Difference between revisions of "ABCD2Concepts"

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==Metadata==
 
==Metadata==
−
Metadata describe the dataset as whole - as opposed to individual specimens.  
+
Metadata describe the dataset as whole - as opposed to individual specimens/observations.  
  
 
=== General metadata ===
 
=== General metadata ===
 
{| class="wikitable"
 
{| class="wikitable"
−
! width="120px" | Group
+
!Group
 
!Element
 
!Element
 
!Example
 
!Example
−
!Remarks
+
!Remark
 
|-
 
|-
  
−
|rowspan="4" | ContentContact
+
|rowspan="4" | ContentContact*
 
|Name*
 
|Name*
 
|John Doe
 
|John Doe
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|-
 
|-
 
|Phone
 
|Phone
−
| +49 30 838 99999999
+
| +49 30 838 99999
 
|-
 
|-
  
−
|rowspan="4" | TechnicalContact
+
|rowspan="4" | TechnicalContact*
 
|Name*
 
|Name*
 
|John Doe
 
|John Doe
Line 41: Line 41:
 
|-
 
|-
 
|Phone
 
|Phone
−
| +49 30 838 99999999
+
| +49 30 838 99999
 
|-
 
|-
  
Line 50: Line 50:
 
|-
 
|-
  
−
|rowspan="2" | Metadata/RevisionData
+
|rowspan="2" | Metadata/RevisionData*
 
|DateCreated
 
|DateCreated
 
|2018-07-19
 
|2018-07-19
Line 71: Line 71:
 
|-
 
|-
  
−
|rowspan="4" | Metadata/Description/Representation
+
|rowspan="4" | Metadata/Description/Representation*
 
|Title*
 
|Title*
 
|Herbarium Berolinense
 
|Herbarium Berolinense
Line 95: Line 95:
 
|-
 
|-
 
|TelephoneNumbers/TelephoneNumber
 
|TelephoneNumbers/TelephoneNumber
−
| +49 30 838 99999999
+
| +49 30 838 99999
 
|-
 
|-
 
|URIs/URL
 
|URIs/URL
Line 122: Line 122:
 
|Acknowledgements
 
|Acknowledgements
 
|The project was funded by the German Federal Ministry of Education and Research (BMBF)
 
|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.).
 
|-
 
|-
  
Line 132: Line 132:
 
|Disclaimer
 
|Disclaimer
 
|No responsibility is accepted for the accuracy of the information in this database.
 
|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).
 
|-
 
|-
  
Line 145: Line 145:
 
|-
 
|-
 
|}
 
|}
 +
 +
'''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].
  
 
==Specimen 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.
+
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===
 
===General unit data===
Line 175: Line 177:
  
 
|CollectorsFieldNumber
 
|CollectorsFieldNumber
−
|1055
+
|765/10
 
|The original number assigned to the unit by the collector or observer.
 
|The original number assigned to the unit by the collector or observer.
 
|-
 
|-
 
|RecordBasis
 
|RecordBasis
−
|PreservedSpecimen
+
|LivingSpecimen
−
|An indication of what the unit record describes; needs to comply with a coontrolled vocabulary.
+
|An indication of what the unit record describes; needs to comply with a [https://dwc.tdwg.org/terms/#basisOfRecord controlled vocabulary].
 
|-
 
|-
 
|KindOfUnit
 
|KindOfUnit
−
|Whole plant
+
|Seed; (whole) plant
 
|Part(s), physical state, or class of materials represented by this specimen.  
 
|Part(s), physical state, or class of materials represented by this specimen.  
 
|-
 
|-
Line 208: Line 210:
 
|}
 
|}
  
−
===The sample identifiers===
+
===Gathering event===
−
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 ''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''.
 +
 
 
{| class="wikitable"
 
{| class="wikitable"
−
! width="120px" | Group
+
!Group
 
!Element
 
!Element
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 +
|-
 +
|rowspan="2" | 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).
 
