Difference between revisions of "GGBN Data Standard"
Gabi Dröge (Talk | contribs) (→Single Read Vocabulary) |
Gabi Dröge (Talk | contribs) (→GGBN Data Standard Terms) |
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{{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | {{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:permitType | ggbn: | + | {{!}} [[#ggbn:permitType | ggbn:Permit Type]] {{!}} |
| − | {{!}} [[#ggbn:permitStatus | ggbn: | + | {{!}} [[#ggbn:permitStatus | ggbn:Permit Status]] {{!}} |
| − | {{!}} [[#ggbn:permitURI | ggbn: | + | {{!}} [[#ggbn:permitURI | ggbn:Permit URI]] {{!}} |
| − | {{!}} [[#ggbn:permitText | ggbn: | + | {{!}} [[#ggbn:permitText | ggbn:Permit Text]] {{!}} |
=== Loan Vocabulary === | === Loan Vocabulary === | ||
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{{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | {{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:blockedUntil | ggbn: | + | {{!}} [[#ggbn:blockedUntil | ggbn:Blocked Until]] {{!}} |
| − | {{!}} [[#ggbn:blocked | ggbn: | + | {{!}} [[#ggbn:blocked | ggbn:Blocked]] {{!}} |
| − | {{!}} [[#ggbn:loanConditions | ggbn: | + | {{!}} [[#ggbn:loanConditions | ggbn:Loan Conditions]] {{!}} |
{{!}} [[#dwc:disposition | dwc:disposition]] {{!}} | {{!}} [[#dwc:disposition | dwc:disposition]] {{!}} | ||
{{!}} [[#abcd:AcquiredFrom | abcd:AcquiredFrom]] {{!}} | {{!}} [[#abcd:AcquiredFrom | abcd:AcquiredFrom]] {{!}} | ||
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{{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | {{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:preservationType | ggbn: | + | {{!}} [[#ggbn:preservationType | ggbn:Preservation Type]] {{!}} |
| − | {{!}} [[#ggbn:preservationTemperature | ggbn: | + | {{!}} [[#ggbn:preservationTemperature | ggbn:Preservation Temperature]] {{!}} |
| − | {{!}} [[#ggbn:preservationDateBegin | ggbn: | + | {{!}} [[#ggbn:preservationDateBegin | ggbn:Preservation Date Begin]] {{!}} |
| − | {{!}} [[# | + | {{!}} [[#ggbn:sequence | ggbn:Sequence (order)]] {{!}} |
=== Preparation Vocabulary === | === Preparation Vocabulary === | ||
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{{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | {{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:preparationType | ggbn: | + | {{!}} [[#ggbn:preparationType | ggbn:Preparation Type]] {{!}} |
| − | {{!}} [[#ggbn:preparationProcess | ggbn: | + | {{!}} [[#ggbn:preparationProcess | ggbn:Preparation Process]] {{!}} |
| − | {{!}} [[#ggbn:preparationMaterials | ggbn: | + | {{!}} [[#ggbn:preparationMaterials | ggbn:Preparation Materials]] {{!}} |
| − | {{!}} [[#ggbn:preparedBy | ggbn: | + | {{!}} [[#ggbn:preparedBy | ggbn:Prepared By]] {{!}} |
| − | {{!}} [[#ggbn:preparationDate | ggbn: | + | {{!}} [[#ggbn:preparationDate | ggbn:Preparation Date]] {{!}} |
{{!}} [[#dwc:associatedReferences | dwc:associatedReferences (DwC)]] {{!}} | {{!}} [[#dwc:associatedReferences | dwc:associatedReferences (DwC)]] {{!}} | ||
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{{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | {{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:purificationMethod | ggbn: | + | {{!}} [[#ggbn:purificationMethod | ggbn:Purification Method]] {{!}} |
