NMC DSP Technical Terms
This page contains the definitions used within the NMC DSP.
- 1 Study (project)
- 2 StudyType
- 3 StudyTypeMetaTemplate
- 4 MetaTemplate
- 5 MetaTemplateMetaField
- 6 MetaField
- 7 MetaFieldOption
- 8 MetaFieldType
- 9 MetaFieldGroup
- 10 MetaData
- 11 MetaObject
- 12 Experiment
- 13 ExperimentSample
- 14 Sample
- 15 SampleType
- 16 Source (biological source)
- 17 Species
- 18 Strain
- 19 Data
- 20 DataType
Describes the whole project/study to be done. For example a description on what subjects will be studied and what is the goal of the research.
Describes the type of study done, several types of studie can be:
- Metabolite identification
- Nutritional research
- Clinical research
A study template can belong to one or more studytypes.
The template name and creation date.
Contains the fields used in a specific template. The template being used is defined in the MetaTemplate. The field is chosen from the MetaField table. The object (table) the field is belonging/related to is stored in the MetaObject.
Describes a unique fieldname which can be reused in a template. Some examples of fieldnames (per category):
Contains options which belong to a field. See the following examples where bold is a field and indented the list of options:
- High-pressure sodium grow lamp
- Incandescent grow lights
- Fluorescent grow lamp
- LED grow lamp
Describes a type of field and how it is formatted.
A field can belong to a group. A group can be self referencing. Examples of groups are:
- Growth environment
- Body height
The actual real metadata with a key/value combination where the key is a reference to a key in one of the objects. Take for example the Experiment table (object):
PK Description 101 First experiment 102 Second experiment 103 Third experiment
The key/value combination could be:
Key Value 101 BLOB: metadata with text 102 BLOB: metadata with numerical value 103 BLOB: metadata with text
A list of objects where metadata can be attached to. Currently to - at least - the following objects (tables) metadata can be attached:
The experiment describes the whole setup and techniques used for achieving the goal.
- Date : 2009/01/19
- Hour : 11h00
- Tomato seeds: MoneyMaker 95/2 (2 filter paper with 50 seeds)
- Room : BZ
- Temperature : 25 C
- Photoperiod : 8/16h, 45 μmol m−2 s−1
- Objective : Find a good experimental system for the culture of tomato seedlings
- Determination of hypocotyls elongation
- Results : Experiment/Vic2-090119
- Harvested : 28/01/09
- Grinding : 30/01/09 (little pestle and eppendorf)
- Extraction : 30/01/09
- Injection : 02/02/09
This is used for re-using samples within different experiments.
A sample taken from a (biological) source.
- Name: label used in the labatory to identify the sample
Defines the type of sample taken from a (biological source).
Source (biological source)
Describes the unique individual source where samples are taken from.
- Human (patient)
- Quality control
A taxonomic rank of organisms. An overview of existing species can be found here. Of a Species both the common name and a scientific name is captured. For example:
- Mouse, Mus Musculus
- Black Rat, Rattus rattus
- Tomato, Solanum lycopersicum
The nomenclature for strains for mice can be found at JAX.
Mouse (overview here)
A mouse or a rat strain is a group of animals that is genetically uniform. Strains are used in laboratory experiments. Mouse strains can be inbred, mutated or genetically engineered, while rat strains are usually inbred. Example mouse strains:
The term "strain" is used mostly in the case of micro organisms, where as in plants a 'strain' is a designated group of offspring that have descended from a modified plant, produced either by conventional breeding or by biotechnological means or result from genetic mutation. Variety/genotype/ecotype/cultivars are the terms used instead in the case of plants.
- Plant: Columbia ecotype of Arabidopsis Thaliana -> imbred line B73
- Rice : rice (oryza sativa) -> nipponbare
- Tomato : Solanum lycopersicum -> Money Maker/ M82
Cell (overview here)
- Bruce 4
Contains the actual raw (unprocessed) data coming from a mass spectrometry device. References to files on disk are stored. The most used formats are netCDF and mzXML, which are ASCII human readable files. Data can have a reference to itself, meaning that one starts with for example raw data (parent) and processes this, resulting in children from that original raw dataset.
Specifies the type of data, this can be raw data or processed data.
- examples of other raw data/ processed data type file names:
- all peaks.CPR