GGBN Amplification Extension

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

Support for DNA Amplifications as an extension for Material Sample core sample data in Darwin Core. Intended to be a one to many relation to the Material Sample core.

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


Properties



Amplification

amplificationDate
Date when the amplification was carried out
See also http://terms.tdwg.org/wiki/ggbn:amplificationDate
Examples: 2008-10-17, May 2007
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/amplificationDate
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
amplificationStaff
Person or Institution who performed the amplification
See also http://terms.tdwg.org/wiki/ggbn:amplificationStaff
Examples: Jon Doe, NMNH
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/amplificationStaff
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
amplificationSuccess
true/false or yes/no whether the ampliciation was successful in general; highly recommended to report unsuccessful runs
See also http://terms.tdwg.org/wiki/ggbn:amplificationSuccess
Examples: yes, no, true, false
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/amplificationSuccess
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
amplificationSuccessDetails
Details about the amplification, e.g. including why it has failed
See also http://terms.tdwg.org/wiki/ggbn:amplificationSuccessDetails
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/amplificationSuccessDetails
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
amplificationMethod
Method used for amplification
See also http://terms.tdwg.org/wiki/ggbn:amplificationMethod
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/amplificationMethod
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
primerSequenceForward
Sequence of forward primer used for this amplification
See also http://terms.tdwg.org/wiki/ggbn:primerSequenceForward
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerSequenceForward
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
primerNameForward
Name of forward primer used for this amplification
See also http://terms.tdwg.org/wiki/ggbn:primerNameForward
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerNameForward
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
primerReferenceCitationForward
First reference of the primer
See also http://terms.tdwg.org/wiki/ggbn:primerReferenceCitationForward
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationForward
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
primerReferenceLinkForward
Link to the first reference of the primer
See also http://terms.tdwg.org/wiki/ggbn:primerReferenceLinkForward
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkForward
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type uri
Requiredfalse
primerSequenceReverse
Sequence of reverse primer used for this amplification
See also http://terms.tdwg.org/wiki/ggbn:primerSequenceReverse
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerSequenceReverse
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
primerNameReverse
Name of reverse primer used for this amplification
See also http://terms.tdwg.org/wiki/ggbn:primerNameForward
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerNameReverse
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
primerReferenceCitationReverse
First reference of the primer
See also http://terms.tdwg.org/wiki/ggbn:primerReferenceCitationReverse
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationReverse
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
primerReferenceLinkReverse
Link to the first reference of the primer
See also http://terms.tdwg.org/wiki/ggbn:primerReferenceURIForward
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkReverse
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type uri
Requiredfalse
purificationMethod
Method or protocol used to purify the PCR product
See also http://terms.tdwg.org/wiki/ggbn:purificationMethod
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/purificationMethod
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
consensusSequence
Consensus sequence derived from all individual sequences
See also http://terms.tdwg.org/wiki/ggbn:consensusSequence
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/consensusSequence
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
consensusSequenceLength
Length of the consensus sequence (number of base pairs)
See also http://terms.tdwg.org/wiki/ggbn:consensusSequenceLength
Examples: 697
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/consensusSequenceLength
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type integer
Requiredfalse
consensusSequenceChromatogramFileURI
Link to the chromatogram of the consensus sequence
See also http://terms.tdwg.org/wiki/ggbn:consensusSequenceChromatogramFileURI
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/consensusSequenceChromatogramFileURI
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type uri
Requiredfalse
barcodeSequence
DNA Barcode sequence (part or 100% of the consensus sequence)
See also http://terms.tdwg.org/wiki/ggbn:barcodeSequence
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/barcodeSequence
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
haplotype
Name of the haplotype, if applicable
See also http://terms.tdwg.org/wiki/ggbn:haplotype
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/haplotype
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
marker
Genetic locus/marker or DNA fragment amplified by PCR
See also http://terms.tdwg.org/wiki/ggbn:marker
Examples: COI, rbcL
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/marker
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
markerSubfragment
Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes
See also http://terms.tdwg.org/wiki/ggbn:markerSubfragment
Examples: V6
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/markerSubfragment
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
geneticAccessionNumber
Definite number or ID under which the DNA sequence is deposited in a public database (GenBank/EMBL/DDBJ accession number)
See also http://terms.tdwg.org/wiki/ggbn:geneticAccessionNumber
Examples: AJ675356
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/geneticAccessionNumber
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
BOLDProcessID
Definite number or ID under which the DNA sequence is deposited in the BOLD database
See also http://terms.tdwg.org/wiki/ggbn:BOLDProcessID
Examples: KBPBK324-08
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/BOLDProcessID
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
geneticAccessionURI
URI of the related record in a public database (GenBank/DDBJ/EMBL record).
See also http://terms.tdwg.org/wiki/ggbn:geneticAccessionURI
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/geneticAccessionURI
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type uri
Requiredfalse
GC-content
guanine-cytosine content in mol %
See also http://terms.tdwg.org/wiki/ggbn:GC-content
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/GC-content
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
chimera_check
A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point
See also http://gensc.org/ns/mixs/#chimera_check
Examples:
Qualified Namehttp://gensc.org/ns/mixs/chimera_check
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse
assembly
How was the assembly done (e.g. with a text based assembler like phrap or a flowgram assembler etc). Input: CV
See also http://gensc.org/ns/mixs/#assembly
Examples:
Qualified Namehttp://gensc.org/ns/mixs/assembly
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse
sop
Relevant standard operating procedures
See also http://gensc.org/ns/mixs/#sop
Examples:
Qualified Namehttp://gensc.org/ns/mixs/sop
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse
finishing_strategy
Was the genome project intended to produce a complete or draft genome, Coverage, the fold coverage of the sequencing expressed as 2x, 3x, 18x etc, and how many contigs were produced for the genome
See also http://gensc.org/ns/mixs/#finishing_strategy
Examples:
Qualified Namehttp://gensc.org/ns/mixs/finishing_strategy
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse
annot_source
For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
See also http://gensc.org/ns/mixs/#annot_source
Examples:
Qualified Namehttp://gensc.org/ns/mixs/annot_source
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse
markerAccordance
Result of comparison of two markers of two specimens or strains. Name or TAX-ID (NCBI) of compared specimens/strain and the relative identity percentage must be given
See also http://terms.tdwg.org/wiki/ggbn:markerAccordance
Examples:
Qualified Namehttp://data.ggbn.org/schemas/ggbn/terms/markerAccordance
Namespacehttp://data.ggbn.org/schemas/ggbn/terms/
GroupAmplification
Data Type string
Requiredfalse
seq_quality_check
Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA e.g. none or manually edited
See also http://gensc.org/ns/mixs/#seq_quality_check
Examples:
Qualified Namehttp://gensc.org/ns/mixs/seq_quality_check
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse
adapters
Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
See also http://gensc.org/ns/mixs/#adapters
Examples:
Qualified Namehttp://gensc.org/ns/mixs/adapters
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse
mid
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
See also http://gensc.org/ns/mixs/#mid
Examples:
Qualified Namehttp://gensc.org/ns/mixs/mid
Namespacehttp://gensc.org/ns/mixs/
GroupAmplification
Data Type string
Requiredfalse