Using OBIS to Provide Reliable Estimates of Population Indices

for Marine Species from Research

Trawl Surveys Ocean Biodiversity Informatics ConferenceHamburg Germany, November 29, 2004

Robert M. Branton1, Daniel Ricard2

1Bedford Institute of Oceanography, 2Dalhousie UniversityNova Scotia, Canada

brantonb@mar.dfo-mpo.gc.ca

Background

• Traditionally trawl surveys are species rich (100s) with analysis focus on commercial species (~10s).

• Recently other species have been added to sampling protocols thus enabling investigation of ecosystem issues.

• OBIS is expected to provide a basis for interoperability of these data with other scientific disciplines.

Presentation focus:

1. DFO/NOAA trawl data

2. Trawl data quality

3. DFO’s OBIS provider service

4. Ways to improve OBIS

DFO - Canada Dept. of Fisheries and OceansNOAA - USA National Ocean and Atmospheric Agency

1) DFO/NOAA trawl data• ECNASAP database

created in 1995 :– 5 laboratories– 1970-94– 50,000 fishing sets – 276 species.

• Static copy of DFO 4VWX summer survey posted on OBIS in 2002.

Year = 1988

Maps produced using DFO - ACON

ECNASAP – East Coast North America Strategic Assessment Project

Status

• ECNASAP available from DFO/NOAA staff:– 300+ column SPSS file on CD– not updated since ‘95 although surveys are ongoing.

• DFO now testing OBIS views for ECNASAP and various other DFO trawl surveys:– basis for ‘Status of Ecosystem Reports’.

• OBIS-ECNASAP exported to U. of Southern Maine:– basis for ‘Gulf of Maine Ocean Data Partnership’.

Fishing Set Metadata

Observed Numbers and

Weights

LengthCounts

SpecimenDetails

SpeciesMetadata

SurveyMetadata

AreaMetadata

Database Content

AgeReadings

Parasites and/orStomach Content

Sex And Maturity

Fishing Set Metadata

Observed Numbers and

Weights

SpeciesMetadata

SpecimenDetails

Fishing Set Metadata

Observed Numbers and

Weights

SpeciesMetadata

DFO/NOAA

ECNASAP

OBIS

2) Trawl Data quality

• Validate survey species lists using ITIS:– Get most current scientific names and hierarchies– Taxonomists / survey staff review discrepancies,

correct lists, note species difficult to identify and/or not routinely sampled.

• Add hierarchy data to species lists:– Use cumulative discovery curves for each hierarchy

level to investigate protocol changes vs. new discoveries in survey area.

ITIS - Integrated Taxonomic Information System

Average = 0.255 / tow

Taking care of zeros

• Zero catches & counts usually not recorded:– not looking = NULL, – looking but not finding = 0.

• Zeros are important when mapping distribution and calculating averages.

• Augment species list to indicate when and where to assume zero.

Average = 2.405 / tow

Standardizing Observations

• General recommendations:– Define Collection Codes for each survey vessel, sampling

gear, stratification plan & season combination (series)– Adjust Observed Individual Count and Weight (at length,

sex & maturity) by sampling ratio (e.g. total/sample)– Don’t include damaged sets.

• Indicate if data are standardized or estimated:– fishing sets for distance towed (e.g. standard/observed),

species for catchability by gear (e.g. proportion caught at length), …

– numbers at age using stock specific age length keys (e.g. proportion at age for given length), …

Confidence Limits

0

10

20

30

40

50

1990 1992 1994 1996 1998 2000 2002 2004

Year

Aer

age

Wei

gh

t p

er S

tan

dar

d T

ow

(K

gs)

• Relative indices such as ‘average per standard tow’ should include variance or standard error.

• Absolute estimates such as ‘total biomass’ and ‘total abundance’ should also be peer reviewed.– give links to citable

publications. 0

10

20

30

40

50

1990 1992 1994 1996 1998 2000 2002 2004

Year

Aer

age

Wei

gh

t p

er S

tan

dar

d T

ow

(K

gs)

3) DFO’s OBIS provider service

• Inputs– FTP for small databases (e.g. museums)– SQL*net for large databases (e.g. research labs)

• Output– DiGIR XML to OBIS global cache portal at

Rutgers U.

Architecture Diagram

DMZOracle

DB

DiGIRProvider

BIO DMZDFO Firewall

OBIS Portal

Pre-ScheduledExports Only

OperationalOracleDBs

SQL*net

SQL*net

ODBC

FTP

Large RemoteData Bases

Small RemoteData Bases

MSAccessDBs

RemoteOracle DBs

Large LocalData Bases

Trawl Survey & Ecosystem Reporting

http://www.dfo-mpo.gc.ca/CSAS/CSAS/English/Research_Years/2003/2003_089_E.htm

4) Ways to improve OBIS

Enhance existing schema concepts:• Basis of Record – stratum average, stock estimate• Locality – stratum, ecozone, grid square, stock area• Life Stage – maturity stage, age class.

Add new concepts to schema:• Number of Samples and Sampling Units in Locality• Length Class of Observed Individuals• Observed Individual Count Variances or Error Estimate• Observed Weight Variances or Error Estimate• Parent Catalog Number (for stomach contents and parasites).

…/

Add new schemas:• Collection/survey metadata • Area gazetteer (e.g. stratum, ecozone, grid square and

stock areas).

Enhance end-user interface:• Collection based multi-species mapping and reporting

– expanding pie symbol maps (shown earlier)– species by row or column

• missing values as zeroes or nulls• species catchability standardization • summary statistics by stratum, ecozones, ...

Expected Benefits

• Systematic basis for ongoing enhancement and extension of the OBIS schema and interface.– Ability to integrate data from disparate

sampling schemes – Capacity to derive population/community

indices of abundance, diversity, production, etc. around the world.

e.g. Trophic Cascade models (using Trawl and CPR data) being developed for Scotian

Shelf could also be tested on North Sea.

Compliments of Ken Frank, DFO