Download presentation
Presentation is loading. Please wait.
Published byBlaze Barton Modified over 8 years ago
1
The Vertebrate Bridging Ontology (VBO) Ravensara Travillian, James Malone, Chao Pang, John Hancock, Peter W.H. Holland, Paul Schofield, and Helen Parkinson Email: raven@ebi.ac.uk
2
VBO project Goal: fill critical gap in data annotation—computational cross-species integration of data between key model vert organisms Most Recent Common Ancestor (MRCA) 2 VBO Zebrafish Anatomy Ontology Rat Anatomy Ontology Mouse Anatomy Ontology Mouse Subspecies Anatomy Ontologies Xenopus Ontology Human Anatomy Ontology
3
Use cases that homology enables Key questions evolutionary community may wish to ask: 1. Compare expression of (a) a named gene or (b) gene family or (c) combination of genes between species (query: which anatomical features? same/different? 2. Compare anatomical structure between species (query: same or different genes expressed?) 3. Test hypothesis of homology using gene expression similarity/difference between species? How to do so: view curated info through Atlas interface 3
4
Homology as basis for cross-species query http://www.newworldencyclopedia.org/entry/Image:Evolution_pl.png 4
5
Clades, homology groupings, and MRCA/LCA 5
6
Homology mapping: top-down or bottom-up? Two theoretical approaches In practice, a hybrid approach, depending on evidence 6 MRCAHomology chaining Specified homology Inferred homology
7
Relations in VBO Relations defined in regard to homology 1. homologous-to: Example: chambers of mammalian heart; Indicative of evolutionary conservation 2.homologous-to some part-of: less specific, e.g. Tibia (Homo sapiens) and Fibula (Homo sapiens ) homo-logous- to some part-of Tibiofibula (Xenopus laevis ); Indicative of evolutionary event 3.not-homologous-to (for lexical matches): because of open- world assumption; Human frontal bone not-homologous-to zebrafish frontal bone 7
8
Homology relations: pairwise mappings 8 Structure Species in Structure Species in relation Source: GXA, MRC, EP Prove- nance
9
Pairwise mappings 9
10
Pairwise homology mappings Travillian: VBO workshop 2 7-8 February 2011 10
11
Mappings in Protégé Travillian: VBO workshop 2 7-8 February 2011 11
12
Homology: a maximally-connected graph Example: tetrapod acetabulum (concave surface on pelvis where femur meets) Symmetric Reflexive Transitive Maximally connected for homologous vertebrate structures Travillian: VBO workshop 2 7-8 February 2011 12
13
Limitations of Protégé in modelling homology Protégé cannot leverage subsumption to programmatically create maximally-connected graph Chao developed tool to create maximally-connected graph from pairwise mappings in spreadsheet Travillian: VBO workshop 2 7-8 February 2011 13
14
not-homologous-to: connected graph Travillian: VBO workshop 2 7-8 February 2011 14 Mammalian acetabula Taenia saginata asiatica acetabulum Notomega- rhynchus navonae acetabulum
15
Multi-species interface Travillian: VBO workshop 2 7-8 February 2011 15
16
What can the user query from Atlas/VBO? Once VBO is integrated, user can ask: What structure in what species is homologous to what other structure in what other species? (validated and/or presumed) At what taxonomic level does this homology occcur (e.g., vertebrate, tetrapod, mammal) What lexically-matching structures are not actually homologous? What is the evidence for the claimed relationship? 7-8 February 2011 16 Travillian: VBO workshop 2
17
Thanks to: Tony Burdett, Tomasz Adamusiak, Onard Mejino, Melissa Haendel, Ann-Marie Mallon and Michael Gruenberger Jonathan Bard, Michael Ashburner, David Osumi- Sutherland Monte Westerfield, Terry Hayamizu, Hilmar Lapp, Paula Mabee, George Gkoutos Biotechnology and Biological Sciences Research Council (grant #BB/G022755/1)
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.