GenBank Huge amounts of data, easily accessible

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GenBank Huge amounts of data, easily accessible
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Rate of growth of phylogenetic knowledge
Number of papers with molecular and phylogeny
in Web of Science
Number of studies in TreeBASE
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Why have a phylogeny database?

• Archive data and trees (repeat old analyses with
  new tools)
• Synthesize new data sets and trees (supermatrices
  and supertrees)
• Big scale questions (tree shape, bias in tree
  building methods, stability of trees over time)
• Hypothesis testing find all phylogenies for
  taxa with members in Gondwana -- do they show
  similar area cladograms, amounts of sequence
  divergence, etc.
• Who knows(we wont know until we try)

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Obstacles in the way

• Ontologies (consistent names for organisms,
  genes, and other kinds of data)
• How to store and query trees (what kind of
  queries do we want?)
• Summarising information in trees (supertrees) and
  matrices (supermatrices)
• Visualising very big trees

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Peruvian Diving-petrel(or, whats in a name?)

• ITIS Pelecanoides garnotii
• NCBI Pelecanoides garnoti
• TreeBASE Pelecanoides garnoti AF076073

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TreeBASE Names Projecthttp//darwin.zoology.gla.a
c.uk/rpage/TreeBASE/

• Aim is to map every name in TreeBASE onto a valid
  taxonomic name (i.e., a name in a database, or in
  the literature)
• Use exact-, substring-, and approximate string
  matching ( BLAST)
• So far 26819 out of 35084 names mapped

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Hemideina maori (weta)
18 TreeBASE names 1 real name
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catodon
catadon
macrocephalus
3 TreeBASE names 1 real name
Physeter catodon (Sperm Whale)
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The case of the Harp seal
TreeBASE and GenBank have harp seals under two
different names, only ITIS knows that they are
the same thing
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(No Transcript)
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• There are known knowns, things we know that we
  know
• There are known unknowns, things we now know we
  dont know
• But there are also unknown unknowns, things we do
  not know we don't know

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Why taxonomy matters
(or
vs.
)
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Searching on Aves in TreeBASEfinds 4 studies
with birds

• Study 1 Gauthier, J., A.G. Kluge, and T. Rowe.
  1988. Amniote phylogeny and the importance of
  fossils.
• Study 2 Harshman, J., C. J. Huddleston, J. P.
  Bollback, T. J. Parsons, and M. J. Braun. 2003
  inpress. True and False Gavials A Nuclear Gene
  Phylogeny of Crocodylia.
• Hedges, S. B., K. D. Moberg, and L. R.
  Maxson.1990. Tetrapod phylogeny inferred from 18s
  and 28s ribosomal RNA sequences and a review of
  the evidence for amniote relationships.
• van Dijk, M. A. M., E. Paradis, F. Catzeflis, and
  W. de Jong. 1999. The virtues of gaps Xenarthran
  (Edentate) monophyly supported by a unique
  deletion in alphaA-crystallin.

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but there are other birds in TreeBASE!
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Tree space in TreeBASE (overlap 1)
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There are 24 bird studies in TreeBASE, but tree
surfing wont find them
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Fig. 1. The data availability matrix' for green
plant protein sequences from GenBank (release
132). A set of 130304 sequences for 14667 species
sequences were clustered into 61117 groups of
homologous proteins by a combination of BLAST and
single-linkage clustering (using the program
Blastclust from the NCBI Blast toolkit
http//www.ncbi.nlm.nih.gov/BLAST/ ). A column
represents a protein or protein family a row
represents one of the species in the dataset and
a dot indicates the existence of a sequence for
that species and protein. Species are sorted
vertically by their number of sequences the
most-represented species ( Arabidopsis thaliana )
is at the top. Proteins are sorted horizontally
by the number of taxa for which they have been
sequenced the most heavily sequenced gene ( rbcL
) is on the right. This figure shows the most
heavily sampled corner of the data availability
matrix the remainder of the matrix is even more
sparse.
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Seeing the tree (best seen when printed on 1.5 m
wide paper)
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http//darwin.zoology.gla.ac.uk/rpage/MyToL/www
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Demo 1
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Demo 2
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Comparing classificationsfor Psocoptera
Lienhard Smithers (2002) courtesy of Kevin
Johnson 4363 species
NCBI (GenBank) 9 species
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Bioinformatics envy - GenBank should NOT be our
role model
www.biomoby.org www.gmod.org
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From journal to database
Problem not enough data and trees in journals
make it into databases
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Elseviers journal Molecular Phylogenetics and
Evolution is a criminal waste of our efforts
Text, data, trees locked up in paper and PDF
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the database is the journal

1. Data trees go into database
2. Text (annotation) added
3. Automatically generate a report summarising the
   results
4. The report is the publication (can have a DOI)
5. Open Access data and text