lab

 

In some sense the information in this category could be a repeat of metadata in the sampleprep category. I went back to the metadata originally in sampleprep and moved some of it here as it seemed to fit better.  I also changed the name of the category to sample metadata (from matrix metadata) because the sample matrix (while important) is only one piece of metadata that describes a sample and how it was sampled.  So, the metadata is broadly about the sample, how it was collected, and how it was stored.  Thoughts?  Email This email address is being protected from spambots. You need JavaScript enabled to view it..

  • identifier: the unique identifier of the sample (string) [10-02-14]
  • amount: the mass or volume of the sample received or collected (float/decimal) [10-02-14]
  • amount unit: the unit of the quantity of the sample amount (string/enum/vocab) [10-02-14]
  • aggregation: if the sample was obtained by collecting it at multiple locations and combining then it should be described here (string) [10-02-14]
  • matrix: description of the type of sample material (from a controlled vocabulary) (string) [10-02-14]
  • physical state: the phase of the sample (e.g. solid, liquid, gas, slurry, etc.) (enum) [10-02-14]
  • homogeneity: the homogeneity of the sample at collection (e.g. homogeneous, heterogeneous, emulsion) (enum) [10-02-14]
  • sampling event: was the sample collected as part of a specific trip/exploration/voyage? (string) [10-02-14]
  • sampling location: a description of or GPS coordinates for where the sample was obtained (string) [10-02-14]
  • sampling depth: the depth below sea level the sample was collected (string) [10-02-14]
  • sampling depth unit: the unit for the sampling depth (string/enum/vocab) [03-01-15]
  • sampling altitude: the altitude above sea level the sample was collected (string)  [10-02-14]
  • sampling altitude unit: the unit for the sampling altitude (string/enum/vocab) [03-01-15]
  • sampling conditions: what were the environmental conditions (weather) where the sample was collected (string) [10-02-14]
  • sampling protocol: how the sample was collected (string) [10-02-14]
  • sampling equipment: the apparatus used to collect the sample (string) [10-02-14]
  • field stabilization: a description of the any processes used to stabilize the sample in the field (string) [was 'field prep' 02-16-15]
  • field additives: list of substances  added to the sample to stabilize the concentration of the analyte(s) to be determined (string) [was 'field prep' 02-16-15]
  • storage container: container that the collected is stored/placed in for transport/storage (should include material type as well as container type) (string) [02-16-15] (replaced 'vessel' with 'container')
  • storage conditions: how/where the sample is stored after collection, prior to lab processing and/or analysis (string) [10-02-14]

On this page I am going to collect anything that can be used as a part of controlled vocabulary for sample matrix.  This can be from existing databases, industry specifications, or government standards.  If you have any suggestions to add to this list please let This email address is being protected from spambots. You need JavaScript enabled to view it. know.

General

Specific Areas

Sample preparation is key to good analytical results as in most cases analytical instruments give inaccurate results with real samples.  Because preparation of a sample requires a procedure, there is a decision to be made around inclusion of the complete procedure or just a reference to the procedure (either formal standard or in-house).  While I think that it is important to provide a mechanism to allow users to articulate each step in sample preparation, I imagine that referencing a procedure will be significantly more common.  Anything missing? If so, email This email address is being protected from spambots. You need JavaScript enabled to view it..

10-02-14: Moved some of the metadata to the 'Sample" category and made some new items here for subsamples
04-28-15: Moved interference to the description category

  • sample name: the name given to the sample (string) [09-23-14]
  • subsample id: the unique identifier(s) of the subsample(s) (e.g. sample identifier + discriminator) (string) [09-23-14]
  • subsample amount: the mass or volume of the subsample(s) processed for analysis (float/decimal) [10-02-14]
  • subsample unit: the unit of the quantity of the subsample amount(s) (string) [10-02-14]
  • procedure: a textual description of the procedural steps used to convert the raw sample into a sample ready for analysis (string) [09-23-14]
    -- OR --
    step(s): each procedural step separately recorded with some indication of the order the steps were taken (e.g. 1-10, A thru M) (string) [09-23-14]
  • storage conditions: how/where the sample is stored after laboratory processing but prior to analysis (string) [09-23-14]
  • analysis timeframe: how long the analyst has to analyze the sample to maintain accuracy of the procedure (float/decimal) [new 04-28-15]
  • chain of custody: whether a chain-of-custody was maintained for the sample during the preparation (string) [09-23-14]
  • interferences: information about interferences that can be an issue in the sample preparation (string) [09-23-14] (moved to description 04-28-15)
  • safety: any safety issues relative the sample preparation [09-23-14]
  • waste: information about waste generated from the preparation procedure [09-23-14]
  • keyword(s): any important terms that characterize the sample preparation process [09-23-14]
    (e.g. liquid/liquid extraction, solid phase extraction, preconcentration, mesh sieving, hot-plate digestion, microwave digestion, etc.)
  • reference: a formatted citation to a published version of the procedure used [09-23-14]

This category of metadata seems pretty straightforward if you think about the analysis of one single analyte for its solution concentration, however the metadata here must be comprehensive enough to cover all analysis possibilities.  Please let This email address is being protected from spambots. You need JavaScript enabled to view it. know there are any additional metadata items needed. (names update 2-12-15)

  • substance: a discrete chemical species identified by its InChI string [09-23-14]
  • substance class: named group of chemical substances identified as a specific class by structure, use, size, or action determined in chemical analysis procedures [09-23-14] (e.g. PCB's, amino acids, PAH's, pharmaceuticals, heavy metals, enzymes, etc.)
  • functional group: chemical test for an organic functional group [02-26-15]
  • biological property: a property specific to a biological process [02-26-15]
    (e.g. biological activity, QSAR)
  • chemical property: any property to due with a chemical reaction [02-26-15]
    ( e.g. heat of combustion, enthalpy of formation, toxicity, chemical stability, flammability, rate of reaction, etc.)
  • physical property: measurement of a bulk (material) property, or characteristic substance property [02-26-15]
    (e.g. solubility, refractive index, electrical conductivity, color, thermal conductivity, etc. - anything other than concentration)
  • analyzed form: a descriptive term to indicate the state of the analyte as it was measured (not the oxidation state) [09-23-14]
    (e.g. dissolved, labile, total, volatile, extractable, free, residual, etc.)