GGBN Data Standard
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Revision as of 18:28, 9 October 2014 by Katharine Barker (Talk | contribs)
Namespace URI: http://data.ggbn.org/schemas/ggbn/terms/ with preferred namespace prefix “ggbn”.
Collections in GGBN Data Standard:
GGBN Amplification Vocabulary • GGBN DNA Cloning Vocabulary • GGBN Gel Image Vocabulary • GGBN Loan Vocabulary • GGBN Material Sample Vocabulary • GGBN Permit Vocabulary • GGBN Preparation Vocabulary • GGBN Preservation Vocabulary • GGBN Single Read Vocabulary
Concepts in GGBN Data Standard (grouped by collection):
GGBN Amplification Vocabulary
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
GGBN DNA Cloning Vocabulary
By label: Clone Strain • Cloning Date • Cloning Method • Cloning Staff • Plasmid • 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) • library construction method • library reads sequenced • library screening strategy • library size • library vector
By concept name: ggbn:cloneStrain • ggbn:cloningDate • ggbn:cloningMethod • ggbn:cloningStaff • ggbn:plasmid • ggbn:primerName • ggbn:primerNameForward • ggbn:primerNameReverse • ggbn:primerReferenceCitation • ggbn:primerReferenceCitationForward • ggbn:primerReferenceCitationReverse • ggbn:primerReferenceLink • ggbn:primerReferenceLinkForward • ggbn:primerReferenceLinkReverse • ggbn:primerSequence • ggbn:primerSequenceForward • ggbn:primerSequenceReverse • mixs:lib const meth • mixs:lib reads seqd • mixs:lib screen • mixs:lib size • mixs:lib vector
GGBN Gel Image Vocabulary
By label: DNA Threshold • Gel Buffer • Gel Concentration • Gel Duration • Gel Ladder • Gel Remarks • Gel Stain • Gel Stain Concentration • Gel Voltage • Identifier • Percent above Threshold • Staining Method
By concept name: dcterms:identifier • ggbn:DNAThreshold • ggbn:gelBuffer • ggbn:gelConcentration • ggbn:gelDuration • ggbn:gelLadder • ggbn:gelRemarks • ggbn:gelStain • ggbn:gelStainConcentration • ggbn:gelVoltage • ggbn:percentAboveThreshold • ggbn:stainingMethod
GGBN Loan Vocabulary
By label: Blocked • Blocked Until • Disposition • Loan Conditions • Loan Date • Loan Destination,Loaned To • Loan Identifier,Loan Number • Received From
By concept name: dwc:disposition • ggbn:blocked • ggbn:blockedUntil • ggbn:loanConditions • ggbn:loanDate • ggbn:loanDestination • ggbn:loanIdentifier • ggbn:receivedFrom
GGBN Material Sample Vocabulary
By label: Concentration (DNA) • DNA Melting Point • DNA-DNA Hybridization • High • Low • Material Sample Type • Medium • Method used for Determination of Concentration and Ratios of Absorbance (DNA) • Method used for Determination of Weight • Purification Method (DNA or Amplification) • Quality • Quality Check Date • Quality Remarks • Quality Vocabulary • Ratio of Absorbance 260/230 (DNA) • Ratio of Absorbance 260/280 (DNA) • Sample Designation • Unit of Concentration (DNA) • Unit of Volume • Unit of Weight • Volume • Weight • estimated Size • sample size
By concept name: ggbn:concentration • ggbn:concentrationUnit • ggbn:DNADNAHybridization • ggbn:DNAMeltingPoint • ggbn:materialSampleType • ggbn:methodDeterminationConcentrationAndRatios • ggbn:methodDeterminationWeight • ggbn:purificationMethod • ggbn:quality • ggbn:qualityCheckDate • ggbn:qualityRemarks • ggbn:ratioOfAbsorbance260 230 • ggbn:ratioOfAbsorbance260 280 • ggbn:sampleDesignation • ggbn:volume • ggbn:volumeUnit • ggbn:weight • ggbn:weightUnit • ggbnvoc:high • ggbnvoc:low • ggbnvoc:medium • ggbnvoc:quality vocabulary • mixs:estimated size • mixs:samp size
GGBN Permit Vocabulary
By label: Collecting Permit • Contract • Copyright • Data use • Expemtion Permit • Export Permit • Genetically Modified Organism • Human Pathogens • Import Permit • Intellectual Property Rights (IPR) • Internationally Recognized Certificate of Compliance (IRCC) • Material Transfer Agreement (MTA) • Memorandum of Cooperation (MoC) • Memorandum of Understanding (MoU) • Other • Patent • Permit Status • Permit Status Qualifier • Permit Text • Permit Type • Permit URI • Permit available • Permit not available • Permit not required • Phytosanitary • Salvage • Unknown • Veterinary Certificate • permitStatus Vocabulary • permitType vocabulary
By concept name: ggbn:permitStatus • ggbn:permitStatusQualifier • ggbn:permitText • ggbn:permitType • ggbn:permitURI • ggbnvoc:Collecting Permit • ggbnvoc:Contract • ggbnvoc:Copyright • ggbnvoc:Data use • ggbnvoc:Exemption Permit • ggbnvoc:Export Permit • ggbnvoc:Genetically Modified Organism • ggbnvoc:Human Pathogens • ggbnvoc:Import Permit • ggbnvoc:Intellectual Property Rights • ggbnvoc:Internationally Recognized Certificate of Compliance • ggbnvoc:Material Transfer Agreement • ggbnvoc:Memorandum of Cooperation • ggbnvoc:Memorandum of Understanding • ggbnvoc:Other • ggbnvoc:Patent • ggbnvoc:Permit available • ggbnvoc:Permit not available • ggbnvoc:Permit not required • ggbnvoc:permitStatus vocabulary • ggbnvoc:permitType vocabulary • ggbnvoc:Phytosanitary • ggbnvoc:Salvage • ggbnvoc:Unknown • ggbnvoc:Veterinary Certificate
GGBN Preparation Vocabulary
By label: Associated References • Preparation Date • Preparation Materials • Preparation Process • Preparation Type • Prepared By
By concept name: dwc:associatedReferences • ggbn:preparationDate • ggbn:preparationMaterials • ggbn:preparationProcess • ggbn:preparationType • ggbn:preparedBy
GGBN Preservation Vocabulary
By concept name: ggbn:preservationDateBegin • ggbn:preservationTemperature • ggbn:preservationType • ggbn:sequence
GGBN Single Read Vocabulary
By label: Chromatogram File URI • Fragment Length • Primer Name • Primer Reference Citation • Primer Reference Link • Primer Sequence • Sequencing Date • Sequencing Direction • Sequencing Method • Sequencing Staff • Single Sequence • Single Sequence Length
By concept name: ggbn:chromatogramFileURI • ggbn:fragmentLength • ggbn:primerName • ggbn:primerReferenceCitation • ggbn:primerReferenceLink • ggbn:primerSequence • ggbn:sequencingDate • ggbn:sequencingDirection • ggbn:sequencingMethod • ggbn:sequencingStaff • ggbn:singleSequence • ggbn:singleSequenceLength
The Global Genome Biodiversity Network (GGBN) is a global network of well-managed collections of genomic tissue samples from across the Tree of Life, benefiting society through biodiversity research, development and conservation. This network will foster collaborations among repositories of molecular biodiversity in order to ensure quality standards, improve best practices, secure interoperability, and harmonize exchange of material in accordance with national and international legislation and conventions.