| − | {{!}} [[#ggbn:ratioOfAbsorbance260_230 | ggbn: | + | {{!}} [[#ggbn:ratioOfAbsorbance260_230 | ggbn:Ratio Of Absorbance 260/230]] {{!}} |
| − | {{!}} [[#ggbn:ratioOfAbsorbance260_280 | ggbn: | + | {{!}} [[#ggbn:ratioOfAbsorbance260_280 | ggbn:Ratio Of Absorbance 260/280]] {{!}} |
| − | {{!}} [[#ggbn:concentration | ggbn: | + | {{!}} [[#ggbn:concentration | ggbn:Concentration]] {{!}} |
| − | {{!}} [[#ggbn:concentrationUnit | ggbn: | + | {{!}} [[#ggbn:concentrationUnit | ggbn:Concentration Unit]] {{!}} |
| − | {{!}} [[#ggbn:methodDeterminationConcentrationAndRatios | ggbn: | + | {{!}} [[#ggbn:methodDeterminationConcentrationAndRatios | ggbn:Method Determination Concentration And Ratios]] {{!}} |
| − | {{!}} [[#ggbn:weight | ggbn: | + | {{!}} [[#ggbn:weight | ggbn:Weight]] {{!}} |
| − | {{!}} [[#ggbn:weightUnit | ggbn: | + | {{!}} [[#ggbn:weightUnit | ggbn:Weight Unit]] {{!}} |
| − | {{!}} [[#ggbn:methodDeterminationWeight | ggbn: | + | {{!}} [[#ggbn:methodDeterminationWeight | ggbn:Method Determination Weight]] {{!}} |
| − | {{!}} [[#ggbn:volume | ggbn: | + | {{!}} [[#ggbn:volume | ggbn:Volume]] {{!}} |
| − | {{!}} [[#ggbn:volumeUnit | ggbn: | + | {{!}} [[#ggbn:volumeUnit | ggbn:Volume Unit]] {{!}} |
| − | {{!}} [[#ggbn:quality | ggbn: | + | {{!}} [[#ggbn:quality | ggbn:Quality]] {{!}} |
| − | {{!}} [[#ggbn:qualityCheckDate | ggbn: | + | {{!}} [[#ggbn:qualityCheckDate | ggbn:Quality Check Date]] {{!}} |
| − | {{!}} [[#ggbn:qualityRemarks | ggbn: | + | {{!}} [[#ggbn:qualityRemarks | ggbn:Quality Remarks]] {{!}} |
| − | {{!}} [[#ggbn:DNADNAHybridization | ggbn: | + | {{!}} [[#ggbn:DNADNAHybridization | ggbn:DNA-DNA Hybridization]] {{!}} |
| − | {{!}} [[#ggbn:DNAMeltingPoint | ggbn: | + | {{!}} [[#ggbn:DNAMeltingPoint | ggbn:DNA Melting Point]] {{!}} |
| − | {{!}} [[#mixs:estimatedSize | mixs: | + | {{!}} [[#mixs:estimatedSize | mixs:Estimated Size]] {{!}} |
| − | {{!}} [[#mixs:poolingDNAExtracts | mixs: | + | {{!}} [[#mixs:poolingDNAExtracts | mixs:Pooling DNA Extracts]] {{!}} |
| − | {{!}} [[#mixs:sampleSize | mixs: | + | {{!}} [[#mixs:sampleSize | mixs:Sample Size]] {{!}} |
| − | {{!}} [[#mixs:sieving | mixs: | + | {{!}} [[#mixs:sieving | mixs:Sieving]] {{!}} |
=== Gel Image Vocabulary === | === Gel Image Vocabulary === | ||
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{{!}} [[#dcterms:identifier | dcterms:identifier (DwC)]] {{!}} | {{!}} [[#dcterms:identifier | dcterms:identifier (DwC)]] {{!}} | ||
{{!}} [[#dcterms:description | dcterms:description (DwC)]] {{!}} | {{!}} [[#dcterms:description | dcterms:description (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:gelVoltage | ggbn:dcterms: | + | {{!}} [[#ggbn:gelVoltage | ggbn:dcterms:Gel Voltage]] {{!}} |
| − | {{!}} [[#ggbn:gelConcentration | ggbn: | + | {{!}} [[#ggbn:gelConcentration | ggbn:Gel Concentration]] {{!}} |
| − | {{!}} [[#ggbn:gelDuration | ggbn: | + | {{!}} [[#ggbn:gelDuration | ggbn:Gel Duration]] {{!}} |
| − | {{!}} [[#ggbn:gelLadder | ggbn: | + | {{!}} [[#ggbn:gelLadder | ggbn:Gel Ladder]] {{!}} |
| − | {{!}} [[#ggbn:gelStain | ggbn: | + | {{!}} [[#ggbn:gelStain | ggbn:Gel Stain]] {{!}} |
=== Amplification Vocabulary === | === Amplification Vocabulary === | ||
{{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | {{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:amplificationDate | ggbn: | + | {{!}} [[#ggbn:amplificationDate | ggbn:Amplification Date]] {{!}} |
