GGBN Data Standard
The GGBN Data Standard is a set of vocabularies designed to represent tissue, DNA or RNA samples associated to voucher specimens and collections. Contributors: xxx.
Introduction
GGBN Data Standard Terms
The GGBN Data Standard is intended to be used with ABCD or Darwin Core and is not a stand-alone solution! Loan, Permit, Preparation, and Preservation terms can be used for specimens too and most of them were missing in ABCD/DwC so far. Referencing to underlying specimen or tissue is done by relatedResource (DwC) or UnitAssociation (ABCD) respectively.
Permit Vocabulary
This vocabulary can be used for tissues, DNA/RNA samples, or specimens, depending on mappig source
| dwc:materialSampleID (DwC) | | ggbn:permitType | | ggbn:permitStatus | | ggbn:permitURI | | ggbn:permitText |
Loan Vocabulary
This vocabulary can be used for tissues, DNA/RNA samples, or specimens, depending on mappig source
| dwc:materialSampleID (DwC) | | ggbn:blockedUntil | | ggbn:blocked | | ggbn:loanConditions | | dwc:disposition | | abcd:AcquiredFrom |
Preservation Vocabulary
This vocabulary can be used for tissues, DNA/RNA samples, or specimens, depending on mappig source
| dwc:materialSampleID (DwC) | | ggbn:preservationType | | ggbn:preservationTemperature | | ggbn:preservationDateBegin | | dwc:sequence |
Preparation Vocabulary
This vocabulary can be used for tissues, DNA/RNA samples, or specimens, depending on mappig source. It can be used in addition to existing DwC term (dwc:preparations)
| dwc:materialSampleID (DwC) | | ggbn:preparationType | | ggbn:preparationProcess | | ggbn:preparationMaterials | | ggbn:preparedBy | | ggbn:preparationDate | | dwc:associatedReferences (DwC) |
DNA/RNA Vocabulary
| dwc:materialSampleID (DwC) | | ggbn:purificationMethod | | ggbn:ratioOfAbsorbance260_230 | | ggbn:ratioOfAbsorbance260_280 | | ggbn:concentration | | ggbn:concentrationUnit | | ggbn:methodDeterminationConcentrationAndRatios | | ggbn:weight | | ggbn:weightUnit | | ggbn:methodDeterminationWeight | | ggbn:volume | | ggbn:volumeUnit | | ggbn:quality | | ggbn:qualityCheckDate | | ggbn:qualityRemarks | | ggbn:DNADNAHybridization | | ggbn:DNAMeltingPoint | | mixs:estimatedSize | | mixs:PoolingDNAExtracts | | mixs:sampleSize | | mixs:sieving |
Gel Image Vocabulary
| dwc:materialSampleID (DwC) | | dcterms:identifier (DwC) | | dcterms:description (DwC) | | ggbn:dcterms:gelVoltage | | ggbn:dcterms:gelConcentration | | ggbn:dcterms:gelDuration | | ggbn:dcterms:gelLadder | | ggbn:dcterms:gelStain |
Amplification Vocabulary
| dwc:materialSampleID (DwC) | | ggbn:amplificationDate | | ggbn:amplificationStaff | | ggbn:amplificationSuccess | | ggbn:amplificationSuccessDetails | | ggbn:purificationMethod | | ggbn:consensusSequence | | ggbn:consensusSequenceLength | | ggbn:consensusSequenceChromatogramFileURI | | ggbn:barcodeSequence | | ggbn:haplotype | | ggbn:primerName (ABCD) | | ggbn:primerNameForward (DwC) | | ggbn:primerNameReverse (DwC) | | ggbn:primerReferenceCitation (ABCD) | | ggbn:primerReferenceCitationForward (DwC) | | ggbn:primerReferenceCitationReverse (DwC) | | ggbn:primerReferenceLink (ABCD) | | ggbn:primerReferenceLinkForward (DwC) | | ggbn:primerReferenceLinkReverse (DwC) | | ggbn:primerSequence (ABCD) | | ggbn:primerSequenceForward (DwC) | | ggbn:primerSequenceReverse (DwC) | | ggbn:geneticAccessionNumber | | ggbn:geneticAccessionURI | | ggbn:BOLDProcessID | | ggbn:marker | | ggbn:Subfragment | | ggbn:GC-Content | | mixs:chimeraCheck | | mixs:assembly | | mixs:sop | | mixs:finishingStrategy | | mixs:annotationSource | | ggbn:markerAccordance | | mixs:seqQualityCheck | | mixs:adapters | | mixs:mid (multiplex identifiers) |
DNA Cloning Vocabulary
| dwc:materialSampleID (DwC) | | ggbn:cloningDate | | ggbn:cloningStaff | | ggbn:cloningMethod | | ggbn:cloneStrain | | ggbn:primerName (ABCD) | | ggbn:primerNameForward (DwC) | | ggbn:primerNameReverse (DwC) | | ggbn:primerReferenceCitation (ABCD) | | ggbn:primerReferenceCitationForward (DwC) | | ggbn:primerReferenceCitationReverse (DwC) | | ggbn:primerReferenceLink (ABCD) | | ggbn:primerReferenceLinkForward (DwC) | | ggbn:primerReferenceLinkReverse (DwC) | | ggbn:primerSequence (ABCD) | | ggbn:primerSequenceForward (DwC) | | ggbn:primerSequenceReverse (DwC) | | mixs:libReadsSeqd | | mixs:libScreen | | mixs:libSize | | mixs:libVector | | mixs:libConstMeth | | ggbn:plasmid |
Single Read Vocabulary
Currently implemented in ABCD only and not in DwC-A, due to star schema restrictions (1:n:n relation).
| ggbn:sequencingDirection | | ggbn:sequencingDate | | ggbn:sequencingStaff | | ggbn:sequencingMethod | | ggbn:singleSequence | | ggbn:singleSequenceLength | | ggbn:fragmentLength | | ggbn:chromatogramFileURI | | ggbn:primerName | | ggbn:primerReferenceCitation | | ggbn:primerReferenceLink | | ggbn:primerSequence |