The GGBN Data Standard is a set of vocabularies designed to represent tissue, DNA or RNA samples associated to voucher specimens, tissue samples and collections. Contributors: Gabriele Droege, Birgit Gemeinholzer, Holger Zetzsche, Astrid Schories, Jörg Holetschek, Enrique Arbeláez Cortés, Katharine Barker, Sean Brady, Boyke Bunk, Margaret Casey, Jonathan Coddington, John Deck, René Dekker, Sonya Dyhrman, Elisabeth Haring, Hans-Peter Klenk, Patricia Kelbert, Thomas Knebelsberger, Renzo Kortmann, Christopher Lewis, Jacqueline Mackenzie-Dodds, Christopher Meyer, Jon Norenburg, Michael Raupach, Thomas von Rintelen, Ole Seberg, Larissa Smirnova, Carola Söhngen, Sun Ying, Lee A. Weigt, Kenneth Wurdack, Pelin Yilmaz, Elizabeth Zimmer, Thomas Orrell, Jamie Whitacre, Xin Zhou..
Introduction
The GGBN Data Standard is based on ABCDDNA, that has been developed within the DNA Bank Network. The current GGBN Data Standard is a result of further reviews of ABCDDNA done with the GGBN community. The GGBN Data Standard is intended to be used with ABCD or Darwin Core and is not a stand-alone solution! Test implementations are now available for both ABCD and DarwinCore-Archive. June 2014: New version of GGBN Data Standard will be tested with BioCASe and IPT and included into the GGBN Harvester and GGBN Index. Please visit this page to find updates on currently running tests with IPT.
GGBN Data Standard Terms
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.
Dynamic Term List
Index to concepts (all collections combined)
By label: Amplification Date • Amplification Method • Amplification Staff • Amplification Success • Amplification Success Details • Associated References • BOLD Process ID • Barcode Sequence • Blocked • Blocked Until • Chromatogram File URI • Clone Strain • Cloning Date • Cloning Method • Cloning Staff • Collecting Permit • Concentration (DNA) • Consensus Sequence • Consensus Sequence Chromatogram URI • Consensus Sequence Length • Contract • Copyright • DNA Melting Point • DNA Threshold • DNA-DNA Hybridization • Data use • Disposition • End Repair • Expemtion Permit • Export Permit • Fragment Length • Gel Buffer • Gel Concentration • Gel Duration • Gel Ladder • Gel Remarks • Gel Stain • Gel Stain Concentration • Gel Voltage • Genetic Accession Number • Genetic Accession URI • Genetically Modified Organism • Guanin-Cytosine content • Haplotype • High • Human Pathogens • Identifier • Import Permit • Intellectual Property Rights (IPR) • Internationally Recognized Certificate of Compliance (IRCC) • Loan Conditions • Loan Date • Loan Destination,Loaned To • Loan Identifier,Loan Number • Low • Marker • Marker Accordance • Marker Subfragment • Material Sample Type • Material Transfer Agreement (MTA) • Medium • Memorandum of Cooperation (MoC) • Memorandum of Understanding (MoU) • Method used for Determination of Concentration and Ratios of Absorbance (DNA) • Method used for Determination of Weight • Other • PCR Cycle Number • PCR Replicate Number • Patent • Percent above Threshold • Permit Status • Permit Status Qualifier • Permit Text • Permit Type • Permit URI • Permit available • Permit not available • Permit not required • Phytosanitary • Plasmid • Preparation Date • Preparation Materials • Preparation Process • Preparation Type • Prepared By • Preservation Date Begin • Preservation Temperature • Preservation Type • 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) • Quality • Quality Check Date • Quality Remarks • Quality Vocabulary • Ratio of Absorbance 260/230 (DNA) • Ratio of Absorbance 260/280 (DNA) • Received From • Salvage • Sample Designation • Sequence (order) • Sequencing Date • Sequencing Direction • Sequencing Method • Sequencing Staff • Single Sequence • Single Sequence Length • Staining Method • Unit of Concentration (DNA) • Unit of Volume • Unit of Weight • Unknown • Veterinary Certificate • Volume • Weight • adapters • annotation source • assembly • chimera check • estimated Size • finishing strategy • library construction method • library reads sequenced • library screening strategy • library size • library vector • multiplex identifiers • permitStatus Vocabulary • permitType vocabulary • relevant standard operating procedures • sample size • sequence quality check
By concept name: dcterms:identifier • dwc:associatedReferences • dwc:disposition • ggbn:BOLDProcessID • ggbn:DNADNAHybridization • ggbn:DNAMeltingPoint • ggbn:DNAThreshold • ggbn:GC-content • ggbn:amplificationDate • ggbn:amplificationMethod • ggbn:amplificationStaff • ggbn:amplificationSuccess • ggbn:amplificationSuccessDetails • ggbn:barcodeSequence • ggbn:blocked • ggbn:blockedUntil • ggbn:chromatogramFileURI • ggbn:cloneStrain • ggbn:cloningDate • ggbn:cloningMethod • ggbn:cloningStaff • ggbn:concentration • ggbn:concentrationUnit • ggbn:consensusSequence • ggbn:consensusSequenceChromatogramFileURI • ggbn:consensusSequenceLength • ggbn:endRepair • ggbn:fragmentLength • ggbn:gelBuffer • ggbn:gelConcentration • ggbn:gelDuration • ggbn:gelLadder • ggbn:gelRemarks • ggbn:gelStain • ggbn:gelStainConcentration • ggbn:gelVoltage • ggbn:geneticAccessionNumber • ggbn:geneticAccessionURI • ggbn:haplotype • ggbn:loanConditions • ggbn:loanDate • ggbn:loanDestination • ggbn:loanIdentifier • ggbn:marker • ggbn:markerAccordance • ggbn:markerSubfragment • ggbn:materialSampleType • ggbn:methodDeterminationConcentrationAndRatios • ggbn:methodDeterminationWeight • ggbn:pcrCycleNumber • ggbn:pcrReplicateNumber • ggbn:percentAboveThreshold • ggbn:permitStatus • ggbn:permitStatusQualifier • ggbn:permitText • ggbn:permitType • ggbn:permitURI • ggbn:plasmid • ggbn:preparationDate • ggbn:preparationMaterials • ggbn:preparationProcess • ggbn:preparationType • ggbn:preparedBy • ggbn:preservationDateBegin • ggbn:preservationTemperature • ggbn:preservationType • 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 • ggbn:quality • ggbn:qualityCheckDate • ggbn:qualityRemarks • ggbn:ratioOfAbsorbance260 230 • ggbn:ratioOfAbsorbance260 280 • ggbn:receivedFrom • ggbn:sampleDesignation • ggbn:sequence • ggbn:sequencingDate • ggbn:sequencingDirection • ggbn:sequencingMethod • ggbn:sequencingStaff • ggbn:singleSequence • ggbn:singleSequenceLength • ggbn:stainingMethod • ggbn:volume • ggbn:volumeUnit • ggbn:weight • ggbn:weightUnit • ggbnvoc:Collecting Permit • ggbnvoc:Contract • ggbnvoc:Copyright • ggbnvoc:Data use • ggbnvoc:Exemption Permit • ggbnvoc:Export Permit • ggbnvoc:Genetically Modified Organism • ggbnvoc:Human Pathogens • ggbnvoc:Import Permit • ggbnvoc:Intellectual Property Rights • ggbnvoc:Internationally Recognized Certificate of Compliance • ggbnvoc:Material Transfer Agreement • ggbnvoc:Memorandum of Cooperation • ggbnvoc:Memorandum of Understanding • ggbnvoc:Other • ggbnvoc:Patent • ggbnvoc:Permit available • ggbnvoc:Permit not available • ggbnvoc:Permit not required • ggbnvoc:Phytosanitary • ggbnvoc:Salvage • ggbnvoc:Unknown • ggbnvoc:Veterinary Certificate • ggbnvoc:high • ggbnvoc:low • ggbnvoc:medium • ggbnvoc:permitStatus vocabulary • ggbnvoc:permitType vocabulary • ggbnvoc:quality vocabulary • mixs:adapters • mixs:annot source • mixs:assembly • mixs:chimera check • mixs:estimated size • mixs:finishing strategy • mixs:lib const meth • mixs:lib reads seqd • mixs:lib screen • mixs:lib size • mixs:lib vector • mixs:mid • mixs:samp size • mixs:seq quality check • mixs:sop
GGBN Amplification Vocabulary
Index to GGBN Amplification Vocabulary
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:BOLDProcessID • ggbn:GC-content • ggbn:amplificationDate • ggbn:amplificationMethod • ggbn:amplificationStaff • ggbn:amplificationSuccess • ggbn:amplificationSuccessDetails • ggbn:barcodeSequence • ggbn:consensusSequence • ggbn:consensusSequenceChromatogramFileURI • ggbn:consensusSequenceLength • ggbn:endRepair • 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
Concept definitions in GGBN Amplification Vocabulary
| Concept Name: | ggbn:amplificationDate |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/amplificationDate |
| Label | Amplification Date |
| Definition | Date when the amplification was carried out |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | 2008-10-17, May 2007 |
| Notes: | freetext since mostly exact date is unknown |
| Concept Name: | ggbn:amplificationMethod |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/amplificationMethod |
| Label | Amplification Method |
| Definition | Method used for amplification/PCR. |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:amplificationStaff |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/amplificationStaff |
| Label | Amplification Staff |
| Definition | Person or Institution who performed the amplification |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | Jon Doe, NMNH |
| Concept Name: | ggbn:amplificationSuccess |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/amplificationSuccess |
| Label | Amplification Success |
| Definition | true/false or yes/no whether the ampliciation was successful in general; highly recommended to report unsuccessful runs |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | yes, no, true, false |
