Difference between revisions of "ABCD2Concepts"

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=Introduction=
+
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 [https://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki].
−
ABCD and DarwinCore both contain hundreds of elements. Some are mandatory. The curator of the DNA Bank has to define the Metadata of the DNA Bank collection first. After that the real mapping can begin. You can use [http://www.biocase.org BioCASe] or [http://www.gbif.org/ipt IPT] to provide data to GGBN, but have to make sure you use the extensions for the [http://terms.tdwg.org/wiki/GGBN_Data_Standard GGBN Data Standard]. DarwinCore and ABCD have a lot of terms in common, but use different names for the terms. Therefore the following section are splitted into ABCD and DwC. GGBN supports both standards, both have pros and cons and work well for GGBN. It depends on your data and if your institution is already providing data to GBIF which one fits better. Please contact us if you need help.
 
  
−
<div id="wikinote">
+
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.
  
−
'''Asterisk (*) means mandatory for GGBN, all others are recommended.
+
==Metadata==
−
 
+
Metadata describe the dataset as whole - as opposed to individual specimens/observations.  
−
Separate mappings for voucher specimens (mapping 1) and tissue and DNA samples (mapping 2) are preferred. This enables third parties such as GBIF or GGBN to harvest only those data that are relevant.
 
−
 
 
−
All metadata information should be in English! Please map as many elements as possible, the better your data visible and searchable in GBIF and GGBN the better for other scientists and at the end for yourself!</div>
 
−
 
 
−
=Mapping principles=
 
−
You can provide your data to GGBN in different ways. It depends on your other collections and the way you provide your data already to GBIF which one fits best for you. GGBN can handle all of the examples below, but it might make a difference for your occurrences at GBIF. Most important is, that you provide the references between the records in a standardized way. DNA collections comprise many difference use cases. Not in all cases you will have a physicial tissue or a physicial specimen. Please contact us if you need help.
 
−
 
 
−
==Mapping with Specimens==
 
−
A specimen in terms of GGBN and GBIF is a preserved specimen from wild origin or a living specimen (cultivated plant, captivated animal, cell culture). In case your collection or certain DNA samples have no corresponding tissue sample, you should refer to the "mother" specimen directly.
 
−
<div id="wikinote">Specimens are often deposited in external collections. If you provide the proper identifiers the GGBN Data Portal can aggregate this information! We know that it is impossible to track this information back for all legacy data. But if you keep this in mind in your daily workflows for all new records and samples the quality and value of your data and collection will increase enormously.</div>
 
  
 +
=== General metadata ===
 
{| class="wikitable"
 
{| class="wikitable"
−
! Mapping all at once !! Mapping two sources !! Mapping three sources
+
!Group
−
|-
+
!Element
−
|[[File:GGBN mapping one source.png|Thumb|300px]] || [[File:GGBN mapping two sources.png|Thumb|300px]] || [[File:GGBN mapping three sources.png|Thumb|300px]]
+
!Example
 +
!Remark
 
|-
 
|-
−
|'''Pros:''' - only one mapping needed
 
−
 
−
'''Cons:''' - double occurrences at GBIF, since GBIF can't handle associataions
 
−
||'''Pros:''' - Only underlying specimens records are provided, no double entries at GBIF
 
−
 
−
'''Cons:''' - two mappings needed (but can be easily copied)
 
−
||'''Pros:''' -  Only underlying specimens records are provided, no double entries at GBIF
 
−
 
−
- Clear distinction between collections, some managers prefer this mapping type
 
  
−
'''Cons:''' - three mappings needed (but can be easily copied)
+
|rowspan="4" | ContentContact*
−
|}
+
|Name*
−
 
+
|John Doe
−
==Mapping without Specimens==
+
|rowspan="4" | Contact information for the curator of the dataset.
−
Often tissue samples are collected without collecting/killing the whole organism. There are two ways to handle this.
 
−
{| class="wikitable"
 
−
! Mapping eVouchers  !! Mapping tissues only
 
 
|-
 
|-
−
|style="width: 50%;"|[[File:GGBN mapping evoucher.png|Thumb|300px]] ||[[File:GGBN mapping tissues only.png|Thumb|300px]]
+
|Address
 +
|Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany
 
|-
 
|-
−
|In case you want to track an individual, sampled multiple times (e.g. vertebrates caught multiple times and marked individually, trees) you should add an Observation record as top level. This could also be accompanied by images, then called eVoucher.
+
|Email
−
||In case you don't want to track individuals, just provide your tissue records to GBIF as top level occurrence.
+
|john.doe@acme.com
−
|}
 
−
==Environmental Samples==
 
−
Environmental Samples and even more environmental DNA can currently be provided to GGBN and GBIF in a very basic way only. We are working on a proposal how to map these important sample information in a way they deserve it. Have a look at our [[Use_Cases_Enviro | Environmental DNA use case]]
 
−
 
 
−
=ABCD=
 
−
 
 
−
==Metadata of your DNA and tissue bank==
 
−
Metadata are very important. They will be displayed with every single DNA record in the portal. Be careful with the IPR statements!
 
−
 
 
−
{| class="wikitable"
 
−
! width="120px" | Group
 
−
!Element
 
−
!Remarks
 
−
!Example
 
 
|-
 
|-
−
|ContentContact
+
|Phone
−
|*Address
+
| +49 30 838 99999
−
|Complete Address of the responsible person
 
−
|Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
 
 
|-
 
|-
−
|ContentContact
+
 
−
|*Email
+
|rowspan="4" | TechnicalContact*
−
|valid email address; will be used by the web portal for sending you annotations etc.
+
|Name*
−
|please use @ instead of masquerades like "[at]"
+
|John Doe
 +
|rowspan="4" | Contact information of the person that is responsible for the BioCASe installation - in most cases, this will be the IT department.
 
|-
 
|-
−
|ContentContact
+
|Address
−
|*Name
+
|Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany
−
|Person, person team responsible for curation of your DNA Bank
 
−
|Gabi Droege
 
 
|-
 
|-
−
|Description/Representation
+
|Email
−
|*Details
+
|john.doe@acme.com
−
|Short text to describe the focus and number of samples in your DNA collection. '''It should include the following phrase:''' ''The DNA bank is part of the Global Genome Biodiversity Network (GGBN) which was founded in 2011. The network provides a technically optimized DNA collection service facility for all biological research accessible via one central web portal. The network promotes deposition of well documented reference DNA samples after project completion or data publication from scientists of other universities and institutions.''
 
