Systematics Collections Data

Data

This page provides a brief description of the fields used in the search, results and/or record details pages.

Assigned reference numbers

A list of other reference numbers that have been assigned to this specimen (e.g., NZRCC number for ICMP cultures; Fungal Network of NZ Fungal Foray Numbers (FUNNZ) for PDD specimens). This list does not include accession numbers from other herbaria.

Search title: otherReferenceNo
Assigned reference numbers

This is the value of another reference number assigned to the specimen.

Search title: otherReferenceNoType
Other reference number type

The is a name or acronym of the numbering system of an other reference number assigned to the specimen.

Batches

The term 'batch' is used to refer to a set of samples that were prepared at the same time and from the same material for a particular ICMP accession when the stock of that culture had become low.

Original viability

The viability of this culture batch when it was created.

Physical location

The physical storage location of this culture batch.

Search title: storageMethod
Storage method

A list of any notes that are associated with the specimen. Each note will provide the type of note (as the title), the note text, followed by the note author and date if they are available.

Search title: cultureViability
Viability

The viability of this culture when it was last tested.

[Batches] Note

Any notes regarding this culture batch.

Collection event

Most specimens are derived from a single collecting event. However, some specimens are derived from a series of 'collecting events'.

For example specimens of plants grown in cultivation or reared insects.

For these specimens the SCD system records all of these collecting events to provide the full provenance of the specimen. One of these collecting events, usually the most recent or the collecting event when the material was originally gathered in the field, is designated the 'primary collection event'.

Search title: abundance
Abundance

Abundance of the collected taxon at the location and time of the collecting event.

Search title: altitude
Altitudes

The verbatim elevation converted into metres at which the collecting event occurred.

Search title: collectionEventCode
Collection Event Code

A reference code assigned to the collecting event, or the name of an expedition.

Search title: collectionMethod
Collection Method

The method used to collect this specimen.

For example: trap, pitfall

Search title: verbatimCollectionDate
Collection date

The verbatim collection date is the verbatim date, or date range, for the collecting event, as recorded by the collector.

This field may contain the verbatim or standardised value of the collection date depending on the context.

 Standard valueVerbatim value
Location/UseLabelExampleLabelExample
Search field namecollectionDatecollectionDate:20240201verbatimCollectionDateverbatimCollectionDate:1 Feb 2024
FacetsCollection year2024  
 Collection monthFeb  
 Collection date2024-02-01  
Results - Grid viewCollection date2024-02-01  
Results - Map viewCollection monthMay  
 Collection year2024  
 Collection decade2020's  
Details pageStart date2024-05-01Verbatim date1-3 May 2024
 End date2024-05-03  
Download TSV fileCollectionDateISO_CE*2024-05-01CollectionDate_CE*1 May 2024

The standard collection date is the verbatim date converted, if possible, to ISO format.

Collection decade

The decade of collection.  Derived from Collection date​​​​​​​.

Search title: collectionEventContext
Collection event type

Indicates whether this collecting event was known to have occurred in the field, or under artificial growing conditions (culture, cultivation, reared) or this information is unknown.

Search title: collectionMonth
Collection month

The month of collection.

Derived from Collection date.

Search title: collectionYear
Collection year

The year of collection.

Derived from Collection date.

Search title: collector
Collector

The name of the person who made the gathering. In some cases this may be more than one person.

This field may contain the verbatim or standardised value of the collector depending on the context.

 Standard valueVerbatim value
Location/UseLabelExampleLabelExample
Search titlecollectorcollector:William R. SykesverbatimCollectorverbatimCollector: W.R. Sykes
FacetsCollectorWilliam R. Sykes  
Results - Grid viewStandardised CollectorWilliam R. Sykes  
Details pageStandardised collectorWilliam R. SykesVerbatim collectorW.R. Sykes
Download TSV file  Collector_CE*W.R. Sykes
Search title: collectorsNumber
Collectors reference no.

The collector's personal reference number for this collecting event.

Search title: habitat
Habitat

A description of the habitat provided by the collector.

Search title: keyword
Keywords

Ecological keywords associated with collection events.

For example: keyword:Forest

Search title: localHeight
Local heights

A height or depth offset from the elevation for the collecting event. This may, for example, indicate the depth below a water surface or the height up a tree.

