that has been divided into separate, smaller parts, usually liquid, which are typically stored in separate containers as individual samples. The term aliquot may also be used as a noun to denote a single sample (ISBER 2005).

Annotation. Explanatory or extra information associated with a particular biospecimen. Annotations may be added by either the pathologist or the resource collector.

ASTROTM (Archival Specimen Tracking and Retrieval Operations) system. Customized data management software used in the CASPIRTM (CDC-ATSDR Specimen Packaging, Inventory, and Repository) biorepository.

Audit. A documented review of procedures, records, personnel functions, equipment materials, facilities, and/or vendors in order to evaluate adherence to written SOPs or government laws and regulations (ISBER 2005).

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 (as defined by the NIH Biomedical Information Science and Technology Initiative Consortium (http://www.bisti.nih.gov/CompuBioDef.pdf) (Eiseman et al. 2003).

Biorepository. A place, room, or container where biospecimens are stored. Biorepositories vary considerably, ranging from formal organizations to informal collections of materials in an individual researcher’s freezer.

Biorepository informatics system. The software, hardware, written documents, support, and training that are necessary to annotate, track, and distribute biospecimens within a biorepository or biorepositories.

Biospecimen or specimen. A quantity of tissue, blood, urine, or other biologically derived material used for diagnosis and analysis. A single biopsy may generate several specimens, including multiple paraffin blocks or frozen specimens. A specimen can include everything from subcellular structures (DNA) to cells, tissue (bone, muscle, connective tissue, and skin), organs (e.g., liver, bladder, heart, kidney), blood, gametes (sperm and ova), embryos, fetal tissue, and waste (urine, feces, sweat, hair and nail clippings, shed epithelial cells, and placenta).

C

caDSR (cancer Data Standards Repository). The standards repository that hosts CDEs developed by various NCI-sponsored organizations. caDSR components are instrumental in the collection of metadata associated with clinical trials. caDSR tools facilitate the search and retrieval of CDEs and caDSR is the single, authoritative source of common data.

CASPIRTM (CDC-ATSDR Specimen Packaging, Inventory, and Repository) biorepository. A central facility to store biological and environmental biospecimens that the CDC-ATSDR began to develop in 1995. The mission of this biorepository is “to provide storage for valuable, mostly human, biological samples that have been collected from CDC and ATSDR diagnostic studies, epidemiologic outbreaks, and research studies for possible future use." It has initial storage capacity of more than 6 million biospecimens and is managed through customized data management software, the Archival Specimen Tracking and Retrieval Operations (ASTROTM) system. Currently, the biorepository stores approximately 4 million biospecimens at the central biorepository and a number of satellite biorepositories in individual CDC centers. Daily operations of the biorepository functions are conducted by a contractor, with oversight by a CDC project officer.

caTIES (cancer Text Information Extraction System). A project that will focus on two important challenges of biomedical informatics; namely, information extraction from free text and access to tissue. Specifically, caTIES has three primary goals: (1) extract coded information from free-text surgical pathology reports using controlled terminologies to populate caBIG-compliant data structures, (2) provide researchers with the ability to query, browse, and acquire annotated tissue data and physical material across a network of federated sources, (3) pioneer research for distributed text information extraction within the context of caBIG. caTIES modules will be developed as generalized components available on the caBIG, in order to facilitate reuse by other caBIG projects requiring tissue information extraction.

caTISSUE. A modular, open-source specimen inventory and tracking system that will encompass a core database module for those Centers in need of new solutions, as well as application programming interfaces (APIs), software development toolkits (SDKs), and additional annotation modules for those centers with legacy systems that wish to link into the virtual tissue repositories and query across Cancer Centers. The caBIGTM Tissue Banks and Pathology Tools Workspace (TBPTW) is responsible for the release of caTISSUE.

Centers for Disease Control and Prevention and Agency for Toxic Substances and Disease Registry (ATSDR) (CDC-ATSDR). A registry formed to centrally track and store biospecimens collected for a range of CDC activities.