| Notes: | should be used together with ggbn:amplificationSuccessDetails |
| Concept Name: | ggbn:amplificationSuccessDetails |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/amplificationSuccessDetails |
| Label | Amplification Success Details |
| Definition | Details about the amplification, e.g. including why it has failed |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | should be used together with ggbn:amplificationSuccess |
| Concept Name: | ggbn:barcodeSequence |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/barcodeSequence |
| Label | Barcode Sequence |
| Definition | DNA Barcode sequence (part or 100% of the consensus sequence) |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:BOLDProcessID |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/BOLDProcessID |
| Label | BOLD Process ID |
| Definition | Definite number or ID under which the DNA sequence is deposited in the BOLD database |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | often a BOLD record has also a genetic accession number at NCBI/EMBL/DDBJ in addition |
| Concept Name: | ggbn:consensusSequence |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/consensusSequence |
| Label | Consensus Sequence |
| Definition | Consensus sequence derived from all individual sequences |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:consensusSequenceChromatogramFileURI |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/consensusSequenceChromatogramFileURI |
| Label | Consensus Sequence Chromatogram URI |
| Definition | Link to the chromatogram of the consensus sequence |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | should start with http:// |
| Concept Name: | ggbn:consensusSequenceLength |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/consensusSequenceLength |
| Label | Consensus Sequence Length |
| Definition | Length of the consensus sequence (number of base pairs) |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | 697, integer value |
| Concept Name: | ggbn:endRepair |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/endRepair |
| Label | End Repair |
| Definition | State if end repair was conducted |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | under review HTS library terms |
| Concept Name: | ggbn:GC-content |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/GC-content |
| Label | Guanin-Cytosine content |
| Definition | guanine-cytosine content in mol % |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:geneticAccessionNumber |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/geneticAccessionNumber |
| Label | Genetic Accession Number |
| Definition | Definite number or ID under which the DNA sequence is deposited in a public database (GenBank/EMBL/DDBJ accession number) |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:geneticAccessionURI |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/geneticAccessionURI |
| Label | Genetic Accession URI |
| Definition | URI of the related record in a public database (GenBank/DDBJ/EMBL record) |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | should start with http:// |
| Notes: | this is to enable the provider to decide where to point to |
| Concept Name: | ggbn:haplotype |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/haplotype |
| Label | Haplotype |
| Definition | Name of the haplotype |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | H4, A23 |
| Concept Name: | ggbn:marker |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/marker |
| Label | Marker |
| Definition | Genetic locus/marker or DNA fragment amplified by PCR |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | COI, rbcL |
| Concept Name: | ggbn:markerAccordance |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/markerAccordance |
| Label | Marker Accordance |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:markerSubfragment |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/markerSubfragment |
| Label | Marker Subfragment |
| Definition | Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | V6 |
| Concept Name: | ggbn:pcrCycleNumber |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/pcrCycleNumber |
| Label | PCR Cycle Number |
| Definition | Number of cycles used for the PCR |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | under review HTS library terms |
| Concept Name: | ggbn:pcrReplicateNumber |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/pcrReplicateNumber |
| Label | PCR Replicate Number |
| Definition | Number of PCR replicates, that are subsequently pooled and used for sequencing |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | under review HTS library terms |
| Concept Name: | ggbn:primerName |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerName |
| Label | Primer Name |
| Definition | Name of primer used for this amplification, cloning, or single read |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerNameForward or ggbn:primerNameReverse |
| Concept Name: | ggbn:primerNameForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerNameForward |
| Label | Primer Name (Forward) |
| Definition | Name of primer used for this amplification, cloning, or single read |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName |
| Concept Name: | ggbn:primerNameReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerNameReverse |
| Label | Primer Name (Reverse) |
| Definition | Name of reverse primer used for this amplification, cloning, or single read |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName |
| Concept Name: | ggbn:primerReferenceCitation |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitation |
| Label | Primer Reference Citation |
| Definition | Forst reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceCitationForward or ggbn:primerReferenceCitationReverse |
| Concept Name: | ggbn:primerReferenceCitationForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationForward |
| Label | Primer Reference Citation (Forward) |
| Definition | First reference of the forward rimer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation |
| Concept Name: | ggbn:primerReferenceCitationReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationReverse |
| Label | Primer Reference Citation (Reverse) |
| Definition | First reference of the reverse primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation |
| Concept Name: | ggbn:primerReferenceLink |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLink |
| Label | Primer Reference Link |
| Definition | Link to the first reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceLinkForward or ggbn:primerReferenceLinkReverse |
| Concept Name: | ggbn:primerReferenceLinkForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkForward |
| Label | Primer Reference Link (Forward) |
| Definition | Link to the first reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink |
| Concept Name: | ggbn:primerReferenceLinkReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkReverse |
| Label | Primer Reference Link (Reverse) |
| Definition | Link to the first reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink |
| Concept Name: | ggbn:primerSequence |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerSequence |
| Label | Primer Sequence |
| Definition | DNA sequence of the primer (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerSequenceForward or ggbn:primerSequenceReverse |
| Concept Name: | ggbn:primerSequenceForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerSequenceForward |
| Label | Primer Sequence (Forward) |
| Definition | DNA sequence of the forward primer (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence |
| Concept Name: | ggbn:primerSequenceReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerSequenceReverse |
| Label | Primer Sequence (Reverse) |
| Definition | DNA sequence of the reverse primer (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence |
| Concept Name: | ggbn:purificationMethod |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/purificationMethod |
| Label | Purification Method (DNA or Amplification) |
| Definition | Method or protocol used for secundary purification of already extracted genomic DNA or of PCR product |
| Defined By | http://data.ggbn.org/schemas/ggbn/terms/ |
| Required: No — Repeatable: Yes | |
| Examples | QIAamp DNA Mini Kit |
| Notes: | no controlled vocabulary; this element should be used both for DNA and Amplification product; repeatable only within GGBN Amplification Vocabulary |
| Concept Name: | mixs:adapters |
| Normative URI | http://gensc.org/ns/mixs/adapters |
| Label | adapters |
| Definition | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | mixs:annot source |
| Normative URI | http://gensc.org/ns/mixs/annot_source |
| Label | annotation source |
| Definition | For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | mixs:assembly |
| Normative URI | http://gensc.org/ns/mixs/assembly |
| Label | assembly |
