what is “ phyloinformatics ”?
DESCRIPTION
What is “ phyloinformatics ”?. Linking biodiversity data together. Apomys datae. Apomys specimen. How do we integrate these data?. Why integrate?. Learn stuff we don’t know. There are known knowns , things we know that we know There are known unknowns , things we now know we don’t know - PowerPoint PPT PresentationTRANSCRIPT
What is “phyloinformatics”?
Linking biodiversity data together
Apomys datae
Apomys specimen
How do we integrate these data?
Why integrate?
Learn stuff we don’t know
• There are known knowns, things we know that we know
• There are known unknowns, things we now know we don’t know
• But there are also unknown unknowns, things we do not know we don't know
Unknown knowns
Things we know …without knowing that we know
Melissotarsus insularis
Melissotarsus insularis no hit
CASENT0107663-D01 DQ176312
Melissotarsus sp. BLF m1DQ176312
CASENT0107663-D01Melissotarsus insularis
1
Melissotarsus insularisMelissotarsus sp. BLF m1 =
No one source has all the answers
19
Single source
Many sources
Combine sources
ispecies.org
Linking
• Finding information about organisms
• Linking together in “mashups”
Geography
@rdmpage
@andrewxhill
Geography
• Species distributions
• Geophylogenies
Taxonomy
36
Names can change…Leptodactylus fuscus (Schneider)
1799 Rana fusca Schneider1802 Rana typhonia Sonnini & Latreille1803 Rana typhonia Daudin1824 Rana sibilatrix Wied1826 Leptodactylus typhonius Fitzinger1841 Cystignathus typhonius Dumeril & Bibron1843 Leptodactylus typhonius Fitzinger1858 Cystignathus fuscus Günther1882 Leptodactylus typhonius Boulenger1927 Leptodactylus sibilatrix Müller1935 Leptodactylus sibilatrix Parker1968 Leptodactylus fuscus Heyer
Taxonomy as a source of data
“Dark taxa”
Classification
http://synthesis.eol.org/media/treemap/
@kzelnio Think how great of a tool that could be at museumson a large flat screen at 4 year old height.
Taxonomy
• Names
• Synonyms
• Classifications
• Visualisation
Phylogeny
0
1000
2000
3000
4000
5000
6000
7000
1975 1980 1985 1990 1995 2000 2005
Year
Cumulative number
Rate of growth of phylogenetic knowledge
Number of papers with “molecular” and “phylogeny” in Web of Science
Number of studies in TreeBASE
@dr_pi
Phylogeny
• Finding a phylogeny for a group of organisms
• Displaying on the web (visualisation)
Data mining
Text mining
Morphological and molecular description of Haematoloechus meridionalis n. sp. (Digenea: Plagiorchioidea: Haematoloechidae) from Rana vaillanti brocchi of Guanacaste, Costa Rica
Halipegus eschi n. sp. (Digenea: Hemiuridae) in Rana vaillanti from Guanacaste Province, Costa Rica
Haematoloechus danbrooksi n. sp. (Digenea: Plagiorchioidea) from Rana vaillanti from Los Tuxtlas, Veracruz, Mexico
What do crustaceans live on?
Greenplants
Bacteria
FungiVertebrates
Arthropods
What do insects live on?
Greenplants
Bacteria
FungiVertebrates
Arthropods
Data mining
• Extracting information from the literature
• Extracting information from databases
The End