Clinical data. Data pertaining to or founded on actual observation and treatment of patients.

Clinical trial research. Research studies that evaluate new interventions, drugs, or medical therapies given to patients in strictly scientifically controlled settings. The purpose of such trials is to determine whether one or more screening, prevention, and/or treatment options are safe, effective, and better than current standard care.

Code of Federal Regulations (CFR). The Code of Federal Regulations is a publication that codifies the general and permanent rules published in the Federal Register by the executive departments and agencies of the Federal Government. It is published by the Office of the Federal Register, National Archives and Records Administration, Washington, DC (ISBER 2003).

Coded samples. Sometimes termed “linked” or “identifiable,” these samples are supplied by biorepositories to investigators from identified specimens with a code rather than with personally identifying information, such as a name or Social Security number.

Collection. See Retrieval.

Common Data Elements (CDEs). CDEs standardize metadata between a series of software systems. Such standardization ensures that the same meaning of words is used and that data model and application components are reusable. In addition, it eases the integration of systems.

Confidentiality. A principle emergent from a relationship in which something about an individual, information, or material has been shared (with some degree of loss of privacy) in confidence (NBN Blueprint 2003).

Container. Enclosure for one unit or units of specimen(s) (ISBER 2005).

Cooperative Human Tissue Network (CHTN). A six-division, decentralized, NCI-funded, infrastructure that provides biomedical researchers with access to human tissue. Established in response to a Request for Applications in 1987, the CHTN has provided more than 500,000 high-quality tissue biospecimens from a variety of organs to more than 1,000 investigators for the conduct of basic and developmental cancer research. Eighty percent of these researchers are from academic or government institutions; only 20 percent of users are from industry.

Cryoprotectant. An additive that serves to minimize osmotic imbalances that occur with the progression of freezing fronts through a substance and is intended to limit the amount of cell damage due to cell shrinkage and intracellular ice formation (ISBER 2005).

Custodianship. Relates to the caretaking responsibility for the specimen collection, including management and documentation, as well as rights to determine the conditions under which the specimens are accessed and used.

D

Data. Values derived from scientific experiments or diagnostic procedures organized especially for scientific analysis in a numerical form suitable for processing by computer (NBN Blueprint 2003).

De-identified protected health information. Health information that does not identify an individual and with respect to which there is no reasonable basis to believe that the information can be used to identify an individual. Such information is not individually identifiable health information (45 C.F.R. §164.514(a)-(c)) (Eiseman et al. 2003).

Demographic data. Data relating to statistical characteristics of human populations (e.g., age, gender).

Deviation. An intentional or unintentional event that is a departure from a procedure or a normal practice (ISBER 2005).

Disposition. Final destination of specimens (ISBER 2005).

Distribution. A process that includes receipt of request for specimens, selection of appropriate specimens, and final inspection, in conjunction with subsequent shipment and delivery of specimens to another biorepository, specimen collection center, or laboratory (ISBER 2005).

Dry ice. Solid-phase carbon dioxide.

E

F

G

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.

H

Honest broker. A neutral intermediary between the individual whose tissue and data are being studied and the researcher. The honest broker collects and collates pertinent information regarding the tissue source, replaces identifiers with a code, and releases only coded information to the researcher (Eiseman et al. 2003).

Human subject. A living individual about whom an investigator conducting research obtains (1) data through intervention or interaction with the individual or (2) identifiable private information (NBN Blueprint 2003).

I

Indemnify. To secure against hurt, loss, or damage.

Informatics. The use of science, computer science, information technologies, and other technologies to provide data, information, and knowledge to an individual or an organization. The term is synonymous with information science. See also biorepository informatics system.

Informatics system. Refers to the software, hardware, written documents, support, and training necessary to annotate, track, and distribute biospecimens within a biorepository or biorepositories.

Informed consent. An educational process between the investigator and the prospective subject (or the subject’s legally authorized representative) as a means to ensure respect for persons; mutual understanding of research procedures, risks, rights, and responsibilities; and continuous voluntary participation (NBN Blueprint 2003).

