A merger of multi-species anatomy ontologies or An experiment in knowledge management Biocuration 2013 Chris Mungall, Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte , Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzi Lewis, Paula Mabee, Anne Niknejad, Melissa Haendel
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A merger of multi-species anatomy ontologies
orAn experiment in knowledge management
Biocuration 2013
Chris Mungall, Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte , Wasila Dahdul , Alex
Dececchi, Nizar Ibrahim, Suzi Lewis, Paula Mabee, Anne Niknejad, Melissa Haendel
Vertebrata
Ascidians
Arthropoda
Annelida
Mollusca
Echinodermata
tetrapod limbs
ampullae
tube feet
parapodia
We want to understand gene function across taxa
Anatomy ontologies are used to describe morphological variation
Anatomy ontologies built for one species will not work for others
Use of Uberon Annotation extensions GOA/UniProtKB [Chris’ talk] Construction of GO terms [Heiko's talk] Bgee cross-model homology-based expression search
[Frederic’s talk] Annotation of biospecimens from diverse taxa [eagle-i.org] Phenotype similarity analyses to identify disease gene
candidates and models New project “Monarch Initiative” to build tools and
services for navigating phenotypes [see our poster tonight]
Modern diversity only a fraction of evolutionary diversity
Missing evolutionary transitions e.g. fin to limb
Extant ontologies not always compatible with fossil data
Different data sources and resolution between extinct and extant
Shubin et al. 2006
And so over time…
… additional multi-species ontologies evolved
But…
…they had a hard time maintaining relationships to one another
And there was asynchrony in the universe
The big roll-up
The new Uberon-ext Contents:
– Over 8,000 classes (terms), 2500+ added by Phenoscape– Multiple relationships, including subclass, part-of and develops-from
Scope: metazoa (animals)– Current focus is chordates– Includes teleost, amniote, and amphibian specific classes
Uberon classes are generic / species neutral– ‘mammary gland’: you can use this class for any mammal!– ‘lung’: you can use this class for any vertebrate (that has lungs)
Model organism anatomies were difficult to query across
Uberon was developed to help integrate human and model organism anatomy
Uberon has been useful to align model organism anatomy ontologies
Palaeontolosts and evo-devo biologists needed wider coverage
A core set of vertebrate terms was needed by all=> So we merged the ontologies, and now we can have dinosaur bone data, model organism data, and human data all integrated and queryable in one database!
Conclusions
Thanks!
Chris Mungall, Jim Balhoff, Frederic Bastian, David
Blackburn, Aurelie Comte , Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzi Lewis, Paula
Mabee, Anne Niknejad
Looking for a post-doc?
http://nescent.org/about/employment.php#PostDoc2
We are recruiting a postdoc with training in bioinformatics who is interested in studying phenotypic evolution by combining model organism genetic data with comparative anatomical data from throughout the vertebrates. Projects may range from primarily computational to primarily biological.