Barcode of Life initiative FishBoL Workshop

1
Barcode of LifeinitiativeFish-BoL Workshop
6 June 2005University of Guelph, Ontario Canada

• Nicolas BAILLY
• WorldFish Center Philippines Office, Los Baños
• n.bailly_at_cgiar.org

2
Available in DVD, CD-ROM and on the
web(www.fishbase.org 4 mirrors)
FishBase, a global public good developed as a
decision-support system for conservation and
management of aquatic biodiversity and ecosystems.
Book in English, Spanish, French,
Portuguese Multi-language (13) on-line access
(Main Pages) 16 Non-roman scripts for common names
3
FishBase and the private life of a fish
Reproduction and Life History Maturity
Spawning Eggs Larvae Broodstock Fry
nurseryLarval dynamics Larval speed
Morphology and PhysiologyMetabolism
Gill area Vision Disease Brain
AbnormalitiesEcotoxicology Swim mode
Distribution Occurrence FAO areas
Country Ecosystem
Genetics AquacultureElectrophoresis
HeritabilityStrains Introductions
Fish as FoodProcessing Ciguatera FAO
catches Aquaculture (production)
Trophic Ecology Ecology PredatorsFood items
Diet composition Food consumption Ration
Other Tables Pictures Keys Sounds
Class Order Family Species
Common Name
Population Dynamics Growth/Mortality
L/W relations Maximum sizes RecruitmentL/L
relations Length frequency
4
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 (gt 24,800 species, 43
  museums)
• 4.48 million records (2 Gb 180 database tables)

5
FishBase as a web service
6
FishBase basic structure
Species descriptionand life history
BiologyEcologyFisheries
Fishnames
Fishcollections
Fish literature
Collaborators
7
FishBase basic structure
8
(No Transcript)
9
(No Transcript)
10
xml file for common names
11
xml file for common names
12
(No Transcript)
13
(No Transcript)
14
Encoding of records in Table Species
15
Drown by numbers again

• Species total 2000/2005
• Fresh 13779 46.4 747 59.1
• Brackish 86 0.3 4 0.3
• Marine 15758 53.3 513 40.6
• Total 28920 1263

After FB, June 2005Miss 270 spp. 2004
After CoF, Mai 2005
16
Checking, validation, quality assurance

• Internal checks by queries
• Checks by specialists (taxonomy, other
  specialties)
• Checks by area specialists
• Cross-check with CoF
• Classification Nelson -gt Eschmeyer
  Authors Difficulty to coordinate all changes
• Problem what is to be complete?

17
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)
18
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)

19
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
20
Mapping in SAUP (Fisheries Centre, UBC, Vancouver)
21
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

22
Common Access and Interoperability
Data providers
Portal
1 to n
23
FishBase and Common Access
Data providers
FishBase
User
Gadus morhua
Answer
Data
Request
1 to n
24
FishBase and Interoperability
Data providers
FishBase
User
Gadus morhua
URLs
1 to n
25
How to deep-link in FishBase
26
(No Transcript)
27
(No Transcript)
28
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

29
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)

30
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

31
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

32
fishbase.org fishbase.de fishbase.fr fishbase.se
fishbase.tw fishbase.org.ph