| Definition | How was the assembly done (e.g. with a text based assembler like phrap or a flowgram assembler); estimated error rate associated with the finished sequences (e.g. error rate of 1 in 1000 bp); and the method of calculation |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | mixs:chimera check |
| Normative URI | http://gensc.org/ns/mixs/chimera_check |
| Label | chimera check |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | mixs:finishing strategy |
| Normative URI | http://gensc.org/ns/mixs/finishing_strategy |
| Label | finishing strategy |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | mixs:mid |
| Normative URI | http://gensc.org/ns/mixs/mid |
| Label | multiplex identifiers |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | mixs:seq quality check |
| Normative URI | http://gensc.org/ns/mixs/seq_quality_check |
| Label | sequence quality check |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | mixs:sop |
| Normative URI | http://gensc.org/ns/mixs/sop |
| Label | relevant standard operating procedures |
| Definition | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences |
| Defined By | |
| Required: No — Repeatable: Yes |
GGBN DNA Cloning Vocabulary
Index to GGBN DNA Cloning Vocabulary
By label: Clone Strain • Cloning Date • Cloning Method • Cloning Staff • Plasmid • 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) • library construction method • library reads sequenced • library screening strategy • library size • library vector
By concept name: ggbn:cloneStrain • ggbn:cloningDate • ggbn:cloningMethod • ggbn:cloningStaff • ggbn:plasmid • ggbn:primerName • ggbn:primerNameForward • ggbn:primerNameReverse • ggbn:primerReferenceCitation • ggbn:primerReferenceCitationForward • ggbn:primerReferenceCitationReverse • ggbn:primerReferenceLink • ggbn:primerReferenceLinkForward • ggbn:primerReferenceLinkReverse • ggbn:primerSequence • ggbn:primerSequenceForward • ggbn:primerSequenceReverse • mixs:lib const meth • mixs:lib reads seqd • mixs:lib screen • mixs:lib size • mixs:lib vector
Concept definitions in GGBN DNA Cloning Vocabulary
| Concept Name: | ggbn:cloneStrain |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/cloneStrain |
| Label | Clone Strain |
| Definition | Name of the individual DNA clone |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:cloningDate |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/cloningDate |
| Label | Cloning Date |
| Definition | Date when the DNA cloning was carried out |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 2014-05-18, May 2013 |
| Concept Name: | ggbn:cloningMethod |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/cloningMethod |
| Label | Cloning Method |
| Definition | Method or protocol used for DNA cloning |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:cloningStaff |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/cloningStaff |
| Label | Cloning Staff |
| Definition | Person or Institution who performed the cloning |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | Jane Doe, NMNH |
| Concept Name: | ggbn:plasmid |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/plasmid |
| Label | Plasmid |
| Definition | Name of Plasmid used for sequencing |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:primerName |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerName |
| Label | Primer Name |
| Definition | Name of primer used for this amplification, cloning, or single read |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerNameForward or ggbn:primerNameReverse |
| Concept Name: | ggbn:primerNameForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerNameForward |
| Label | Primer Name (Forward) |
| Definition | Name of primer used for this amplification, cloning, or single read |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName |
| Concept Name: | ggbn:primerNameReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerNameReverse |
| Label | Primer Name (Reverse) |
| Definition | Name of reverse primer used for this amplification, cloning, or single read |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName |
| Concept Name: | ggbn:primerReferenceCitation |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitation |
| Label | Primer Reference Citation |
| Definition | Forst reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceCitationForward or ggbn:primerReferenceCitationReverse |
| Concept Name: | ggbn:primerReferenceCitationForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationForward |
| Label | Primer Reference Citation (Forward) |
| Definition | First reference of the forward rimer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation |
| Concept Name: | ggbn:primerReferenceCitationReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationReverse |
| Label | Primer Reference Citation (Reverse) |
| Definition | First reference of the reverse primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation |
| Concept Name: | ggbn:primerReferenceLink |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLink |
| Label | Primer Reference Link |
| Definition | Link to the first reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceLinkForward or ggbn:primerReferenceLinkReverse |
| Concept Name: | ggbn:primerReferenceLinkForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkForward |
| Label | Primer Reference Link (Forward) |
| Definition | Link to the first reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink |
| Concept Name: | ggbn:primerReferenceLinkReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkReverse |
| Label | Primer Reference Link (Reverse) |
| Definition | Link to the first reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink |
| Concept Name: | ggbn:primerSequence |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerSequence |
| Label | Primer Sequence |
| Definition | DNA sequence of the primer (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerSequenceForward or ggbn:primerSequenceReverse |
| Concept Name: | ggbn:primerSequenceForward |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerSequenceForward |
| Label | Primer Sequence (Forward) |
| Definition | DNA sequence of the forward primer (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence |
| Concept Name: | ggbn:primerSequenceReverse |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerSequenceReverse |
| Label | Primer Sequence (Reverse) |
| Definition | DNA sequence of the reverse primer (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence |
| Concept Name: | mixs:lib const meth |
| Normative URI | http://gensc.org/ns/mixs/lib_const_meth |
| Label | library construction method |
| Definition | Library construction method used for clone libraries |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | paired-end,single,vector |
| Concept Name: | mixs:lib reads seqd |
| Normative URI | http://gensc.org/ns/mixs/lib_reads_seqd |
| Label | library reads sequenced |
| Definition | Total number of clones sequenced from the library |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | mixs:lib screen |
| Normative URI | http://gensc.org/ns/mixs/lib_screen |
| Label | library screening strategy |
| Definition | Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | enriched, screened, normalized |
| Concept Name: | mixs:lib size |
| Normative URI | http://gensc.org/ns/mixs/lib_size |
| Label | library size |
| Definition | Total number of clones in the library prepared for the project |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | mixs:lib vector |
| Normative URI | http://gensc.org/ns/mixs/lib_vector |
| Label | library vector |
| Definition | Cloning vector type(s) used in construction of libraries |
| Defined By | |
| Required: No — Repeatable: No |
GGBN Gel Image Vocabulary
Index to GGBN Gel Image Vocabulary
By label: DNA Threshold • Gel Buffer • Gel Concentration • Gel Duration • Gel Ladder • Gel Remarks • Gel Stain • Gel Stain Concentration • Gel Voltage • Identifier • Percent above Threshold • Staining Method
By concept name: dcterms:identifier • ggbn:DNAThreshold • ggbn:gelBuffer • ggbn:gelConcentration • ggbn:gelDuration • ggbn:gelLadder • ggbn:gelRemarks • ggbn:gelStain • ggbn:gelStainConcentration • ggbn:gelVoltage • ggbn:percentAboveThreshold • ggbn:stainingMethod
Concept definitions in GGBN Gel Image Vocabulary
| Concept Name: | dcterms:identifier |
| Normative URI | http://purl.org/dc/terms/identifier |
| Label | Identifier |
| Definition | An unambiguous reference to the resource within a given context. |
| Defined By | http://dublincore.org/documents/dcmi-terms/#terms-identifier |
| Required: No — Repeatable: No | |
| Notes: | Dublin Core: Recommended best practice is to identify the resource by means of a string conforming to a formal identification system. Audubon Core: An arbitrary code that is unique for the resource, with the resource being either a provider, collection, or media item. Using multiple identifiers implies that they have a same-as relationship, i.e. they all identify the same object (e. g. an object may have an http-URL, an lsid-URI, and a UUID-number).
