Persistent Identifiers Herbarieworkshop, Kongsvoll Fjellstue September 2014. Dag Endresen, NHM.

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Presentation transcript:

Persistent Identifiers Herbarieworkshop, Kongsvoll Fjellstue September Dag Endresen, NHM

Name ambiguity: George

Identify the thing that you care about The specimen itself (the physical entity) Image of the specimen Description of the specimen Location where the specimen was captured The occurrence event when the specimen was captured…

Record-level Terms dcterms:type | dcterms:modified | dcterms:language | dcterms:rights | dcterms:rightsHolder | dcterms:accessRights | dcterms:bibliographicCitation | dcterms:references | institutionID | collectionID | datasetID | institutionCode | collectionCode | datasetName | ownerInstitutionCode | basisOfRecord | informationWithheld | dataGeneralizations | dynamicProperties Occurrence occurrenceID | catalogNumber | occurrenceRemarks | recordNumber | recordedBy | individualID | individualCount | sex | lifeStage | reproductiveCondition | behavior | establishmentMeans | occurrenceStatus | preparations | disposition | otherCatalogNumbers | previousIdentifications | associatedMedia | associatedReferences | associatedOccurrences | associatedSequences | associatedTaxa MaterialSample materialSampleID Event eventID | samplingProtocol | samplingEffort | eventDate | eventTime | startDayOfYear | endDayOfYear | year | month | day | verbatimEventDate | habitat | fieldNumber | fieldNotes | eventRemarks dcterms:Location locationID | higherGeographyID | higherGeography | continent | waterBody | islandGroup | island | country | countryCode | stateProvince | county | municipality | locality | verbatimLocality | verbatimElevation | minimumElevationInMeters | maximumElevationInMeters | verbatimDepth | minimumDepthInMeters | maximumDepthInMeters | minimumDistanceAboveSurfaceInMeters | maximumDistanceAboveSurfaceInMeters | locationAccordingTo | locationRemarks | verbatimCoordinates | verbatimLatitude | verbatimLongitude | verbatimCoordinateSystem | verbatimSRS | decimalLatitude | decimalLongitude | geodeticDatum | coordinateUncertaintyInMeters | coordinatePrecision | pointRadiusSpatialFit | footprintWKT | footprintSRS | footprintSpatialFit | georeferencedBy | georeferencedDate | georeferenceProtocol | georeferenceSources | georeferenceVerificationStatus | georeferenceRemarks GeologicalContext geologicalContextID | earliestEonOrLowestEonothem | latestEonOrHighestEonothem | earliestEraOrLowestErathem | latestEraOrHighestErathem | earliestPeriodOrLowestSystem | latestPeriodOrHighestSystem | earliestEpochOrLowestSeries | latestEpochOrHighestSeries | earliestAgeOrLowestStage | latestAgeOrHighestStage | lowestBiostratigraphicZone | highestBiostratigraphicZone | lithostratigraphicTerms | group | formation | member | bed Identification identificationID | identifiedBy | dateIdentified | identificationReferences | identificationVerificationStatus | identificationRemarks | identificationQualifier | typeStatus Taxon taxonID | scientificNameID | acceptedNameUsageID | parentNameUsageID | originalNameUsageID | nameAccordingToID | namePublishedInID | taxonConceptID | scientificName | acceptedNameUsage | parentNameUsage | originalNameUsage | nameAccordingTo | namePublishedIn | namePublishedInYear | higherClassification | kingdom | phylum | class | order | family | genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank | scientificNameAuthorship | vernacularName | nomenclaturalCode | taxonomicStatus | nomenclaturalStatus | taxonRemarks ResourceRelationship (Auxiliary Terms) resourceRelationshipID | resourceID | relatedResourceID | relationshipOfResource | relationshipAccordingTo | relationshipEstablishedDate | relationshipRemarks MeasurementOrFact (Auxiliary Terms) measurementID | measurementType | measurementValue | measurementAccuracy | measurementUnit | measurementDeterminedDate | measurementDeterminedBy | measurementMethod | measurementRemarks

Term name:occurrenceID Identifier: Class: Definition:An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. Comment:For a specimen in the absence of a bona fide global unique identifier, for example, use the form: "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]". Examples: "urn:lsid:nhm.ku.edu:Herps:32", "urn:catalog:FMNH:Mammal:145732". For discussion see

Persistent Identifier (PID) Globally Unique Identifier (GUID) Universal Resource Identifier (URI) Persistent Uniform Resource Locator (PURL) Life Science Identifier (LSID) Digital Object Identifier (DOI) Handle system (Handle) Archival Resource Key (ARK, EZID) Universally Unique Identifier (UUID) Reuse existing identifiers!

Photo: Smithsonian National Museum of Natural History, USNM Eutoxeres-aquila urn:lsid:Orthoptera.speciesfile.org:TaxonName:xx urn:lsid:catalogueoflife.org:taxon:d755ba3e-29c1-102b-9a4a f820:ac2009 PURL Reuse existing identifiers

Illustration by Miroslav Šašek (1963)

Globally unique Scalability, number of IDs Community acceptance Long-term life-cycle Resolvable, resolution service(s) Cost per identifier People-friendly or machine-friendly Solution for the generation of new IDs – Central generation, PID issuer – Distributed generation at source

A UUID is a 16-octet (128-bit) 36-chars number. Example: C37E3F9B-BCAF EB7-3346A2DB2373 C37E3F9B-BCAF EB7-3346A2DB2373 The probability of one duplicate would be about 50% if every person on earth create 600 million UUIDs. Allows for easy generation at source in a distributed network.

IdentifierResolver LocationSpecimen

http – PURL – UUID

Including machine readable formats

Quick Response Code (QR code). A type of matrix barcode (or two- dimensional code). Popular due to its fast readability and large storage capacity. The use of QR Codes is free of any license. The QR Code is clearly defined and published as an ISO standard. Invented in Japan by the Toyota subsidiary Denso Wave in 1994.

UUID QR codes for museum objects at NHM-UiO provides: Machine-readable identifiers (using a simple smart phone - or a barcode reader) Allows for new and efficient workflows for collection management. Deployment for stable identifiers appropriate for data-basing.

Peer review option for biodiversity data sets. Authors get scientific credit for data publication. Meeting concerns over data quality. Meeting concerns over data citation mechanism. Towards  Each data set published through GBIF accompanied by a data paper…? Data set identifier DOI  dwc:datasetID …?

Why publish your data Citable publication Establish scientific priority Increase collaboration Link data to bigger network Re-use and multiply effect Respond to funding requirements Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur T, Mueller G, Dikow T, Helgen K, Frank J, Agosti D, Roberts D, Penev L (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal 1: e995. DOI: /BDJ.1.e995

Globally unique identifiers are one of the three core components in the TDWG technical architecture.

Status 27. August 2014 GBIF enables free and open access to biodiversity data online. We are an international government-initiated and funded initiative focused on making biodiversity data available to all and anyone, for scientific research, conservation and sustainable development.

GBIF provides a data discovery system global registry data portal

Thanks for listening! Dag Endresen