Standards within the Directory

As a Centre we have a firm commitment not to create duplication within an already disparate field. To that end we are seeking to re-use existing standards as appropriate. Within the UKCRC Tissue Directory this has two main impacts.

SNOMED-CT

The Centre has selected SNOMED-CT for all health related classifications, such as diseases or human health related conditions and incidents. As someone searching the Directory or a Biobank adding information then you will need to use SNOMED-CT terms at some point.

As a researcher, what do I need to know?


Take a look at the list of SNOMED-CT terms that Biobanks have used within our Directory as you will need to use one of them to start a search.

As a Biobank, what do I need to know?


We did not simply load the full SNOMED-CT terminology into our Directory. This was to prevent different Biobanks using different levels of detail to represent the same disease. Therefore, when you come to add your collection, you may not find what you are looking for. In that case, get in contact with us and we either let you know of the relevant term of add as needed.

Explanation of Terms used

We have started to compile a list of definitions for the fields that are most commonly asked about. This list will be updated over time.

Terms

The definitions were taken from the MIABIS data standard

Item NameDefinitionSourceLink
Case-controlA case-control study design compares two groups of subjects: those with the disease or condition under study (cases) and a very similar group of subjects who do not have the disease or condition (controls).EMBL (EFO)http://www.ebi.ac.uk/efo/EFO_0001427
CohortA form of longitudinal study for the analysis of risk factors following a group of people who do not have a disease, and uses correlations to determine the absolute risk of subject contraction.Wikipedia (rewritten)
Cross-sectionalA type of observational study that involves data collection from a population, or a representative subset, at one specific point in time.Wikipedia
LongitudinalResearch studies involving repeated observations of the same entity over time. In the biobank context, longitudinal studies sample a group of people in a given time period, and study them at intervals by the acquisition and analyses of data and/or samples over time.P3Ghttp://www.p3gobservatory.org/lexicon/list.htm#l
Twin-studyTwin studies measure the contribution of genetics (as opposed to environment) to a given trait or condition of interest.
Quality controlA quality control testing study design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance.EMBL (EFO)http://www.ebi.ac.uk/efo/EFO_0001774
Population-basedStudy done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.Wikipedia (rewritten)
Disease specificA study or biobank for which material and information is collected from subjects that have already developed a particular disease.EMBL (EFO)http://www.ebi.ac.uk/efo/EFO_0001430
Birth cohortA corhort study for which the subjects are followed from the time of birth usually including information about gestation and follow up.
Definitions taken from the work of the Confederation of Cancer Biobanks

Item NameDefinition
Open to applicantsAccess procedures are in place to accept applications from any researcher - there are no restrictions
Open in response to specific callsAccess is time-limited and there will be specific periods when researchers can request access
Open only through collaborationAccess is only available via a research collaboration with the biobank staff
Data access onlyNo samples are released, only data can be made available
Access restricted at presentSome restrictions may be in place, this may a temporary geographical restriction or a pre-set group of researchers
Closed to accessCurrently no access is provided
An adapted version of the MIABIS data standard

Item NameDefinitionSourceLinkNew value
DNAA long linear double-stranded polymer formed from nucleotides attached to a deoxyribose backbone and found in the nucleus of a cell; associated with the transmission of genetic information.NCIDNA
RNAOne of two types of nucleic acid made by cells. RNA contains information that has been copied from DNA (the other type of nucleic acid). Cells make several different forms of RNA, and each form has a specific job in the cell. Many forms of RNA have functions related to making proteins. RNA is also the genetic material of some viruses instead of DNA. RNA can be made in the laboratory and used in research studies. Also called ribonucleic acid.NCIRNA
cDNA/mRNASingle-stranded DNA that is complementary to messenger RNA or DNA that has been synthesized from messenger RNA by reverse transcriptase/A class of RNA molecule containing protein-coding information in its nucleotide sequence that can be translated into the amino acid sequence of a protein.NCIRNA
microRNAA type of RNA found in cells and in blood. MicroRNAs are smaller than many other types of RNA and can bind to messenger RNAs (mRNAs) to block them from making proteins. MicroRNAs are being studied in the diagnosis (NCI) and treatment of cancer.NCIRNA
Whole bloodBlood that has not been separated into its various components; blood that has not been modified except for the addition of an anticoagulant.NCIBlood
Peripheral blood cellsA general term describing the three cellular components of blood (white blood cells, red blood cells, and platelets), all which are made in the bone marrow.Lymphoma Information Network GlossaryBlood
PlasmaPlasma is the fluid (acellular) portion of the circulating blood, as distinguished from the serum that is the fluid portion of the blood obtained by removal of the fibrin clot and blood cells after coagulation.NCIPlasma
SerumThe clear portion of the blood that remains after the removal of the blood cells and the clotting proteins.NCISerum
Tissue, cryo preservedAn anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function. Preserved by freezing in liquid nitrogenNCITissue (Frozen)
Tissue, paraffin preservedTissue that is preserved and embedded in paraffin.NCITissue (FFPE)
Cell linesCells of a single type (human, animal, or plant) that have been adapted to grow continuously in the laboratory and are used in research.NCIImmortalized Cell Lines
UrineThe fluid that is excreted by the kidneys. It is stored in the bladder and discharged through the urethra.NCIUrine
SalivaA clear liquid secreted into the mouth by the salivary glands and mucous glands of the mouth; moistens the mouth and starts the digestion of starches.NCISaliva
FaecesThe material discharged from the bowel during defecation. It consists of undigested food, intestinal mucus, epithelial cells, and bacteria.NCIFaeces
PathogenA biological agent causing disease; a disease producer e.g. virus, bacterium, prion, other microorganism etc.Isolated Pathogen