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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Making the tree of life accessible for research

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

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

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


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

THE “TREE OF LIFE” =

* Proper phylogenies as well as phylogeny-based taxonomic hierarchies


Architecture overview

ARCHITECTURE OVERVIEW

Species1

Species2

Species3

condition1

condition2

Phylotastic


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


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

HACKATHON #1, JUNE 4 TO 8 @ NESCENT

  • 30 participants

    • high diversity

    • 2 remote sites


Phylotastic org

PHYLOTASTIC.ORG

It’s all open source

Screencasts & live demonstrations


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:

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;


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

SCREENCAST: MESQUITE-O-TASTIC

Peter Midford

NESCent

Arlin Stoltzfus

NIST


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

RECONCILIOTASTIC


Role of tnrs in phylotastic brief

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


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

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

THE OTHER KIND OF DATING WITH FOSSILS

r8s, pathd8, Multidivtime

Calibrating a tree using fossil timepoints


Datelife

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

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


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

WHAT’S NEXT?


Acknowledgements

www.phylotastic.org

Send feedback to Arlin Stoltzfus ([email protected])

ACKNOWLEDGEMENTS

HIP Leadership Team

Participants

Sponsors


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