| − | {{!}} [[#ggbn:amplificationStaff | ggbn: | + | {{!}} [[#ggbn:amplificationStaff | ggbn:Amplification Staff]] {{!}} |
| − | {{!}} [[#ggbn:amplificationSuccess | ggbn: | + | {{!}} [[#ggbn:amplificationSuccess | ggbn:Amplification Success]] {{!}} |
| − | {{!}} [[#ggbn:amplificationSuccessDetails | ggbn: | + | {{!}} [[#ggbn:amplificationSuccessDetails | ggbn:Amplification Success Details]] {{!}} |
| − | {{!}} [[#ggbn:purificationMethod | ggbn: | + | {{!}} [[#ggbn:purificationMethod | ggbn:Purification Method]] {{!}} |
| − | {{!}} [[#ggbn:consensusSequence | ggbn: | + | {{!}} [[#ggbn:consensusSequence | ggbn:Consensus Sequence]] {{!}} |
| − | {{!}} [[#ggbn:consensusSequenceLength | ggbn: | + | {{!}} [[#ggbn:consensusSequenceLength | ggbn:Consensus Sequence Length]] {{!}} |
| − | {{!}} [[#ggbn:consensusSequenceChromatogramFileURI | ggbn: | + | {{!}} [[#ggbn:consensusSequenceChromatogramFileURI | ggbn:Consensus Sequence Chromatogram File URI]] {{!}} |
| − | {{!}} [[#ggbn:barcodeSequence | ggbn: | + | {{!}} [[#ggbn:barcodeSequence | ggbn:BarcodeSequence]] {{!}} |
| − | {{!}} [[#ggbn:haplotype | ggbn: | + | {{!}} [[#ggbn:haplotype | ggbn:Haplotype]] {{!}} |
| − | {{!}} [[#ggbn:primerName | ggbn: | + | {{!}} [[#ggbn:primerName | ggbn:Primer Name (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerNameForward | ggbn: | + | {{!}} [[#ggbn:primerNameForward | ggbn:Primer Name Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerNameReverse | ggbn: | + | {{!}} [[#ggbn:primerNameReverse | ggbn:Primer Name Reverse (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceCitation | ggbn: | + | {{!}} [[#ggbn:primerReferenceCitation | ggbn:Primer Reference Citation (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceCitationForward | ggbn: | + | {{!}} [[#ggbn:primerReferenceCitationForward | ggbn:Primer Reference Citation Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceCitationReverse | ggbn: | + | {{!}} [[#ggbn:primerReferenceCitationReverse | ggbn:Primer Reference Citation Reverse (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceLink | ggbn: | + | {{!}} [[#ggbn:primerReferenceLink | ggbn:Primer Reference Link (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceLinkForward | ggbn: | + | {{!}} [[#ggbn:primerReferenceLinkForward | ggbn:Primer Reference Link Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceLinkReverse | ggbn: | + | {{!}} [[#ggbn:primerReferenceLinkReverse | ggbn:Primer Reference Link Reverse (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerSequence | ggbn: | + | {{!}} [[#ggbn:primerSequence | ggbn:Primer Sequence (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerSequenceForward | ggbn: | + | {{!}} [[#ggbn:primerSequenceForward | ggbn:Primer Sequence Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerSequenceReverse | ggbn: | + | {{!}} [[#ggbn:primerSequenceReverse | ggbn:Primer Sequence Reverse (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:geneticAccessionNumber | ggbn: | + | {{!}} [[#ggbn:geneticAccessionNumber | ggbn:Genetic Accession Number]] {{!}} |
| − | {{!}} [[#ggbn:geneticAccessionURI | ggbn: | + | {{!}} [[#ggbn:geneticAccessionURI | ggbn:Genetic Accession URI]] {{!}} |
| − | {{!}} [[#ggbn:BOLDProcessID | ggbn: | + | {{!}} [[#ggbn:BOLDProcessID | ggbn:BOLD Process ID]] {{!}} |