Institutional review board. A specially constituted review body established or designated by an entity to protect the welfare of human subjects recruited to participate in biomedical or behavioral research.

Intellectual property. Creative ideas and expressions of the human mind that have commercial value and receive the legal protection of a property right. The major legal mechanisms for protecting intellectual property rights are copyrights, patents, and trademarks. Intellectual property rights enable owners to select who may access and use their property and to protect it from unauthorized use.

Interoperability. The ability of two or more systems or components to exchange information and to use the information that has been exchanged.

Invention. A new and useful process, machine, manufacture or composition of matter, or any new and useful improvement, finding, or product that clearly advances the state of the art or practice and may be patentable.

J

K

L

Label. Any written, printed, or graphic material on or affixed to a specimen container or package (ISBER 2005).

Liquid nitrogen dry shipper. A container used for sending samples in the vapor phase of liquid nitrogen (ISBER 2005).

Longitudinal data. Clinical data acquired over the course of time.

M

Material Transfer Agreement (MTA). A binding legal agreement between the owner of research materials and the recipient of the materials that sets forth conditions of transfer and use, protects proprietary interests, and restricts distribution of the material. An important aspect of the MTA is that it removes liability on the part of the provider that might arise from use of the research material.

Minimal risk. The probability and magnitude of harm or discomfort anticipated in the research that are not greater in and of themselves than those ordinarily encountered in daily life or during the performance of routine physical or psychological examinations or tests.

N

O

P

Package. A labeled carton, receptacle, or wrapper containing one or more containers and accompanying labeling material (ISBER 2005).

Paraffin-embedded. Tissue that is formalin fixed and then embedded in wax. (Note: Other alternative fixation methods may be used to fix the tissue).

Patent. A property right granted by the Federal Government to an inventor. In order to be patentable, an invention must contain an idea that serves some utility, is novel, and is “nonobvious” to an average person “skilled in the arts of the specified field” (NBN Blueprint 2003).

Patient. A person undergoing medical treatment.

Preservation. Use of chemical agents, alterations in environmental conditions, or other means during processing to prevent or retard biological or physical deterioration of a specimen (ISBER 2005).

Prevalence. Number of cases of a disease, infected persons, or persons with some other attribute present during a particular interval of time.

Privacy. The state or condition of limited access to an individual and/or to information about that individual.

Procedure. A series of steps designed to result in a specific outcome when followed in order (ISBER 2005).

Process validation studies. The process of demonstrating that a specific procedure will consistently produce expected results within predetermined specifications (ISBER 2005).

Processing. Any procedure employed after specimen collection but prior to its distribution, including preparation, testing, and releasing the specimen to inventory and labeling (ISBER 2005).

Prospective. When an intervention of interest is performed and all relevant information and observations on its effects are gathered after entry into the study. By contrast, “retrospective” studies focus on information that has already been collected.

Protected health information (PHI). Any health information that is collected by a covered entity and is individually identifiable (NBN Blueprint 2003). Also, a subset of individually identifiable information that can be disclosed only under the following conditions: (1) the use or disclosure is sought solely to review PHI as necessary to prepare the research protocol or other similar preparatory purposes, (2) no PHI is removed from the covered entity during review, and (3) the PHI that the researcher seeks to use or access is necessary for the research purposes. PHI can be de-identified by removing all 18 identifiers listed in Section 164.514(b)(2) of the Federal regulations or by having a qualified statistician perform an analysis stating that the risk of the information being used is small (ISBER 2005).

Proteomics. The study of the full set of proteins encoded by a genome; the study of the identities, quantities, structures, and biochemical and cellular functions of all proteins in an organism, organ, or organelle and how these properties vary in space, time, and physiological state.

Q

Quality assurance (QA). An integrated system of management activities involving planning, implementation, documentation, assessment, and improvement to ensure that a process or item is of the type and quality needed for the project. Same as quality management system (QMS) (ISBER 2005).