|-
 
|-
−
|Unit
+
|GatheringAgent/AgentText
−
|*<span style="color:red">SourceID</span>
+
|Sipman
−
|short description of relevant collection
+
|Name of an individual gathering agent. The element ''GatheringAgent'' is repeatable, so it can be provided several times in case of a gathering team.
−
|should be "DNA Bank" or "tissue collection"
 
 
|-
 
|-
−
|Unit
+
 
−
|*<span style="color:red">SourceInstitutionID</span>
+
|rowspan="4" | Altitude
−
|short name/abbreviation of relevant institution
+
|MeasurementOrFactText
−
|BGBM
+
|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.
 
|-
 
|-
−
|Unit
+
 
−
|*<span style="color:red">UnitID</span>
+
|MeasurementOrFactAtomised/LowerValue*
−
|DNA extraction number or tissue number
+
|1500
−
|DNA 123
+
|The lower or only value of the gathering site altitude.
 
|-
 
|-
−
|Unit
 
−
|UnitGUID
 
−
|sample record GUID
 
−
|f6c7fd5a-2f04-4dcb-ba38-0230bf196d30
 
−
|}
 
  
−
===GGBN terms===
+
|MeasurementOrFactAtomised/UpperValue
−
The following fields are highly recommended, some are mandatory (marked with *), but feel free to map more!
+
|1600
−
<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>
+
|The upper value for the measured gathering site altitude, if there is a range.  
−
{| class="wikitable"
 
−
! width="120px" | Group
 
−
!Element
 
−
!Remarks
 
−
!Example
 
 
|-
 
|-
−
|
+
 
−
|*RecordBasis
+
|MeasurementOrFactAtomised/UnitOfMeasurement
−
|The specific nature of the data record, controlled vocabulary!
+
|m
−
|"PreservedSpecimen", "MaterialSample", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"; for Tissue or DNA samples use "MaterialSample"
+
|The unit of measurement used to measure the gathering site altitude.
 
|-
 
|-
−
|
+
 
−
|*materialSampleType
+
|rowspan="2" | Country
−
|Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type
+
|ISO3166Code
−
|"tissue", "DNA", "specimen"
+
|US
 +
|ISO code of the country where the voucher was collected/observed.
 
|-
 
|-
−
|SpecimenUnit/Preparation
+
 
−
|*preparationType
+
|Name*
−
|description of type of material, free text
+
|United States of America
−
|or DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood
+
|Name of the gathering country.
 
|-
 
|-
−
|SpecimenUnit/Preparation
+
 
−
|*preparationDate
+
|rowspan="3" | DateTime
−
|date of DNA extraction
+
|DateText
−
|if unknown type "unknown"
+
|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.
 
|-
 
|-
−
|SpecimenUnit/Preparation
+
 
−
|*preparatioMaterials
+
|ISODateTimeBegin
−
|extraction kit or protocoll
+
|2012-08-17
−
|if unknown type "unknown"
+
|Gathering date in ISO format. If you want to provide a time span, this will be the start of the time span.
 
|-
 
|-
−
|SpecimenUnit/Preparation
+
 
−
|*preparedBy
+
|ISODateTimeEnd
−
|extraction staff
+
|2012-08-19
−
|if unknown type "unknown"
+
|End datetime (in ISO format) if the gathering covers a time span.
 
|-
 
|-
−
|SpecimenUnit/Preservation
+
 
−
|preservation
+
|
−
|preservation of the tissue or DNA
+
|LocalityText
−
|if unknown type "unknown"
+
|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.
 
|-
 
|-
−
|SpecimenUnit/Loan/Permit
+
 
−
|*permitStatus
+
|rowspan="2" | NamedArea
−
|Information about the presence, absence or other basic status of permits associated with the sample(s), controlled vocabulary!
+
|AreaName
−
|Permit available, Permit not required, Permit not available, '''Unknown Material collected after 2014-10-12 cannot be in "Unknown" permit status!'''
+
|Europe
 +
|Any geographic term that is neither a country (use ''Country'' element) nor the exact locality description (use ''LocalityText'').
 
