From 16 to 17 January 2018 biological data experts was meeting in Brussels to exchange experiences and use cases for the (relatively) new Darwin Core Event core and how the standard can be used in Marine and terrestrial contexts. By discussing use cases we aimed at providing guidelines on best practices of this new standard. See also: http://www.gbif.no/news/2018/gbif_obis_event_core_workshop.html http://www.gbif.no/news/2018/documents/2018-01-17_event_core_mof_dwciri.pptx

1. Event core for measurement or fact data
GBIF/OBIS hackathon, Belspo, Brussel, January 16, 2018
Slides, CC-BY Dag Endresen, GBIF.no

2. Event core and measurements
• Event core (since 2015) opens up new
functionality for data published in GBIF!
• Limitations of the star-schema is a frequently
mentioned obstacle…
– E.g. when connecting measurement or facts (MoF)
only core entities can be described.
• "OBIS eMoF" provides flexible solutions that
could be further generalized and suggested as
the new updated "GBIF:MoF" standard…?

3. DwC archive – application schema
DwC Event (since 2015)
– http://rs.gbif.org/core/dwc_event_2016_06_21.xml
DwC Occurrence
– http://rs.gbif.org/core/dwc_occurrence_2015-07-02.xml
DwC Measurement or fact (want link to event and occ!)
– http://rs.gbif.org/extension/dwc/measurements_or_facts.xml
OBIS Extended measurement or fact (proposed 2017)
– http://rs.gbif.org/extension/obis/extended_measurement_or_fact.xml
DwC Resource relationship (possible solution?)
– http://rs.gbif.org/extension/dwc/resource_relation.xml

4. Use case : Measurements for both events
and occurrences in the same dataset
OBIS expeditions are sampling more data than
only organism occurrences (e.g. environment).
--> development of a new extended measurement
and fact extension (for DwC-archives)

5. Integrated Publishing Toolkit
Star Schema (DwC-archive)
Occurrence core
MoF Extension
1
Event core
Occurrence
Extension
MoF Extension
1 1
MoF = Measurement or Fact
∞
∞
∞ Here: MoF describes
only the Occurrences
Sample event is the DwC core
Here: MoF describes
only the Event
Slide by:
OBIS-ENV-DATA
International Oceanographic
Data and Information Exchange

8. The extended MeasurementOrFact extension
allows for parameter standardization (linking to
external URI of a controlled vocabulary)
ID: Link to the core record (here: a link to the event)
occurrenceID (new): identifier to link the eMoF with the occurrence extension
measurementType: The nature of the measurement or fact (MoF)
measurementTypeID (new): identifier for the measurementType (global unique identifier, URI)
measurementValue: the value of the MoF
measurementValueID (new): identifier for facts reported as measurementValue (URI)
measurementAccuracy: description of the potential error or accuracy of the MoF
measurementUnit: measurement unit (SI unit; meter, gram, etc)
measurementUnitID (new): identifier for the measurementUnit (URI)
measurementDeterminedDate: date on which the MOF was made
measurementDeterminedBy: list of people, groups, or organizations who recorded the MoF
measurementMethod: description or reference to (publication, URI) for the method or protocol used
measurementRemarks: Comments or notes to the MoF
Slide by:
OBIS-ENV-DATA

9. eMoF propose minting three new terms
measurementType: The nature of the measurement or fact (MoF)
measurementTypeID (new): identifier for the measurementType (global unique identifier, URI)
http://rs.iobis.org/obis/terms/measurementTypeID
measurementValue: the value of the MoF
measurementValueID (new): identifier for facts reported as measurementValue (URI)
http://rs.iobis.org/obis/terms/measurementValueID
measurementUnit: measurement unit (SI unit; meter, gram, etc)
measurementUnitID (new): identifier for the measurementUnit (URI)
http://rs.iobis.org/obis/terms/measurementUnitID
Let's explore the Darwin Core RDF Guide first…

10. Darwin Core RDF Guide
(2015)

12. dwciri: namespace
The dwciri: namespace is intended for use
exclusively with non-literal objects.
http://rs.tdwg.org/dwc/iri/
Baskauf S, Wieczorek J, Deck J, Webb C, Morris PJ and Schildhauer M (2015) Darwin Core RDF Guide,
Biodiversity Information Standards http://rs.tdwg.org/dwc/terms/guides/rdf/
Baskauf SJ, Wieczorek J, Deck J, Webb CO (2016) Lessons learned from adapting the Darwin Core
vocabulary standard for use in RDF. Semantic Web 7(6): 617-627, DOI: 10.3233/SW-150199

13. dwciri: and dwc: terms
• If a term in the dwciri: namespace has an
analogue in the dwc: namespace having the
same local name, the dwciri: term will have the
same meaning as its dwc: counterpart, but is
intended to have an IRI-reference object.