−
|The DNA bank of the Botanic Garden and Botanical Museum Berlin-Dahlem holds currently a collection of 20000 plant DNA and tissue samples growing constantly. Its core collection focuses on the flora of Germany but it comprises botanical samples collected worldwide.
 
 
|-
 
|-
−
|Description/Representation
+
|Phone
−
|*@language
+
| +49 30 838 99999
−
|language of description
 
−
|should be "en" as literal
 
 
|-
 
|-
−
|Description/Representation
+
 
−
|*Title
+
|Metadata
−
|Short title that describes your DNA collection
+
|IconURI
−
|DNA Bank of the Herbarium Berolinense
+
|http://ww3.bgbm.org/providerResources/BGBM.jpg
 +
|Link to an image that represents the dataset.
 
|-
 
|-
−
|IPRStatements/Citation
+
 
−
|*Text
+
|rowspan="2" | Metadata/RevisionData*
−
|
+
|DateCreated
−
|Droege, G. (Ed.) 2008 - (continuously updated): DNA samples of the DNA bank at the BGBM (Botanic Garden and Botanical Museum Berlin-Dahlem).
+
|2018-07-19
 +
|rowspan="2" | Date when the dataset has been first published (DateCreated) and of the last changes/additions/removals (DateModified).
 
|-
 
|-
−
|IPRStatements/Citation
+
|DateModified*
−
|*@language
+
|2018-09-27
−
|language of citation
 
−
|should be "en" as literal
 
 
|-
 
|-
−
|IPRStatements/Copyright
+
 
−
|*Text
+
|rowspan="3" | Metadata/Version
−
|
+
|DateIssued
−
|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.
+
|2018-09-27
 +
|rowspan="3" | If you keep track of dataset versions, the info can be specified in this section.
 
|-
 
|-
−
|IPRStatements/Copyright
+
|Major*
−
|*@language
+
|3
−
|language of copyright
 
−
|should be "en" as literal
 
 
|-
 
|-
−
|IPRStatements/TermsOfUse
+
|Minor
−
|*Text
+
|1
−
|
 
−
|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
+
|rowspan="4" | Metadata/Description/Representation*
−
|language of the terms of use
+
|Title*
−
|should be "en" as literal
+
|Herbarium Berolinense
 +
|rowspan="4" | Short description of the dataset (preferrably in english), consisting of a title, a 2-3 sentences long description and an optional URL.
 
|-
 
|-
−
|
+
|@language*
−
|IconURI
+
|en
−
|complete url path to the logo of your institution
 
−
|
 
 
|-
 
|-
−
|Owner
+
|Description
−
|*Address
+
|The herbarium of the Botanic Garden and Botanical Museum Berlin-Dahlem (herbarium acronym: B) is  ...
−
|Complete Address of the institution that owns the DNA bank samples and data
 
−
|
 
 
|-
 
|-
−
|Owner/Representation
+
|URL
−
|*Text
+
|https://www.bgbm.org/en/herbarium
−
|name of your institution
 
−
|Botanic Garden an Botanical Museum Berlin-Dahlem (Freie Universität Berlin)
 
 
|-
 
|-
−
|Owner
+
 
−
|*URL
+
|rowspan="7" | Metadata/Owners/Owner  
−
|path to website of your institution
+
|Addresses/Address
−
|http://www.bgbm.org
+
|Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany
 +
|rowspan="7" | Institution that owns the dataset.  
 
|-
 
|-
−
|RevisionData
+
|EmailAddresses/EmailAddress
−
|*DateModified
+
|john.doe@acme.com
−
|date of last modification of your data
 
−
|
 
 
|-
 
|-
−
|TechnicalContact
+
|TelephoneNumbers/TelephoneNumber
−
|*Address
+
| +49 30 838 99999
−
|Complete Address of the responsible person
 
−
|Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
 
 
|-
 
|-
−
|TechnicalContact
+
|URIs/URL
−
|*Email
+
|https://www.bgbm.org
−
|valid email address; will be used by the web portal for sending you annotations etc.
 
−
|please use @ instead of masquerades like "[at]"
 
 
|-
 
|-
−
|TechnicalContact
+
|LogoURI
−
|*Name
+
|http://ww3.bgbm.org/providerResources/BGBM.jpg
−
|Person, person team responsible for technical issues of your database
 
−
|Gabriele Droege
 
 
|-
 
|-
−
|Unit
+
|Organisation/Name/Representation/Text*
−
|*RecordBasis
+
|Botanic Garden and Botanical Museum Berlin-Dahlem
−
|this value must be part of the ABCD vocabulary
 
−
|must be "MaterialSample"
 
 
|-
 
|-
−
|Unit
+
|Organisation/Name/Representation/Abbrevation
−
|*KindOfUnit
+
|BGBM
−
|the type of sample
 
−
|e.g. DNA
 
 
|}
 
|}
  
−
==Sample data==
+
=== IPR Statements ===
−
===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.
+
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:
 +
 
 
{| class="wikitable"
 
{| class="wikitable"
−
! width="120px" | Group
+
!Section
−
!Element
 
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 
|-
 
|-
−
|Unit
+
 
−
|*<span style="color:red">SourceID</span>
+
|Acknowledgements
−
|short description of relevant collection
+
|The project was funded by the German Federal Ministry of Education and Research (BMBF)
−
|should be "DNA Bank" or "tissue collection"
+
|A free text acknowledging support for the dataset (e.g. grant money, help, permission to reuse published material, etc.).
 
|-
 
|-
−
|Unit
+
 
−
|*<span style="color:red">SourceInstitutionID</span>
+
|Citation
−
|short name/abbreviation of relevant institution
+
|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].
−
|BGBM
+
|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 [https://creativecommons.org/licenses/ here].
 
|-
 
|-
−
|Unit
+
 
−
|*<span style="color:red">UnitID</span>
+
|TermsOfUse
−
|DNA extraction number or tissue number
+
|Textual metadata on specimens from the Herbarium Berolinense (B) are released under the Creative Commons 1.0 Public Domain Dedication waiver.
−
|DNA 123
+
|Terms for using the published data.
 
|-
 
|-
−
|Unit
 
−
|UnitGUID
 
−
|sample record GUID
 
−
|f6c7fd5a-2f04-4dcb-ba38-0230bf196d30
 
 
|}
 
|}
  
−
===GGBN terms===
+
'''Note:''' If you publish your data to GBIF, you are required to specify a license in the ''License'' node with the ''language'' attribute and the elements ''Text'' and ''URI''. The latter should contain a link to a well-defined license, for example https://creativecommons.org/publicdomain/zero/1.0/. More details on GBIF licensing can be found [http://www.gbif.org/terms/licences here].
−
The following fields are highly recommended, some are mandatory (marked with *), but feel free to map more!
+
 
−
<div id="wikinote">'''Please have a look at the [http://terms.tdwg.org/wiki/GGBN_Data_Standard 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.'''</div>
+
==Specimen Data==
 +
In ACBD terminology, a single specimen/observation 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===
 +
 