| − | {{!}} [[#ggbn:marker | ggbn: | + | {{!}} [[#ggbn:marker | ggbn:Marker]] {{!}} |
| − | {{!}} [[#ggbn:markerSubfragment | ggbn:Subfragment]] {{!}} | + | {{!}} [[#ggbn:markerSubfragment | ggbn:Marker Subfragment]] {{!}} |
{{!}} [[#ggbn:GC-Content | ggbn:GC-Content]] {{!}} | {{!}} [[#ggbn:GC-Content | ggbn:GC-Content]] {{!}} | ||
| − | {{!}} [[#mixs:chimeraCheck | mixs: | + | {{!}} [[#mixs:chimeraCheck | mixs:Chimera Check]] {{!}} |
| − | {{!}} [[#mixs:assembly | mixs: | + | {{!}} [[#mixs:assembly | mixs:Assembly]] {{!}} |
| − | {{!}} [[#mixs:sop | mixs: | + | {{!}} [[#mixs:sop | mixs:Standard Operating Procedures]] {{!}} |
| − | {{!}} [[#mixs:finishingStrategy | mixs: | + | {{!}} [[#mixs:finishingStrategy | mixs:Finishing Strategy]] {{!}} |
| − | {{!}} [[#mixs:annotationSource | mixs: | + | {{!}} [[#mixs:annotationSource | mixs:Annotation Source]] {{!}} |
| − | {{!}} [[#ggbn:markerAccordance | ggbn: | + | {{!}} [[#ggbn:markerAccordance | ggbn:Marker Accordance]] {{!}} |
| − | {{!}} [[#mixs:seqQualityCheck | mixs: | + | {{!}} [[#mixs:seqQualityCheck | mixs:Sequence Quality Check]] {{!}} |
| − | {{!}} [[#mixs:adapters | mixs: | + | {{!}} [[#mixs:adapters | mixs:Adapters]] {{!}} |
| − | {{!}} [[#mixs:mid | mixs: | + | {{!}} [[#mixs:mid | mixs:Multiplex Identifiers]] {{!}} |
=== DNA Cloning Vocabulary === | === DNA Cloning Vocabulary === | ||
{{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | {{!}} [[#dwc:materialSampleID | dwc:materialSampleID (DwC)]] {{!}} | ||
| − | {{!}} [[#ggbn:cloningDate | ggbn: | + | {{!}} [[#ggbn:cloningDate | ggbn:Cloning Date]] {{!}} |
| − | {{!}} [[#ggbn:cloningStaff | ggbn: | + | {{!}} [[#ggbn:cloningStaff | ggbn:Cloning Staff]] {{!}} |
| − | {{!}} [[#ggbn:cloningMethod | ggbn: | + | {{!}} [[#ggbn:cloningMethod | ggbn:Cloning Method]] {{!}} |
| − | {{!}} [[#ggbn:cloneStrain | ggbn: | + | {{!}} [[#ggbn:cloneStrain | ggbn:Clone Strain]] {{!}} |
| − | {{!}} [[#ggbn:primerName | ggbn: | + | {{!}} [[#ggbn:primerName | ggbn:Primer Name (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerNameForward | ggbn: | + | {{!}} [[#ggbn:primerNameForward | ggbn:Primer Name Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerNameReverse | ggbn: | + | {{!}} [[#ggbn:primerNameReverse | ggbn:Primer Name Reverse (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceCitation | ggbn: | + | {{!}} [[#ggbn:primerReferenceCitation | ggbn:Primer Reference Citation (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceCitationForward | ggbn: | + | {{!}} [[#ggbn:primerReferenceCitationForward | ggbn:Primer Reference Citation Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceCitationReverse | ggbn: | + | {{!}} [[#ggbn:primerReferenceCitationReverse | ggbn:Primer Reference Citation Reverse (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceLink | ggbn: | + | {{!}} [[#ggbn:primerReferenceLink | ggbn:Primer Reference Link (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceLinkForward | ggbn: | + | {{!}} [[#ggbn:primerReferenceLinkForward | ggbn:Primer Reference Link Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceLinkReverse | ggbn: | + | {{!}} [[#ggbn:primerReferenceLinkReverse | ggbn:Primer Reference Link Reverse (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerSequence | ggbn: | + | {{!}} [[#ggbn:primerSequence | ggbn:Primer Sequence (ABCD)]] {{!}} |
