Structured data and lists

Matt Styles edited this page Mar 18, 2018 · 44 revisions

Index

Structured data

Lists

Structured data


Contact information

MIABIS-2.0-07

Attribute Code Attribute Name Allowed Values Description
MIABIS-2.0-07-A First name Text Textual string of letters denoting the first name of the Contact
MIABIS-2.0-07-B Last name Text Textual string of letters denoting the last name of the Contact
MIABIS-2.0-07-C Phone Formated Text Phone to the Contact including international call prefix
MIABIS-2.0-07-D Email Text Email address of the Contact person
MIABIS-2.0-07-E Address Text Street name and street number or PO Box of the Contact person
MIABIS-2.0-07-F ZIP Text ZIP of the Contact person
MIABIS-2.0-07-G City Text City of the Contact person
MIABIS-2.0-07-H Country Text Country of the Contact person

Researcher information

MIABIS-2.0-23

Attribute Code Attribute Name Allowed Values Description
MIABIS-2.0-23A Juristic Person Text Textual string of letters denoting the juristic person e.g. a university, concern, county council etc.
MIABIS-2.0-23B Department Text Department (e.g. division), or corresponding affiliation of the Contact person
MIABIS-2.0-23C ORCID Text The persistent digital identifier that distinguishes researchers. As defined by ORCID

Disease

MIABIS-2.0-17

Attribute Code Attribute Name Allowed Values Description
MIABIS-2.0-17A Disease Ontology Text Name of ontology used for disease. Can be several values e.g. ICD, SNOMED
MIABIS-2.0-17B Disease Ontology Version Text Version of selected ontology for disease e.g. ICD-9, ICD-10, SNOMED-CT
MIABIS-2.0-17C Disease Ontology Code Text Disease code from the selected Disease Ontology Version e.g. C61
MIABIS-2.0-17D Disease Ontology Description Text Description from the selected Disease Ontology Code e.g : Malignant neoplasm of prostate
MIABIS-2.0-17E Disease Free Text Text Explanation about disease or symptom in case of unknown disease or insufficient information

Vendor

MIABIS-2.0-nn (proposal)

Attribute Code Attribute Name Allowed Values Description
MIABIS-2.0-nnA Name Text Legal name of the Vendor
MIABIS-2.0-nnB Website URL Website of the Vendor

Example

Name Website
Affymetrix http://www.affymetrix.com/estore/
Life Technologies http://www.lifetechnologies.com/se/en/home.html
Roche Applied Science http://www.roche-applied-science.com/
Illumina http://www.illumina.com/

Lists


Sex

MIABIS-2.0-09

Item Name Definition Source Link
Male male
Female female
Unknown a proper value is applicable but not known
Undifferentiated undifferentiated, the gender could not be uniquely identified such as hermaphrodite

Material type

MIABIS-2.0-14

Item Name Definition Source Link
Blood Blood that has not been separated into its various components; blood that has not been modified except for the addition of an anticoagulant. NCI
DNA A 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. NCI
Faeces The material discharged from the bowel during defecation. It consists of undigested food, intestinal mucus, epithelial cells, and bacteria. NCI
Immortalized Cell Lines Cells of a single type (human, animal, or plant) that have been adapted to grow continuously in the laboratory and are used in research. NCI
Isolated Pathogen An isolated biological agent causing disease; a disease producer e.g. virus, bacterium, prion, other microorganism etc. NCI
Other Any other type of material taken from a biological entity, e.g. amniotic fluid, cerebrospinal fluid (CSV), mitochondrial RNA. NCI
Plasma Plasma 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. NCI
RNA One 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. NCI
Saliva A 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. NCI
Serum The clear portion of the blood that remains after the removal of the blood cells and the clotting proteins. NCI
Tissue (Frozen) An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function.
Tissue (FFPE) Tissue, formalin fixated and paraffin preserved or equivalent.
Urine The fluid that is excreted by the kidneys. It is stored in the bladder and discharged through the urethra. NCI

Until September the following list was in use, there is a one way transformation to the new list above.

