GGBN Material Sample Extension

http://data.ggbn.org/schemas/ggbn/terms/MaterialSample

Support for material sample properties (e.g. tissues, DNA, RNA) as an extension to a Material Sample core. Intended to be a one to one relation to the Material Sample core.

Link: http://terms.tdwg.org/wiki/GGBN_Material_Sample_Vocabulary


Properties



MaterialSample

materialSampleType
Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type. Please use preparationType for further specification such as "leg","blood","gDNA","axenic culture". Equal to KindOfUnit in ABCD!
See also http://terms.tdwg.org/wiki/ggbn:materialSampleType
Examples: tissue, culture strain, specimen, DNA, RNA, Protein.
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/materialSampleType
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredtrue
concentration
Concentration of DNA (weight ng/volume µl)
See also http://terms.tdwg.org/wiki/ggbn:concentration
Examples: 67.5
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/concentration
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type decimal
Requiredfalse
concentrationUnit
Unit used for concentration measurement
See also http://terms.tdwg.org/wiki/ggbn:concentrationUnit
Examples: ng/µl
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/concentrationUnit
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
methodDeterminationConcentrationAndRatios
Description of method used for concentration measurement
See also http://terms.tdwg.org/wiki/ggbn:methodDeterminationConcentrationAndRatios
Examples: Nanodrop, Qubit
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/methodDeterminationConcentrationAndRatios
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
ratioOfAbsorbance260_230
Ratio of absorbance at 260 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only).
See also http://terms.tdwg.org/wiki/ggbn:ratioOfAbsorbance260_230
Examples: 1.89
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_230
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type decimal
Requiredfalse
ratioOfAbsorbance260_280
Ratio of absorbance at 280 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only).
See also http://terms.tdwg.org/wiki/ggbn:ratioOfAbsorbance260_280
Examples: 1.91
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_280
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type decimal
Requiredfalse
volume
Volume of sample
See also http://terms.tdwg.org/wiki/ggbn:volume
Examples: 30, 150
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/volume
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type decimal
Requiredfalse
volumeUnit
Unit used for volume measurement
See also http://terms.tdwg.org/wiki/ggbn:volumeUnit
Examples: µl, ml
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/volumeUnit
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
weight
Weight of sample
See also http://terms.tdwg.org/wiki/ggbn:weight
Examples: 10
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/weight
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type decimal
Requiredfalse
weightUnit
Unit used for weight measurement
See also http://terms.tdwg.org/wiki/ggbn:weightUnit
Examples: ng, g
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/weightUnit
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
methodDeterminationWeight
Description of method used for weight measurement
See also http://terms.tdwg.org/wiki/ggbn:methodDeterminationWeight
Examples: Agarose gel, bioanalyzer, tape station
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/methodDeterminationWeight
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
purificationMethod
DNA purification kit (company/product name) or protocol.
See also http://terms.tdwg.org/wiki/ggbn:purificationMethod
Examples: QIAquick Purification Kit Qiagen
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/purificationMethod
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
qualityCheckDate
Date of quality check (e.g. Nanodrop measurement (DNA))
See also http://terms.tdwg.org/wiki/ggbn:qualityCheckDate
Examples: 2008-11-27
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/qualityCheckDate
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
quality
Sample quality estimation based on parameters described at QualityRemarks
See also http://terms.tdwg.org/wiki/ggbn:quality
Examples: low, medium, high
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/quality
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type GGBN Quality Vocabulary
Requiredfalse
qualityRemarks
Description of methods and parameters defining low, medium or high quality of a sample
See also http://terms.tdwg.org/wiki/ggbn:qualityRemarks
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/qualityRemarks
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
samp_size
Amount or size of sample (volume, mass or area) that was collected
See also http://gensc.org/ns/mixs/#sample_size
Examples:
Qualified Namehttp://gensc.org/ns/mixs/samp_size
Namespacehttp://gensc.org/ns/mixs/
GroupMaterialSample
Data Type string
Requiredfalse
sieving
collection design of pooled samples and/or sieve size and amount of sample sieved
See also http://gensc.org/ns/mixs/#sieving
Examples:
Qualified Namehttp://gensc.org/ns/mixs/sieving
Namespacehttp://gensc.org/ns/mixs/
GroupMaterialSample
Data Type string
Requiredfalse
DNADNAHybridization
Result of DNA-DNA hybridization, e.g. strain: measurement value percentage
See also http://terms.tdwg.org/wiki/ggbn:DNADNAHybridization
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/DNADNAHybridization
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
DNAMeltingPoint
result of melting temperature (Tm) analysis, e.g. measurement value unit
See also http://terms.tdwg.org/wiki/ggbn:DNAMeltingPoint
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/DNAMeltingPoint
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse
estimated_size
The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period
See also http://gensc.org/ns/mixs/#estimated_size
Examples: 300000 bp
Qualified Namehttp://gensc.org/ns/mixs/estimated_size
Namespacehttp://gensc.org/ns/mixs/
GroupMaterialSample
Data Type string
Requiredfalse
pool_dna_extracts
Pooling of DNA extracts (if done). Were multiple DNA extractions mixed? How many?
See also http://gensc.org/ns/mixs/#pool_dna_extracts
Examples:
Qualified Namehttp://gensc.org/ns/mixs/pool_dna_extracts
Namespacehttp://gensc.org/ns/mixs/
GroupMaterialSample
Data Type string
Requiredfalse
sampleDesignation
Additional lab or project numbers used for the DNA or tissue sample
See also http://terms.tdwg.org/wiki/ggbn:DNADNAHybridization
Examples: CAM123;CrCro456
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/sampleDesignation
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupMaterialSample
Data Type string
Requiredfalse