Required for media collections, No for media resources (but preferred if available). In context of GGBN used as gel image uri. |
| Concept Name: | ggbn:DNAThreshold |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/DNAThreshold |
| Label | DNA Threshold |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 564; 2,027; 2,322; 4,361, 6,557; 9,416; 23,130. The hindIII ladder has fragment sizes (in base-pairs, bp): 564; 2,027; 2,322; 4,361, 6,557; 9,416; 23,130 |
| Concept Name: | ggbn:gelBuffer |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelBuffer |
| Label | Gel Buffer |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | Tris-Boric Acid-EDTA |
| Concept Name: | ggbn:gelConcentration |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelConcentration |
| Label | Gel Concentration |
| Definition | Concentration of your gel |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 0.7x, 1x, 1.5x |
| Concept Name: | ggbn:gelDuration |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelDuration |
| Label | Gel Duration |
| Definition | Duration of Gel with unit |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:gelLadder |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelLadder |
| Label | Gel Ladder |
| Definition | 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. |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | HindIII |
| Concept Name: | ggbn:gelRemarks |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelRemarks |
| Label | Gel Remarks |
| Definition | General remarks on your gel. |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:gelStain |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelStain |
| Label | Gel Stain |
| Definition | Type of gel stain used. Gel stain is a substance that binds to DNA and fluoresces under ultraviolet (UV) light. |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | GelRed; SYBR-Safe; Ethidium Bromide (EtBr) |
| Concept Name: | ggbn:gelStainConcentration |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelStainConcentration |
| Label | Gel Stain Concentration |
| Definition | Concentration of your gel stain |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 5ul of 10,000x into 50 ml of TBE buffer |
| Concept Name: | ggbn:gelVoltage |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/gelVoltage |
| Label | Gel Voltage |
| Definition | Voltage of Gel (in V) |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:percentAboveThreshold |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/percentAboveThreshold |
| Label | Percent above Threshold |
| Definition | Percent of your DNA at or above the size of the threshold |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 10%, 35%, 50%, 80%. Usually a protocol considers 50% of fragments ≥ 9KB to be high genomic quality |
| Concept Name: | ggbn:stainingMethod |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/stainingMethod |
| Label | Staining Method |
| Definition | 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 |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | Precast stain; Post stain; Stain in loading buffer |
GGBN Loan Vocabulary
Index to GGBN Loan Vocabulary
By label: Blocked • Blocked Until • Disposition • Loan Conditions • Loan Date • Loan Destination,Loaned To • Loan Identifier,Loan Number • Received From
By concept name: dwc:disposition • ggbn:blocked • ggbn:blockedUntil • ggbn:loanConditions • ggbn:loanDate • ggbn:loanDestination • ggbn:loanIdentifier • ggbn:receivedFrom
Concept definitions in GGBN Loan Vocabulary
| Concept Name: | dwc:disposition |
| Normative URI | http://rs.tdwg.org/dwc/terms/disposition |
| Label | Disposition |
| Definition | The current state of a specimen with respect to the collection identified in collectionCode or collectionID. Recommended best practice is to use a controlled vocabulary. |
| Defined By | http://rs.tdwg.org/dwc/terms/ |
| Required: No — Repeatable: Yes | |
| Examples | "in collection", "missing", "voucher elsewhere", "duplicates elsewhere" |
| Notes: | For discussion see http://code.google.com/p/darwincore/wiki/Occurrence Remark by GGBN: "consumed" as another example |
| Concept Name: | ggbn:blocked |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/blocked |
| Label | Blocked |
| Definition | Sample or specimen data can not be ordered/loaned in general, but are visible via portals. |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | yes, no |
| Notes: | Records/samples/specimens not to be published should be blocked on database level. If they are available via Darwin Core or ABCD, they are visible for everyone. This element is to be used for samples/specimens that cannot be loaned. |
| Concept Name: | ggbn:blockedUntil |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/blockedUntil |
| Label | Blocked Until |
| Definition | Sample or specimen data can not be ordered/loaned until the given date, but are visible via portals |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | 2016-03-31, format YYYY-MM-DD |
| Notes: | in GGBN context the record is visible at the portal but blocked for ordering until the given date |
| Concept Name: | ggbn:loanConditions |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/loanConditions |
| Label | Loan Conditions |
| Definition | Sample can be ordered under certain conditions, that are described here |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | for non-commercial institutions only; only with permission of material supplier |
| Concept Name: | ggbn:loanDate |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/loanDate |
| Label | Loan Date |
| Definition | Date when loan has been sent by the lender. |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | based on HISPID extension for ABCD |
| Concept Name: | ggbn:loanDestination |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/loanDestination |
| Label | Loan Destination,Loaned To |
| Definition | Name of person and/or organization the unit was sent to. Person/Institution who received the material. |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | Jane Doe, NMNH |
| Notes: | based on HISPID extension for ABCD; in this instance, “sent” is not equivalent to “shipped”. A shipment can be directed to a recipient who is not the actual intended responsible party; many organizations have shipping offices to handle packages. |
| Concept Name: | ggbn:loanIdentifier |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/loanIdentifier |
| Label | Loan Identifier,Loan Number |
| Definition | The unique institutional loan number to uniquely identify a specimen on loan |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | 2014/123 |
| Notes: | based on HISPID extension for ABCD |
| Concept Name: | ggbn:receivedFrom |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/receivedFrom |
| Label | Received From |
| Definition | Name of person and/or organization the unit was received from. Person/Institution who authorized the loan of the material. From the perspective of the owner of the material, this type of loan is incoming. |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | e.g. lender or recipient of a strain, sample, specimen etc. |
GGBN Material Sample Vocabulary
Index to GGBN Material Sample Vocabulary
By label: Concentration (DNA) • DNA Melting Point • DNA-DNA Hybridization • High • Low • Material Sample Type • Medium • Method used for Determination of Concentration and Ratios of Absorbance (DNA) • Method used for Determination of Weight • Purification Method (DNA or Amplification) • Quality • Quality Check Date • Quality Remarks • Quality Vocabulary • Ratio of Absorbance 260/230 (DNA) • Ratio of Absorbance 260/280 (DNA) • Sample Designation • Unit of Concentration (DNA) • Unit of Volume • Unit of Weight • Volume • Weight • estimated Size • sample size
By concept name: ggbn:DNADNAHybridization • ggbn:DNAMeltingPoint • ggbn:concentration • ggbn:concentrationUnit • ggbn:materialSampleType • ggbn:methodDeterminationConcentrationAndRatios • ggbn:methodDeterminationWeight • ggbn:purificationMethod • ggbn:quality • ggbn:qualityCheckDate • ggbn:qualityRemarks • ggbn:ratioOfAbsorbance260 230 • ggbn:ratioOfAbsorbance260 280 • ggbn:sampleDesignation • ggbn:volume • ggbn:volumeUnit • ggbn:weight • ggbn:weightUnit • ggbnvoc:high • ggbnvoc:low • ggbnvoc:medium • ggbnvoc:quality vocabulary • mixs:estimated size • mixs:samp size
Concept definitions in GGBN Material Sample Vocabulary
| Concept Name: | ggbn:concentration |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/concentration |
| Label | Concentration (DNA) |
| Definition | Concentration of DNA (weight ng/volume µl) |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 67.5 |