14. Darwin Core RDF guide and the dwciri: namespace term
already have alternatives for some of the new terms
minted by the OBIS eMoF.
emof = http://rs.iobis.org/obis/terms/
dwciri = http://rs.tdwg.org/dwc/iri/
emof:measurementTypeID = dwciri:measurementType
emof:measurementUnitID = dwciri:measurementUnit
emof:measurementValueID (no analogue in dwciri - useful addition)
see also:
dwciri:measurementDeterminedBy
dwciri:measurementMethod
dwciri:samplingProtocol
DwC RDF Guide: http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm#2.9_MeasurementOrFact_instances

15. Linking MoF instances to resources
• "Darwin Core does not provide the object properties
that would be required to describe precisely how the
dwc:MeasurementOrFact instance was related to the
dwc:Occurrence instance, the dwc:Organism whose
occurrence was recorded, or the
dwc:PreservedSpecimen that was collected".
• Examples of the DwC RDF Guide use
dcterms:relation to link MoF instances to the
respective resources.
Baskauf et al. 2015, Darwin Core RDF Guide, chapter 2.9

16. DwC RDF Guide MoF example 31
Example 31 - Turtle
<http://mczbase.mcz.harvard.edu/guid/MCZ:Mamm:67231>
a dwc:Occurrence;
dcterms:relation [a dwc:MeasurementOrFact ;
dwc:measurementType "tail length" ;
dwciri:measurementType <http://purl.obolibrary.org/obo/VT_0002758> ;
dwc:measurementValue "25"^^xsd:int ; dwc:measurementUnit "mm" ;
dwciri:measurementUnit <http://mimi.case.edu/ontologies/2009/1/
UnitsOntology#millimeter> ;
dwc:measurementAccuracy "0.5"^^xsd:decimal ;
dwc:measurementDeterminedDate "2009-08-22"^^xsd:date ;
dwc:measurementDeterminedBy "Ryan B Stephens" ;
dwciri:measurementDeterminedBy <http://scholar.google.com/citations?
user=RAsUdjoAAAAJ> ;
dwc:measurementMethod "unspecified" ;
dwciri:measurementMethod <http://purl.obolibrary.org/obo/MMO_0000160> ;
dwc:measurementRemarks "Accuracy from significant digits."@en].

17. Unintended consequences of ID terms
• In its normative definition, each Darwin Core ID
term is declared to be rdfs:subPropertyOf
dcterms:identifier.
• In RDF, the purpose of a subproperty
declaration is to allow a client with reasoning
capability to infer a triple containing a broader
(and presumably more well-known) property.
• (Applicable to RDF-serialization, less so to text-
or XML-serialization).

18. DwC RDF Guide ID term example 23
Example 23 : Turtle (incorrect usage)
<http://guid.mvz.org/identifications/23459>
a dwc:Identification; dwc:identifiedBy "Richard Sage";
dwc:dateIdentified "2000"^^xsd:gYear;
dwc:taxonID "http://lsid.tdwg.org/
urn:lsid:catalogueoflife.org:taxon:d79c11aa-29c1-102b-9a4a-00304854f
820:col20120721".
possible incorrect inference:
dcterms:identifier "http://lsid.tdwg.org/
urn:lsid:catalogueoflife.org:taxon:d79c11aa-29c1-102b-9a4a-00304854f
820:col20120721".

19. Darwin Core Resource
Relationship

20. DwC Resource Relationship
Term Name: ResourceRelationship
• Identifier: http://rs.tdwg.org/dwc/terms/ResourceRelationship
• Definition: A relationship of one rdfs:Resource (http://
www.w3.org/2000/01/rdf-schema#Resource) to another.
• Comment: Resources can be thought of as identifiable records or
instances of classes and may include, but need not be limited to
Occurrences, Organisms, MaterialSamples, Events, Locations,
GeologicalContexts, Identifications, or Taxa. Example: An instance of
an Organism is the mother of another instance of an Organism. For
discussion see http://terms.tdwg.org/wiki/dwc:ResourceRelationship
ResourceRelationship terms -- resourceRelationshipID | resourceID |
relatedResourceID | relationshipOfResource | relationshipAccordingTo |
relationshipEstablishedDate | relationshipRemarks

21. Use case for Resource Relationship
CORE entity is dwc:Event, measurement is on a
dwc:Occurrence organized in a DwCA extension
• resourceRelationshipID = "relationship1"
• resourceID = "organism1"^^dwc:Occurrence
• relatedResourceID = "measurement1"
• relationshipOfResource =
"measurement_of_occurrence"

22. Use case for Resource Relationship
CORE entity is dwc:Occurrence, but the measurement
is on one of the entities flattened into the simple
Darwin Core data record (Event, Location, Multimedia,
Materialsample, ...)
• resourceRelationshipID = "relationship1"
• resourceID = "organism1"^^dwc:Organism |
"event1"^^dwc:Event
• relatedResourceID = "measurement1"
• relationshipOfResource =
"measurement_of_organism/event..."