Search title: locality
Locality

Standard locality is the collecting location following a standardised gazetteer of locations for each collection. These locations are provided to assist with the interpretation of the verbatim locality.

Verbatim locality is the collecting location as provided by the collector.

This field may contain the verbatim or standardised value of the collection locality depending on the context.

 Standard valueVerbatim value
Location/UseLabelExampleLabelExample
Search title  localitylocality:Landcare Research experimental nursery
Results - List viewStandard localityLincoln, Landcare Research  
Details pageStandard locality - LocationLincoln, Landcare ResearchVerbatim localityLincoln, Landcare Research experimental nursery
Download TSV fileStandardLocality_CE*Lincoln, Landcare ResearchLocality_CE1*Lincoln, Landcare Research experimental nursery
Search title: microHabitat
Microhabitat

A description of the microhabitat provided by the collector.

Search title: collectionEventNote
Notes

Any additional notes provided by the collector.

Search title: observedSpecies
Observed species

A list of species observed at the collecting site by the collector, unless indicated by the word 'derived'. If the species are indicated as 'derived' they have been added using supplementary information by the collector or a later worker.

Components

Most specimens consist of material from a single taxon or individual, but some specimens are composed of material from more than one taxon or individual. In SCD we refer to each taxon or distinct part that makes up a specimen as a 'component'. These components may be associated through a particular relationship (e.g. host–parasite), or may simply have been collected together (e.g. many bryophyte collections). When there is more than one component present, one of the components is flagged as the 'Primary component' – this is deemed to be the taxa of most interest at the time of accessioning and is the taxon under which the specimen is stored.

Association

The category of association (e.g., host) and taxonomic name of the associated organism.

Search title: associationType
Association type

The type of association between two components.

Search title: partAffected
Part affected

Description of the part of the component affected by the association.

Search title: substrate
Substrate

Description of the substrate from which the specimen or culture was collected.

Duplicates

When a duplicate specimen is known to be held by another collection, we provide a list with the acronym of the other collection(s) followed by their accession number (if known).

For example, for CHR 486272 this field displays as AK: AK 227406 because a duplicate specimen (AK 227406) is held in the herbarium at the Auckland War Memorial Museum (AK).

Date received

The date the duplicate was sent or received.

Direction

The direction of the duplicate i.e. sent, received or duplicate

Search title: duplicates
Duplicates at

The acronym of the other collection(s).

Search title: duplicateAccessionNumber
Other catalog numbers

The accession number (if known) of the other collection.

Geographic regions

The geographic region(s) within which the collection event occurred. A collection event may have geographic regions indicated for one or more of the schemas.

Search title: botanicalDistrict
Botanical District

The name of the Botanical District from which this specimen or culture was collected. See Cockayne, L. 1958: The Vegetation of New Zealand (3 e.d.) Weinheim: J.Cramer. 456 p. p;s 1-87, 3 end maps

Search title: country
Country

The name at the time of collection for the country from which this specimen or culture was collected.

This field may contain the verbatim or standardised value of the country depending on the context. The standardised value is based on ISO country list.

 Standard valueVerbatim value
Location/UseLabelExampleLabelExample
Search field namecountrycountry:New Zealand  
Facets Country​​​​​​​​​​​​​​ New Zealand  
Results - Grid viewCountryNew Zealand  
Details pageCountryNew Zealand  
Download TSV fileCountry_CE*New ZealandVerbatimCountry_CE*N.Z.
Search title: ecologicalDistrict
Ecological District

The standard name of the Ecological District  (following McEwen 1987) from which this specimen or culture was collected.

Search title: ecologicalRegion
Ecological Region

The standard name of the Ecological Region  (following McEwen 1987) from which this specimen or culture was collected.

Search title: landDistrict
Land district

The name of the Land District from which this specimen or culture was collected. Land Districts were established under the Land Act 1948 (and earlier Acts). Boundaries are displayed on NZMS 311A or see Marshall & Kelly (1986) Atlas of New Zealand Boundaries. Department of Geography, University of Auckland Occasional Publication No. 20.