Quality control (QC). Specific tests defined by the QA or QMS Program to be performed to monitor procurement, processing, preservation and storage, specimen quality, and test accuracy. These may include but are not limited to performance evaluations, testing, and controls used to determine accuracy and reliability of the biorepository’s equipment and operational procedures as well as monitoring of the supplies, reagents, equipment, and facilities (ISBER 2005).

Quality management system (QMS). Same as Quality assurance (QA) (ISBER 2005).

Quality. Conformance of a specimen or process with preestablished specifications or standards (ISBER 2005).

R

Reach-through provisions. Material transfer agreements do not usually require financial payments at the time of the transfer, but many allow the provider to either own, or license exclusively, or obtain payments upon the sale of, developments that the recipient makes with the provider’s materials. These are loosely termed “reach-through” provisions and are considered by many providers to be desirable because they allow the provider to obtain rights in subject matter to which the provider would not otherwise have rights through its ownership or patent coverage of the material alone. Reach-through provisions are considered undesirable by many recipients because they burden all the developments created after the use of the material and because they are seen as providing an unfairly high level of compensation to the provider for use of the material.

Repository. See Biorepository.

Research. Systematic investigation, including research development, testing, and evaluation, designed to develop or contribute to generalizable knowledge.

Retrieval. The removal, acquisition, recovery, harvesting, or collection of specimens (ISBER 2005). Safety. Processes, procedures, and technologies to ensure freedom from danger or harm. Sample. Portions of specimens distributed to researchers (Eiseman et al. 2003). Semantics. Refers to the ways that information in a data file should be interpreted by others. Shipping manifest. A written description of the contents of the shipped package (ISBER 2005).

S

Specimen. A portion of tissue, blood, urine, or other material used for diagnosis and analysis. A single biopsy may generate several specimens, including a number of slides, paraffin blocks, and/or frozen specimens. See Biospecimen.

Standard operating procedures (SOPs) manual. A group of standard operating procedures detailing the specific policies of a biorepository and the procedures used by the staff/personnel (ISBER 2005).

Storage. Maintenance of specimens for future use.

Syntax. Refers to the ways that information is structured in a data file.

T

Tissue. Refers generally to a biologic collection of cells, and the extracellular matrix and/or intercellular substances surrounding them. Tissue is most often referred to in the context of solid tissue, as originating from a solid organ; however, tissue can also be defined broadly to include collections of cells and intercellular substances from bodily fluids such as blood.

Tissue Banks and Pathology Tools Workspace (TBPTW). As one of three caBIGTM pilot domain workspaces, the goal of the TBPTW is to develop a set of tools to inventory, track, mine, and visualize tissue samples and related information from a geographically dispersed biorepository. This Workspace provides an opportunity to bind Cancer Center systems together into a unified resource through a shared informatics infrastructure. Cancer Centers with experience in successfully developing tools in this domain are acting as developers, while other Centers are included as testing and validation sites. Cancer Centers that have expressed an interest in sharing information regarding specimen repositories and data sets are participating as early test sites, providing an opportunity to demonstrate how the tools perform in actual practice.

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

U

Uniform Biological Material Transfer Agreement (UBMTA). A standardized material transfer agreement with generic language for biological material transfers. It was created to increase the efficiency of the process by decreasing delays in research progress during negotiation of material transfer agreements, while providing uniform protection for biological materials. The National Institutes of Health published the Uniform Biological Material Transfer Agreement in 1995 and recommends its use by all public and nonprofit research institutions.

Use case. A description of the process used to perform a particular modeling task on a particular model. It is a user-centered description of the activities performed by a user to accomplish a particular goal. The collected use cases specify all the ways the system can be used.

V

W

Waterfall development. A method of software development by which development activities happen in sequence, and a given step is not performed until the previous one is complete. For example, a system design is performed only when all requirements have been gathered; additional requirements cannot be gathered once design has started.

X

Y

Z