Making the tree of life accessible for research
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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.

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Making the Tree of Life Accessible for Research

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http://phylotastic.org/

A project of the NESCent HIP (hackathons, interoperability, phyogenies) working group.

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).


RE-USE OF TREES

“Most attempts at re-use seem to end in disappointment” [1]

Consumers (re-users)

Producers

Repositories

[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


USE CASE: LEAF VEIN EVOLUTION

?

aextoxicaceae/aextoxicon/aextoxicon_puntatum

anacardiaceae/anacardium/anacardium_excelum

anacardiaceae/rhus/rhus_glabra

annonaceae/dugetia/dugetia_furfuraceae

. . .

R.L. Walls with Linnaeus

Input list from Walls, 2011

Phylomatic

98-species tree of Walls, 2011

APG framework with 1566 taxa


  • 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

THE “TREE OF LIFE” =

* Proper phylogenies as well as phylogeny-based taxonomic hierarchies


ARCHITECTURE OVERVIEW

Species1

Species2

Species3

condition1

condition2

Phylotastic


  • Phy· lo· tas· tic/fī lō ˈtăs tĭk/

    • Adjective: providing computable, convenient and credible access to expert knowledge of the phylogeny of species

    • 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

PHYLOTASTIC

* Hackathons, Interoperability, Phylogenies, a NESCent working group


  • 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

HACKATHON #1, JUNE 4 TO 8 @ NESCENT

  • 30 participants

    • high diversity

    • 2 remote sites


PHYLOTASTIC.ORG

It’s all open source

Screencasts & live demonstrations


  • 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:

SCREENCAST: SCRIPTABLE PRUNER, WEB FORM

Rutger Vos

#!/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;


  • YouTube screencast at http://bit.ly/QjymbK (3 min)

  • Installable Mesquite module is here:

    • https://github.com/phylotastic/mesquite-o-tastic

SCREENCAST: MESQUITE-O-TASTIC

Peter Midford

NESCent

Arlin Stoltzfus

NIST


  • 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

RECONCILIOTASTIC


ROLE OF TNRS IN PHYLOTASTIC (BRIEF)

<1 minute

Phylotastic

36 species + 2 extras*

auto-extract species names from text

5 minutes

Copy & paste species named in Table 1

Phylotastic

Riek, 2011 (Mammalian Biology 76(1):3-11)

33 species

12 minutes

Manually key in species list from tree image

Phylotastic

36 species

Hours or days

Manually reconcile names with names in source tree

Phylotastic

40 species

40 species

* named in text but not used in phylogenetic analysis


  • 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

ROLE OF TNRS — MORE DETAIL

TNRS team

Naim Matasci

iPlant

Gaurav Vaidya

U. Colorado

Siavash Mirarab

UT Austin


THE OTHER KIND OF DATING WITH FOSSILS

r8s, pathd8, Multidivtime

Calibrating a tree using fossil timepoints


11 studies

>4,000 trees

6,973 taxa

620,868 leaves

DATELIFE

http://www.datelife.org

DateLife engine

(R, FastRWeb, Rserve)

PHP


CURRENT STATUS - WYSIWYG

Branches could shift without warning

There are some holes

You might crash

We haven’t put the pieces together yet

The interfaces are unstable


  • 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

WHAT’S NEXT?


www.phylotastic.org

Send feedback to Arlin Stoltzfus ([email protected])

ACKNOWLEDGEMENTS

HIP Leadership Team

Participants

Sponsors


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