Search title: nzAreaCodeFull (full name)
NZ Area Code

The name of the New Zealand Area from which this specimen or culture was collected. See Crosby et al. (1998) Area codes for recording specimen localities in the New Zealand subregion. New Zealand Journal of Zoology 25(2): 175–183.

Native lands

The name of the territory, or territories, from which this specimen or culture was collected. The territory boundaries are defined by  Native Land Digital, which is updated often, therefore we periodcally refresh this information.

Search title: stateProvince
State/Province

The state or province from which this specimen or culture was collected.

Search title: worldGeographicRegion
World Geographic Scheme for Recording Plant Distribution

The name from the World Geographic Scheme from which this specimen or culture was collected. See  https://www.tdwg.org/standards/wgsrpd/ for details on the Scheme.

Georeferences

The georeferences recorded by the collector or a later worker.

Search title: decimalLatitude
Decimal latitude

The decimal latitude (WGS 1984).

Derived from  Georeference.

Search title: decimalLongitude
Decimal longitude

The decimal longitude (WGS 1984).

Derived from  Georeference.

Search title: georeference
Georeferences

The georeferences recorded by the collector or a later worker.

Identifications

The identification fields provide information about the current and historical identifications that have been applied to the specimen. Within SCD, identifications are recorded for each  component allowing for full identification histories to be recorded regardless of how many components are present. For each component the identifications are separated into the Active identification and Other identifications.

Active

This indicates which identification is the active identification. There can only be one active identification per component.

Search title: class
Class

For the active identification, the name of the taxonomic class under which the specimen is classified.

Search title: identificationUncertain
Confidence of identification

This indicates whether the determiner/ identifier is certain or not certain of their identification.

Search example: identificationUncertain:Uncertain

Search title: taxonomicName
Determined name

The verbatim taxonomic name provided by the determiner.

Search title: determiner
Determiner

The Verbatim determiner is the person who provided the determination/identification.

The Standard determiner is the standarised name of the person(s), if known,

This field may contain the verbatim or standardised value of the collector depending on the context.

 Standard valueVerbatim value
Location/UseLabelExampleLabelExample
Search titledeterminerdeterminer:William R. Sykes  
FacetsDeterminerWilliam R. SykesDeterminerW.R. Sykes
Details pageDeterminerSykes WR  
Download TSV file  Determiner_C*W.R. Sykes
Determiners reference number

The identifier's reference number for this identification.

Search title: family
Family

For the active identification, the name of the taxonomic family under which the specimen is classified.

Search title: genus
Genus

The genus name associated with any identifications applied to the specimen

Search title: identificationDate
Identification date [ISO]

The verbatim determination date is the date on which the determiner identified the specimen.

This field may contain the verbatim or standardised value of the identificaiton date depending on the context.

 Standard valueVerbatim value
Location/UseLabelExampleLabelExample
Search field nameidentificationDateidentificationDate:20240501  
FacetsIdentification date2024-05-01  
Details pageIdentification date2024-05-01(Verbatim:1 May 2024)
Download TSV fileIdentificationDateISO_C*2024-05-01  

The standard determination date is the verbatim date converted, if possible, to ISO format.

Search title: typeOfIdentification
Identification type

For each identification, the type of identification that was applied by the determiner. The type of identification varies between each collection.

Type of identificationDefinitionUsed by
ConfirmationA critical examination of the specimen that confirms a previous identification.CHR; ICMP
DeterminationA critical examination of the specimen that changes a previous identification.CHR; FLAX; ICMP; NZAC; PDD
Implicit...PDD
Nomenclatural curationAn technical change that has been applied to the specimen to update the scientific name of the specimen. These identifications do not critically examine the matter, rather they are based on an early determination that has been applied to the specimen and are usually made following a recent revision or monograph of a taxonomic group.CHR; PDD
Received asThe identification applied to the culture when it was received by ICMP.ICMP
Taxonomic curationA change that has been applied to the specimen to update the scientific name of the specimen following a recent revision or monograph that has resulted in a different taxonomic treatment for the taxon to which the specimen is identified. These 'identifications' do not critically examine the matter, rather they are based on an early determination that has been applied to the specimen and are always made following a recent revision or monograph of a taxonomic group.CHR; PDD
Search title: identificationNote
Note

A note relating to the identification, if any, made by the determiner.