 
{| class="wikitable"
 
{| class="wikitable"
−
! width="120px" | Group
+
!ABCD element
−
!Element
 
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 
|-
 
|-
−
|
+
|SourceID*
−
|*RecordBasis
+
|Herbarium Berolinense
−
|The specific nature of the data record, controlled vocabulary!
+
|The name or code of the data source.
−
|"PreservedSpecimen", "MaterialSample", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"; for Tissue or DNA samples use "MaterialSample"
 
 
|-
 
|-
−
|
+
|SourceInstitutionID*
−
|*materialSampleType
+
|B
−
|Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type
+
|The unique identifier (code or name) of the institution holding the original data source.
−
|"tissue", "DNA", "specimen"
 
 
|-
 
|-
−
|SpecimenUnit/Preparation
+
|UnitID*
−
|*preparationType
+
|B -W 08738 -01 0
−
|description of type of material, free text
+
|A unique identifier for the unit record within the data source.
−
|or DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood
 
 
|-
 
|-
−
|SpecimenUnit/Preparation
+
 
−
|*preparationDate
+
|UnitGUID
−
|date of DNA extraction
+
|http://herbarium.bgbm.org/object/BW08738010
−
|if unknown type "unknown"
+
|A globally unique identifier for the unit record.
 
|-
 
|-
−
|SpecimenUnit/Preparation
+
 
−
|*preparatioMaterials
+
|CollectorsFieldNumber
−
|extraction kit or protocoll
+
|765/10
−
|if unknown type "unknown"
+
|The original number assigned to the unit by the collector or observer.
−
|-
 
−
|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
+
|RecordBasis
−
|geneticAccessionNumber
+
|LivingSpecimen
−
|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
+
|An indication of what the unit record describes; needs to comply with a [https://dwc.tdwg.org/terms/#basisOfRecord controlled vocabulary].
−
|e.g. AJ45567
 
 
|-
 
|-
−
|GGBN/Amplification
+
|KindOfUnit
−
|genBankNumber-URI
+
|Seed; (whole) plant
−
|complete link to the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD
+
|Part(s), physical state, or class of materials represented by this specimen.
−
|
 
 
|-
 
|-
−
|SpecimenUnit
+
|Sex
−
|blockedUntil
+
|Male
−
|in case the sample is blocked until a specific date it's nevertheless searchable but customers cannot order it
+
|Sex of the unit.
−
|ISO format
 
 
|-
 
|-
−
|SpecimenUnit
+
|RecordURI
−
|blocked
+
|http://herbarium.bgbm.org/object/BW08738010
−
|sample is blocked (e.g. because it is consumed), but data are still available
+
|The web address of the page where more information on this particular unit record can be found.
−
|Yes/No
 
 
|-
 
|-
−
|GGBN
+
|Notes
−
|concentration
+
|Specimen examined in a review of the genera of the tribe Eupatorieae, R. M. King & H. Robinson 1968-1969
−
|concentration of the DNA
+
|A free text description of the unit. Any notes that do not fit elsewhere.
−
|65,34
 
 
|-
 
|-
−
|GGBN
+
|DateLastEdited
−
|@unit
+
|2009-030-7
−
|unit of the concentration
+
|The date of the creation of or last change to this unit record.
−
|µg/ml
 
 
|-
 
|-
−
|GGBN
+
|LastEditor
−
|ratioOfAbsorbance260_230
+
|John Doe
−
|map only if filled with content
+
|The name or other indication of the person or team that created or last edited this record.
−
|1,2
 
 
|-
 
|-
−
|GGBN
 
−
|ratioOfAbsorbance260_280
 
−
|map only if filled with content
 
−
|1,8
 
 
|}
 
|}
  
−
==Related Specimen Data==
+
===Gathering event===
−
<div id="wikinote">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.</div>
+
The ''Gathering'' subsection of ABCD covers all details about the gathering site and the gathering agents. All the follwing groups and elements are located in ''Units/Unit/Gathering''.
−
[[File:Relationships.jpg|thumb|500px|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===
 
 
{| class="wikitable"
 
{| class="wikitable"
−
! width="120px" | Group
+
!Group
 
!Element
 
!Element
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 
|-
 
|-
−
|Associations/UnitAssociation
+
|rowspan="2" | Agents
−
|*UnitID
+
|GatheringAgentsText
−
|the UnitID or CatalogueNumber used for GBIF
+
|Scholz, Sipman
−
|e.g. the barcode number of your specimens
+
|A free text representation or concatenated version of those responsible for collecting or recording. In case of a gathering team, it is advised not to provide a concatenated text of the collectors, but individual gathering agents (see below).
 
|-
 
|-
−
|Associations/UnitAssociation
+
|GatheringAgent/AgentText
−
|*SourceInstitutionID
+
|Sipman
−
|the SourceInstitutionID or InstitutionCode used for GBIF
+
|Name of an individual gathering agent. The element ''GatheringAgent'' is repeatable, so it can be provided several times in case of a gathering team.
−
|e.g. the acronym of your institution
 
 
|-
 
|-
−
|Associations/UnitAssociation
+
 
−
|*SourceName
+
|rowspan="4" | Altitude
−
|the SourceID or CollectionCode used for GBIF
+
|MeasurementOrFactText
−
|e.g. the name of the collection where the specimen belongs to, e.g. "Birds"
+
|1500-1600m
 +
|Use this element if you have the altitude stored as a free text, that is as a single, concatenated text. If the boundaries of a range are stored as separate values in your database, use the ''MeasurementOrFactAtomised'' elements below.
 
|-
 
|-
−
|Associations/UnitAssociation
+
 
−
|*AssociationType
+
|MeasurementOrFactAtomised/LowerValue*
−
|the Relation between the DNA and the voucher
+
|1500
−
|e.g. "DNA and voucher from same individual"
+
|The lower or only value of the gathering site altitude.
 
|-
 
|-
−
|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===
+
|MeasurementOrFactAtomised/UpperValue
−
'''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.
+
|1600
 +
|The upper value for the measured gathering site altitude, if there is a range.  
 +
|-
  
−
{| class="wikitable"
+
|MeasurementOrFactAtomised/UnitOfMeasurement
−
! | Group
+
|m
−
!Element
+
|The unit of measurement used to measure the gathering site altitude.
−
!Remarks
+
|-
−
!Example
+
 
 +
|rowspan="2" | Country
 +
|ISO3166Code
 +
|US
 +
|ISO code of the country where the voucher was collected/observed.
 
|-
 
|-
−
|
+
 
−
|*CollectorsFieldNumber
+
|Name*
−
|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
+
|United States of America
−
|e.g. 765/10
+
|Name of the gathering country.
 
