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 knownknowns, things we know that we  know• There are knownunknowns, things we now know  we don’t know• But the...
Unknown knowns
Things we know…without knowing that we know
Melissotarsus insularis
1Melissotarsusinsularis         no hitMelissotarsus insularis   CASENT0107663-D01CASENT0107663-D01             DQ176312   ...
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)  1799Rana fusca Schneider  1802 Ranatyphonia Sonnini & Latreille  1803 R...
Taxonomy as a source of data
“Dark taxa”
Classification
http://synthesis.eol.org/media/treemap/
Taxonomy• Names• Synonyms• Classifications• Visualisation
Phylogeny
Rate of growth of phylogenetic knowledge       Number of       papers with       “molecular”       and       “phylogeny” i...
Phylogeny• Finding a phylogeny for a group of organisms• Displaying on the web (visualisation)
Data mining
Text mining
Morphological and molecular description ofHaematoloechusmeridionalis n. sp. (Digenea:Plagiorchioidea: Haematoloechidae) fr...
What do crustaceans live on?  Fungi                  Arthropods                           VertebratesGreenplants          ...
What do insects live on?  Fungi                     Arthropods                              VertebratesGreenplants        ...
Data mining• Extracting information from the literature• Extracting information from databases
The End
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
Phyloinformatics: Introduction
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Phyloinformatics: Introduction

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  • http://www.eol.org
  • http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html
  • http://systbio.org/?q=node/184, see http://dx.doi.org/10.1080/10635150701266848
  • http://www.perceptivepixel.com/ and http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html
  • Petra Isenberg, see “Interactive tree comparison for co-located collaborative information visualization” http://www.ncbi.nlm.nih.gov/pubmed/17968069 and http://innovis.cpsc.ucalgary.ca/Research/CollaborativeTreeComparison
  • Transcript of "Phyloinformatics: Introduction"

    1. 1. What is “phyloinformatics”?
    2. 2. Linking biodiversity data together
    3. 3. Apomys datae
    4. 4. Apomys specimen
    5. 5. How do we integrate these data?
    6. 6. Why integrate?
    7. 7. Learn stuff we don’t know
    8. 8. • There are knownknowns, things we know that we know• There are knownunknowns, things we now know we don’t know• But there are also unknownunknowns, things we do not know we dont know
    9. 9. Unknown knowns
    10. 10. Things we know…without knowing that we know
    11. 11. Melissotarsus insularis
    12. 12. 1Melissotarsusinsularis no hitMelissotarsus insularis CASENT0107663-D01CASENT0107663-D01 DQ176312 DQ176312 Melissotarsus sp.Melissotarsus sp.BLF m1 = Melissotarsus insu
    13. 13. No one source has all the answers
    14. 14. 19
    15. 15. Single source
    16. 16. Many sources
    17. 17. Combine sources
    18. 18. ispecies.org
    19. 19. Linking• Finding information about organisms• Linking together in “mashups”
    20. 20. Geography
    21. 21. @rdmpage
    22. 22. @andrewxhill
    23. 23. Geography• Species distributions• Geophylogenies
    24. 24. Taxonomy
    25. 25. 36
    26. 26. Names can change…Leptodactylus fuscus (Schneider) 1799Rana fusca Schneider 1802 Ranatyphonia Sonnini & Latreille 1803 Ranatyphonia Daudin 1824 Ranasibilatrix Wied 1826 Leptodactylustyphonius Fitzinger 1841 Cystignathustyphonius Dumeril & Bibron 1843 Leptodactylustyphonius Fitzinger 1858 Cystignathusfuscus Günther 1882 Leptodactylustyphonius Boulenger 1927 Leptodactylussibilatrix Müller 1935 Leptodactylussibilatrix Parker 1968 Leptodactylusfuscus Heyer
    27. 27. Taxonomy as a source of data
    28. 28. “Dark taxa”
    29. 29. Classification
    30. 30. http://synthesis.eol.org/media/treemap/
    31. 31. Taxonomy• Names• Synonyms• Classifications• Visualisation
    32. 32. Phylogeny
    33. 33. Rate of growth of phylogenetic knowledge Number of papers with “molecular” and “phylogeny” in Web of Science Number of studie s in TreeBA SE
    34. 34. Phylogeny• Finding a phylogeny for a group of organisms• Displaying on the web (visualisation)
    35. 35. Data mining
    36. 36. Text mining
    37. 37. Morphological and molecular description ofHaematoloechusmeridionalis n. sp. (Digenea:Plagiorchioidea: Haematoloechidae) fromRanavaillantibrocchi of Guanacaste, Costa RicaHalipeguseschi n. sp. (Digenea: Hemiuridae) inRanavaillanti from Guanacaste Province, Costa RicaHaematoloechusdanbrooksi n. sp. (Digenea:Plagiorchioidea) from Ranavaillanti from Los Tuxtlas,Veracruz, Mexico
    38. 38. What do crustaceans live on? Fungi Arthropods VertebratesGreenplants Bacteria
    39. 39. What do insects live on? Fungi Arthropods VertebratesGreenplants Bacteria
    40. 40. Data mining• Extracting information from the literature• Extracting information from databases
    41. 41. The End
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