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GenBank Huge amounts of data, easily accessible. Rate of growth of phylogenetic knowledge Number of papers with molecular and phylogeny in Web of Science.

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Presentation on theme: "GenBank Huge amounts of data, easily accessible. Rate of growth of phylogenetic knowledge Number of papers with molecular and phylogeny in Web of Science."— Presentation transcript:

1 GenBank Huge amounts of data, easily accessible

2 Rate of growth of phylogenetic knowledge Number of papers with molecular and phylogeny in Web of Science Number of studies in TreeBASE

3 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)

4 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

5 Peruvian Diving-petrel (or, whats in a name?) ITIS Pelecanoides garnotii NCBI Pelecanoides garnoti TreeBASE Pelecanoides garnoti AF076073

6 TreeBASE Names Project http://darwin.zoology.gla.ac.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

7 Hemideina maori (weta) 18 TreeBASE names = 1 real name

8 3 TreeBASE names = 1 real name catodon catadon macrocephalus Physeter catodon (Sperm Whale)

9 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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11 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

12 Why taxonomy matters (or vs.)

13 Searching on Aves in TreeBASE finds 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.

14 …but there are other birds in TreeBASE!

15 Tree space in TreeBASE (overlap = 1)

16 There are 24 bird studies in TreeBASE, but tree surfing wont find them

17 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. rbcL Arabidopsis

18 Seeing the tree (best seen when printed on 1.5 m wide paper…)

19 http://darwin.zoology.gla.ac.uk/~rpage/MyToL/www

20 Demo 1

21 Demo 2

22 Comparing classifications for Psocoptera NCBI (GenBank) 9 species Lienhard & Smithers (2002) [courtesy of Kevin Johnson] 4363 species

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24 www.biomoby.org www.gmod.org Bioinformatics envy - GenBank should NOT be our role model

25 From journal to database… Problem: not enough data and trees in journals make it into databases

26 Elseviers journal Molecular Phylogenetics and Evolution is a criminal waste of our efforts Text, data, trees locked up in paper and PDF

27 … 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 Oh, the vision thing George Bush (snr), 1987


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