|-
 
|-
−
|Gathering/Agents/GatheringAgent
+
 
−
|*FullName
+
|rowspan="3" | DateTime
−
|the Collector or Collector Team
+
|DateText
−
|e.g. Scholz & Sipman
+
|August 2012
 +
|Date when voucher was collected if it doesn't conform to a specific date format and is stored just as a freet text.
 
|-
 
|-
−
|Gathering/Altitude
+
 
−
|*LowerValue
+
|ISODateTimeBegin
−
|if you have both the lower and upper value in different columns map both field, if not map LowerValue only
+
|2012-08-17
−
|e.g. 100
+
|Gathering date in ISO format. If you want to provide a time span, this will be the start of the time span.
 
|-
 
|-
−
|Gathering/Altitude
+
 
−
|UpperValue
+
|ISODateTimeEnd
−
|
+
|2012-08-19
−
|e.g. 200
+
|End datetime (in ISO format) if the gathering covers a time span.
 
|-
 
|-
−
|Gathering/Altitude
+
 
−
|*Unit
 
 
|
 
|
−
|e.g. m
+
|LocalityText
 +
|Landkreis Neustrelitz, Feldberger Seengebiet, Carwitz, ca. 1 km SW von Carwitz.
 +
|The original gathering locality data as appearing on a label or in an original entry, as a text string. This field should be transcribed verbatim from the specimen label.
 
|-
 
|-
−
|Gathering/Country
+
 
−
|*ISO3166Code
+
|rowspan="2" | NamedArea
−
|ISO code of the country where the voucher was collected
+
|AreaName
−
|e.g. US
+
|Europe
 +
|Any geographic term that is neither a country (use ''Country'' element) nor the exact locality description (use ''LocalityText'').
 
|-
 
|-
−
|Gathering/Country
+
 
−
|*Name
+
|AreaClass
−
|english Name of the country
+
|Continent
−
|e.g. United States of America
+
|Type of geographic term provided in ''AreaName''
 
|-
 
|-
−
|Gathering/DateTime
+
 
−
|*DateText
+
|Biotope
−
|date when voucher was collected, if you have content yuo can also use ISO format
+
|Text
−
|e.g. 21. April 1951
+
|Amongst rocks and stones, calcareous soil and screes
 +
|Gathering site biotope description.
 
|-
 
|-
−
|Gathering/Locality
+
 
−
|*LocalityText
+
| -
 +
|AreaDetail
 
|
 
|
−
|e.g. 5km NO Berlin
+
|A free text description of further details pertaining to the observation, sampling, or collection locality which which did not fit into the one of the other elements.
 
|-
 
|-
−
|Gathering/NamedArea
+
 
−
|AreaName
+
|rowspan="8" | SiteCoordinateSets/ SiteCoordinates/ CoordinatesLatLong
−
|name of continent
+
|../CoordinateMethod
−
|e.g. Europe
+
|Inferred map reference
 +
|Method of coordinates determination (GPS vs. inferred from description).
 
|-
 
|-
−
|Gathering/NamedArea
+
 
−
|@language
+
|LatitudeDecimal
−
|language of the name of continent
+
|52.49179
−
|e.g. "en"
+
|Latitude in decimal degrees.
 
|-
 
|-
−
|Gathering/SiteCoordinates
+
 
−
|*LatitudeDecimal
+
|LongitudeDecimal
−
|
+
|13.23589
−
|e.g. -15,88876
+
|Longitude in decimal degreed.
 
|-
 
|-
−
|Gathering/SiteCoordinates
 
−
|*LongitudeDecimal
 
−
|
 
−
|e.g. 72,88876
 
−
|}
 
  
−
===Identification history of the voucher===
+
|CoordinatesText
−
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.
+
|52°30' N 13°23' E
−
{| class="wikitable"
+
|An alternative concatenated text representation of the lat/lon coordinates if they can't be provided as separate lat/lon values.
−
! | Group
 
−
!Element
 
−
!Remarks
 
−
!Example
 
 
|-
 
|-
−
|Identification
+
 
−
|*PreferredFlag
+
|SpatialDatum
−
|mark the presently preferred Identification
+
|WGS 84
−
|e.g. true, false, 0, 1
+
|A mathematical surface on which the mapping and coordinate system used for the geocodes of the gathering site are based.  
 
|-
 
|-
−
|Identification/HigherTaxon
+
 
−
|*HigherTaxonName
+
|CoordinateErrorDistanceInMeters
−
|the name of the higher taxon, please have a look at the BioCASE Wiki for how to prepare your database for the [http://wiki.bgbm.org/bps/index.php/Preparation#Repeatable_Elements_in_ABCD repeatable elements]
+
|500
−
|e.g. Asteraceae, Animalia
+
|An estimate of how tightly the collecting locality was specified, expressed as a distance in meters corresponding to a radius around the lat/long coordinates.
 
|-
 
|-
−
|Identification/HigherTaxon
+
 
−
|*HigherTaxonRank
+
|AccuracyStatement
−
|the rank of the taxon in english or latin
+
|Coordinates rounded to 2 decimal places.
−
|e.g. familia, regnum, phylum
+
|A free text statement of the degree of accuracy of the latitude and longitude coordinates.  
 
|-
 
|-
−
|Identification/ScientificName
+
 
−
|*FullScientificName
+
|CoordinateErrorMethod
−
|the complete name of the taxon including Authors (and years for animals)
+
|Maximum error defined by dimensions of original ordinance survey map.
−
|e.g. Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi
+
|Verbatim statement of how the Coordinate Error was determined.  
 
|-
 
|-
−
|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.)
+
|Notes
−
|e.g. factorovskyi
 
−
|-
 
−
|Identification/ScientificName/NameAtomised
 
−
|*GenusOrMonomial
 
 
|
 
|
−
|e.g. Aaronsohnia
+
|Further text relating to the gathering event that does not fit one of the specified elements.  
 
|-
 
|-
−
|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===
+
===Identification history===
−
These should be mapped in the specimen mapping, not the DNA mapping.
+
Most specimen databases record the complete determination or identification history of a single specimen. ABCD allows to provide this complete history; each determination becomes an ''Identifications/Identification'' subtree.
−
 
 
−
=Darwin Core=
 
−
We recommend using [http://www.gbif.org/ipt/ IPT] for providing data as Darwin Core-Archive.
 
−
 
 
−
'''Mandatory for GGBN:''' Select '''occurrence''' as core and add '''GGBN Material Sample''' and '''Darwin Core Resource Relationship''' as extensions.
 
