ABCD2Concepts

ABCD2Concepts

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

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

General metadata

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	+49 30 838 99999999
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	+49 30 838 99999999
Metadata	IconURI	http://ww3.bgbm.org/providerResources/BGBM.jpg	Link to an image that represents the dataset.
Metadata/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
Metadata/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/Owners/Owner	Addresses/Address	Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany	Institution that owns the dataset.
	EmailAddresses/EmailAddress	john.doe@acme.com
	TelephoneNumbers/TelephoneNumber	+49 30 838 99999999
	URIs/URL	https://www.bgbm.org
	LogoURI	http://ww3.bgbm.org/providerResources/BGBM.jpg
	Organisation/Name/Representation/Text*	Botanic Garden and Botanical Museum Berlin-Dahlem
	Organisation/Name/Representation/Abbrevation	BGBM

IPR Statements

The section Metadata/IPRStatements contains several sub-sections that allow to provide IPR (intellectual property rights) statements. Each sub-section contains the mandatory element Text for the statement and the optional elements Details and URI for delivering more details and/or a link to a web page mit more information. The seven sections are as follows:

Section	Example	Remark
Acknowledgements	The project was funded by the German Federal Ministry of Education and Research (BMBF)	A free text acknowledging support for the dataset (e.g. grant money, help, permission to reuse published material, etc.).
Citation	Röpert D. (ed.) 2000+ [continuously updated]: Digital specimen images at the Herbarium Berolinense. - Published at http://ww2.bgbm.org/herbarium/default.cfm [accessed dd Mmm yyyy].	Citation guidline for using the data in publications.
Disclaimer	No responsibility is accepted for the accuracy of the information in this database.	A disclaimer statement for the dataset (e. g. concerning responsibility for data quality or legal implications).
License	Creative Commons 1.0 Public Domain Dedication waiver	The license for using the data; we suggest one of the Creative Commons licenses that can be found at here.
TermsOfUse	Textual metadata on specimens from the Herbarium Berolinense (B) are released under the Creative Commons 1.0 Public Domain Dedication waiver.	Terms for using the published data.

Specimen Data

In ACBD terminology, a specimen is called a Unit; for each specimen, one Units/Unit will be created. Below you'll find the most commonly used ABCD elements in this sub-tree.

General unit data

ABCD element	Example	Remark
SourceID*	Herbarium Berolinense	The name or code of the data source.
SourceInstitutionID*	B	The unique identifier (code or name) of the institution holding the original data source.
UnitID*	B -W 08738 -01 0	A unique identifier for the unit record within the data source.
UnitGUID	http://herbarium.bgbm.org/object/BW08738010	A globally unique identifier for the unit record.
CollectorsFieldNumber	1055	The original number assigned to the unit by the collector or observer.
RecordBasis	PreservedSpecimen	An indication of what the unit record describes; needs to comply with a coontrolled vocabulary.
KindOfUnit	Whole plant	Part(s), physical state, or class of materials represented by this specimen.
Sex	Male	Sex of the unit.
RecordURI	http://herbarium.bgbm.org/object/BW08738010	The web address of the page where more information on this particular unit record can be found.
Notes	Specimen examined in a review of the genera of the tribe Eupatorieae, R. M. King & H. Robinson 1968-1969	A free text description of the unit. Any notes that do not fit elsewhere.
DateLastEdited	2009-030-7	The date of the creation of or last change to this unit record.
LastEditor	John Doe	The name or other indication of the person or team that created or last edited this record.

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.

File:Relationships.jpg

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
	IPR
	TechnicalContact
Unit	UnitID