Expanding OBIS beyond species occurrence data, with

an extension for environmental data

Photo credits Molly Timmers - NOAA w.appeltans@unesco.org

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

download

versioning

upload

PUBLISH

OBIS 2.0 developments

github.com/iobis/api-docs

github.com/iobis/robis

github.com/iobis/pyobis

github.com/iobis/training

@WrdAppltns

THANK YOU

info@iobis.org

WWW www.iobis.org