making the tree of life accessible for research

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.

http://phylotastic.org/

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

http://bit.ly/RWRgIc

http://bi.ly/Poaoci


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

?


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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


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ARCHITECTURE OVERVIEWSpecies1Species2Species3conditio

n1conditio

n2

Phylotastic


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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


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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


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PHYLOTASTIC.ORG

It’s all open

sourceScreencasts &

live demonstrations


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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


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http://bit.ly/U1VGA1


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


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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


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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


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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


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THE OTHER KIND OF DATING WITH FOSSILS

r8s, pathd8,

Multidivtime

Calibrating a tree using fossil timepoints


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PHP

11 studies>4,000 trees6,973 taxa

620,868 leavesDateLife engine

(R, FastRWeb, Rserve)

http://www.datelife.orgDATELIFE


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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


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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


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ACKNOWLEDGEMENTS www.phylotastic.org Send feedback to Arlin

Stoltzfus ([email protected]) HIP Leadership Team

ParticipantsSponsors


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making the tree of life accessible for research

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