| Notes: | in ABCD this element has stringUnit as attribute (example ng/µl) in DarwinCore this element has to be used together with ggbn:concentrationUnit |
| Concept Name: | ggbn:concentrationUnit |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/concentrationUnit |
| Label | Unit of Concentration (DNA) |
| Definition | Unit used for concentration measurement (DNA) |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | ng/µl |
| Notes: | in DarwinCore this element has to be used together with ggbn:concentration this element is not required in ABCD (see ggbn:concentration for details) |
| Concept Name: | ggbn:DNADNAHybridization |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/DNADNAHybridization |
| Label | DNA-DNA Hybridization |
| Definition | Result of DNA-DNA hybridization, e.g. strain: measurement value percentage |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:DNAMeltingPoint |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/DNAMeltingPoint |
| Label | DNA Melting Point |
| Definition | result of melting temperature (Tm) analysis, e.g. measurement value unit |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbn:materialSampleType |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/materialSampleType |
| Label | Material Sample Type |
| Definition | Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type. |
| Defined By | |
| Required: Yes — Repeatable: No | |
| Examples | tissue, culture strain, specimen, DNA, RNA, Protein, environmental sample, genome library, transcriptome library |
| Notes: | Please use preparationType for further specification such as 'leg','blood','gDNA','axenic culture','whole genome library','environmental barcoding library', 'Reduced representation sequencing library'. Equal to KindOfUnit in ABCD! |
| Concept Name: | ggbn:methodDeterminationConcentrationAndRatios |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/methodDeterminationConcentrationAndRatios |
| Label | Method used for Determination of Concentration and Ratios of Absorbance (DNA) |
| Definition | Description of method used for concentration measurement (DNA) |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | Nanodrop, Qubit |
| Concept Name: | ggbn:methodDeterminationWeight |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/methodDeterminationWeight |
| Label | Method used for Determination of Weight |
| Definition | Description of method used for weight measurement |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | Agarose gel, bioanalyzer, tape station |
| Notes: | This element can be used for both DNA and tissue samples (or specimens) |
| Concept Name: | ggbn:purificationMethod |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/purificationMethod |
| Label | Purification Method (DNA or Amplification) |
| Definition | Method or protocol used for secundary purification of already extracted genomic DNA or of PCR product |
| Defined By | http://data.ggbn.org/schemas/ggbn/terms/ |
| Required: No — Repeatable: Yes | |
| Examples | QIAamp DNA Mini Kit |
| Notes: | no controlled vocabulary; this element should be used both for DNA and Amplification product; repeatable only within GGBN Amplification Vocabulary |
| Concept Name: | ggbn:quality |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/quality |
| Label | Quality |
| Definition | Sample quality estimation based on parameters described at QualityRemarks |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | high, medium, low |
| Notes: | Predefined vocabulary! See: quality vocabulary |
| Concept Name: | ggbn:qualityCheckDate |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/qualityCheckDate |
| Label | Quality Check Date |
| Definition | Date of quality check (e.g. Nanodrop measurement (DNA)) |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | ISO format: 2013-01-27 |
| Notes: | this element can be used for DNA, tissues or specimens |
| Concept Name: | ggbn:qualityRemarks |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/qualityRemarks |
| Label | Quality Remarks |
| Definition | Description of methods and parameters defining low, medium or high quality of a sample |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | to be used together with ggbn:quality |
| Concept Name: | ggbn:ratioOfAbsorbance260 230 |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_230 |
| Label | Ratio of Absorbance 260/230 (DNA) |
| Definition | Ratio of absorbance at 260 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only) |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 1.89 |
| Concept Name: | ggbn:ratioOfAbsorbance260 280 |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_280 |
| Label | Ratio of Absorbance 260/280 (DNA) |
| Definition | Ratio of absorbance at 280 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only) |
| Defined By | http://data.ggbn.org/schemas/ggbn/terms |
| Required: No — Repeatable: No | |
| Examples | 1.8 |
| Notes: | no controlled vocabulary |
| Concept Name: | ggbn:sampleDesignation |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/sampleDesignation |
| Label | Sample Designation |
| Definition | Additional lab or project numbers used for the DNA or tissue sample. |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | CAM123;CrCro456 |
| Notes: | In case of multiple numbers please separate them with ";" |
| Concept Name: | ggbn:volume |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/volume |
| Label | Volume |
| Definition | Volume of sample |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 30, 150 |
| Notes: | this element can be used for DNA or tissue samples
in ABCD this element has stringUnit as attribute (example µl, ml) in DarwinCore this element has to be used together with ggbn:volumeUnit |
| Concept Name: | ggbn:volumeUnit |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/volumeUnit |
| Label | Unit of Volume |
| Definition | Unit used for volume measurement |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | µl, ml |
| Notes: | in DarwinCore this element has to be used together with ggbn:volume this element is not required in ABCD (see ggbn:volume for details) |
| Concept Name: | ggbn:weight |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/weight |
| Label | Weight |
| Definition | Weight of sample |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 10 |
| Notes: | this element can be used for DNA or tissue samples
in ABCD this element has stringUnit as attribute (example ng, mg, g) in DarwinCore this element has to be used together with ggbn:weightUnit |
| Concept Name: | ggbn:weightUnit |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/weightUnit |
| Label | Unit of Weight |
| Definition | Unit used for weight measurement |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | ng, mg, g |
| Notes: | in DarwinCore this element has to be used together with ggbn:weight this element is not required in ABCD (see ggbn:weight for details) |
| Concept Name: | ggbnvoc:high |
| Normative URI | |
| Label | High |
| Definition | A value for the ggbnvoc:quality_vocabulary |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbnvoc:low |
| Normative URI | |
| Label | Low |
| Definition | A value for the ggbnvoc:quality_vocabulary |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbnvoc:medium |
| Normative URI | |
| Label | Medium |
| Definition | A value for the ggbnvoc:quality_vocabulary |
| Defined By | |
| Required: No — Repeatable: No | |
| Concept Name: | ggbnvoc:quality vocabulary |
| Normative URI | |
| Label | Quality Vocabulary |
| Definition | Vocabulary of ggbn:quality term |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | ggbnvoc:high, ggbnvoc:medium, ggbnvoc:low |
| Notes: | Methods and parameters defining low, medium or high quality of a sample are described with ggbn:qualityRemarks |
| Concept Name: | mixs:estimated size |
| Normative URI | http://gensc.org/ns/mixs/estimated_size |
| Label | estimated Size |
| Definition | The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | 300000 bp |
| Concept Name: | mixs:samp size |
| Normative URI | http://gensc.org/ns/mixs/samp_size |
| Label | sample size |
| Definition | Amount or size of sample (volume, mass or area) that was collected |
| Defined By | |
| Required: No — Repeatable: No |
GGBN Permit Vocabulary
Index to GGBN Permit Vocabulary
By label: Collecting Permit • Contract • Copyright • Data use • Expemtion Permit • Export Permit • Genetically Modified Organism • Human Pathogens • Import Permit • Intellectual Property Rights (IPR) • Internationally Recognized Certificate of Compliance (IRCC) • Material Transfer Agreement (MTA) • Memorandum of Cooperation (MoC) • Memorandum of Understanding (MoU) • Other • Patent • Permit Status • Permit Status Qualifier • Permit Text • Permit Type • Permit URI • Permit available • Permit not available • Permit not required • Phytosanitary • Salvage • Unknown • Veterinary Certificate • permitStatus Vocabulary • permitType vocabulary