−
 
 
−
==Metadata of your DNA and tissue bank==
 
−
Please follow the example in the IPT documentation: https://github.com/gbif/ipt/wiki/IPT2ManualNotes.wiki#basic-metadata
 
−
 
 
−
'''Note:''' The description of your dataset should contain the following phrase: ''The DNA bank is part of the Global Genome Biodiversity Network (GGBN) which was founded in 2011. The network provides a technically optimized DNA collection service facility for all biological research accessible via one central web portal. The network promotes deposition of well documented reference DNA samples after project completion or data publication from scientists of other universities and institutions.''
 
−
 
 
−
==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 CatalogNumber should be unique in one database!''' Mostly the extraction number is used for it.
 
 
{| class="wikitable"
 
{| class="wikitable"
−
! width="120px" | Group
+
!Group
 +
!Subgroup
 
!Element
 
!Element
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 +
|-
 +
 +
| -
 +
| -
 +
|PreferredFlag
 +
|1
 +
|The currently preferred determination should be marked with ''1'' or ''True'', historic determinations with ''0'' or ''False''.
 
|-
 
|-
−
|Occurrence
+
 
−
|*<span style="color:red">institutionCode</span>
+
|Date
−
|short description of relevant collection
+
| -
−
|should be "DNA Bank" or "tissue collection"
+
|DateText/ISODateTimeBegin
 +
|2018-08-17
 +
|Date of the unit identification event. If in ISO format, use ''ISODateTimeBegin'', ''DateText'' otherwise.
 
|-
 
|-
−
|Occurrence
+
 
−
|*<span style="color:red">collectionCode</span>
+
|rowspan="2" | Identifiers
−
|short name/abbreviation of relevant institution
+
| -
−
|NMNH
+
|IdentifiersText
 +
|Humboldt & Bonpland
 +
|Text indicating the person, person team, or organisation that made the identification. If it is a team, individual ''Identifier'' subtrees should be provided, if possible (see below).
 
|-
 
|-
−
|Occurrence
+
 
−
|*<span style="color:red">catalogNumber</span>
+
|Identifier/PersonName
−
|DNA extraction number or tissue number
+
|FullName
−
|DNA 123
+
|Humboldt
 +
|Person that made the identification.
 +
|-
 +
 
 +
|rowspan="9" | Result/TaxonIdentified
 +
|rowspan="2" | HigherTaxa/HigherTaxon
 +
|HigherTaxonName*
 +
|Asteraceae
 +
|Name of the higher taxon. Please have a look at the BioCASE Wiki for how to prepare your database for the [http://wiki.bgbm.org/bps/index.php/Preparation#Repeatable_Elements_in_ABCD repeatable elements]
 
|-
 
|-
−
|Occurrence
 
−
|occurrenceID
 
−
|sample record GUID
 
−
| http://n2t.net/ark:/65665/304ed89be-b1ed-4e71-b210-dbbddfadb776
 
−
|}
 
  
−
===GGBN terms===
+
|HigherTaxonRank
−
The following fields are highly recommended, some are mandatory (marked with *), but feel free to map more!
+
|familia
−
<div id="wikinote">'''Please have a look at the [http://terms.tdwg.org/wiki/GGBN_Data_Standard 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.'''</div>
+
|Rame of the higher taxon.
−
{| class="wikitable"
 
−
! width="120px" | Group
 
−
!Element
 
−
!Remarks
 
−
!Example
 
 
|-
 
|-
−
|Occurrence Core
+
 
−
|*basisOfRecord
+
|ScientificName
−
|The specific nature of the data record, controlled vocabulary!
+
|FullScientificNameString*
−
|"PreservedSpecimen", "MaterialSample", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"; for Tissue or DNA samples use "MaterialSample"
+
|Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi
 +
|Complete name of the taxon including Authors (and years for animals).
 
|-
 
|-
−
|Material Sample Extension
+
 
−
|*materialSampleType
+
|rowspan="5" | ScientificName/NameAtomised/Botanical
−
|Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type
+
|GenusOrMonomial
−
|"tissue", "DNA", "specimen"
+
|Aaronsohnia
 +
|rowspan="5" | ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.)
 
|-
 
|-
−
|Preparation Extension
+
 
−
|*preparationType
+
|FirstEpithet
−
|description of type of material, free text
+
|factorovskyi
−
|or DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood
 
 
|-
 
|-
−
|Preparation Extension
+
 
−
|*preparationDate
+
|InfraspecificEpithet
−
|date of DNA extraction
+
|factorovskyi
−
|if unknown type "unknown"
 
 
|-
 
|-
−
|Preparation Extension
+
 
−
|*preparatioMaterials
+
|Rank
−
|extraction kit or protocoll
+
|var.
−
|if unknown type "unknown"
 
 
|-
 
|-
−
|Preparation Extension
+
 
−
|*preparationStaff
+
|AuthorTeam
−
|extraction staff
+
|Warb. & Eig.
−
|if unknown type "unknown"
 
 
|-
 
|-
−
|Preservation Extension
+
 
−
|preservation
+
| -
−
|preservation of the tissue or DNA
+
|NameComments
−
|if unknown type "unknown"
+
|
 +
|Free text comments related to the name identified for the unit.
 
|-
 
|-
−
|Permit Extension
+
 
−
|*permitStatus
+
|rowspan="2" | References/Reference
−
|Information about the presence, absence or other basic status of permits associated with the sample(s), controlled vocabulary!
+
|rowspan="2" | -
−
|Permit available, Permit not required, Permit not available, '''Unknown Material collected after 2014-10-12 cannot be in "Unknown" permit status!'''
+
|TitleCitation
 +
|Ralfs, J: The British Desmidieae, London 1848
 +
|rowspan="2" | A reference (e.g. an article or monograph) that was used as the base for the identifier's taxon identification (e.g. by means of providing a key or a description of the taxon).
 
|-
 
|-
−
|Permit Extension
+
 
−
|*permitStatusQualifier
+
|CitationDetail
−
|Description of why a certain permit was not required or why Permit Status is unknown
+
|p.  22 + 226, 35 pl.
−
|"no national requirement for a permit at date of access", "officially authorized illegal holder", "collected on private land", "pre-Nagoya"
 
 
|-
 
|-
−
|Permit Extension
+
 
−
|*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
+
|Notes
 +
|Invalid publication as: Echinella rotata Greville in W.J. Hooker 1833: British Flora Vol II, pp. 432, London, p.398
 +
|Supplementary remarks about the unit identification.
 
|-
 
|-
−
|Permit Extension
+
 
−
|*permitText
+
 
−
|The text of a permit related to the gathering/shipping or further details
+
|}
−
|
+
 
