Difference between revisions of "ABCD2Concepts"

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|Link to an image that represents the dataset.

Revision as of 10:56, 27 September 2018

This page provides an overview of the most commonly used ABCD elements with short explanations and sample values. If you're looking for a complete list of ABCD elements, please refer to the full documentation at the ABCD Wiki.

Mandatory fields are marked with an asterisk. If you don't provide them, the element - and potentially non-mandatory sibling/parental elements - will be removed from the ABCD document.


Metadata describe the dataset as whole - as opposed to individual specimens.

Group Element Example Remarks
ContentContact Name* John Doe Contact information for the curator of the dataset.
Address Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany
Email john.doe@acme.com
Phone john.doe@acme.com
TechnicalContact Name* John Doe Contact information of the person that is responsible for the BioCASe installation - in most cases, this will be the IT department.
Address Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany
Email john.doe@acme.com
Phone john.doe@acme.com
RevisionData DateCreated 2018-07-19 Date when the dataset has been first published (DateCreated) and of the last changes/additions/removals (DateModified).
DateModified* 2018-09-27
Version DateIssued 2018-09-27 If you keep track of dataset versions, the info can be specified in this section.
Major* 3
Minor 1
Metadata/Description/Representation Title* Herbarium Berolinense Short description of the dataset (preferrably in english), consisting of a title, a 2-3 sentences long description and an optional URL.
@language* en
Description The herbarium of the Botanic Garden and Botanical Museum Berlin-Dahlem (herbarium acronym: B) is ...
URL https://www.bgbm.org/en/herbarium
Metadata IconURI http://ww3.bgbm.org/providerResources/BGBM.jpg Link to an image that represents the dataset.
IPRStatements/Citation *Text Droege, G. (Ed.) 2008 - (continuously updated): DNA samples of the DNA bank at the BGBM (Botanic Garden and Botanical Museum Berlin-Dahlem).
IPRStatements/Citation *@language language of citation should be "en" as literal
IPRStatements/Copyright *Text The copyright for any material created by the DNA bank of the BGBM is reserved. The duplication or use of information and data such as texts or images is only permitted with the indication of the source or with prior approval by the BGBM.
IPRStatements/Copyright *@language language of copyright should be "en" as literal
IPRStatements/TermsOfUse *Text The use of the data is allowed only for non-profit scientific use and for non-profit nature conservation purpose. The data bases or part of it may only be used or copied by the written permission from the legal owner.
IPRStatements/TermsOfUse *@language language of the terms of use should be "en" as literal
IconURI complete url path to the logo of your institution
Owner *Address Complete Address of the institution that owns the DNA bank samples and data
Owner/Representation *Text name of your institution Botanic Garden an Botanical Museum Berlin-Dahlem (Freie Universität Berlin)
Owner *URL path to website of your institution http://www.bgbm.org
Unit *RecordBasis this value must be part of the ABCD vocabulary must be "MaterialSample"
Unit *KindOfUnit the type of sample e.g. DNA

Sample data

The sample identifiers

We use identifier the same way as GBIF does. In addition to the traditional triple ID (see below) you can also provide the GUID. Please note that UnitID should be unique in one database! Mostly the extraction number is used for it.

Group Element Remarks Example
Unit *SourceID short description of relevant collection should be "DNA Bank" or "tissue collection"
Unit *SourceInstitutionID short name/abbreviation of relevant institution BGBM
Unit *UnitID DNA extraction number or tissue number DNA 123
Unit UnitGUID sample record GUID f6c7fd5a-2f04-4dcb-ba38-0230bf196d30

GGBN terms

The following fields are highly recommended, some are mandatory (marked with *), but feel free to map more!