|-
 
|-
−
|SpecimenUnit/Loan/Permit
+
 
−
|*permitStatusQualifier
+
|AreaClass
−
|Description of why a certain permit was not required or why Permit Status is unknown
+
|Continent
−
|"no national requirement for a permit at date of access", "officially authorized illegal holder", "collected on private land", "pre-Nagoya"
+
|Type of geographic term provided in ''AreaName''
 
|-
 
|-
−
|SpecimenUnit/Loan/Permit
+
 
−
|*permitType
+
|Biotope
−
|A permit is a document that allows someone to take an action that otherwise would not be allowed, controlled vocabulary!
+
|Text
−
|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
+
|Amongst rocks and stones, calcareous soil and screes
 +
|Gathering site biotope description.
 
|-
 
|-
−
|SpecimenUnit/Loan/Permit
+
 
−
|*permitText
+
| -
−
|The text of a permit related to the gathering/shipping or further details
+
|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.
 
|-
 
|-
−
|GGBN/Amplification
+
 
−
|amplificationDate
+
|rowspan="8" | SiteCoordinateSets/ SiteCoordinates/ CoordinatesLatLong
−
|date of amplification; if unknown or general without content you don't have to map it
+
|../CoordinateMethod
−
|should be ISO format yyyy-mm-dd
+
|Inferred map reference
 +
|Method of coordinates determination (GPS vs. inferred from description).
 
|-
 
|-
−
|GGBN/Amplification
+
 
−
|marker
+
|LatitudeDecimal
−
|
+
|52.49179
−
|COX1
+
|Latitude in decimal degrees.
 
|-
 
|-
−
|GGBN/Amplification
+
 
−
|geneticAccessionNumber
+
|LongitudeDecimal
−
|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
+
|13.23589
−
|e.g. AJ45567
+
|Longitude in decimal degreed.
 
|-
 
|-
−
|GGBN/Amplification
+
 
−
|genBankNumber-URI
+
|CoordinatesText
−
|complete link to the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD
+
|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.
 
|-
 
|-
−
|SpecimenUnit
+
 
−
|blockedUntil
+
|SpatialDatum
−
|in case the sample is blocked until a specific date it's nevertheless searchable but customers cannot order it
+
|WGS 84
−
|ISO format
+
|A mathematical surface on which the mapping and coordinate system used for the geocodes of the gathering site are based.
 
|-
 
|-
−
|SpecimenUnit
+
 
−
|blocked
+
|CoordinateErrorDistanceInMeters
−
|sample is blocked (e.g. because it is consumed), but data are still available
+
|500
−
|Yes/No
+
|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.
 
|-
 
|-
−
|GGBN
+
 
−
|concentration
+
|AccuracyStatement
−
|concentration of the DNA
+
|Coordinates rounded to 2 decimal places.
−
|65,34
+
|A free text statement of the degree of accuracy of the latitude and longitude coordinates.
 
|-
 
|-
−
|GGBN
+
 
−
|@unit
+
|CoordinateErrorMethod
−
|unit of the concentration
+
|Maximum error defined by dimensions of original ordinance survey map.
−
|µg/ml
+
|Verbatim statement of how the Coordinate Error was determined.
 
|-
 
|-
−
|GGBN
+
 
−
|ratioOfAbsorbance260_230
+
| -
−
|map only if filled with content
+
|Notes
−
|1,2
+
|
 +
|Further text relating to the gathering event that does not fit one of the specified elements.
 
|-
 
|-
−
|GGBN
+
 
−
|ratioOfAbsorbance260_280
 
−
|map only if filled with content
 
−
|1,8
 
 
|}
 
|}
  
−
==Related Specimen Data==
+
===Identification history===
−
<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>
+
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.
−
[[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
 +
!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''.
 +
|-
 +
 +
|Date
 +
| -
 +
|DateText/ISODateTimeBegin
 +
|2018-08-17
 +
|Date of the unit identification event. If in ISO format, use ''ISODateTimeBegin'', ''DateText'' otherwise.
 
|-
 
|-
−
|Associations/UnitAssociation
+
 
−
|*UnitID
+
|rowspan="2" | Identifiers
−
|the UnitID or CatalogueNumber used for GBIF
+
| -
−
|e.g. the barcode number of your specimens
+
|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).
 