 +
===Botanical Garden Unit===
 +
 
 +
{| class="wikitable"
 +
!ABCD element
 +
!Example
 +
!Remark
 
|-
 
|-
−
|Amplification Extension
+
|AccessionStatus
−
|amplificationDate
+
|C
−
|date of amplification; if unknown or general without content you don't have to map it
+
|The current status of the accession in the garden. Possible values are
−
|should be ISO format yyyy-mm-dd
+
* C (current accession in the living collection)
 +
* D (non-current due to death)
 +
* T (non current due to transfer to another record system, normally another garden)
 +
* S (stored in a dormant state)
 +
* O (other accession status - different from those above)
 
|-
 
|-
−
|Amplification Extension
+
|Cultivation
−
|marker
 
 
|
 
|
−
|COX1
+
|Allows for cultivation information to be passed as free text in order to help the receiving garden care for the transferred accession or to record the garden's experience made with this accession.
 
|-
 
|-
−
|Amplification Extension
+
|DonorCategory
−
|geneticAccessionNumber
+
|E
−
|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
+
|A code to indicate the type of the immediate donor from which the accession was obtained. This may not necessarily be the original collector of wild material. One or more of the following characters: E, G, B, R, S, U, H, M, N, I, O, U. For a description of these values, please refer to https://www.bgci.org/files/Databases/itf2.pdf, section E.5 (donor type flag). Gardens4Science data providers should also see the note below.
−
|e.g. AJ45567
 
 
|-
 
|-
−
|Amplification Extension
+
|Hardiness
−
|genBankNumber-URI
+
|1
−
|complete link to the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD
+
|A flag indicating that the accession is grown outdoors in the botanical garden.
−
|
 
 
|-
 
|-
−
|Loan Extension
+
|HybridFlag
−
|blockedUntil
+
| x
−
|in case the sample is blocked until a specific date it's nevertheless searchable but customers cannot order it
+
|Indicates the type of hybrid (if appropriate), according to
−
|ISO format
+
* no hybrid: <empty>
 +
* named hybrid: x
 +
* graft chimaera: +
 +
* any other type of hybrid: "hybrid"
 +
gardens4science providers should also see the notes below.
 
|-
 
|-
−
|Loan Extension
+
|IPEN
−
|blocked
+
|XX-0-HEID-3253
−
|sample is blocked (e.g. because it is consumed), but data are still available
+
|A unique number given to plant materials accessioned in conformance with the rules of the International Plant Exchange Network.
−
|Yes/No
 
 
|-
 
|-
−
|Material Sample Extension
+
|LocationInGarden
−
|concentration
+
|MD4
−
|concentration of the DNA
+
|The current location of the living plant in the botanical garden.
−
|65,34
 
 
|-
 
|-
−
|Material Sample Extension
+
|Perennation
−
|@unit
+
|
−
|unit of the concentration
+
|A code to indicate the means of perennation.
−
|µg/ml
 
 
|-
 
|-
−
|Material Sample Extension
+
|PlantingDate
−
|ratioOfAbsorbance260_230
+
|2007-07-07
−
|map only if filled with content
+
|The date in ISO format the plant was planted at its current location in the botanical garden.
−
|1,2
 
 
|-
 
|-
−
|Material Sample Extension
 
−
|ratioOfAbsorbance260_280
 
−
|map only if filled with content
 
−
|1,8
 
 
|}
 
|}
  
−
==Related Specimen Data==
+
'''Note for gardens4Science data providers:'''
−
<div id="wikinote">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.</div>
+
# Whether or not a given record will be visible in the public view of the [http://gardens4science.biocase.org gardens4science data portal] (that is, without being logged in) is determined by the value of the ''DonorCategory'' field: Records "O = other" will be visible only for logged-in curators; if the field is filled with "I = individual" or empty, the record will also show up for unregistered users.
−
[[File:Relationships.jpg|thumb|500px|In the database and the mapping the child record should refer to its mother record in opposite to the real world example]]
+
# Use ''HybridFlag'' in addition to the correct [https://www.bgci.org/files/Databases/itf2.pdf nomenclature of hybrid or graft chimera names] in ''fullScientificName'' (e.g. ''xDisoselenicereus fulgidus (Hook.f.) E.Meier''; ''Epiphyllum x floribundum Kimnach''; ''+Crataegomespilus potsdamiensis''; ''Echinopsis hybrid''). The https://terms.tdwg.org/wiki/abcd2:TaxonIdentified-HybridFlag-@insertionpoint does not need to be mapped/filled and can be ignored (value will be taken from ''fullScientificName'').
 +
 
 +
===SpecimenUnit/Accessions===
  
−
===The voucher identifiers===
 
−
Please use the Darwin Core Resource Relationship Class
 
 
{| class="wikitable"
 
{| class="wikitable"
−
! width="120px" | Group
+
!ABCD element
−
!Element
 
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 +
|-
 +
|AccessionCatalogue
 +
|
 +
|Identifier of an accessions catalogue or numbering scheme
 
|-
 
|-
−
|Resource Relationship
+
|AccessionDate
−
|*resourceRelationshipID
+
|2007-07-07
−
|concatenated string with the triple id used for GBIF plus the accesspoint of the IPT archive providing this record and the guid (the latter one is not mandatory, but recommended)
+
|Date on which the accession was recorded
−
|e.g. catalogNumber=11718653&collectionCode=Botany&institutionCode=US&accesspoint=http://collections.mnh.si.edu/ipt/archive.do?r=nmnhdwca&guid=http://n2t.net/ark:/65665/303e7eecb-4e8d-4fce-a251-6c8fa3f2863d
+
|-
 +
|AccessionNumber
 +
|001010680
 +
|Institutional number applied to an accession and recorded in the accessions register.
 
|-
 
|-
−
| Resource Relationship
 
−
|*relationshipOfResource
 
−
|the Relation between the DNA and the voucher or the tissue and the voucher
 
−
|e.g. " same individual", “same population”, “same ex situ individual”
 
 
|}
 
|}
  
−
===Gathering event of the voucher===
+
===Multimedia===
−
'''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.
+
For providing links to associated images, videos and sounds, the sub-tree ''MultimediaObjects'' can be used. Each ABCD unit can have multiple multimedia objects, each represented by its own ''MultimediaObject'' with the following elements:
  
 
{| class="wikitable"
 
{| class="wikitable"
−
! | Group
+
!ABCD element
−
!Element
 
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 
|-
 
|-
−
|Occurrence Core
+
 
−
|*recordNumber
+
|FileURI*
−
|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
+
|http://ww2.bgbm.org/herbarium/images/B/-W/14/61/B_-W_14616%20-00%200.jpg
−
|e.g. 765/10
+
|The Universal Resource Identifier (URI) of the underlying multimedia file.
 