23. Use case for Resource Relationship
CORE entity is dwc:Event (measurement event, not the
collecting event), measurement is on a dwc:Occurrence
published in another dataset
• resourceRelationshipID = "relationship1" |
http:urn:uuid:UUID^^resourceRelationship
• resourceID = "http:urn:uuid:UUID"^^dwc:Occurrence
• relatedResourceID =
http:urn:uuid:UUID^^dwc:MeasurementOrFact
• relationshipOfResource =
"measurement_of_occurrence_in_another_dataset"

24. Some other use cases

25. Use case : linking between multiple archives
Joint collecting expeditions collecting material
that end up in different museums, herbaria, and
genebanks.
(1) Collecting events published in one DwC-archive
(2) Collection specimens in other DwC-archive(s)
(3) … and experiments in a third set of DwC-archives

26. Example of a joint, collaborative collection mission:
same sampling event – but specimens sent to to different museum collections
Dannevig collections (280 collecting events)
http://doi.org/10.15468/hwvr0m
UiT : Arthropod collection
http://doi.org/10.15468/vjkvxg
NTNU : Algae herbarium
https://doi.org/10.15468/elzhsu
UiB : Cephalaspidean Gastropods
http://doi.org/10.15468/sbomfu
UiO : Dannevig- and Drobak-
collections Polychaeta
https://doi.org/10.15468/y6cctp
Material from the same
expedition –> 4 herbaria,
and 4 datasets (DwC-A).

27. Event core for measurement or fact data
GBIF/OBIS hackathon, Belspo, Brussel, January 16, 2018
Image CC-BY Dag Endresen

28. cultivated
corn, maize
wild tomato
cultivated
tomato
wild teosinte
28
cultivation

30. Biodiversity
Collecting Mission
Database
158 252 occurrences
doi:10.15468/ulk1iz
Dataset published
in GBIF June 2017

31. The Global Crop Wild
Relative Occurrence
Database include data
from hundreds of
data sources –
including GBIF
The CWR Database
was published in
GBIF (2016)
(excluding the data records
originating from GBIF)
doi:10.15468/jyrthk

33. Powdery Mildew,
Blumeria graminis
Leaf spots
Ascochyta sp.
Yellow rust
Puccinia strilformis
Black stem rust
Puccinia graminis 33 Apple, Malus domestica Borkh.
Cultivar “Nanna” by Stein H Hjeltnes
Rhubarb, Rheum x hybridum Murray, DKRHE43, by Gitte K. Bjørn

34. Proposing a new use case:
Measurement events as dwc:Event
Experiments with living specimens
at a location and date that is
different from the collecting event.

35. Collecting expeditions Genebank, collections Field/lab experiments
Seeds from
collecting trip
expeditions are
deposited in
genebank
collections. Living seeds from
genebank
collections are
used for field or
laboratory
experiments.

36. Germplasm material flow
• Material samples from many different collecting
missions are deposited in different genebanks.
• Material from public genebanks are included in
other genebank collections (and breeders
collections).
• Material from different genebanks (and thus
many different collecting events) are included in
each field trial experiment.
• Collecting Event ≠ Measurement Event (MoF)

37. European meeting on C&E ("MoF")
• Aim to publish trait data (characterization and
evaluation, C&E) from online crop portals.
• European genebank meeting in Bonn May 2009
(ECPGR ICT Group).
• Developed guidelines & data exchange models.
• Some harmonization with Darwin Core and DwC
Measurement or Fact (MoF).
à DwC germplasm extension, released 2012.
à GBIF data fitness for use in agrobiodiversity, 2016.
à EURISCO C&E data models, implemented 2017.

38. May 2009

39. ECPGR C&E trait data model (1/2)
ECPGR trait data
• Genotype : Identity of the germplasm material
• Trait : Type of measurement, protocol
– Method : How the trait was scored
• Experiment : Location and date of the
experiment (dwc:Event)
• Score: Measurement value (dwc:MoF)

40. ECPGR C&E trait data model (2/2)
• DATASET
– uploadercode (FK)
– dataset_remark
– (dataset_id)
• GENOTYPE
– genotype_number (PK)
– genotype_nicode
– genotype_instcode
– genotype_accenumb
– genotype_genus
• TRAIT
– trait_number (PK)
– trait_name
– trait_remark
– trait_method
• EXPERIMENT
– experiment_number (PK)
– experiment_description
– experiment_year
– experiment_longitude
– experiment_latitude
– experiment_report
• SCORE
– genotype_number (FK)
– experiment_number (FK)
– trait_number (FK)
– score
-