|-
 
|-
−
|Associations/UnitAssociation
+
 
−
|*SourceInstitutionID
+
|Identifier/PersonName
−
|the SourceInstitutionID or InstitutionCode used for GBIF
+
|FullName
−
|e.g. the acronym of your institution
+
|Humboldt
 +
|Person that made the identification.
 
|-
 
|-
−
|Associations/UnitAssociation
+
 
−
|*SourceName
+
|rowspan="9" | Result/TaxonIdentified
−
|the SourceID or CollectionCode used for GBIF
+
|rowspan="2" | HigherTaxa/HigherTaxon
−
|e.g. the name of the collection where the specimen belongs to, e.g. "Birds"
+
|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]
 
|-
 
|-
−
|Associations/UnitAssociation
+
 
−
|*AssociationType
+
|HigherTaxonRank
−
|the Relation between the DNA and the voucher
+
|familia
−
|e.g. "DNA and voucher from same individual"
+
|Rame of the higher taxon.
 +
|-
 +
 
 +
|ScientificName
 +
|FullScientificNameString*
 +
|Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi
 +
|Complete name of the taxon including Authors (and years for animals).
 
|-
 
|-
−
|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===
+
|rowspan="5" | ScientificName/NameAtomised/Botanical
−
'''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.
+
|GenusOrMonomial
 +
|Aaronsohnia
 +
|rowspan="5" | ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.)
 +
|-
  
−
{| class="wikitable"
+
|FirstEpithet
−
! | Group
+
|factorovskyi
−
!Element
 
−
!Remarks
 
−
!Example
 
 
|-
 
|-
−
|
+
 
−
|*CollectorsFieldNumber
+
|InfraspecificEpithet
−
|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
+
|factorovskyi
−
|e.g. 765/10
 
 
|-
 
|-
−
|Gathering/Agents/GatheringAgent
+
 
−
|*FullName
+
|Rank
−
|the Collector or Collector Team
+
|var.
−
|e.g. Scholz & Sipman
 
 
|-
 
|-
−
|Gathering/Altitude
+
 
−
|*LowerValue
+
|AuthorTeam
−
|if you have both the lower and upper value in different columns map both field, if not map LowerValue only
+
|Warb. & Eig.
−
|e.g. 100
 
 
|-
 
|-
−
|Gathering/Altitude
+
 
−
|UpperValue
+
| -
 +
|NameComments
 
|
 
|
−
|e.g. 200
+
|Free text comments related to the name identified for the unit.
 
|-
 
|-
−
|Gathering/Altitude
+
 
−
|*Unit
+
|rowspan="2" | References/Reference
−
|
+
|rowspan="2" | -
−
|e.g. m
+
|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).
 
|-
 
|-
−
|Gathering/Country
+
 
−
|*ISO3166Code
+
|CitationDetail
−
|ISO code of the country where the voucher was collected
+
|p. 22 + 226, 35 pl.
−
|e.g. US
 
 
|-
 
|-
−
|Gathering/Country
+
 
−
|*Name
+
| -
−
|english Name of the country
+
| -
−
|e.g. United States of America
+
|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.
 
|-
 
|-
−
|Gathering/DateTime
+
 
−
|*DateText
+
 
−
|date when voucher was collected, if you have content yuo can also use ISO format
+
|}
−
|e.g. 21. April 1951
+
 
 +
===Botanical Garden Unit===
 +
 
 +
{| class="wikitable"
 +
!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)
 
|-
 
|-
−
|Gathering/Locality
+
|Cultivation
−
|*LocalityText
 
 
|
 
|
−
|e.g. 5km NO Berlin
+
|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.
 
|-
 
|-
−
|Gathering/NamedArea
+
|Hardiness
−
|AreaName
+
|1
−
|name of continent
+
|A flag indicating that the accession is grown outdoors in the botanical garden.
−
|e.g. Europe
+
|-
 +
|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.
 
|-
 
|-
−
|Gathering/NamedArea
+
|LocationInGarden
−
|@language
+
|MD4
−
|language of the name of continent
+
|The current location of the living plant in the botanical garden.
−
|e.g. "en"
 
 
|-
 
|-
−
|Gathering/SiteCoordinates
+
|Perennation
−
|*LatitudeDecimal
 
 
|
 
|
−
|e.g. -15,88876
+
|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.
 