|-
 
|-
−
| Occurrence Core
+
 
−
|*recordedBy
+
|ProductURI
−
|the Collector or Collector Team
+
|http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=726
−
|e.g. Scholz & Sipman
+
|The Universal Resource Identifier of an electronic source of a multimedia object including HTML, Javascript or similar means delivering rendered output.
 
|-
 
|-
−
| Occurrence Core
+
 
−
|*minimumElevationInMeters
+
|Comment
−
|if you have both the lower and upper value in different columns map both field, if not map LowerValue only
+
|Image of herbarium specimen E00732880 by Specimen Digitisation Pipeline.
−
|e.g. 100
+
|Short description of the multimedia object.
 
|-
 
|-
−
| Occurrence Core
+
 
−
|maximumElevationInMeters
+
|Format
−
|
+
|image/jpeg
−
|e.g. 200
+
|A code or descriptive term for the file or object format.  
 
|-
 
|-
−
|Occurrence Core
+
 
−
|*countryCode
+
|FileSize
−
|ISO code of the country where the voucher was collected
+
|2365
−
|e.g. US
+
|The size in Kb of the file referred to by the URI or filename for the multimedia object.  
 
|-
 
|-
−
| Occurrence Core
+
 
−
|*country
+
|Creator
−
|english Name of the country
+
|Paris, Museum National d'Histoire Naturelle, OD
−
|e.g. United States of America
+
|The identifier (e.g. name or other id) of personnel who has taken the image.
 
|-
 
|-
−
| Occurrence Core
+
 
−
|*eventDate
+
|CreatedDate
−
|date when voucher was collected, if you have content you can also use ISO format
+
|2012-07-07
−
|e.g. 21. April 1951
+
|The date the multimedia object was created.
 
|-
 
|-
−
| Occurrence Core
+
 
−
|*locality
+
|ID
−
|
+
|22658
−
|e.g. 5km NO Berlin
+
|Identifier for the multimedia object relating to or forming the unit. This may be a filename.
 
|-
 
|-
−
| Occurrence Core
+
 
−
|continent
+
|IPR
−
|name of continent
 
−
|e.g. Europe
 
−
|-
 
−
| Occurrence Core
 
−
|*decimalLatitude
 
 
|
 
|
−
|e.g. -15,88876
+
|Intellectual Property Rights relating specifically to the multimedia object. This subtree has the same elements as ''Metadata/IPRStatements''. Fore more details, see the respective [[ABCD2Concepts#General_metadata | remarks]].
 
|-
 
|-
−
| Occurrence Core
 
−
|*decimalLongitude
 
−
|
 
−
|e.g. 72,88876
 
−
|}
 
  
−
===Scientific Name of the voucher===
 
−
{| class="wikitable"
 
−
! | Group
 
−
!Element
 
−
!Remarks
 
−
!Example
 
−
|-
 
−
|Occurrence Core
 
−
|*Family
 
−
|Please provide at least one higher taxon, usually family
 
−
|e.g. Asteraceae, Paridae
 
−
|-
 
−
|Occurrence Core
 
−
|*scientificName
 
−
|the complete name of the taxon including Authors (and years for animals)
 
−
|e.g. Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi
 
−
|-
 
−
|Occurrence Core
 
−
|*specificEpithet
 
−
|
 
−
|e.g. factorovskyi
 
−
|-
 
−
|Occurrence Core
 
−
|*genus
 
−
|
 
−
|e.g. Aaronsohnia
 
−
|-
 
−
|Occurrence Core
 
−
|*infraspecificEpithet
 
−
|
 
−
|e.g. factorovskyi
 
−
|-
 
−
|Identification/ScientificName/NameAtomised
 
−
|*taxonRank
 
−
|
 
−
|e.g. var.
 
 
|}
 
|}
−
===Multimedia items of the voucher===
 
−
These should be mapped in the specimen mapping, not the DNA/tissue mapping. If you have histological images you should map them here.
 

Latest revision as of 16:17, 5 February 2021

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/observations.

General metadata

Group Element Example Remark
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 99999
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 99999
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 99999
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.

Note: If you publish your data to GBIF, you are required to specify a license in the License node with the language attribute and the elements Text and URI. The latter should contain a link to a well-defined license, for example https://creativecommons.org/publicdomain/zero/1.0/. More details on GBIF licensing can be found here.

Specimen Data

In ACBD terminology, a single specimen/observation 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 765/10 The original number assigned to the unit by the collector or observer.
RecordBasis LivingSpecimen An indication of what the unit record describes; needs to comply with a controlled vocabulary.
KindOfUnit Seed; (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.

Gathering event

The Gathering subsection of ABCD covers all details about the gathering site and the gathering agents. All the follwing groups and elements are located in Units/Unit/Gathering.

Group Element Example Remark
Agents GatheringAgentsText Scholz, Sipman A free text representation or concatenated version of those responsible for collecting or recording. In case of a gathering team, it is advised not to provide a concatenated text of the collectors, but individual gathering agents (see below).
GatheringAgent/AgentText Sipman Name of an individual gathering agent. The element GatheringAgent is repeatable, so it can be provided several times in case of a gathering team.
Altitude MeasurementOrFactText 1500-1600m Use this element if you have the altitude stored as a free text, that is as a single, concatenated text. If the boundaries of a range are stored as separate values in your database, use the MeasurementOrFactAtomised elements below.
MeasurementOrFactAtomised/LowerValue* 1500 The lower or only value of the gathering site altitude.
MeasurementOrFactAtomised/UpperValue 1600 The upper value for the measured gathering site altitude, if there is a range.
MeasurementOrFactAtomised/UnitOfMeasurement m The unit of measurement used to measure the gathering site altitude.
Country ISO3166Code US ISO code of the country where the voucher was collected/observed.
Name* United States of America Name of the gathering country.
DateTime DateText August 2012 Date when voucher was collected if it doesn't conform to a specific date format and is stored just as a freet text.
ISODateTimeBegin 2012-08-17 Gathering date in ISO format. If you want to provide a time span, this will be the start of the time span.
ISODateTimeEnd 2012-08-19 End datetime (in ISO format) if the gathering covers a time span.
LocalityText Landkreis Neustrelitz, Feldberger Seengebiet, Carwitz, ca. 1 km SW von Carwitz. The original gathering locality data as appearing on a label or in an original entry, as a text string. This field should be transcribed verbatim from the specimen label.
NamedArea AreaName Europe Any geographic term that is neither a country (use Country element) nor the exact locality description (use LocalityText).
AreaClass Continent Type of geographic term provided in AreaName
Biotope Text Amongst rocks and stones, calcareous soil and screes Gathering site biotope description.
- AreaDetail A free text description of further details pertaining to the observation, sampling, or collection locality which which did not fit into the one of the other elements.
SiteCoordinateSets/ SiteCoordinates/ CoordinatesLatLong ../CoordinateMethod Inferred map reference Method of coordinates determination (GPS vs. inferred from description).
LatitudeDecimal 52.49179 Latitude in decimal degrees.
LongitudeDecimal 13.23589 Longitude in decimal degreed.
CoordinatesText 52°30' N 13°23' E An alternative concatenated text representation of the lat/lon coordinates if they can't be provided as separate lat/lon values.
SpatialDatum WGS 84 A mathematical surface on which the mapping and coordinate system used for the geocodes of the gathering site are based.
CoordinateErrorDistanceInMeters 500 An estimate of how tightly the collecting locality was specified, expressed as a distance in meters corresponding to a radius around the lat/long coordinates.
AccuracyStatement Coordinates rounded to 2 decimal places. A free text statement of the degree of accuracy of the latitude and longitude coordinates.
CoordinateErrorMethod Maximum error defined by dimensions of original ordinance survey map. Verbatim statement of how the Coordinate Error was determined.
- Notes Further text relating to the gathering event that does not fit one of the specified elements.

