GGBN Data Standard v1
From GGBN Wiki
This page describes the GGBN Data Standard version 1 (v1), released on 04. October 2016.
Citation: Droege et al. (2016): The Global Genome Biodiversity Network (GGBN) Standard Specification. DATABASE. doi: 10.1093/database/baw125
Note: Ongoing discussions and updates of the GGBN Data Standard will be documented at http://terms.tdwg.org/GGBN_Data_Standard
The GGBN Data Standard is intended to be used with ABCD or Darwin Core and is not a stand-alone solution! Implementations are available for both ABCD and DarwinCore-Archive. For ABCD two implementations have been made. One for single species samples ABCDGGBN and one for environmental samples ABCDGGBN-Enviro. Please check out the TDWG wiki for updates.
A new stable version of the standard will be released earliest at the end of 2019.
The GGBN Data Standard is a set of terms and controlled vocabularies designed to represent sample facts. It does not cover e.g., scientific name, geography, or physiological facts. This allows combining the GGBN Data Standard with other complementary standards, such as DwC, ABCD or MIxS. Potentially, the standard can be used not only for non-human genomic samples but also human samples. It builds upon existing standards commonly used within the communities extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard incorporates all molecular terms of MIxS, and can also handle SPREC and large parts of BRISQ. It has been developed as a cross-domain effort lead by the Global Genome Biodiversity Network together with colleagues from DwC, ABCD, MIxS, GBIF, ESBB and others over the last years.
Contributors: Gabi Droege, Katharine Barker, Walter G. Berendsohn, Sean Brady, Carol Butler, E. Margaret Casey, Jonathan Coddington, John Deck, David Fichtmüller, Birgit Gemeinholzer, Anton Güntsch, Jörg Holetschek, Tom Hollowell, Patricia Kelbert, Hans-Peter Klenk, Renzo Kottmann, Christopher Lewis, Chris Lyal, Jacqueline Mackenzie-Dodds, Christopher Meyer, Daniel Mulcahy, Éamonn Ó Tuama, Thomas Orrell, Gitte Petersen, Astrid Schories, Ole Seberg, Jamie Whitacre, Pelin Yilmaz, Holger Zetzsche, Yong Zhang, Xin Zhou, Erica Benson, Boyke Bunk, Enrique Arbeláez Cortés, Boyke Bunk, René Dekker, Markus Döring, Sonya Dyhrman, Paul Flemons, Elisabeth Haring, Thomas Knebelsberger, Ivayolo Kostadinov, Rita T. Lawlor, Jon Norenburg, Sara Y. Nussbeck, Michael Raupach, Thomas von Rintelen, Tim Robertson, Larissa Smirnova, Carola Söhngen, Sun Ying, Lee A. Weigt, John Wieczorek, Kenneth Wurdack, Elizabeth Zimmer.
Namespace URI: http://data.ggbn.org/schemas/ggbn/terms/ with preferred namespace prefix “ggbn”.
A list of mandatory and recommended fields for sharing data with GGBN as well as information on how to map your data can be found here.
Contents
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 • Genetic Accession Number • Genetic Accession URI • Guanin-Cytosine content • Haplotype • Marker • Marker Accordance • Marker Subfragment • 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 • 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 |
| Required: No — Repeatable: Yes | |
| Examples | 2008-10-17, May 2007 |
| Notes: | freetext since mostly extact 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. |
| 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 |
| 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 |
| 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 |
| 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) |
| 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 |
| 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 |
| 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 |
| 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) |
| Required: No — Repeatable: Yes | |
| Examples | 697, integer value |
| 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 % |
| 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) |
| 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) |
| 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 |
| 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 |
| 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 |
| 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 |
| Required: No — Repeatable: Yes | |
| Examples | V6 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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') |
| 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') |
| 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') |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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: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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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') |
| 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') |
| 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') |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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. |
| 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 |
| 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 |
| 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 |
| 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 |
| 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. |
| 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. |
| 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. |
| 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 |
| 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) |
| 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 |
| 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 |
| Required: No — Repeatable: No | |
| Examples | Precast stain; Post stain; Stain in loading buffer |
| 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. |
| 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. |
| 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 |
| 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 |
| 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. |
| 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. |
| 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 |
| 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. |
| 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) |
| 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) |
| 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 |
| 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 |
| 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. |
| Required: Yes — Repeatable: No | |
| Examples | tissue, culture strain, specimen, DNA, RNA, Protein, environmental sample |
| Notes: | Please use preparationType for further specification such as 'leg','blood','gDNA','axenic culture'.