By concept name: ggbn:permitStatus • ggbn:permitStatusQualifier • ggbn:permitText • ggbn:permitType • ggbn:permitURI • ggbnvoc:Collecting Permit • ggbnvoc:Contract • ggbnvoc:Copyright • ggbnvoc:Data use • ggbnvoc:Exemption Permit • ggbnvoc:Export Permit • ggbnvoc:Genetically Modified Organism • ggbnvoc:Human Pathogens • ggbnvoc:Import Permit • ggbnvoc:Intellectual Property Rights • ggbnvoc:Internationally Recognized Certificate of Compliance • ggbnvoc:Material Transfer Agreement • ggbnvoc:Memorandum of Cooperation • ggbnvoc:Memorandum of Understanding • ggbnvoc:Other • ggbnvoc:Patent • ggbnvoc:Permit available • ggbnvoc:Permit not available • ggbnvoc:Permit not required • ggbnvoc:Phytosanitary • ggbnvoc:Salvage • ggbnvoc:Unknown • ggbnvoc:Veterinary Certificate • ggbnvoc:permitStatus vocabulary • ggbnvoc:permitType vocabulary
Concept definitions in GGBN Permit Vocabulary
| Concept Name: | ggbn:permitStatus |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitStatus |
| Label | Permit Status |
| Definition | Information about the presence, absence or other basic status of permits associated with the sample(s). |
| Defined By | |
| Required: Yes — Repeatable: Yes | |
| Examples | Permit available, Permit not required, Permit not available, Unknown Material collected after 2014-10-12 cannot be in "Unknown" permit status! |
| Notes: | Predefined vocabulary, See permitStatus vocabulary; entry of data is mandatory |
| Concept Name: | ggbn:permitStatusQualifier |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitStatusQualifier |
| Label | Permit Status Qualifier |
| Definition | Description of why a certain permit was not required or why Permit Status is unknown |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | "no national requirement for a permit at date of access", "officially authorized illegal holder", "collected on private land", "pre-Nagoya" |
| Concept Name: | ggbn:permitText |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitText |
| Label | Permit Text |
| Definition | The text of a permit related to the gathering/shipping or further details |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:permitType |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitType |
| Label | Permit Type |
| Definition | A permit is a document that allows someone to take an action that otherwise would not be allowed. |
| Defined By | |
| Required: Yes — Repeatable: Yes | |
| Examples | Collecting Permit, Import Permit, Export Permit, Intellectual Property Rights, Copyright, Patent, Data use, Phytosanitary, Salvage, Exemption Permit, Material Transfer Agreement, Internationally Recognized Certificate of Compliance, Contract, Memorandum of Understanding, Memorandum of Cooperation, Veterinary Certificate, Human Pathogens, Genetically Modified Organism, Other |
| Notes: | Predefined vocabulary! See permitType vocabulary |
| Concept Name: | ggbn:permitURI |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Permit URI |
| Definition | A reference to the permit related to the gathering or shipping event |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | One will eventually need a direct link to IRCC in the future. |
| Concept Name: | ggbnvoc:Collecting Permit |
| Normative URI | |
| Label | Collecting Permit |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Contract |
| Normative URI | |
| Label | Contract |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Copyright |
| Normative URI | |
| Label | Copyright |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Data use |
| Normative URI | |
| Label | Data use |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Exemption Permit |
| Normative URI | |
| Label | Expemtion Permit |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Export Permit |
| Normative URI | |
| Label | Export Permit |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Genetically Modified Organism |
| Normative URI | |
| Label | Genetically Modified Organism |
| Definition | A value for the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | Currently a placeholder only, might be renamed in the future |
| Concept Name: | ggbnvoc:Human Pathogens |
| Normative URI | |
| Label | Human Pathogens |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Import Permit |
| Normative URI | |
| Label | Import Permit |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Intellectual Property Rights |
| Normative URI | |
| Label | Intellectual Property Rights (IPR) |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Internationally Recognized Certificate of Compliance |
| Normative URI | |
| Label | Internationally Recognized Certificate of Compliance (IRCC) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Material Transfer Agreement |
| Normative URI | |
| Label | Material Transfer Agreement (MTA) |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Memorandum of Cooperation |
| Normative URI | |
| Label | Memorandum of Cooperation (MoC) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Memorandum of Understanding |
| Normative URI | |
| Label | Memorandum of Understanding (MoU) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Other |
| Normative URI | |
| Label | Other |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Patent |
| Normative URI | |
| Label | Patent |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Permit available |
| Normative URI | |
| Label | Permit available |
| Definition | A value of ggbnvoc:permitStatus_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Permit not available |
| Normative URI | |
| Label | Permit not available |
| Definition | A value for the ggbnvoc:permitStatus_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Permit not required |
| Normative URI | |
| Label | Permit not required |
| Definition | A value for the ggbnvoc:permitStatus_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:permitStatus vocabulary |
| Normative URI | |
| Label | permitStatus Vocabulary |
| Definition | Vocabulary of ggbn:permitStatus term |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | Permit available, Permit not required, Permit not available, Unknown |
| Concept Name: | ggbnvoc:permitType vocabulary |
| Normative URI | |
| Label | permitType vocabulary |
| Definition | Vocabulary of ggbn:permitType term |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | Collecting Permit, Import Permit, Export Permit, Intellectual Property Rights, Copyright, Patent, Data use, Phytosanitary, Salvage, Exemption Permit, Material Transfer Agreement, Internationally Recognized Certificate of Compliance, contract, Memorandum of Understanding, Memorandum of Cooperation, Veterinary Certificate, Human Pathogens, Genetically Modified Organism, Other |
| Concept Name: | ggbnvoc:Phytosanitary |
| Normative URI | |
| Label | Phytosanitary |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Salvage |
| Normative URI | |
| Label | Salvage |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Unknown |
| Normative URI | |
| Label | Unknown |
| Definition | A value for the ggbnvoc:permitStatus_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Veterinary Certificate |
| Normative URI | |
| Label | Veterinary Certificate |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Defined By | |
| Required: No — Repeatable: Yes |
GGBN Preparation Vocabulary
Index to GGBN Preparation Vocabulary
By label: Associated References • Preparation Date • Preparation Materials • Preparation Process • Preparation Type • Prepared By
By concept name: dwc:associatedReferences • ggbn:preparationDate • ggbn:preparationMaterials • ggbn:preparationProcess • ggbn:preparationType • ggbn:preparedBy
Concept definitions in GGBN Preparation Vocabulary
| Concept Name: | dwc:associatedReferences |
| Normative URI | http://rs.tdwg.org/dwc/terms/associatedReferences |
| Label | Associated References |
| Definition | A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence. |
| Defined By | http://rs.tdwg.org/dwc/terms/ |
| Required: No — Repeatable: Yes | |
| Examples | The recommended best practice is to separate the values with a vertical bar (' | '). Examples: "http://www.sciencemag.org/cgi/content/abstract/322/5899/261", "Christopher J. Conroy, Jennifer L. Neuwald. 2008. Phylogeographic study of the California vole, Microtus californicus Journal of Mammalogy, 89(3):755-767.", "Steven R. Hoofer and Ronald A. Van Den Bussche. 2001. Phylogenetic Relationships of Plecotine Bats and Allies Based on Mitochondrial Ribosomal Sequences. Journal of Mammalogy 82(1):131-137. | Walker, Faith M., Jeffrey T. Foster, Kevin P. Drees, Carol L. Chambers. 2014. Spotted bat (Euderma maculatum) microsatellite discovery using illumina sequencing. Conservation Genetics Resources.". |
