Development of the skeleton is a good example of a process that is highly regulated, requires a lot of precision, is conserved and important relationships across species, and is fairly easy to detect when it’s gone awry. I mean–it’s hard to know at a glance if all the neurons in an organism got to the right place at the right time or if all the liver cells are in the right place still. But skeletal morphology–length, shape, location, abnormalities can be apparent and are amenable to straightforward observations and measurements. Some of these have been collected for decades by fish researchers. This makes them a good model for creating a searchable, stored, phenotype collection.
The team at Phenoscape is trying to wrangle this sort of phenotype information. I completely agree with this statement of the need:
Although the emphasis has been on genomic data (Pennisi, 2011), there is growing recognition that a corresponding sea of phenomic data must also be organized and made computable in relation to genomic data.
They have over half a million phenotype observations cataloged. These include observations in thousands of fish taxa. They created and used an annotation suite of tools called Phenex to facilitate this. They describe Phenex as:
Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.
That’s great data to capture to provide important context for all the sequencing data we are now able to obtain. I think this is a nice example of combining important physical observations, mutant studies, and more, with genomics to begin to get at questions about evolutionary relationships among genes and regulatory regions that aren’t obvious only from the sequence data. You may not be personally interested in fish skeletons–but as an informative way to think about structuring these data types across species to make them useful for hypothesis generation–this is a useful example.
Here’s a intro video provided by the Phenoscape team that walks you through a search starting with a gene of interest, and taking you through the kinds of things you can find.
So have a look around Phenoscape to see a way to go from the physical observations of phenotype to gene details, or vice versa.
Mabee B.P., Balhoff J.P., Dahdul W.M., Lapp H., Midford P.E., Vision T.J. & Westerfield M. (2012). 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton., Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology, PMID: http://www.ncbi.nlm.nih.gov/pubmed/22736877
Balhoff J.P., Cartik R. Kothari, Hilmar Lapp, John G. Lundberg, Paula Mabee, Peter E. Midford, Monte Westerfield & Todd J. Vision (2010). Phenex: Ontological Annotation of Phenotypic Diversity, PLoS ONE, 5 (5) e10500. DOI: http://dx.doi.org/10.1371/journal.pone.0010500