Identification history

Most specimen databases record the complete determination or identification history of a single specimen. ABCD allows to provide this complete history; each determination becomes an Identifications/Identification subtree.

Group Subgroup Element Example Remark
- - PreferredFlag 1 The currently preferred determination should be marked with 1 or True, historic determinations with 0 or False.
Date - DateText/ISODateTimeBegin 2018-08-17 Date of the unit identification event. If in ISO format, use ISODateTimeBegin, DateText otherwise.
Identifiers - IdentifiersText Humboldt & Bonpland Text indicating the person, person team, or organisation that made the identification. If it is a team, individual Identifier subtrees should be provided, if possible (see below).
Identifier/PersonName FullName Humboldt Person that made the identification.
Result/TaxonIdentified HigherTaxa/HigherTaxon HigherTaxonName* Asteraceae Name of the higher taxon. Please have a look at the BioCASE Wiki for how to prepare your database for the repeatable elements
HigherTaxonRank familia Rame of the higher taxon.
ScientificName FullScientificNameString* Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi Complete name of the taxon including Authors (and years for animals).
ScientificName/NameAtomised/Botanical GenusOrMonomial Aaronsohnia ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.)
FirstEpithet factorovskyi
InfraspecificEpithet factorovskyi
Rank var.
AuthorTeam Warb. & Eig.
- NameComments Free text comments related to the name identified for the unit.
References/Reference - TitleCitation Ralfs, J: The British Desmidieae, London 1848 A reference (e.g. an article or monograph) that was used as the base for the identifier's taxon identification (e.g. by means of providing a key or a description of the taxon).
CitationDetail p. 22 + 226, 35 pl.
- - Notes Invalid publication as: Echinella rotata Greville in W.J. Hooker 1833: British Flora Vol II, pp. 432, London, p.398 Supplementary remarks about the unit identification.

Botanical Garden Unit

ABCD element Example Remark
AccessionStatus C The current status of the accession in the garden. Possible values are
  • C (current accession in the living collection)
  • D (non-current due to death)
  • T (non current due to transfer to another record system, normally another garden)
  • S (stored in a dormant state)
  • O (other accession status - different from those above)
Cultivation Allows for cultivation information to be passed as free text in order to help the receiving garden care for the transferred accession or to record the garden's experience made with this accession.
DonorCategory E A code to indicate the type of the immediate donor from which the accession was obtained. This may not necessarily be the original collector of wild material. One or more of the following characters: E, G, B, R, S, U, H, M, N, I, O, U. For a description of these values, please refer to https://www.bgci.org/files/Databases/itf2.pdf, section E.5 (donor type flag). Gardens4Science data providers should also see the note below.
Hardiness 1 A flag indicating that the accession is grown outdoors in the botanical garden.
HybridFlag x Indicates the type of hybrid (if appropriate), according to
  • no hybrid: <empty>
  • named hybrid: x
  • graft chimaera: +
  • any other type of hybrid: "hybrid"

gardens4science providers should also see the notes below.

IPEN XX-0-HEID-3253 A unique number given to plant materials accessioned in conformance with the rules of the International Plant Exchange Network.
LocationInGarden MD4 The current location of the living plant in the botanical garden.
Perennation A code to indicate the means of perennation.
PlantingDate 2007-07-07 The date in ISO format the plant was planted at its current location in the botanical garden.

Note for gardens4Science data providers:

  1. Whether or not a given record will be visible in the public view of the gardens4science data portal (that is, without being logged in) is determined by the value of the DonorCategory field: Records "O = other" will be visible only for logged-in curators; if the field is filled with "I = individual" or empty, the record will also show up for unregistered users.
  2. Use HybridFlag in addition to the correct nomenclature of hybrid or graft chimera names in fullScientificName (e.g. xDisoselenicereus fulgidus (Hook.f.) E.Meier; Epiphyllum x floribundum Kimnach; +Crataegomespilus potsdamiensis; Echinopsis hybrid). The https://terms.tdwg.org/wiki/abcd2:TaxonIdentified-HybridFlag-@insertionpoint does not need to be mapped/filled and can be ignored (value will be taken from fullScientificName).

SpecimenUnit/Accessions

ABCD element Example Remark
AccessionCatalogue Identifier of an accessions catalogue or numbering scheme
AccessionDate 2007-07-07 Date on which the accession was recorded
AccessionNumber 001010680 Institutional number applied to an accession and recorded in the accessions register.

Multimedia

For providing links to associated images, videos and sounds, the sub-tree MultimediaObjects can be used. Each ABCD unit can have multiple multimedia objects, each represented by its own MultimediaObject with the following elements:

ABCD element Example Remark
FileURI* http://ww2.bgbm.org/herbarium/images/B/-W/14/61/B_-W_14616%20-00%200.jpg The Universal Resource Identifier (URI) of the underlying multimedia file.
ProductURI http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=726 The Universal Resource Identifier of an electronic source of a multimedia object including HTML, Javascript or similar means delivering rendered output.
Comment Image of herbarium specimen E00732880 by Specimen Digitisation Pipeline. Short description of the multimedia object.
Format image/jpeg A code or descriptive term for the file or object format.
FileSize 2365 The size in Kb of the file referred to by the URI or filename for the multimedia object.
Creator Paris, Museum National d'Histoire Naturelle, OD The identifier (e.g. name or other id) of personnel who has taken the image.
CreatedDate 2012-07-07 The date the multimedia object was created.
ID 22658 Identifier for the multimedia object relating to or forming the unit. This may be a filename.
IPR Intellectual Property Rights relating specifically to the multimedia object. This subtree has the same elements as Metadata/IPRStatements. Fore more details, see the respective remarks.
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