Please have a look at the GGBN Data Standard documentation where all GGBN terms are described in detail. The table below is just listing the most important ones. Since the Nagoya Protocol has come into force we higly recommend to map the Permit fields. They will become mandatory for providing data to GGBN at the end of 2020. Until then all core members must have implemented the required fields in their databases.
Group Element Remarks Example
*RecordBasis The specific nature of the data record, controlled vocabulary! "PreservedSpecimen", "MaterialSample", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"; for Tissue or DNA samples use "MaterialSample"
*materialSampleType Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type "tissue", "DNA", "specimen"
SpecimenUnit/Preparation *preparationType description of type of material, free text or DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood
SpecimenUnit/Preparation *preparationDate date of DNA extraction if unknown type "unknown"
SpecimenUnit/Preparation *preparatioMaterials extraction kit or protocoll if unknown type "unknown"
SpecimenUnit/Preparation *preparedBy extraction staff if unknown type "unknown"
SpecimenUnit/Preservation preservation preservation of the tissue or DNA if unknown type "unknown"
SpecimenUnit/Loan/Permit *permitStatus Information about the presence, absence or other basic status of permits associated with the sample(s), controlled vocabulary! Permit available, Permit not required, Permit not available, Unknown Material collected after 2014-10-12 cannot be in "Unknown" permit status!
SpecimenUnit/Loan/Permit *permitStatusQualifier Description of why a certain permit was not required or why Permit Status is unknown "no national requirement for a permit at date of access", "officially authorized illegal holder", "collected on private land", "pre-Nagoya"
SpecimenUnit/Loan/Permit *permitType A permit is a document that allows someone to take an action that otherwise would not be allowed, controlled vocabulary! 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
SpecimenUnit/Loan/Permit *permitText The text of a permit related to the gathering/shipping or further details
GGBN/Amplification amplificationDate date of amplification; if unknown or general without content you don't have to map it should be ISO format yyyy-mm-dd
GGBN/Amplification marker COX1
GGBN/Amplification geneticAccessionNumber the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD; this is a repeatable element, you can provide as much as you want e.g. AJ45567
GGBN/Amplification genBankNumber-URI complete link to the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD
SpecimenUnit blockedUntil in case the sample is blocked until a specific date it's nevertheless searchable but customers cannot order it ISO format
SpecimenUnit blocked sample is blocked (e.g. because it is consumed), but data are still available Yes/No
GGBN concentration concentration of the DNA 65,34
GGBN @unit unit of the concentration µg/ml
GGBN ratioOfAbsorbance260_230 map only if filled with content 1,2
GGBN ratioOfAbsorbance260_280 map only if filled with content 1,8

Related Specimen Data

All specimen voucher information must be available via a GBIF compliant database! Both Darwin Core-Archive and BioCASE specimen providers are possibe! To provide the underlying specimen data you can use your existing GBIF dataset mapping.
In the database and the mapping the child record should refer to its mother record in opposite to the real world example

The voucher identifiers

Group Element Remarks Example
Associations/UnitAssociation *UnitID the UnitID or CatalogueNumber used for GBIF e.g. the barcode number of your specimens
Associations/UnitAssociation *SourceInstitutionID the SourceInstitutionID or InstitutionCode used for GBIF e.g. the acronym of your institution
Associations/UnitAssociation *SourceName the SourceID or CollectionCode used for GBIF e.g. the name of the collection where the specimen belongs to, e.g. "Birds"
Associations/UnitAssociation *AssociationType the Relation between the DNA and the voucher e.g. "DNA and voucher from same individual"
Associations/UnitAssociation *DatasetAccessPoint the wrapper url of the voucher record e.g. "http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar"

Gathering event of the voucher

All elements marked with * will be indexed and must be mapped! Mapping these gathering facts twice (one for the specimen database and one for the DNA mapping) is required because of indexing and later search purposes.

Group Element Remarks Example
*CollectorsFieldNumber the number the collector gave to the specimen in the field, often used in Botany but not in Zoology; map it if you have content e.g. 765/10
Gathering/Agents/GatheringAgent *FullName the Collector or Collector Team e.g. Scholz & Sipman
Gathering/Altitude *LowerValue if you have both the lower and upper value in different columns map both field, if not map LowerValue only e.g. 100
Gathering/Altitude UpperValue e.g. 200
Gathering/Altitude *Unit e.g. m
Gathering/Country *ISO3166Code ISO code of the country where the voucher was collected e.g. US
Gathering/Country *Name english Name of the country e.g. United States of America
Gathering/DateTime *DateText date when voucher was collected, if you have content yuo can also use ISO format e.g. 21. April 1951
Gathering/Locality *LocalityText e.g. 5km NO Berlin
Gathering/NamedArea AreaName name of continent e.g. Europe
Gathering/NamedArea @language language of the name of continent e.g. "en"
Gathering/SiteCoordinates *LatitudeDecimal e.g. -15,88876
Gathering/SiteCoordinates *LongitudeDecimal e.g. 72,88876

Identification history of the voucher

Mostly specimen databases record the complete determination or identification history of a single specimen. For GGBN we try to get all available information into the portal.

Group Element Remarks Example
Identification *PreferredFlag mark the presently preferred Identification e.g. true, false, 0, 1
Identification/HigherTaxon *HigherTaxonName the name of the higher taxon, please have a look at the BioCASE Wiki for how to prepare your database for the repeatable elements e.g. Asteraceae, Animalia
Identification/HigherTaxon *HigherTaxonRank the rank of the taxon in english or latin e.g. familia, regnum, phylum
Identification/ScientificName *FullScientificName the complete name of the taxon including Authors (and years for animals) e.g. Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi
Identification/ScientificName/NameAtomised *FirstEpithet Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.) e.g. factorovskyi
Identification/ScientificName/NameAtomised *GenusOrMonomial e.g. Aaronsohnia
Identification/ScientificName/NameAtomised *InfraspecificEpithet Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.) e.g. factorovskyi
Identification/ScientificName/NameAtomised *Rank Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.) e.g. var.

Multimedia items of the voucher

These should be mapped in the specimen mapping, not the DNA mapping.

Category Element Discription Comment
Metadata Title
Unit UnitID