Transcript TDW-10 - BioDaSys

BioDaSys
Biological Database System
Sylvain Caillot – FEMA - OFP
TDW10: 28/04/2016, Noumea, New Caledonia
Overview
Tell me more about it
-
What is biological sampling?
History of BioDaSys
BioDaSys to support the tuna tissue bank
Next step: The Pacific Marine Specimen Bank
Going even further…
What?
Up to 8 samples collected from fish
All labelled to be uniquely identified
-
Stomach
Muscle
Liver
Gonad
Otolith
Spine
Blood
Fin
How?
… are they collected?
- At sea:
- Observer programs, tagging cruises, scientific trips
- At port during disembarking:
- Port sampling program, consultants
- Specific training, assessment, assistance, financial incentive
- Targeted sampling : Species/length frequency/Type of samples
Why?
- Ecosystem approach of fisheries management
- Diet, micronekton
- Support stock assessment with estimation of species’ biology
- Reproductive biology, growth rate, stock boundaries
- Scientific studies with implication in fisheries management
- Contaminant
ECOSYSTEM
History
From S’Danger to BioDaSys
S’Danger
- First release in 2003 as an Access database
- Only stomach samples & analysis
- Only tuna
BioDaSys
To support the tuna tissue bank:
- Collection of biological sampling all over the Pacific
- Since 2001 on behalf of member countries
- Last release in Avril 2016
- 11 different biological samples & 9 different analyses
- All species
BioDaSys now
To continue supporting the tissue bank
- To collect all information related to biological sampling
from A to Z
- Desktop front-end used by SPC staff
- Webmapping front-end for data visualisation
accessible to the public
- SQL Server database with >100 tables
What is BioDaSys?
From paper to the Web
BioDaSys
Desktop front-end - Skeleton
Trip
Fish
Sample
Analysis
BioDaSys
Few numbers…
Trips
8
890
Fish
28,600
Observer trips, port sampling, scientific
cruises, tagging cruises, ships of opportunity
274 different species: Tuna, billfish, wahoo,
shark, snapper, gelatinous, crustacean…
Samples 81,800
61,300 samples still available in dedicated freezers
8
Analyses 24,500
+ 1,000 analyses still being processed
BioDaSys
and a map…
Trip
BioDaSys
Fish
Sample
Analysis
Samples
Increase of the number of samples per year
1,000
3,000
7,500
12,000
2001
2006
2010
2015
Diversity of samples
OO
ST
MU
GO
LI
17,400 muscles
14,700 livers
13,900 gonads
13,800 stomachs
13,700 otoliths
…
Stored all over the Pacific
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SPC premises
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Australia
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Marshall Isl.
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Solomon Isl.
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American Samoa
-
7 other countries
Trip
BioDaSys
Fish
Sample
Analysis
Analysis
- 10 laboratories all over the world
- 7 current analyses available
- 2 new analyses to come
10,600
Stomach
content
4,500
Fatmeter
4,400
Ageing
2,500
Histology
2,500
Isotope
154 Lipid
92 Contaminant
DNA
Micro-chemistry
Data consolidation
From A to Z
Sampling tracker
• Labels / Kits
• Collection
• Freight
• Finance
• Storage
• Availability
• Sampling quality
• Access to scans, payslips
Data consolidation
Daily management
Laboratory logistic
- Kit preparation, items stock
Sample movement
Data quality
Data entry, data checking & reporting tools
- Data imported from Excel files
- Constraints & controls
- Typing mistakes
- Calculated fields, pre-cooked data extractions
- Data harmonization
- References lookup tables
- Reports
Data validation
Connection with external datasets
Fishing positions cross-checked with
• Obs. logbooks
• VMS
• Logsheets
Tuna tissue bank
Webmapping front end
- Simple searchable view of all collected samples
- Scientists can request samples for their studies
What’s next?
The Pacific Marine Specimen Bank
- Full-featured web-portal for browsing biological sampling data
- Supported by WCPFC and managed by SPC
Pacific Marine Specimen Bank
Unique repository for all biological data
-
Search tools
Reporting & mapping interfaces
Easy deposits and withdrawals of samples using baskets
Optimized data access based on user credentials
Better collaboration between samplers, coordinators, users
Based on robust and modern technologies
First version in 2016
Pacific Marine Specimen Bank
Going even further…
Make relevant biological information available online
• Species identification fact sheets
• Photo library
• X-rays library
Thank you
Any questions? – [email protected] , [email protected]
DEMO: http://www.spc.int/tagging/webtagging/BioDaSys/BioDaSys/Samples