GGBN Amplification Vocabulary

Principal usage: The GGBN Amplification Vocabulary is meant to be used with a 1:many relation for 1 DNA record. This is to cover all amplifications done with a single DNA sample. Within a Darwin Core-Archive implementation it has to be used with the new defined Material Sample Core (not the Occurrence Core). Within ABCD please use the ABCDGGBN implementation. GGBN requirements and recommendations for usage and example content will follow soon.

Scheme: GGBN Data Standard

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Description: These terms have been developed for specific GGBN purposes but can be used in any other molecular context. The amplification vocabulary terms are specific to the aspects of amplification, sequencing, and genetic accession numbers. It also contains terms from MIxS. It does not cover single read information (see GGBN Single Read Vocabulary). The vocabulary is still under review. We appreciate any input or feedback. To do so please contact the GGBN secretariat at ggbn[at]si.edu.

This is a collection within the GGBN Data Standard. It contains the following concepts:

By label: Amplification Date • Amplification Method • Amplification Staff • Amplification Success • Amplification Success Details • BOLD Process ID • Barcode Sequence • Consensus Sequence • Consensus Sequence Chromatogram URI • Consensus Sequence Length • End Repair • Genetic Accession Number • Genetic Accession URI • Guanin-Cytosine content • Haplotype • Marker • Marker Accordance • Marker Subfragment • PCR Cycle Number • PCR Replicate Number • Primer Name • Primer Name (Forward) • Primer Name (Reverse) • Primer Reference Citation • Primer Reference Citation (Forward) • Primer Reference Citation (Reverse) • Primer Reference Link • Primer Reference Link (Forward) • Primer Reference Link (Reverse) • Primer Sequence • Primer Sequence (Forward) • Primer Sequence (Reverse) • Purification Method (DNA or Amplification) • adapters • annotation source • assembly • chimera check • finishing strategy • multiplex identifiers • relevant standard operating procedures • sequence quality check
By concept name: ggbn:amplificationDate • ggbn:amplificationMethod • ggbn:amplificationStaff • ggbn:amplificationSuccess • ggbn:amplificationSuccessDetails • ggbn:barcodeSequence • ggbn:BOLDProcessID • ggbn:consensusSequence • ggbn:consensusSequenceChromatogramFileURI • ggbn:consensusSequenceLength • ggbn:endRepair • ggbn:GC-content • ggbn:geneticAccessionNumber • ggbn:geneticAccessionURI • ggbn:haplotype • ggbn:marker • ggbn:markerAccordance • ggbn:markerSubfragment • ggbn:pcrCycleNumber • ggbn:pcrReplicateNumber • ggbn:primerName • ggbn:primerNameForward • ggbn:primerNameReverse • ggbn:primerReferenceCitation • ggbn:primerReferenceCitationForward • ggbn:primerReferenceCitationReverse • ggbn:primerReferenceLink • ggbn:primerReferenceLinkForward • ggbn:primerReferenceLinkReverse • ggbn:primerSequence • ggbn:primerSequenceForward • ggbn:primerSequenceReverse • ggbn:purificationMethod • mixs:adapters • mixs:annot source • mixs:assembly • mixs:chimera check • mixs:finishing strategy • mixs:mid • mixs:seq quality check • mixs:sop

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GGBN Amplification Vocabulary has a sub-collection:

• GGBN Single Read Vocabulary