|-
 
|-
−
|Gathering/SiteCoordinates
 
−
|*LongitudeDecimal
 
−
|
 
−
|e.g. 72,88876
 
 
|}
 
|}
  
−
===Identification history of the voucher===
+
'''Note for gardens4Science data providers:'''
−
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.
+
# 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.
 +
# 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===
 +
 
 
{| class="wikitable"
 
{| class="wikitable"
−
! | Group
+
!ABCD element
−
!Element
 
−
!Remarks
 
 
!Example
 
!Example
 +
!Remark
 
|-
 
|-
−
|Identification
+
|AccessionCatalogue
−
|*PreferredFlag
+
|
−
|mark the presently preferred Identification
+
|Identifier of an accessions catalogue or numbering scheme
−
|e.g. true, false, 0, 1
 
 
|-
 
|-
−
|Identification/HigherTaxon
+
|AccessionDate
−
|*HigherTaxonName
+
|2007-07-07
−
|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]
+
|Date on which the accession was recorded
−
|e.g. Asteraceae, Animalia
 
 
|-
 
|-
−
|Identification/HigherTaxon
+
|AccessionNumber
−
|*HigherTaxonRank
+
|001010680
−
|the rank of the taxon in english or latin
+
|Institutional number applied to an accession and recorded in the accessions register.
−
|e.g. familia, regnum, phylum
 
 
|-
 
|-
−
|Identification/ScientificName
+
|}
−
|*FullScientificName
+
 
−
|the complete name of the taxon including Authors (and years for animals)
+
===Multimedia===
−
|e.g. Aaronsohnia factorovskyi Warb. & Eig. var. factorovskyi
+
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"
 +
!ABCD element
 +
!Example
 +
!Remark
 
|-
 
|-
−
|Identification/ScientificName/NameAtomised
+
 
−
|*FirstEpithet
+
|FileURI*
−
|Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.)
+
|http://ww2.bgbm.org/herbarium/images/B/-W/14/61/B_-W_14616%20-00%200.jpg
−
|e.g. factorovskyi
+
|The Universal Resource Identifier (URI) of the underlying multimedia file.
 
|-
 
|-
−
|Identification/ScientificName/NameAtomised
+
 
−
|*GenusOrMonomial
+
|ProductURI
−
|
+
|http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=726
−
|e.g. Aaronsohnia
+
|The Universal Resource Identifier of an electronic source of a multimedia object including HTML, Javascript or similar means delivering rendered output.
 
|-
 
|-
−
|Identification/ScientificName/NameAtomised
+
 
−
|*InfraspecificEpithet
+
|Comment
−
|Please note: ABCD has several container for NameAtomised, it depens on your sampes which one to choose (Botanical or Zoology etc.)
+
|Image of herbarium specimen E00732880 by Specimen Digitisation Pipeline.
−
|e.g. factorovskyi
+
|Short description of the multimedia object.
 
|-
 
|-
−
|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===
+
|Format
−
These should be mapped in the specimen mapping, not the DNA mapping.
+
|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.
 +
|-
  
−
{| class="wikitable"
+
|CreatedDate
−
! Category
+
|2012-07-07
−
! Element
+
|The date the multimedia object was created.
−
! Discription
 
−
! Comment
 
 
|-
 
|-
−
| rowspan="3" | Metadata
+
 
−
| Title
+
|ID
−
|  
+
|22658
−
|  
+
|Identifier for the multimedia object relating to or forming the unit. This may be a filename.
 
|-
 
|-
−
| IPR  
+
 
−
|  
+
|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 [[ABCD2Concepts#General_metadata | remarks]].
 
|-
 
|-
−
| TechnicalContact
+
 
−
|
 
−
|
 
−
|-
 
−
| Unit
 
−
| UnitID
 
−
|
 
−
|
 
 
|}
 
|}

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.
Retrieved from "https://wiki.bgbm.org/bps/index.php?title=ABCD2Concepts&oldid=1116"