This is a first pass of gathering and structuring key data to be used to build the CINECA WP3 minimal metadata model - current under development.

The chosen sub-categories are shaped by common data categories collected by major catalogues such as Maelstrom. The chosen variables are either CINECA use case requirements, or variables that can be mapped to by the majority of CINECA cohorts, or typical metadata variables collected by major catalogues. We have applied ontology terms to variables (mostly from NCIT). We are also looking into cross referencing with existing minimal data models.

If you use this work, please attribute CINECA and the primary contacts listed below.

Vivian Jin and Fiona Brinkman (SFU, Canada); Melanie Courtot (EBI, UK).

Create application ontology and structure terms in a hierarchy for easier search. For each variable, specify values and associated ontology terms (eg. for gender - specify male/female/transgender/non-binary).

NOTE: use blank response if answer to question description is N/A

Known num. of cohorts with this data (if greater zero)

The reason for performing a study in terms of the scientific questions to be answered by the analysis of data collected during the study.

A chronological schedule of when activities or events occurred or will occur.

MIABIS codes (Categorical)

A plan detailing how a study will be performed in order to represent the phenomenon under examination, to answer the research questions that have been asked, and defining the methods of data analysis. Study design is driven by research hypothesis being posed, study subject/population/sample available, logistics/resources: technology, support, networking, collaborative support, etc.…

A position, site, or point in space where something can be found.

criteria for enrollment and recruitment procedures

Medical and/or social characteristics which are necessary for a subject to be allowed to participate in a clinical study, as outlined in the study protocol. Meeting inclusion criteria is not a sufficient condition for entry or recruitment of a subject into the study. Characteristics limiting the eligibility of a subject for the clinical study must be considered

The number of subjects entered in a clinical trial.

The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.

gender(s) studied in cohort

The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes.

The fluid that is excreted by the kidneys. It is stored in the bladder and discharged through the urethra.

A liquid tissue; its major function is to transport oxygen throughout the body. It also supplies the tissues with nutrients, removes waste products, and contains various components of the immune system defending the body against infection. Several hormones also travel in the blood.

The material discharged from the bowel during defecation. It consists of undigested food, intestinal mucus, epithelial cells, and bacteria.

The watery fluid in the mouth made by the salivary glands. Saliva moistens food to help digestion and it helps protect the mouth against infections.

The quality of being obtainable or accessible and ready for use or service.

Alphanumeric (or Categorical?)

The system of methods followed in a particular discipline.

MIABIS codes (Categorical)

An administrative activity defined at a global library level that is an action of storing samples.

biosample source/anatomical location

Alphanumeric (or Categorical?)

A request to identify the specimen source site.

Alphanumeric (or Categorical?)

The organization of information according to preset specifications.

DNA Sequencing/Nucleic Acid Sequencing

NCIT:C153598/NCIT:C18881

Whole Genome Sequencing

Sequence variants (CNV, SNP arrays)

Single Nucleotide Polymorphism Profile

The analysis of all of the single nucleotide polymorphisms in the genome of a biological sample.

The analysis of all of the epigenetic DNA modifications in the genome a biological sample.

ERO:0000657 (***ERO is obsolete)

A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research.

Microbiome markers (rRNA, etc)

A procedure that can determine the RNA sequences for all or part of the poly-A tail-containing messenger RNA transcripts in an individual.

eQTL (Cis eQTLs and/or Trans eQTLs)

Expression Quantitative Trait Locus

A stretch of DNA at a particular chromosomal location that is able to regulate the expression of a specific mRNA or protein.

A subset of a larger population, selected for investigation to draw conclusions or make estimates about the larger population.

Alphanumeric (or Categorical?)

The organization of information according to preset specifications.

The quality of being obtainable or accessible and ready for use or service.

The system of methods followed in a particular discipline.

associated cell type/tissue type/biosample

Alphanumeric (or Categorical?)

A request to identify the specimen source site.

NCIT:C985496/NCIT:C16977

Any genetically determined characteristic/The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment.

The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation.

date and time-related information

The date (and time) on which an assessment is completed.

Consent by a patient to a surgical or medical procedure or participation in a clinical study after achieving an understanding of the relevant medical facts and the risks involved.

One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing.

NCIT:C25150/NCIT:C68615

The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.

The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes.

NCIT:C16564/NCIT:C17049

A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease...

Any address at which a person dwells more than temporarily.

The activities of educating or instructing or teaching; activities that impart knowledge or skill.

family and household structure

A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others.

A description of an individual's current and past experience with alcoholic beverage consumption.

Physical Activity Measurement

A measurement of a subject's physical activity or movement.

A natural and periodic state of rest during which consciousness of the world is suspended.

That which is consumed to fuel necessary life processes of an organism.

The physician responsible for the admission of a patient to a hospital or other inpatient health institution. The admitting physician evaluates patients, makes admitting decisions and assesses diagnostic and treatment plans

Hematopoietic and Lymphoid System Disorder

Any deviation from the normal structure or function of the blood or lymphatic system that is manifested by a characteristic set of symptoms and signs.

endocrine/nutritional/metabolic disorders

A non-neoplastic or neoplastic disorder that affects the endocrine system. Representative examples of non-neoplastic disorders include diabetes mellitus, hyperthyroidism, and adrenal gland insufficiency. Representative examples of neoplastic disorders include carcinoid tumor, neuroendocrine carcinoma, and pheochromocytoma.…

mental and behaviour disorders

Psychiatric Disorder/Behavioural Disorder

NCIT:C2893/NCIT:C35470

A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia.…/A specific behavioral problem that occurs in persistent patterns and characteristic clusters and that causes clinically significant impairment.

A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.

A non-neoplastic or neoplastic disorder that affects the gastrointestinal tract, anus, liver, biliary system, and pancreas.

Respiratory System Disorder

A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma.

signs and symptoms (Sign or Symptom NCIT:C100104)

The vertical force exerted by a mass as a result of gravity.

The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension.

The pressure of the circulating blood against the walls of the blood vessels.

The number of heartbeats per unit of time, usually expressed as beats per minute.

non-pharmacological interventions

Vasculature Mechanical or Surgical Intervention

A verbal or written order given by an authorized person instructing a patient to obtain and use a medical device, prescription or undergo a procedure.

The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.

A designation assigned to a particular period during a life cycle, generally defined by chronological parameters.

general research data documents (pdf, ppt, images etc)

summary statistics for additional data from federated sources

Statistical Analysis Documentation

Records pertaining to the statistical analyses and reports of a clinical trial.