Difference between revisions of "ABCD2Concepts"

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(→‎The sample identifiers)
(→‎GGBN terms)
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|The name or other indication of the person or team that created or last edited this record.
 
|The name or other indication of the person or team that created or last edited this record.
 
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===GGBN terms===
 
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The following fields are highly recommended, some are mandatory (marked with *), but feel free to map more!
 
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<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>
 
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{| class="wikitable"
 
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! width="120px" | Group
 
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!Element
 
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!Remarks
 
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!Example
 
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|-
 
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|
 
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|*RecordBasis
 
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|The specific nature of the data record, controlled vocabulary!
 
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|"PreservedSpecimen", "MaterialSample", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"; for Tissue or DNA samples use "MaterialSample"
 
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|-
 
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|
 
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|*materialSampleType
 
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|Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type
 
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|"tissue", "DNA", "specimen"
 
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|-
 
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|SpecimenUnit/Preparation
 
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|*preparationType
 
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|description of type of material, free text
 
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|or DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood
 
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|-
 
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|SpecimenUnit/Preparation
 
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|*preparationDate
 
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|date of DNA extraction
 
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|if unknown type "unknown"
 
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|-
 
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|SpecimenUnit/Preparation
 
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|*preparatioMaterials
 
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|extraction kit or protocoll
 
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|if unknown type "unknown"
 
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|-
 
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|SpecimenUnit/Preparation
 
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|*preparedBy
 
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|extraction staff
 
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|if unknown type "unknown"
 
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|-
 
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|SpecimenUnit/Preservation
 
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|preservation
 
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|preservation of the tissue or DNA
 
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|if unknown type "unknown"
 
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|-
 
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|SpecimenUnit/Loan/Permit
 
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|*permitStatus
 
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|Information about the presence, absence or other basic status of permits associated with the sample(s), controlled vocabulary!
 
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|Permit available, Permit not required, Permit not available, '''Unknown Material collected after 2014-10-12 cannot be in "Unknown" permit status!'''
 
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|-
 
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|SpecimenUnit/Loan/Permit
 
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|*permitStatusQualifier
 
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|Description of why a certain permit was not required or why Permit Status is unknown
 
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|"no national requirement for a permit at date of access", "officially authorized illegal holder", "collected on private land", "pre-Nagoya"
 
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|-
 
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|SpecimenUnit/Loan/Permit
 
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|*permitType
 
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|A permit is a document that allows someone to take an action that otherwise would not be allowed, controlled vocabulary!
 
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|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
 
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|-
 
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|SpecimenUnit/Loan/Permit
 
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|*permitText
 
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|The text of a permit related to the gathering/shipping or further details
 
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|
 
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|-
 
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|GGBN/Amplification
 
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|amplificationDate
 
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|date of amplification; if unknown or general without content you don't have to map it
 
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|should be ISO format yyyy-mm-dd
 
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|-
 
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|GGBN/Amplification
 
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|marker
 
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|
 
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|COX1
 
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|-
 
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|GGBN/Amplification
 
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|geneticAccessionNumber
 
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|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
 
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|e.g. AJ45567
 
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|-
 
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|GGBN/Amplification
 
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|genBankNumber-URI
 
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|complete link to the accession number of NCBI/EMBL/DDBJ or the process ID of BOLD
 
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|
 
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|-
 
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|SpecimenUnit
 
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|blockedUntil
 
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|in case the sample is blocked until a specific date it's nevertheless searchable but customers cannot order it
 
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|ISO format
 
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|-
 
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|SpecimenUnit
 
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|blocked
 
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|sample is blocked (e.g. because it is consumed), but data are still available
 
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|Yes/No
 
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|-
 
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|GGBN
 
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|concentration
 
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|concentration of the DNA
 
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|65,34
 
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|-
 
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|GGBN
 
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|@unit
 
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|unit of the concentration
 
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|µg/ml
 
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|-
 
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|GGBN
 
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|ratioOfAbsorbance260_230
 
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|map only if filled with content
 
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|1,2
 
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|-
 
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|GGBN
 
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|ratioOfAbsorbance260_280
 
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|map only if filled with content
 
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|1,8
 
 
|}
 
|}
  

Revision as of 15:18, 27 September 2018

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

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

Metadata

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

General metadata

Group Element Example Remarks
ContentContact Name* John Doe Contact information for the curator of the dataset.
Address Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany
Email john.doe@acme.com
Phone +49 30 838 99999999
TechnicalContact Name* John Doe Contact information of the person that is responsible for the BioCASe installation - in most cases, this will be the IT department.
Address Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany
Email john.doe@acme.com
Phone +49 30 838 99999999
Metadata IconURI http://ww3.bgbm.org/providerResources/BGBM.jpg Link to an image that represents the dataset.
Metadata/RevisionData DateCreated 2018-07-19 Date when the dataset has been first published (DateCreated) and of the last changes/additions/removals (DateModified).
DateModified* 2018-09-27
Metadata/Version DateIssued 2018-09-27 If you keep track of dataset versions, the info can be specified in this section.
Major* 3
Minor 1
Metadata/Description/Representation Title* Herbarium Berolinense Short description of the dataset (preferrably in english), consisting of a title, a 2-3 sentences long description and an optional URL.
@language* en
Description The herbarium of the Botanic Garden and Botanical Museum Berlin-Dahlem (herbarium acronym: B) is ...
URL https://www.bgbm.org/en/herbarium
Metadata/Owners/Owner Addresses/Address Botanic Garden and Botanical Museum Berlin. Königin-Luise-Str. 6-8; 14195 Berlin, Germany Institution that owns the dataset.
EmailAddresses/EmailAddress john.doe@acme.com
TelephoneNumbers/TelephoneNumber +49 30 838 99999999
URIs/URL https://www.bgbm.org
LogoURI http://ww3.bgbm.org/providerResources/BGBM.jpg
Organisation/Name/Representation/Text* Botanic Garden and Botanical Museum Berlin-Dahlem
Organisation/Name/Representation/Abbrevation BGBM

IPR Statements

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

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

Specimen Data

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

General unit data

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

Related Specimen Data

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

The voucher identifiers

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

Gathering event of the voucher

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

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

Identification history of the voucher

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

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

Multimedia items of the voucher

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


Category Element Discription Comment
Metadata Title
IPR
TechnicalContact
Unit UnitID
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