| Notes: | Remark by GGBN: Material Transfer Agreements (MTAs) |
| Concept Name: | ggbn:preparationDate |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preparationDate |
| Label | Preparation Date |
| Definition | The date of preparation/extraction |
| Defined By | |
| Required: Yes — Repeatable: Yes | |
| Examples | 2011-01-18, unknown, not recorded |
| Notes: | when used for tissues, quite often preparationDate is the same as dwc:eventDate |
| Concept Name: | ggbn:preparationMaterials |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preparationMaterials |
| Label | Preparation Materials |
| Definition | Materials and chemicals used in the preparation of the specimen, tissue, DNA or RNA sample |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | for DNA: DNeasy blood and tissue kit, CTAB; |
| Concept Name: | ggbn:preparationProcess |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preparationProcess |
| Label | Preparation Process |
| Definition | Process used in preparing the specimen or sample, can also be used to describe Phage/Plasmid propagation, Process used in extracting the DNA/RNA; adaptions made; SPREC code |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbn:preparationType |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preparationType |
| Label | Preparation Type |
| Definition | Description of preparation type (specimens, tissues, DNA, HTS Libraries) |
| Defined By | |
| Required: Yes — Repeatable: Yes | |
| Examples | for DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood; for HTs libraries: Whole genome shotgun sequencing, Amplicon sequencing, RAD sequencing |
| Notes: | has close match to: BRISQ:Biospecimen type and BRISQ:Anatomical site BRISQ=Biospecimen Reporting for Improved Study Quality (http://www.ncbi.nlm.nih.gov/pubmed/21433001) |
| Concept Name: | ggbn:preparedBy |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preparedBy |
| Label | Prepared By |
| Definition | Person and/or institution responsible for or effecting the preparation/extraction |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | Jane Doe, NMNH |
GGBN Preservation Vocabulary
Index to GGBN Preservation Vocabulary
By concept name: ggbn:preservationDateBegin • ggbn:preservationTemperature • ggbn:preservationType • ggbn:sequence
Concept definitions in GGBN Preservation Vocabulary
| Concept Name: | ggbn:preservationDateBegin |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preservationDateBegin |
| Label | Preservation Date Begin |
| Definition | Start of current Specimen, Tissue, DNA or RNA Preservation |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | March 2012, 2014-02-19 |
| Concept Name: | ggbn:preservationTemperature |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preservationTemperature |
| Label | Preservation Temperature |
| Definition | Temperature of Specimen, Tissue, DNA or RNA Preservation or Storage |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | -20°C, RT, -80°C, -196°C, LN |
| Notes: | has exact match to: BRISQ:Storage temperature BRISQ=Biospecimen Reporting for Improved Study Quality (http://www.ncbi.nlm.nih.gov/pubmed/21433001) |
| Concept Name: | ggbn:preservationType |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/preservationType |
| Label | Preservation Type |
| Definition | Type of Specimen, Tissue, DNA or RNA Preservation or Storage |
| Defined By | |
| Required: Yes — Repeatable: Yes | |
| Examples | dried, silica, alcohol, FTA card, tube, QIAsafe |
| Notes: | has close match to: BRISQ:Type of long-term preservation and BRISQ:Constitution of preservative BRISQ=Biospecimen Reporting for Improved Study Quality (http://www.ncbi.nlm.nih.gov/pubmed/21433001) |
| Concept Name: | ggbn:sequence |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/sequence |
| Label | Sequence (order) |
| Definition | can be used to describe sequence (order) of different preservations or other issues |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Examples | 1, 2, 3, 4 (1=oldest, 4=latest) |
GGBN Single Read Vocabulary
Index to GGBN Single Read Vocabulary
By label: Chromatogram File URI • Fragment Length • Primer Name • Primer Reference Citation • Primer Reference Link • Primer Sequence • Sequencing Date • Sequencing Direction • Sequencing Method • Sequencing Staff • Single Sequence • Single Sequence Length
By concept name: ggbn:chromatogramFileURI • ggbn:fragmentLength • ggbn:primerName • ggbn:primerReferenceCitation • ggbn:primerReferenceLink • ggbn:primerSequence • ggbn:sequencingDate • ggbn:sequencingDirection • ggbn:sequencingMethod • ggbn:sequencingStaff • ggbn:singleSequence • ggbn:singleSequenceLength
Concept definitions in GGBN Single Read Vocabulary
| Concept Name: | ggbn:chromatogramFileURI |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/chromatogramFileURI |
| Label | Chromatogram File URI |
| Definition | Link to the chromatogram of an individual DNA sequence (single read) |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | currently to be used with ABCD only |
| Concept Name: | ggbn:fragmentLength |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/fragmentLength |
| Label | Fragment Length |
| Definition | Length of fragments (on average or precise) |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | currently to be used with ABCD only |
| Concept Name: | ggbn:primerName |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerName |
| Label | Primer Name |
| Definition | Name of primer used for this amplification, cloning, or single read |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerNameForward or ggbn:primerNameReverse |
| Concept Name: | ggbn:primerReferenceCitation |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitation |
| Label | Primer Reference Citation |
| Definition | Forst reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceCitationForward or ggbn:primerReferenceCitationReverse |
| Concept Name: | ggbn:primerReferenceLink |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLink |
| Label | Primer Reference Link |
| Definition | Link to the first reference of the primer |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceLinkForward or ggbn:primerReferenceLinkReverse |
| Concept Name: | ggbn:primerSequence |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/primerSequence |
| Label | Primer Sequence |
| Definition | DNA sequence of the primer (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: Yes | |
| Notes: | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerSequenceForward or ggbn:primerSequenceReverse |
| Concept Name: | ggbn:sequencingDate |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/sequencingDate |
| Label | Sequencing Date |
| Definition | Date when the DNA sequence/read was produced |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | currently to be used with ABCD only |
| Concept Name: | ggbn:sequencingDirection |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/sequencingDirection |
| Label | Sequencing Direction |
| Definition | Direction of sequencing/read |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | forward, reverse |
| Notes: | currently to be used with ABCD only |
| Concept Name: | ggbn:sequencingMethod |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/sequencingMethod |
| Label | Sequencing Method |
| Definition | Method or protocol used to generate the DNA or RAD sequences/reads |
| Defined By | |
| Required: No — Repeatable: No | |
| Examples | Genotyping-by-sequencing (GBS) |
| Notes: | currently to be used with ABCD only |
| Concept Name: | ggbn:sequencingStaff |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/sequencingStaff |
| Label | Sequencing Staff |
| Definition | Person or institution which performed the sequencing |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | currently to be used with ABCD only |
| Concept Name: | ggbn:singleSequence |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/singleSequence |
| Label | Single Sequence |
| Definition | Sequence of the individual DNA sequence/read (A,T,G,C; 5' to 3') |
| Defined By | |
| Required: No — Repeatable: No | |
| Notes: | currently to be used with ABCD only |
| Concept Name: | ggbn:singleSequenceLength |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/singleSequenceLength |
| Label | Single Sequence Length |
| Definition | Length of the single sequence/read (Number of base pairs ) |
| Defined By | |
| Required: No — Repeatable: No |