Item Name Definition Source Link New value
DNA A 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. NCI DNA
RNA One 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. NCI RNA
cDNA/mRNA Single-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. NCI RNA
microRNA A 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. NCI RNA
Whole blood Blood that has not been separated into its various components; blood that has not been modified except for the addition of an anticoagulant. NCI Blood
Peripheral blood cells A 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 Glossary Blood
Plasma Plasma 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. NCI Plasma
Serum The clear portion of the blood that remains after the removal of the blood cells and the clotting proteins. NCI Serum
Tissue, cryo preserved An 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 nitrogen NCI Tissue (Frozen)
Tissue, paraffin preserved Tissue that is preserved and embedded in paraffin. NCI Tissue (FFPE)
Cell lines Cells of a single type (human, animal, or plant) that have been adapted to grow continuously in the laboratory and are used in research. NCI Immortalized Cell Lines
Urine The fluid that is excreted by the kidneys. It is stored in the bladder and discharged through the urethra. NCI Urine
Saliva A 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. NCI Saliva
Faeces The material discharged from the bowel during defecation. It consists of undigested food, intestinal mucus, epithelial cells, and bacteria. NCI Faeces
Pathogen A biological agent causing disease; a disease producer e.g. virus, bacterium, prion, other microorganism etc. Isolated Pathogen
Other Any other type of material taken from a biological entity, e.g. amniotic fluid, cerebrospinal fluid (CSV), mitochondrial RNA. Other

Storage temperature

MIABIS-2.0-15

Item Name Definition Source Link
RT Room temperature SPREC 2.0
2 °C to 10°C between 2 °C and 10 °C SPREC 2.0
-18 °C to -35 °C between -18 °C and -35 °C SPREC 2.0
-60 °C to -85 °C between -60 °C and -85 °C SPREC 2.0
LN liquid nitrogen, -150 °C to -196 °C
Other, specify any other temperature or long time storage information

Data Categories

MIABIS-2.0-13

Item Name Definition Source Link
Biological samples Y/N if biological samples are collected from the participants in the sample collection/study
Survey data Y/N if information from surveys are collected from the participants in the sample collection/study
Imaging data Y/N if imaging data are collected from the participants in the sample collection/study
Medical records Y/N if medical records are collected from the participants in the sample collection/study
National registries Y/N if register data is associated to the participants in the sample collection/study
Genealogical records Y/N if genealogical records are associated with the participants in the sample collection/study
Physiological/Biochemical measurements Y/N if Measurements/tests performed during a clinical/home visit and from samples taken from donor
Other Other

Collection type

MIABIS-2.0-16 and Study design: MIABIS-2.0-19

Item Name Definition Source Link
Case-control A 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
Cohort A 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-sectional A type of observational study that involves data collection from a population, or a representative subset, at one specific point in time. Wikipedia
Longitudinal Research 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. P3G http://www.p3gobservatory.org/lexicon/list.htm#l
Twin-study Twin studies measure the contribution of genetics (as opposed to environment) to a given trait or condition of interest.
Quality control A 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-based Study 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 specific A 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 cohort A corhort study for which the subjects are followed from the time of birth usually including information about gestation and follow up.
Other

Inclusion Criteria

MIABIS-2.0-22

Item Name Definition Source Link
Health status
Hospital patient
Use of medication
Gravidity
Age group
Familial status
Sex
Country of residence
Ethnic origin
Population representative sampling
Lifestyle/Exposure
Other

Omics Technology

MIABIS-40

Item Name Definition Source Link
Genomics The study of an organism's entire genome. Methods in Molecular Biology 593 DOI:10.1007/978-1-60327-194-3_1 http://www.springerlink.com/content/w048163633774724/#section=614848&page=1
Transcriptomics The study of the transcription, i.e., the expression levels of mRNAs in a given organism, tissue, etc. (under a specific set of conditions). Methods in Molecular Biology 593 DOI:10.1007/978-1-60327-194-3_1 http://www.springerlink.com/content/w048163633774724/#section=614848&page=1
Proteomics The study of proteins, their structures, and their functions, namely the study of the proteome. Methods in Molecular Biology 593 DOI:10.1007/978-1-60327-194-3_1 http://www.springerlink.com/content/w048163633774724/#section=614848&page=1
Metabolomics The identification, quantification, and characterization of the small molecule metabolites in the metabolome (i.e., the set of all small molecule metabolites found in a specific cell, organ, or organism). Methods in Molecular Biology 593 DOI:10.1007/978-1-60327-194-3_1 http://www.springerlink.com/content/w048163633774724/#section=614848&page=1
Other

Ethnic group

MIABIS-50

Item Name Definition Source Link
African
Caucasian
Pacific Islander
East Asian
Native American
Other
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