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BIS TDWG Conference29 October 2014, Jönköping, Sweden
Publishing sample-based data using Darwin Core Archives
Éamonn Ó Tuama, Markus Döring, Kyle Braak, Tim Robertson, Olaf BánkiGlobal Biodiversity Information Facility (GBIF)
Why do this?• Long perceived need by GBIF to
enable publishing of abundance (sample) data;
• Requirement with the EU Project EU BON (http://eubon.eu);
• Meeting the needs of the GEO Biodiversity Observation Network (GEO BON ).
Sample-based data• Output of monitoring programmes;
• Quantitative, calibrated;
• Using standard protocols;
• Repeatable, comparable.
Detect changes and trends in populations
Constraints• Be available for testing in 2015
• Build on existing widely used standards: Darwin Core
• Work within the existing tools ecosystem: IPT
• … while acknowledging the promise of ontologies (BCO, OBOE …)
Caveat
Aim: demonstrate one way data can be exposed to maximize discoverability and reuse. Not in scope: establishing how data should be captured or modelled.
A use case
Enabling the flow of sample based data in support of GEO BON Essential Biodiversity Variables (EBVs).
Essential Biodiversity Variablesintermediate layer between raw data and indicators
GEO BON has identified six EBV classes
a measurement required for study,
reporting and management of
biodiversity change
EBV Class: Species populations
Building onthe
Darwin Corevocabulary
taxonRank
higherClassification
taxonConceptIDcollectionCode
geodeticDatumspecificEpithet
coordinatePosition
collectionCode: The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived. Examples: "Mammals", "Hildebrandt", "eBird".
Darwin Core – a glossary of terms
7 essential terms for encoding sample data
1. eventID2. projectID (new)
3. samplingProtocol4. sampleSize (new)
5. sampleSizeUnit (new)
6. quantity (new)
7. quantityType (new)
New terms requiredeventID: an identifier for the set of information associated with an Event; may be a global unique identifier or an identifier specific to the data set.
projectID: an identifier for a project with which the data is associated; use to link related data sets, e.g., a monitoring series; may be a global unique identifier or an identifier specific to the series.
New terms requiredsampleSize: a numeric value for the time duration, length, area or volume involved in the sampling.
sampleSizeUnit: the unit of measurement used for sampling, e.g., minute, hour, day, metre, metre^2, metre^3.
2 hour3 m217 km1 litre
Unit of measurement vocabulary
Used in IPT as controlled list for sampleSizeUnit
Unit of measurement vocabulary
http://rs.gbif.org/sandbox/vocabulary/gbif/unit_of_measurement.xml
New terms requiredquantity: the number or enumeration value of the entity or category being quantified in the sample. As such it is paired with quantityType.
quantityType: the entity being referred to by quantity, e.g., individuals, a percentage (e.g., species, biomass, biovolume), a scale type
14 Individualsr BraunBlanquetScale0.4 %Species31 %Biomass
Publishing sample data
using the IPT
http://www.gbif.org/ipt
Event Core• An event core is the logical way of
organising a sampling event;
• Related environmental measurements can be included in an extension;
• Vegetation plot data (coverages) can be included separately from “occurrences”.
http://rs.tdwg.org/dwc/terms/guides/text/index.htm
Darwin Core Archive components
Event core
Occurrence ext
Measurement-or-fact ext
Relevé ext
…
meta.xml
EML.xml…
+DwC Archive
Event Core(Event, Location, Geological Context)
eventID, projectID (n), samplingProtocol, sampleSize (n), sampleSizeUnit (n)
Occurrence Extension(Occurrence, Taxon, Identification)
eventID, quantity (n), quantityType (n)
(n) = proposed new term
Placing the terms in a Darwin Core Archive
For term definitions, see http://links.gbif.org/ipt-sample-data-primer
eventID projectID samplingProtocol
sample Size
sampleSizeUnit
event Date location decimal Latitude
decimalLongitude
…
C_1428 RM065 AQEM 1.25 m2 1963-03-01 Kinzig O3 Rothenbergen
48.1333 11.5667 …
C_1538 RM065 AQEM 1.25 m2 1975-01-21 Kinzig W1 Bulau
-34.6033 -58.3817 …
eventID scientificName quantity quantityType …
C_1428 Baetis rhodani 14 individuals …
C_1428 Ephemera danica 15 individuals …
C_1428 Gyraulus albus 2 individuals …
C_1538 Serratella ignita 318 individuals …
A sampling event uses a particular samplingProtocol with sampleSize and sampleSizeUnit, etc. and can record one or more taxa, each of which has a measurement (quantity and quantityType associated with it.
Event core
Occurrence extension
http://rs.gbif.org/sandbox/core/dwc_event.xml
http://rs.gbif.org/sandbox/extension/event_occurrence.xml
Adapting the IPT
http://eubon-ipt.gbif.org
Now with Event Core
This project has received funding from the European Union’s Seventh Programme for research, technological development and demonstration under grant agreement No 308454.
Acknowledgement
EU BON and GEO BON partners, TDWG mailing list contributors and GBIF sample data workshop participants informed this work and are gratefully acknowledged.
Thank you
GBIF SecretariatUniversitetsparken 15DK-2100 Copenhagen ØDenmark
www.gbif.org
E-mail: [email protected]: +45 3532 1470Fax: +45 3532 1480