GGBN Gel Image Extension

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

Support for gel image properties as an extension to an Material Sample core. Intended to be a one to many relation to the Material Sample core.

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


Properties



GelImage

identifier
The public URL that identifies and locates the media file directly, not the html page it might be shown on. Link to a DNA sample image (e.g. agarose gel image); used to determine fragment length profile
See also http://dublincore.org/documents/2012/06/14/dcmi-terms/?v=terms#identifier
Examples:
Qualified Namehttp://purl.org/dc/terms/identifier
Namespacehttp://purl.org/dc/terms/
GroupGelImage
Data Type uri
Requiredtrue
DNAThreshold
Fragment size of the ladder you choose as a standard to measure the percentage of your DNA size, at or above threshold fragment size from ladder
See also http://terms.tdwg.org/wiki/ggbn:DNAThreshold
Examples: The hindIII ladder has fragment sizes (in base-pairs, bp): 564; 2,027; 2,322; 4,361, 6,557; 9,416; 23,130
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/DNAThreshold
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelBuffer
Buffer used to make your gel and buffer in which you run the gel. The gel should be made with the same buffer in which it is run
See also http://terms.tdwg.org/wiki/ggbn:gelBuffer
Examples: Tris-Boric Acid-EDTA
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelBuffer
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelConcentration
Concentration of your gel
See also http://terms.tdwg.org/wiki/ggbn:gelConcentration
Examples: 0.7x, 1x, 1.5x
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelConcentration
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelDuration
Duration of Gel with unit
See also http://terms.tdwg.org/wiki/ggbn:gelDuration
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelDuration
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelLadder
A Gel Ladder is a combination of various known-length fragments of DNA or RNA used to measure DNA or RNA fragments of unknown lengths
See also http://terms.tdwg.org/wiki/ggbn:gelLadder
Examples: HindIII
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelLadder
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelRemarks
General remarks on your gel
See also http://terms.tdwg.org/wiki/ggbn:gelRemarks
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelRemarks
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelStain
Type of gel stain used. Gel stain is a substance that binds to DNA and fluoresces under ultraviolet (UV) light
See also http://terms.tdwg.org/wiki/ggbn:gelStain
Examples: GelRed; SYBR-Safe; Ethidium Bromide (EtBr)
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelStain
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelStainConcentration
Concentration of your gel stain
See also http://terms.tdwg.org/wiki/ggbn:gelStainConcentration
Examples: 5ul of 10,000x into 50 ml of TBE buffer
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelStainConcentration
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
stainingMethod
Method used for staining gels, either precast-adding stain to your gel before casting; post stain-staining your gel after running; stain in loading buffer-adding the stain to the loading buffer
See also http://terms.tdwg.org/wiki/ggbn:stainingMethod
Examples: Precast stain; Post stain; Stain in loading buffer
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/stainingMethod
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
gelVoltage
Voltage of Gel (in V)
See also http://terms.tdwg.org/wiki/ggbn:gelVoltage
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/gelVoltage
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse
percentAboveThreshold
Percent of your DNA at or above the size of the threshold
See also http://terms.tdwg.org/wiki/ggbn:percentAboveThreshold
Examples: 10%, 35%, 50%, 80%. Usually a protocol considers 50% of fragments ≥ 9KB to be high genomic quality
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/percentAboveThreshold
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupGelImage
Data Type string
Requiredfalse