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) |
| 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 |
| 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 |
| 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 |
| Required: No — Repeatable: No | |
| Examples | high, medium, low |
| Notes: | Predefined vocabulary! See: ggbn: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)) |
| 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 |
| 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) |
| 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) |
| 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. |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | http://data.ggbn.org/schemas/ggbn/terms/weightUnit |
| Label | High |
| Definition | A value for the ggbnvoc:quality_vocabulary |
| Required: No — Repeatable: No | |
| Concept Name: | ggbnvoc:low |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/weightUnit |
| Label | Low |
| Definition | A value for the ggbnvoc:quality_vocabulary |
| Required: No — Repeatable: No | |
| Concept Name: | ggbnvoc:medium |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/weightUnit |
| Label | Medium |
| Definition | A value for the ggbnvoc:quality_vocabulary |
| Required: No — Repeatable: No | |
| Concept Name: | ggbnvoc:quality vocabulary |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/weightUnit |
| Label | Quality Vocabulary |
| Definition | Vocabulary of ggbn:quality term |
| 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. |
| 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 |
| 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). |
| 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 |
| 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 |
| 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. |
| 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 |
| Required: No — Repeatable: Yes | |
| Notes: | One will eventually need a direct link to ggbn:IRCC in the future. |
| Concept Name: | ggbnvoc:Collecting Permit |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Collecting Permit |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Contract |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Contract |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Copyright |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Copyright |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Data use |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Data use |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Exemption Permit |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Expemtion Permit |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Export Permit |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Export Permit |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Genetically Modified Organism |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Genetically Modified Organism |
| Definition | A value for the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Notes: | Currently a placeholder only, might be renamed in the future |
| Concept Name: | ggbnvoc:Human Pathogens |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Human Pathogens |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Import Permit |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Import Permit |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Intellectual Property Rights |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Intellectual Property Rights (IPR) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Internationally Recognized Certificate of Compliance |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Internationally Recognized Certificate of Compliance (IRCC) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Material Transfer Agreement |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Material Transfer Agreement (MTA) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Memorandum of Cooperation |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Memorandum of Cooperation (MoC) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Memorandum of Understanding |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Memorandum of Understanding (MoU) |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Other |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Other |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Patent |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Patent |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Permit available |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Permit available |
| Definition | A value of ggbnvoc:permitStatus_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Permit not available |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Permit not available |
| Definition | A value for the ggbnvoc:permitStatus_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Permit not required |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Permit not required |
| Definition | A value for the ggbnvoc:permitStatus_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:permitStatus vocabulary |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | permitStatus Vocabulary |
| Definition | Vocabulary of ggbnvoc:permitStatus term |
| Required: No — Repeatable: No | |
| Examples | Permit available, Permit not required, Permit not available, Unknown |
| Concept Name: | ggbnvoc:permitType vocabulary |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | permitType vocabulary |
| Definition | Vocabulary of ggbn:permitType term |
| 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 | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Phytosanitary |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Salvage |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Salvage |
| Definition | A value of the ggbnvoc:permitType vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Unknown |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Unknown |
| Definition | A value for the ggbnvoc:permitStatus_vocabulary |
| Required: No — Repeatable: Yes | |
| Concept Name: | ggbnvoc:Veterinary Certificate |
| Normative URI | http://data.ggbn.org/schemas/ggbn/terms/permitURI |
| Label | Veterinary Certificate |
| Definition | A value of the ggbnvoc:permitType_vocabulary |
| 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. |
| 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 |
| 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 |
| 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 |
| 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) |
| Required: Yes — Repeatable: Yes | |
| Examples | for DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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) |
| 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) |
| 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 |
| 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 |
| 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 |
| 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') |
| 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 |
| 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 |
| 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 sequences/reads |
| Required: No — Repeatable: No | |
| 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 |
| 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') |
| 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 ) |
| Required: No — Repeatable: No |
