Getting More Phylotastic

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lightning talk for iEvoBio2013, June 25, 2013, delivered by Arlin Stoltzfus on behalf of HIP and the hackathon participants. Phylotastic is a distributed delivery system for expert knowledge of species phylogeny (the tree of life).

Technology Business

Getting more
ArlinStoltzfus
Research Biologist, National Institute of Standards and Technology
A project of the NESCent HIP (hackathons,
interoperability, phyogenies) working group

THE PROBLEM
Tree-of-Life
knowledge
• Mostly locked in pics
• < 5% of trees archived
• Hard to discover &access
Researchers, educators,
& resource-providers
who could use a good
species tree
?

What big-tree methods generate
What users need
APG framework tree Fig. 5 from Butler & King, 2004

~ 5% TO 15% NON-STANDARD NAMES
Figure from Riek, 2011 Phylotastic tree after name corrections
Ovisammon
Oreamnusamerican
us
Felis
catus
Ovisaries
Oreamnos
americanus
Felis
silvestris

Species1
Species2
Species3
condition1
condition2
Phylotastic
Species3
Species1
Species2
Sources & methods

Upstream
steps
Rectify
names
Discover
tree
Prune &
Graft
Add branch
lengths
Integrate
other data
Downstream
analysis

DataOperations
User Controller
Rectify Names
(TNRS) NameBanks
Find matching trees
Source trees
Graft missing taxa
Prune extra taxa
Translate formats
Get branch lengths
Calibrations
Species1
Species2
Species3
condition
1
condition
2
Phylotasti
c

Phylotasti
c
 Goal: access to expert ToL knowledge that is
 convenient – much easier than DIY tree
 computable – logically encoded trees (not pics)
 credible – useable in a scientific paper

HIP HACKATHONS
HIP Leadership Team
Participants

ANNOTATING SOURCE TREES using a formal ontology
See Hilmar Lapp’s lightning talk

TNRS
Oreamnosamericanu
s
Oreamnusamericanus:
No exact match

DATELIFE.ORG
The other kind of Dating with Fossils
Ask Brian O’Meara, Tracy Heath, or Klaus Schliep
-- scales trees by reference to prior calibrations
Dating with Fossils

Reconciled Tree (red=duplication,
green=speciation)

PHYLOTASTIC.ORG
Questions? Ask Arlin or email to
arlin@umd.edu

THANKS!
 www.phylotastic.org
HIP Leadership Team
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Getting More Phylotastic

1. Getting more ArlinStoltzfus Research Biologist, National Institute of Standards and Technology A project of the NESCent HIP (hackathons, interoperability, phyogenies) working group

2. THE PROBLEM Tree-of-Life knowledge • Mostly locked in pics • < 5% of trees archived • Hard to discover &access Researchers, educators, & resource-providers who could use a good species tree ?

3. What big-tree methods generate What users need APG framework tree Fig. 5 from Butler & King, 2004

4. ~ 5% TO 15% NON-STANDARD NAMES Figure from Riek, 2011 Phylotastic tree after name corrections Ovisammon Oreamnusamerican us Felis catus Ovisaries Oreamnos americanus Felis silvestris

5. Species1 Species2 Species3 condition1 condition2 Phylotastic Species3 Species1 Species2 Sources & methods

6. Upstream steps Rectify names Discover tree Prune & Graft Add branch lengths Integrate other data Downstream analysis

7. DataOperations User Controller Rectify Names (TNRS) NameBanks Find matching trees Source trees Graft missing taxa Prune extra taxa Translate formats Get branch lengths Calibrations Species1 Species2 Species3 condition 1 condition 2 Phylotasti c

9. Phylotasti c  Goal: access to expert ToL knowledge that is  convenient – much easier than DIY tree  computable – logically encoded trees (not pics)  credible – useable in a scientific paper

10. HIP HACKATHONS HIP Leadership Team Participants

11. Phylotastic.org demos  pruner

12. ANNOTATING SOURCE TREES using a formal ontology See Hilmar Lapp’s lightning talk

13. TNRS Oreamnosamericanu s Oreamnusamericanus: No exact match

14. DATELIFE.ORG The other kind of Dating with Fossils Ask Brian O’Meara, Tracy Heath, or Klaus Schliep -- scales trees by reference to prior calibrations Dating with Fossils

15. Julie Allen (software bazaar)

16. Reconciled Tree (red=duplication, green=speciation)

17.

18. PHYLOTASTIC.ORG Questions? Ask Arlin or email to arlin@umd.edu

19. Work in progress

20. THANKS!  www.phylotastic.org HIP Leadership Team Participants