| − | {{!}} [[#ggbn:primerSequenceForward | ggbn: | + | {{!}} [[#ggbn:primerSequenceForward | ggbn:Primer Sequence Forward (DwC)]] {{!}} |
| − | {{!}} [[#ggbn:primerSequenceReverse | ggbn: | + | {{!}} [[#ggbn:primerSequenceReverse | ggbn:Primer Sequence Reverse (DwC)]] {{!}} |
| − | {{!}} [[#mixs:libReadsSeqd | mixs: | + | {{!}} [[#mixs:libReadsSeqd | mixs:Library Reads Sequenced]] {{!}} |
| − | {{!}} [[#mixs:libScreen | mixs: | + | {{!}} [[#mixs:libScreen | mixs:Library Screen]] {{!}} |
| − | {{!}} [[#mixs:libSize | mixs: | + | {{!}} [[#mixs:libSize | mixs:Library Size]] {{!}} |
| − | {{!}} [[#mixs:libVector | mixs: | + | {{!}} [[#mixs:libVector | mixs:Library Vector]] {{!}} |
| − | {{!}} [[#mixs:libConstMeth | mixs: | + | {{!}} [[#mixs:libConstMeth | mixs:Library Construction Method]] {{!}} |
| − | {{!}} [[#ggbn:plasmid | ggbn: | + | {{!}} [[#ggbn:plasmid | ggbn:Plasmid]] {{!}} |
=== Single Read Vocabulary === | === Single Read Vocabulary === | ||
Currently implemented in ABCD only and not in DwC-A, due to star schema restrictions (1:n:n relation). | Currently implemented in ABCD only and not in DwC-A, due to star schema restrictions (1:n:n relation). | ||
| − | {{!}} [[#ggbn:sequencingDirection | ggbn: | + | {{!}} [[#ggbn:sequencingDirection | ggbn:Sequencing Direction]] {{!}} |
| − | {{!}} [[#ggbn:sequencingDate | ggbn: | + | {{!}} [[#ggbn:sequencingDate | ggbn:Sequencing Date]] {{!}} |
| − | {{!}} [[#ggbn:sequencingStaff | ggbn: | + | {{!}} [[#ggbn:sequencingStaff | ggbn:Sequencing Staff]] {{!}} |
| − | {{!}} [[#ggbn:sequencingMethod | ggbn: | + | {{!}} [[#ggbn:sequencingMethod | ggbn:Sequencing Method]] {{!}} |
| − | {{!}} [[#ggbn:singleSequence | ggbn: | + | {{!}} [[#ggbn:singleSequence | ggbn:Single Sequence]] {{!}} |
| − | {{!}} [[#ggbn:singleSequenceLength | ggbn: | + | {{!}} [[#ggbn:singleSequenceLength | ggbn:Single Sequence Length]] {{!}} |
| − | {{!}} [[#ggbn:fragmentLength | ggbn: | + | {{!}} [[#ggbn:fragmentLength | ggbn:Fragment Length]] {{!}} |
| − | {{!}} [[#ggbn:chromatogramFileURI | ggbn: | + | {{!}} [[#ggbn:chromatogramFileURI | ggbn:Chromatogram File URI]] {{!}} |
| − | {{!}} [[#ggbn:primerName | ggbn: | + | {{!}} [[#ggbn:primerName | ggbn:Primer Name]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceCitation | ggbn: | + | {{!}} [[#ggbn:primerReferenceCitation | ggbn:Primer Reference Citation]] {{!}} |
| − | {{!}} [[#ggbn:primerReferenceLink | ggbn: | + | {{!}} [[#ggbn:primerReferenceLink | ggbn:Primer Reference Link]] {{!}} |
| − | {{!}} [[#ggbn:primerSequence | ggbn: | + | {{!}} [[#ggbn:primerSequence | ggbn:Primer Sequence]] {{!}} |
== Implementations == | == Implementations == | ||
== References == | == References == | ||
Revision as of 11:36, 23 May 2014
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:Permit Type | | ggbn:Permit Status | | ggbn:Permit URI | | ggbn:Permit Text |
Loan Vocabulary
This vocabulary can be used for tissues, DNA/RNA samples, or specimens, depending on mappig source
| dwc:materialSampleID (DwC) | | ggbn:Blocked Until | | ggbn:Blocked | | ggbn:Loan Conditions | | 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:Preservation Type | | ggbn:Preservation Temperature | | ggbn:Preservation Date Begin | | ggbn:Sequence (order) |
