Expanding OBIS beyond species occurrence data, including sampling event facts and measurements...
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Transcript of Expanding OBIS beyond species occurrence data, including sampling event facts and measurements...
Expanding OBIS beyond species occurrence data, with
an extension for environmental data
Photo credits Molly Timmers - NOAA [email protected]
International OceanographicData and Information Exchange
Co-authors: OBIS-ENV-DATA project consortium
46,000,000 species observations4,600,000 sampling events3,200,000 sampling stations117,000 marine species
1,900 databases in 1 central global database
500 data providers, 56 countries
1,000 papers have cited OBIS(9)
(4)
UNGA resolution (A/RES/70) notes with appreciation the contribution of OBIS to marine scientific research.
Some Statistics
Census of Marine Life2000 - 2010
OBIS was established as the data repository and information dissemination system for
CoML
OBIS @ UNESCO-IOC
In June 2009, the 25th Session of the IOC Assembly decided through Resolution XXV-4 to adopt OBIS as part of IODE, because:
Knowledge of the ocean's biodiversity is of such importance to national and global environmental issues that the responsibility for its continuing success should be assumed by governments.
IntergovernmentalOceanographic Commission
Established in 1960148 Member States
UNCLOS: IOC = competent international organization for Marine Scientific Research and Transfer of Marine Technology
UN focal point for ocean science, ocean observations and services, data and information exchange and capacity building
Darwin Core ArchiveOccurrence core EML Meta.xml
DwC terms managed by TDWG
1. eventDate2. decimalLongitude3. decimalLatitude4. scientificName5. scientificNameID6. occurrenceStatus7. basisOfRecord
WHEN
WHERE
WHAT
BY WHO
HOW MANY
POINTS, LINES, POLYGONSDEPTH
SAMPLINGPROTOCOL
OBIS DATA STANDARD
Sampling more data than just species occurrence
Core sample from a Van Veen grab
Water sample from a Niskin bottle plankton net with CTD
Video plankton recorder
OTN tags
XXIII session of the IOC Committee for IODE, March 2015
Recommendation IODE-XXIII.4ESTABLISHMENT OF THE IODE PILOT PROJECT EXPANDING
OBIS WITH ENVIRONMENTAL DATA (OBIS-ENV-DATA)
OBIS-ENV-DATA1st workshop October 2015
OBIS-ENV-DATA involves 11 institutions from 10 countries in North-America, South-America, Europe, Africa and Oceania.
In collaboration with
14 pilot datasets
ABIOTIC READINGSEnvironmental :
Light Conditions, Ice Coverage, Secchi Disc Depth, Turbidity, Light Transmission, Wind Direction, Bottom Temperature, Surface Salinity
Sediment Sample: Metal Concentrations, Sediment Grain Sizes
Water Sample:Nutrient (NO3) and Chlorophyll a Concentration, Temperature,
SalinitySensor based:
CTD profiles, tracking data, data derived from sensors attached to the sampling device
SAMPLING GEARRMT-1 net: zooplankton, fishCTD-Tracker: marine mammalsVan Veen Grab: macrobenthosSorbe sledge: hyperbenthosVPR:planktonMOCNESS net: zooplanktonThrow-trap: zooplanktonNiskin bottle: phytoplankton
14 pilot datasets
Integrated Publishing Toolkit
Star SchemaOccurrence core
MoF Extension
1
Event core
Occurrence Extension
MoF Extension
1 1
MoF = Measurement or Fact
∞
∞
∞MoF addresses methods, abiotic and biological measurements
Sample event is the DwC core
What we needed
OBIS-ENV-DATA
event 1
occurrence 1
occurrence 2
measurement 1
measurement 2
Not compatible with star schema
Event Core MeasurementOrFacts ExtensionOccurrence Extension
Option 1
event 1 occurrence 1
event 1 occurrence 2
measurement 1
measurement 2
measurement 1
Occurrence Core MeasurementOrFacts Extension
event 1
occurrence 1
occurrence 2
measurement 1
measurement 2
OBIS-ENV-DATA
Event MoF needs to be repeated for each occurrence record
Option 2
event 1
measurement 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence Extension
Not possible when both abundance and biomass measurements are made and can’t record measurements or facts related to the occurrence
OBIS-ENV-DATA
Option 3
event 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence Core
measurement 1
MeasurementOrFacts Extension
Archive 1 Archive 2
Not possible because Event Core requires an occurrence extension file, and 2 archives for one dataset is confusing, need links between archivesOBIS-ENV-DATA
Creating 2 Archives one for Events and abiotic and one for Occurrences and biological measurements
event 1
occurrence 1
occurrence 2
measurement 1
measurement 2
Occurrence Core MeasurementOrFacts Extension
Option 4
OBIS-ENV-DATA
Is abusing the Occurrence Core
Creating dummy occurrence records, treat as an event record
Option 5
event 1
measurement 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence Extension
event 1_1
event 1_2
OBIS-ENV-DATA
Complex and not intuitive.
