taxonomic tree tool

Taxonomic Tree Tool

1Institute of Zoology, CAS, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China2Biodiversity Informatics, Marine Biological Laboratory, Woods Hole, MA 02543, USA.* ji@ioz.ac.cn

- A tool for managing and comparing taxonomic trees

Lin Contian1, Qiao Huijie1,Wang Jiangning1, Ji Liqiang1*, David Patterson2

Outline

Why Taxonomic Tree Tool (TTT)?

Taxonomic Tree Comparison

How Dose TTT Work?

Why TTT? Taxonomic trees are important in the fields

of taxonomy and biodiversity informatics. Taxonomic information is usually scattered

in books, journals, specimen collections, and in the minds of people everywhere. 

Taxonomists need such a tool to gather data from different sources, organize the data, do research on it and share their own data or taxonomic views with others.

Why TTT? Numerous taxonomic trees have been created

due to different views, application of new technology like phylogenetics and different study geographic scopes.

Taxonomists need a tool to explore the differences between their own taxonomic view and others’ for further study

Biodiversity informatics initiatives would like to know what are the differences and then which one to pick up as backbone or how to integrate them

Catalog of Life (COL) seeks to integrated distributed taxonomies into a single authoritative one.

GBIF and GNA store trees in ChecklistBank and Global Names Classification and List Repository (GNACLR) respectively.

None of these projects has successfully been able to integrate the multiple taxonomies into a single flawless tree. Tree comparison will help identify consensus, point to areas of conflict, and promote progress towards large scale authoritative trees

Why TTT?

Taxonomic Tree Comparison

Taxonomic Tree Technically, taxonomic

tree is a special case of mathematical tree: Taxa as nodes are

hierarchically organized into different ranks.

Ranks determine the depth of the tree.

Each taxon has an accepted name as accepted label and may has one or more synonyms as syn-labels.

taxon-node

synonym

Each taxon has an ancestor route and some descendant branches

Since taxon is the unit of taxonomic tree, we should compare taxa when we compare tree.

What of the taxa should be compared?

A BNames

Acestors

Descendants

Nominal Relation (NR) Scientific names are keys to a taxon though

they cannot uniquely represent a taxon. Nominal Relations between two taxa should be:

Accepted – Accepted: 1

Accepted – Synonym: 2

Synonym – Accepted: 3

Synonym – Synonym: 4

None: 0

Ancestors Relation (AR) AR reflects difference of taxonomic position

from top down between two taxa. Value of AR should be:

Equal: 1 e.g. AR(E)TreeA= AR(E)TreeB

Unequal: 0 e.g. AR(D)TreeA ≠ AR(D)TreeB

Descendants Relation(DR) There are five status of DR:

Congruent, DR=1Included, DR=2Include, DR=3Overlap, DR=4Exclude, DR=0

For node B1 and J2, the descendant-branches are congruent, so the DR =1 For node C1 and C2, the descendant-branches are Overlap, so the DR =4

1 2

Is that enough to assess the similarity of the branches?

Node Index (NI) Node Index is calculated as the ratio of the common

nodes. For node E1, NI(E1)=k/m=2/3 For node E2, NI(E2)=k/n=2/3 NIs reflect the similarity of nodes in descendant branches

m nk

E1 E2

1 2

Structure Index (SI) Structure Index is calculated as ratio of common routes. SI(A1 )=1/4 SI(A2 )=1/4 Structure Index is intended for assessing the structure

similarity of the descendant branches

1 2

Taxon Link (TL) What we can do with Nominal Relation (NR),

Ancestors Relation(AR) , Descendants Relation(DR)? Yes, Taxon Link!

Taxon Link is intended for describe the relationship between two taxa. It is represented by a triple tuple.

A BNR

AR

DR

TL(AR, NR, DR)

When all the taxa are compared and all the relative links are found and represented as TL(AR,NR,DR), then the comparison is finished.

Usage of Tree Comparison

Tracking “Split” action

Usage of Tree Comparison

Tracking “Merge” action

Usage of Tree Comparison

Tracking “Move” action

How Dose TTT Work?

http://ttt.biodinfo.org/indexen.asp

select branch select branch

Tree A Tree B

Taxon Link tuple is represented by three different shapes.

Nominal Relation

Ancestor Relation

Descendants Relation

Thank you for your attention! http://ttt.biodinfo.org

Feed back to linct@ioz.ac.cn