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http://phylotastic.or g /. A project of the NESCent HIP (hackathons, interoperability, phyogenies) working group. Making the Tree of Life Accessible for Research. - PowerPoint PPT Presentation
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Making the Tree of Life Accessible for Research
This is a 20-minute overview with links to screencasts and demos, providing an introduction to the project and to the
upcoming 2nd hackathon (Jan 28 to Feb 1, 2013, Tucson, AZ).
http://phylotastic.org/A project of the NESCent HIP (hackathons,
interoperability, phyogenies) working group.
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
RE-USE OF TREES
Producers Consumers (re-users)Repositories
“Most attempts at re-use seem to end in disappointment” [1]
[1] Stoltzfus, et al., 2012, “Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis”, http://www.ncbi.nlm.nih.gov/sites/entrez/23088596
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
USE CASE: LEAF VEIN EVOLUTION
R.L. Walls with
Linnaeus
aextoxicaceae/aextoxicon/aextoxicon_puntatumanacardiaceae/anacardium/anacardium_excelumanacardiaceae/rhus/rhus_glabraannonaceae/dugetia/dugetia_furfuraceae. . .
Phylomatic
Input list from Walls, 2011
APG framework with 1566 taxa 98-species tree of Walls, 2011
?
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
THE “TREE OF LIFE” = Some big trees *
4,500 mammal species 55,473 angiosperm species 1,827 angiosperm taxa 800 fish families 16,000 taxa in ToLWeb 73,060 eukaryotic species 400,000 prokaryotic 16S
rDNAs 250,000 species NCBI taxonomy
And other trees not listed* Proper phylogenies as well as phylogeny-based taxonomic hierarchies
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
ARCHITECTURE OVERVIEWSpecies1Species2Species3conditio
n1conditio
n2
Phylotastic
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
PHYLOTASTIC Phy· lo· tas· tic /fī lō ˈtăs tĭk/
1. Adjective: providing computable, convenient and credible access to expert knowledge of the phylogeny of species
2. Noun: an open-source project of HIP* to prototype and disseminate a distributed, web-services-based phylotastic system
Synonyms: ToL-o-matic Web home: http://www.phylotastic.org
* Hackathons, Interoperability, Phylogenies, a NESCent working group
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
HACKATHON #1, JUNE 4 TO 8 @ NESCENT
Teams: TNRS - taxonomic name resolution TreeStore - triple store with REST API Architecture - controllers, interfaces, pruners Branch lengths - scaling trees using
chronograms Shiny - other demos and cool front-end stuff
30 participants high
diversity 2 remote
sites
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
PHYLOTASTIC.ORG
It’s all open
sourceScreencasts &
live demonstrations
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
SCREENCAST: SCRIPTABLE PRUNER, WEB FORM YouTube video at http://bit.ly/U1VGA1 (3 min) Web form invokes URL API, like this:
http://phylotastic-wg.nescent.org/script/phylotastic.cgi?species=Felis+silvestris%2C+Canis+lupus%2C+Cavia+porcellus&tree=mammals&format=newick
So, you can run it with curl Or with a simple Perl script:
#!/usr/bin/perl –w
my $base = "http://phylotastic-wg.nescent.org/script/phylotastic.cgi";my ( $tree, $taxa ) = @ARGV; $taxa =~ s/[ _]/+/g; $taxa =~ s/,/%2C/g;
system( "curl \"$base?species=$taxa&tree=$tree&format=newick\" > out.tre; open out.tre" ); exit;
Rutger Vos
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
SCREENCAST: MESQUITE-O-TASTIC YouTube screencast at http://bit.ly/QjymbK (3 min) Installable Mesquite module is here:
https://github.com/phylotastic/mesquite-o-tastic
Peter MidfordNESCent
Arlin StoltzfusNIST
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
RECONCILIOTASTIC Reconcile-tree problem
Very common use-case Inputs are gene tree, species tree
Gene tree: easy to get Species tree: hard to get
Approach (see Reconciliotastic demo at http://www.phylotastic.org/demos) Load gene tree (with NCBI identifiers embedded in labels) Compute species list
Extract identifiers from labels Map IDs to species sources via NCBI web service
Get species tree phylotastically Reconcile gene tree and species tree using Zmasek’s SDI library
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
ROLE OF TNRS IN PHYLOTASTIC (BRIEF)
40 species
auto-extract species names
from textRiek, 2011
(Mammalian Biology
76(1):3-11)Manually key in species list
from tree image
36 species + 2 extras*
36 species
Phylotastic
Phylotastic
* named in text but not used in phylogenetic analysis
40 species Phylotastic
Copy & paste species named
in Table 1 33 species Phylotas
tic
5 minutes
<1 minute
12 minutes
Hours or days
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
ROLE OF TNRS — MORE DETAIL screencast: http://bit.ly/T5ikoG (7
min) Riek, 2011 (case study) Cool demo:
PDF auto-extracted names tree What Taxonomic Name Resolvers do What the phylotastic TNRS team did Using the Taxosaurus URL API
http://api.phylotastic.org/tnrs/submit?query=Cephalophus+monticola
TNRS team
Naim MatasciiPlant
Gaurav VaidyaU. Colorado
Siavash MirarabUT Austin
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
THE OTHER KIND OF DATING WITH FOSSILS
r8s, pathd8,
Multidivtime
Calibrating a tree using fossil timepoints
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
PHP
11 studies>4,000 trees6,973 taxa
620,868 leavesDateLife engine
(R, FastRWeb, Rserve)
http://www.datelife.orgDATELIFE
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
CURRENT STATUS - WYSIWYG
There are some holes
We haven’t put the pieces together yetThe interfaces are unstable
Branches could shift without warning
You might crash
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
WHAT’S NEXT?
Phylotastic hackathon #2 (Jan 2013, AZ) Themes
Integration – get components to work together Use-cases – give users what they want More Shiny Stuff — make it look good Your idea here
To apply http://tinyurl.com/PhyloTastic2
More partners & sponsors
Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)
ACKNOWLEDGEMENTS www.phylotastic.org Send feedback to Arlin
Stoltzfus (arlin@umd.ed) HIP Leadership Team
ParticipantsSponsors
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