Search title: order
Order

For the active identification, the name of the taxonomic order under which the specimen is classified.

Search title: phylum
Phylum or Division

For the active identification, the name of the taxonomic division or phylum under which the specimen is classified.

Search title: preferredName
Preferred name

The preferred taxonomic name. This is based on the identification provided by the determiner, but uses taxonomic information from other sources to provide the preferred name for this taxon (see Currency of Data​​​​​​​ for more information).

Previous identification

This shows identifications that are not the active identification. There can be multiple previous identifications per component.

References

The references, if any, associated with this identification by the determiner.

Search title: mainTaxon
Taxonomic name

The standard taxonomic name of the active identification of the primary component. This is used in the Results view.

Search title: vernacularName
Vernacular name

If provided, the vernacular name given by the determiner.

Links

A list of links to external resources that are associated with the specimens. The list provides a short title for each link and the reference text. If available, the reference text is provided as a hyperlink.

Search title: linkSource
External link type

This is the type of external resource i.e. GenBank, Literature etc

Search title: linkValue
Link value

This is the value of the external link. If available, it will be provided as a hyperlink.

Note:

This is an note field that sometimes contains additional information about a link.

Specimen

These fields contain information and metadata about each collection object.

Search title: accessionNumber
Accession number

The catalogue number assigned to this specimen.

CollectionFormatDescription
Allan HerbariumCHR #Primary accession number for a specimen in the Allan Herbarium. These numbers are permanent and may be cited in published works.
International Collection of MicroorganismsICMP #Primary accession number for the culture in the International Collection of Microorganisms. These numbers are permanent and may be cited in published works.
New Zealand FungariumPDD #Primary accession number for the specimen in the New Zealand Fungarium. These numbers are permanent and may be cited in published works.
Arthropod CollectionNZAC#Primary accession and barcode number for the specimen in the New Zealand Arthropod Collection. These numbers are permanent and may be cited in published works.
  NZACAMP#
NZACTFB#
TYPELEP#
TYPEDIP#
Temporary numbers for specimen records in the the New Zealand Arthropod Collection.that were databased historically without permanent accession numbers being applied. These temporary numbers are gradually being replaced as the data are reviewed and permanent accession numbers are assigned.
Barcode

The barcode number assigned to this specimen. This will normally be the same value as the Accession Number​​​​​​​.

Search title: subcollection
Collection

The title for a named component within one of the main collections.

For example: the Allan Herbarium (CHR) has a Spirit (Ethanol) subcollection.

Search title: collection
Data provider

The name or acronym of collection in which the specimen or culture is held.

Search title: dateAdded
Date added

The date the record of this specimen was added to the information system converted, if possible, to ISO format.

Date last edited

The date the record of this specimen was last updated within the information system converted, if possible, to ISO format.

Search title: exsiccata
Exsiccata

When a specimen has been prepared as a duplicate in an exsiccata series this field will contain the title of the exsiccata series.

Search title: hasImages
Images available

Calculated field, based on presence of images. To search with this field, use the values true or false.

Search example: hasImages:True

NZ occurrence:  main taxon

The biostatus of the main taxon​​​​​​​, within New Zealand i.e. Absent, Border intercept, Eradicated, Extinct, Present, Present in captvity/cultivation/culture, Recorded in error, Sometimes present, Uncertain, Wild

NZ origin: main taxon

The origin status of the main taxon​​​​​​​, within New Zealand.

  • Indigenous: found naturally within New Zealand. Contains two subcategories when there is information on whether the organism is naturally found only within this region or is also found in other regions.
    • Endemic: found naturally only in the region. A refinement of Indigenous.
    • Non-endemic: found naturally in the region as well as in other regions.  A refinement of Indigenous.
  • Exotic: originally from outside the region; introduced.
  • Uncertain
Search title: specimenId
Specimen id

A unique identifier for this record.