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:Preparation Type | | ggbn:Preparation Process | | ggbn:Preparation Materials | | ggbn:Prepared By | | ggbn:Preparation Date | | dwc:associatedReferences (DwC) |
DNA/RNA Vocabulary
| dwc:materialSampleID (DwC) | | ggbn:Purification Method | | ggbn:Ratio Of Absorbance 260/230 | | ggbn:Ratio Of Absorbance 260/280 | | ggbn:Concentration | | ggbn:Concentration Unit | | ggbn:Method Determination Concentration And Ratios | | ggbn:Weight | | ggbn:Weight Unit | | ggbn:Method Determination Weight | | ggbn:Volume | | ggbn:Volume Unit | | ggbn:Quality | | ggbn:Quality Check Date | | ggbn:Quality Remarks | | ggbn:DNA-DNA Hybridization | | ggbn:DNA Melting Point | | mixs:Estimated Size | | mixs:Pooling DNA Extracts | | mixs:Sample Size | | mixs:Sieving |
Gel Image Vocabulary
| dwc:materialSampleID (DwC) | | dcterms:identifier (DwC) | | dcterms:description (DwC) | | ggbn:dcterms:Gel Voltage | | ggbn:Gel Concentration | | ggbn:Gel Duration | | ggbn:Gel Ladder | | ggbn:Gel Stain |
Amplification Vocabulary
| dwc:materialSampleID (DwC) | | ggbn:Amplification Date | | ggbn:Amplification Staff | | ggbn:Amplification Success | | ggbn:Amplification Success Details | | ggbn:Purification Method | | ggbn:Consensus Sequence | | ggbn:Consensus Sequence Length | | ggbn:Consensus Sequence Chromatogram File URI | | ggbn:BarcodeSequence | | ggbn:Haplotype | | ggbn:Primer Name (ABCD) | | ggbn:Primer Name Forward (DwC) | | ggbn:Primer Name Reverse (DwC) | | ggbn:Primer Reference Citation (ABCD) | | ggbn:Primer Reference Citation Forward (DwC) | | ggbn:Primer Reference Citation Reverse (DwC) | | ggbn:Primer Reference Link (ABCD) | | ggbn:Primer Reference Link Forward (DwC) | | ggbn:Primer Reference Link Reverse (DwC) | | ggbn:Primer Sequence (ABCD) | | ggbn:Primer Sequence Forward (DwC) | | ggbn:Primer Sequence Reverse (DwC) | | ggbn:Genetic Accession Number | | ggbn:Genetic Accession URI | | ggbn:BOLD Process ID | | ggbn:Marker | | ggbn:Marker Subfragment | | ggbn:GC-Content | | mixs:Chimera Check | | mixs:Assembly | | mixs:Standard Operating Procedures | | mixs:Finishing Strategy | | mixs:Annotation Source | | ggbn:Marker Accordance | | mixs:Sequence Quality Check | | mixs:Adapters | | mixs:Multiplex Identifiers |
DNA Cloning Vocabulary
| dwc:materialSampleID (DwC) | | ggbn:Cloning Date | | ggbn:Cloning Staff | | ggbn:Cloning Method | | ggbn:Clone Strain | | ggbn:Primer Name (ABCD) | | ggbn:Primer Name Forward (DwC) | | ggbn:Primer Name Reverse (DwC) | | ggbn:Primer Reference Citation (ABCD) | | ggbn:Primer Reference Citation Forward (DwC) | | ggbn:Primer Reference Citation Reverse (DwC) | | ggbn:Primer Reference Link (ABCD) | | ggbn:Primer Reference Link Forward (DwC) | | ggbn:Primer Reference Link Reverse (DwC) | | ggbn:Primer Sequence (ABCD) | | ggbn:Primer Sequence Forward (DwC) | | ggbn:Primer Sequence Reverse (DwC) | | mixs:Library Reads Sequenced | | mixs:Library Screen | | mixs:Library Size | | mixs:Library Vector | | mixs:Library Construction Method | | 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:Sequencing Direction | | ggbn:Sequencing Date | | ggbn:Sequencing Staff | | ggbn:Sequencing Method | | ggbn:Single Sequence | | ggbn:Single Sequence Length | | ggbn:Fragment Length | | ggbn:Chromatogram File URI | | ggbn:Primer Name | | ggbn:Primer Reference Citation | | ggbn:Primer Reference Link | | ggbn:Primer Sequence |
