Transcript FishBase - FISH-BOL

Barcode of Life
initiative
Fish-BoL
Workshop
6 June 2005
University of Guelph, Ontario
Canada
Nicolas BAILLY
WorldFish Center
Philippines Office, Los Baños
[email protected]
FishBase, a global public good
developed as a decision-support system
for conservation and management of
aquatic biodiversity and ecosystems.
Available in DVD, CD-ROM and on the web
(www.fishbase.org + 4 mirrors)
Book in English, Spanish, French, Portuguese
Multi-language (13) on-line access (Main Pages)
16 Non-roman scripts for common names
FishBase and the private life of a fish …
Morphology
and Physiology
Metabolism
Gill area
Vision
Disease
Brain
Abnormalities
Ecotoxicology
Swim mode
Reproduction and
Life History
Maturity
Spawning
Eggs
Larvae Broodstock Fry nursery
Larval dynamics Larval speed
Genetics &
Aquaculture
Distribution
Occurrence FAO areas
Country Ecosystem
Fish as Food
Electrophoresis
Heritability
Strains Introductions
Processing Ciguatera
FAO catches
Aquaculture
(production)
Trophic Ecology
Ecology Predators
Food items Diet composition
Food consumption Ration
Population
Dynamics
Growth/Mortality
L/W relations
Maximum sizes Recruitment
L/L relations Length frequency
Other Tables
Pictures
Keys
Sounds
Class
Order
Family
Species
Common Name
Drown by numbers (as of 3rd June 2005)
 28,598 species (incl. 219 with 322 subspecies = 28,920)
 81,190 “synonyms”
 207,403 common names in 264 languages
 160,866 country records for 295 “countries”
 108,813 ecosystem records for 379 ecosystems
 53,388 FAO area records for 27 areas
 12,157 morphology records
 1,158 identification keys for 6,408 species
 41,116 fish images and photos
 36,129 bibliographic references
 2 million occurrences (> 24,800 species, 43 museums)
 4.48 million records (2 Gb; 180 database tables)
FishBase as a web service
FishBase basic structure
Species description
and life history
Fish
collections
Fish
names
Biology
Ecology
Fisheries
…
FB
Fish literature
FB
CoF
Collaborators
CoF
FishBase basic structure
xml file for common names
xml file for common names
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Cumulated number of species entries
Encoding of records in Table Species
30000
25000
60000
20000
50000
15000
40000
30000
10000
20000
10000
5000
0
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Time (years)
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After CoF,
Mai 2005
Drown by numbers again
Fresh
Brackish
Marine
Total
“Species” total 2000/2005
13779 46.4% 747 59.1%
86 0.3%
4
0.3%
15758 53.3% 513 40.6%
28920
1263 After FB, June 2005
Miss 270 spp. 2004
60000
50000
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After CoF, Mai 2005
Checking, validation, quality assurance
 Internal checks by queries
 Checks by specialists (taxonomy, other specialties)
 Checks by area specialists
 Cross-check with CoF
 Classification: Nelson -> Eschmeyer + Authors
Difficulty to coordinate all changes
 Problem: what is to be complete?
Information systems as icebergs: optimal situation
 Distinction between views for end-users …
… and tables for specialists
Views for end-users (VEU)
VEU
VEU
VEU
VEU
VEU
TS
TS
TS
TS
TS
Tables for specialists (TS)
FishBase identification tools
 Quick identification through
outlines down to Families
 Quick identification through
photos by Family, Country,
Ecosystems
 Dichotomous key computerised
(FAO, Ichthyofaunas)
 Matrix approach (computer-aided
identification)
Biogeographic modelling
Occurrence points in can be
mapped and used with available
environmental parameters to
predict other possible occurrences
of the species through mapping
and spatial modelling
Georeferenced records from 43
museum collections and survey data
Mapping in SAUP (Fisheries Centre, UBC, Vancouver)
Common Access and Interoperability
 What is common access?

Accessing at the same time to databases covering
the same topic
 What is interoperability?

Accessing at the same time to databases covering
complementary topics
Common Access
and Interoperability
Data providers
Wrappers
User
Gadus
morhu
a
Portal
Answer
Request
1 to n
Data providers
FishBase and Common Access
User
Gadus
morhu
a
FishBase
Answer
Data
Request
1 to n
Data providers
FishBase and Interoperability
User
FishBase
Gadus
morhu
a
URLs
Fish-BoL
1 to n
How to deep-link in FishBase
What we can provide
 Lists of species by taxononmy, by country, by
ecosystems, by FAO areas
 A fixed English common name
 Deep-links to species pages or others to flesh the
barcode
 Diagnosis, description, photo*, other infromation as
required
 List of "synonyms" and common names
 Link with traditional identification tools
 Link to mapping system
 To discuss: web services through xml
* Depending on author agreement
What we expect
 A new link from FishBase for users
 Widen our collaborator network (new data, data check)
 Importing the survey data
 Complete our photo set (at least one photo per species)
 Taking the opportunity to handle more taxonomic levels
 To root the iceberg for the taxonomy management
(concept approach = potential taxa)
Lessons learned in FishBase
 ‘Science first’ attitude
 ‘Yes’ attitude towards suggestions
 Invite, accept and act on criticism
 Keep in the limits of the project
 Data quantity and quality first
 Keep it simple, software keeps changing
 Invest in people
 Give more credit than expected
FishBase Consortium Members
 WorldFish Center
 Food and Agriculture Organization







of the
United Nations
Leibniz Institute of Marine
Sciences, Kiel
Swedish Museum of Natural
History
Africamuseum, Tervuren
Muséum National d'Histoire
Naturelle
Fisheries Centre, University of
British Columbia
Aristotle University of Thessaloniki
fishbase.org
fishbase.de
fishbase.fr
fishbase.se
fishbase.tw
fishbase.org.ph