Creating a dummy event for each occurrence extension record
event 1
measurement 1
measurement 2
Event Core MeasurementOrFacts Extension
occurrence 1
occurrence 2
Occurrence Extension
OBIS-ENV-DATA
We need to customize the MoF Extension
Event Core
Occurrence Extension
ExtendedMeasurementOrFact Extension
eventID
eventID
eventID
occurrenceID
occurrenceIDOBIS-ENV-DATA
Option 6
Extended MeasurementOrFact(s) Extension allows for parameter standardization (linking to external URI of a controlled vocabulary)
ID: the identifier used by DwC-A standard to link the eMoF to the Core file.
occurrenceID (new): identifier to link the eMoF with the occurrence extension.measurementType: The nature of the measurement, fact, characteristic, or assertion.
measurementTypeID (new): An identifier for the measurementType (global unique identifier, URI)
measurementValue: The value of the measurement, fact, characteristic, or assertion.
measurementValueID (new): An identifier for facts stored in the column measurementValue (global unique identifier, URI)
measurementAccuracy: The description of the potential error associated with the measurementValue.
measurementUnit: The value of the measurement, fact, characteristic, or assertion.
measurementUnitID (new): An identifier for the measurementUnit (global unique identifier, URI)
measurementDeterminedDate: The date on which the MeasurementOrFact was made.
measurementDeterminedBy: A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the MeasurementOrFact.
measurementMethod: A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion.
measurementRemarks: Comments or notes accompanying the MeasurementOrFact.
Event-ID Occurrence-ID MoF-Type MoF-Value MoF-Unit1 Sampling device name Van-Veen grab
1 Area sampled 0.112 m2
1 Sample volume 20 L
1 Sieze mesh size 250 µm
1 Biological entity size sampled 250-1000 µm
1 1 Ash-free dry weight biomass 0.2 Kg/m2
1 1 ObservedindividualCount 112 individuals
1 1 Abundance 1000 individuals/m2
1 1 lifeStage juvenile
EXAMPLE benthic sample Van Veen grab
Extended MeasurementOrFact(s) Extension
ID Occurrence-ID MoF-Type MoF-TypeID MoF-Value MoF-ValueID MoF-Unit MoF-UnitID
1 Sampling device name L19/current/SDNKG01/
Van-Veen grab
L22/current/TOOL0653/
1 Area sampled P01/current/AREABEDS/
0.112 m2 P06/current/UMSQ/
1 Sample volume P01/current/VOLXXXXX/
20 L P06/current/ULIT/
1 Sieze mesh size 250 µm P06/current/UMIC/
1 Biological entity size sampled
250-1000 µm P06/current/UMIC/
1 1 Ash-free dry weight biomass
P01/current/SDBIOL03/
0.2 Kg/m2 P06/current/KMP2/
1 1 ObservedindividualCount
P01/current/OCOUNT01/
112 individuals
1 1 Abundance P01/current/SDBIOL02/
1000 individuals/m2
P06/current/UPMS/
1 1 lifeStage S11/ juvenile S11/current/S1127/
Linking to external URI of a controlled vocabulary for parameter standardization
Event 1
Event 1.1
Event 1.1.1
MoFA1
MoFB1
Occ1
Occ2
Occ3
MoFB2
MoFB3
OBIS-ENV-DATA
EVENT HIERARCHY makes it possible to record differences in sampling time, location, and
depth while still grouping these samples together to the same station visit
MoFA2
CTD and Niskin bottles
Each separate sensor reading can be considered a sub-event of the CTD cast. The Niskin bottle with the biological sample can be linked to the subevent of the CTD cast.
Event1 (station)
Event1.1(depth1)
Event1.2(depth2)
Event1.3(depth3)
MoF1
MoF1.1
MoF1.2
MoF1.3
Occ 1.3
thermocline
CTD and plankton net
If a CTD sensor was placed on a sampling net, the parentEventID to which the sensor readings are linked may represent the deployment of this net, so biological data can be linked directly to this parentEventID.
Event1 (tow)
Event1.1(position1)
Event1.2(position2)
Event1.3(position3)
MoF1.1
MoF1.2
MoF1.3
Bongo nets and CTD unit being deployed from theHenry Bigelow. (Photo by Sammi Ocher, Northeastern University)
Occ 1
MoF1
Animal telemetry
Event1 (entire track)
Event1.1(position1)
Event1.2(position2)
Event1.3(position3)
OTN tags
Each separate sensor reading can be considered a sub-event of a parent event which can be linked to an occurrence record for the animal. The parent event may represent the entire tagging sequence of the animal, or a grouping of sorts for readings recorded at the same period and area, which are then grouped to make up the entire sequence.
MoF1
Occ 1
MoF1.1
MoF1.2
MoF1.3
Video Plankton Recorder
Event1 (tow)
Event1.1(4 seconds)
Event1.1.1(image1)
MoF1.1
MoF1.1.1
Occ 1.1.1 DwC:AssociatedMedia
VPR takes 30 images/sec, software groups by 4 seconds
Pilot datasets on ipt.iobis.org/obis-env
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OBIS 2.0 developments
github.com/iobis/api-docs
github.com/iobis/robis
github.com/iobis/pyobis
github.com/iobis/training