NMC DSP Technical Terms

From BioAssist
Jump to: navigation, search

NMC DSP - Mainpage


This page contains the definitions used within the NMC DSP.

Study (project)

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.

StudyType

Describes the type of study done, several types of studie can be:

  • Metabolite identification
  • Nutritional research
  • Clinical research

StudyTypeMetaTemplate

A study template can belong to one or more studytypes.

MetaTemplate

The template name and creation date.

MetaTemplateMetaField

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.

MetaField

Describes a unique fieldname which can be reused in a template. Some examples of fieldnames (per category):

Human

  • DOB
  • Gender
  • BMI

Plant

  • Soiltype
  • Lighting
  • Humidity

Mouse

  • Caging

MetaFieldOption

Contains options which belong to a field. See the following examples where bold is a field and indented the list of options:

  • Gender
    • Male
    • Female
  • Lighting
    • High-pressure sodium grow lamp
    • Incandescent grow lights
    • Fluorescent grow lamp
    • LED grow lamp

MetaFieldType

Describes a type of field and how it is formatted.

  • Date
  • Integer
  • String

MetaFieldGroup

A field can belong to a group. A group can be self referencing. Examples of groups are:

  • Growth environment
    • Soiltype
    • Humidity
    • Lighting
  • Demographics
    • DOB
    • Gender
  • Anthropometrics
    • Body height

MetaData

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):

Experiment

 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

MetaObject

A list of objects where metadata can be attached to. Currently to - at least - the following objects (tables) metadata can be attached:

Experiment

The experiment describes the whole setup and techniques used for achieving the goal.

  • Example:
    • 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

ExperimentSample

This is used for re-using samples within different experiments.

Sample

A sample taken from a (biological) source.

  • Name: label used in the labatory to identify the sample

SampleType

Defines the type of sample taken from a (biological source).

  • Human
    • Urine
    • Blood
    • CSF
    • Tissue
  • Mouse
    • Urine
    • Blood
    • CSF
    • Tissue
  • Plant
    • Tissue
    • Seeds
    • leaf

Source (biological source)

Describes the unique individual source where samples are taken from.

  • Human (patient)
  • Mouse
  • Quality control
  • Rat
  • Tomato

Species

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
  • etc...

Strain

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:

  • C57BL
  • ...

Plant

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.

Examples:

  • Plant: Columbia ecotype of Arabidopsis Thaliana -> imbred line B73
  • Rice : rice (oryza sativa) -> nipponbare
  • Tomato : Solanum lycopersicum -> Money Maker/ M82


Cell (overview here)

  • AB1
  • ATOM1
  • Bruce 4

Data

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.

DataType

Specifies the type of data, this can be raw data or processed data.

  • examples of other raw data/ processed data type file names:
    • 5phphigh_06.RAW
    • all peaks.CPR
    • metabolites.csv