GGBN Data Standard

The GGBN Data Standard is a set of vocabularies designed to represent tissue, DNA or RNA samples associated to voucher specimens and collections. Contributors: xxx.

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 (Material Sample) 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 |