Search title: kindOfSpecimen
Specimen type

The method used for preparing or mounting the specimen or the kind of culture. These vary between collections:

CollectionTypes of specimens or culture
CHRBag; Box; Packet; Photograph; Sheet; Slide; Vial (30); Vial (125); Vial (250); Vial (500); Vial (1000)
FLAXClone
ICMPBacterial Culture; Fungal Culture; Virus; Yeast Culture
NZACAlcohol; Pin; Slide; Unknown
PDDAlcohol; Dried; Packet
Search title: typeStatus
[icon]

The status of this specimen as a nomenclatural type as governed by the applicable International Code of Nomenclature.

Specimen events

Specimen events are actions or processes that have happened to the specimen after it has been collected. These may include actions that occurred during specimen preparation and deposition (e.g., culture isolation in ICMP), specimen curation or the application of particular treatments (e.g., changing of preservation fluid).

Search title: actionedBy
Actioned by

The standardised name of a person who was responsible for an event (or action) in the history of the specimen.

 Standard value 
Location/UseLabelExample
Search titleactionedByactionedBy:Peter K. Buchanan
FacetsActioned byPeter K. Buchanan
Details pageActioned byPeter K. Buchanan
Download TSV file Isolator
Depositer
Transferred from
TransferredVia
Peter K. Buchanan
Search title: referenceNumberForActionedBy
Actioned by: ... (Reference number ...)

A reference number assigned by the person who actioned the event.

 Verbatim value 
Location/UseLabelExample
Search titlereferenceNumberForActionedByreferenceNumberForActionedBy:BSW196
Facets  
Details page  (Reference number 86/033)
Download TSV file IsolatorsRefNo
DepositersRefNo
TransferrerFromRefNo
TransferredViaRefNo
IsolatorsRefNo AB3
Search title: actionedDate
Actioned date

The eventDateText/Actioned Date is the date the specimen event occurred. If available both the verbatim date and standardised date are provided.

This field may contain the verbatim or standardised value of the actioned date depending on the context.

 Standard valueVerbatim value
Location/UseLabelExampleLabelExample
Search titleActionedDateactionedDate:20240201eventDateTexteventDateText:August to September of 1901
FacetsActioned date2003-02-01  
Details pageDate01 February 2003(Verbatim:01 Feb 2003)
Download TSV file

IsolationDate
DepositedDate
TransferredFromDate
TransferredViaDate

2003-02-01  
Search title: eventNote
Note

A note associated with this specimen event.

Search title: typeOfEvent
Type of specimen event

The type of events recorded vary between the collections. The Event Type is used as the title for the event.

TitleDescriptionCollection
Cold treatment; Fumigation; Irridation; Heat treatment; Treatment historyInformation on a temperature-based or other treatments that has been applied to the specimen.CHR, NZAC
Collection managementInformation on an event associated with management of specimen within the collection.PDD
ContributedInformation on the event when the culture was directly contributed to the collectionICMP
IsolatedInformation on the event when the culture was isolatedICMP
PreparationInformation of an event associated with the preparation of the specimenICMP, NZAC
ReceivedInformation on when the culture was received by the collectionICMP
ViaInformation about the person who sent the culture to the contributorICMP

Specimen flags

Specimen flags are tags that are used to indicate a property or feature of a specimen. They usually provide biological information (e.g., gender) or collection management information (e.g., ICMP's Re-storage). The flags used vary between each collection, and some flags that reflect collection management activities are restricted to registered users.

CollectionType of flagDescription of flagAccess level
CHRSubsetA set of collection management flags used to indicate properties such as the levels of data verification, or the voucher status of the specimenRegistered Users 1
ICMPBACCMPI Border Access and clearance certificate numberRegistered Users 1
 EPA PermitEPA Permit numberRegistered Users 1
 Grade Indicates the level of authenticity of the strain for the culture.
a: there is published information indicating the authenticity
b: the strain has been examined at ICMP and considered to be authentic
?: considered to be atypical or improperly classified
Public
 Import permitMPI Import Permit numberRegistered Users 1
 MPIMPI status flagsPublic
 Price categoryIndicator of price category for purchase of culture.Public
 Re-storageManagement flag to indicate whether re-culturing and storage is requiredCollection Staff
 WarningRisk groupPublic
PDDAlcohol collectionUsed to indicate the presence of an alcohol collection and, if available, record a storage numberRegistered Users 2
 Anamorph stateUsed to indicate the presence of the anamorph (asexual state), teleomorph (sexual state) or holomorph (both states) in the specimenPublic
 MissingSpecimen cannot be located in the collection (usually as a result of misfiling)Registered Users 1
 Rust statesUsed to indicate the presence of one or more of the different states in the rust life cyclePublic
NZACAdditional materialUsed to indicate the presence of additional physical material relating to this specimenPublic
 Data validationAdded when the automatic updated and added dates on the specimen do not represent the actual time of data entry or validationPublic
 GenderUsed to indicate the gender of the specimenPublic
 Life stageUsed to indicate the life stage of the specimen, e.g. egg, immature, larva, instarPublic
 Mounting mediumUsed to record the medium in which the specimen is mountedPublic
 PartFor incomplete specimen this states that part(s) remaining or missingPublic
 Wing developmentUsed to record the stage of wing development for the specimen.Public
Search title: flagValue
Flag value