41. Darwin Core Germplasm extension (1)
• dct = http://purl.org/dc/terms/
• dctype = http://purl.org/dc/dcmitype/
• dsw = http://purl.org/dsw/
• dwc = http://rs.tdwg.org/dwc/terms/
• geo = http://www.w3.org/2003/01/geo/wgs84_pos#
• g = http://purl.org/germplasm/germplasmTerm#
• gtype = http://purl.org/germplasm/germplasmType#
• mcpd = Alercia et al. (2015, 2012, 2001, 1997)
• epgris3 = van Hintum (2009)

42. Darwin Core Germplasm extension (2)
• Germplasm type (class terms)
– dctype:Dataset
– dwc:Taxon
– gtype:GermplasmAccession (dsw:LivingSpecimen)
– gtype:CollectingEvent (dwc:Event)
– gtype:BreedingEvent [dwc:Event]?
– gtype:AcquisitionEvent [dwc:Event]?
– gtype:SafetyDuplication [dwc:Event]?
– gtype:TreatyOrRegulation
– gtype:MeasurementTrait
– gtype:MeasurementTrial (dwc:Event)
– gtype:MeasurementScore (dwc:MeasurementOrFact)

43. Darwin Core Germplasm extension (3)
• gtype:GermplasmAccession (see also:
dsw:Specimen and dsw:LivingSpecimen)
– dwc:occurrenceID
– dwc:catalogNumber (mcpd:ACCENUMB)
– g:germplasmID (epgris3:GENOTYPE_NUMBER)
– g:germplasmIdentifier (mcpd:ACCENAME)
– g:biologicalStatus (mcpd:SAMPSTAT)
– g:storageCondition (mcpd:STORAGE)
– dwc:otherCatalogNumbers (mcpd:OTHERNUMB)
– dwc:occurrenceDetails
– dwc:occurrenceRemarks

44. Darwin Core Germplasm extension (4)
• gtype:MeasurementTrait (measurement methodology,
descriptor)
– g:measurementTraitID
– g:measurementTraitIdentifier (epgris3:TRAIT_NUMBER)
– g:measurementTraitName (epgris3:TRAIT_NAME)
– g:measurementTraitCategory
– g:measurementTraitScale
– g:measurementTraitSource
– g:measurementTraitRemarks (epgris3:TRAIT_REMARK)
– dwc:measurementType
– dwc:measurementMethod

45. Darwin Core Germplasm extension (5)
• gtype:MeasurementTrial (experiment trial season, see
dwc:Event)
– g:measurementTrialID
– g:measurementTrialIdentifier (epgris3:experiment_number)
– g:measurementTrialYear (epgris3:experiment_year)
– geo:location
– geo:lat (epgris3:experiment_latitude)
– geo:long (epgris3:experiment_longitude)
– geo:alt
– g:measurementTrialReport (epgris3:experiment_report)
– g:measurementTrialRemarks (epgris3:experiment_description)

46. Darwin Core Germplasm extension (6)
• gtype:MeasurementScore (see
dwc:MeasurementOrFact)
– dwc:measurementID
– dwc:measurementType
– dwc:measurementValue
– dwc:measurementAccuracy
– dwc:measurementUnit
– dwc:measurementDeterminedDate
– dwc:measurementDeterminedBy
– dwc:measurementMethod
– dwc:measurementRemarks
– g:measurementByInstituteID
– g:measurementGrowthStage
– dwc:occurrenceID
– dwc:catalogNumber
– g:germplasmID
– g:germplasmIdentifier
– g:measurementExperimentID
– g:measurementExperimentIdentifier
– g:measurementMethodID
– g:measurementMethodIdentifier

47. dwc:MeasurementOrFact
g:MeasurementScore (2013)
iode:eMeasurementOrFact (2016)

48. Endresen, D.T.F. and H. Knüpffer (2012). The Darwin Core extension for genebanks opens up new opportunities for
sharing genebank data sets. Biodiversity Informatics 8:11-29. DOI: https://doi.org/10.17161/bi.v8i1.4095

49. Why did we make a Darwin Core
extension for germplasm data?
à Upgrade germplasm data pathways to use
web services
The objective (1) was to enable sharing of germplasm information
using the standard web-service based biodiversity data publishing
toolkits maintained by the Global Biodiversity Information Facility
(GBIF) and the Biodiversity Information Standards (TDWG).
à Upgrade data types to include trait data
The objective (2) was to expand on the germplasm data types
published to germplasm data portal from basic passport data to
include in particular crop trait information.
CC-BY, Dag Endresen

50. DwC Event Core + eMoF
• DwC Event Core + eMoF, as proposed by iOBIS,
opens up promising possibilities for publishing
also crop trait /C&E) data!!
– Using the GBIF infrastructure for data exchange.
– With collaboration on data exchange schema
between thematic domains (terrestrial crops,
marine, etc).