The value associated with a flag.

Search title: typeOfFlag
Type of flag

The type of flag used to indicate a property or feature of a specimen/culture. The flag types vary between each collection.

Search title: flagNote
[Specimen Flag] note

A note associated with a flag. On the details page, this is displayed in brackets.

Specimen notes

This is additonal information associated with the specimen. Often this is information added after collection, e.g. can relate to the history of the specimen.

CollectionType of noteDescriptionAccess level
ICMPAvirulent to Public
NZACBiotaA public specimen note from BiotaCollection Staff Only
ICMPCharacterised as Public
NZACData EntryA public note recording issues with data entry (e.g., legibility of label)Public
CHR, FLAX, ICMP, NZAC, PDDData Quality Public
CHRDeaccession Public
CHRDelete Collection Staff Only
ICMPDet HistoryDetermination history migrated from Access databaseSystematics Researchers
CHRGarden voucher Public
NZACGeneralA public note (that does not fit other categories)Public
CHRGeoreference (derived) Public
CHRGeoreference (original) Public
ICMPGrowth Conditions Public
ICMPHazardHazard categoryCollection Staff Only
CHRHerbarium history Public
CHRInformation withheldA public statement indicating that particular data is withheld.Public
ICMP, NZACMolecular DataA note about or containing molecular data.  Not to be used for external links.Collection Staff Only
ICMPMorphology Systematics Researchers
PDDNoteGeneral noteCollection Staff Only
ICMPNoteGeneral noteSystematics Researchers
CHR, NZAC, FLAXOperatorAny notes from the operator for later data curatorsCollection Staff Only
ICMPOther Details Public
ICMPPathogenic to Public
CHRPrivacyNote added to record request to suppress information for privacy reasons.Collection Staff Only
PDDPublic Note Public
CHRRestricted dataThe information that has been removed from the dedicated fields when the ability to suppress information is not fine enough.Collection Staff Only
ICMPSerotype DataSerotype DataSystematics Researchers
ICMPStrain DataStrain DataPublic
CHRSubsheet Public
CHRSupplementary remarks Public
CHR, FLAX, ICMP, NZAC, PDDSystem AdminNote added to record system adminstration activity.Collection Staff Only
ICMPTest Results Systematics Researchers
CHRType Public
ICMPUnlisted Details Collection Staff Only
CHRVoucher Public
CHRVoucher (cyto) Public
CHRVoucher (DNA) Public
CHRVoucher (pollen) Public
Search title: specimenNote
Specimen note

This is additional information associated with the specimen.

Search title: specimenNoteType
[Specimen note] Type

This is the type of a note containing additional information associated with the specimen for example Herbarium History, Supplementary remarks. Note types vary between collections.

Search title: specimenNoteAuthor
[Specimen note] Author

This is the author of a note containing additional information associated with the specimen.

Transactions

Provides the status, reference number and destination organisation of transactions, so that active transactions can be tracked and searched for.

Search title: loanStatus
Loan status

An indication of the status of the specimen if it is on loan to another institute.

For example: loanStatus:Active.

Loan status values include:

  • Active
  • Requested
  • Lost
  • Transferring
Search title: organisation
Organisation

The standardised name or acronym of the institute to which specimens are on loan.

For example: organisation:WELT

Search title: transactionReferenceNo
Transaction reference number

The reference number assigned to a transaction.

For example: a loan, gift or exchange