May 092012

Left: Maize de*-N738A (Allele) selfed colorless flint M2 origin ear showing thin collapsed defective kernels (cp*-N738A), also segregating for pitted discolored defective kernels (ptd*-N738B) (courtesy of Carolyn Lawrence, MaizeGDB).  Center: Tomato mutant n2326m1 showing low fertility (courtesy of Naama Menda, SGN). Right: Aborted seed phenotype of Arabidopsis hisn2-1 heterozygote with mutant seeds (white, brown) arrested at a preglobular stage of embryo development (courtesy of David Meinke, Oklahoma State University).

The plant working group had a productive meeting as part of the second Phenotype RCN summit meeting in February at NESCent.  We succeeded in bringing some new people into the plant working group while still continuing momentum from our two previous meetings in 2011.

Our discussion continued a thread from previous meetings on how to develop a pilot project that could serve to demonstrate the usefulness of describing plant phenotypes using a common ontology such as the Plant Ontology (PO).  Our goal is to show how a set of phenotype annotations from several species, made using a shared set of ontology terms, can be used to transfer knowledge across species and answer questions that require cross-species comparison.  We came up with a concrete plan for a pilot project that involves gathering a test set of phenotype annotations associated to genes for several plant species and analyzing the resulting dataset.  The plan expands somewhat on our earlier idea to focus on a use case for leaves, and leverages work published recently by David Meinke (Lloyd and Meinke, 2012) to gather a dataset of phenotypes for 2400 Arabidopsis genes ( as well as the efforts by several plant databases to collect phenotype data.

Specific tasks we hope to complete by the next WG meeting in October:

  1. Assemble existing sets of phenotype data for five plant taxa (Arabidopsis, tomato, maize, rice and legumes)
  2. Convert these existing phenotype datasets to entity/quality format, using PO and GO terms for entity and PATO for quality
  3. Calculate ortholog sets for the species included in the phenotype data

We hope to use the fall working group meeting to explore the predictive power of the dataset and plan an analysis phase for the pilot project.

 Posted by on May 9, 2012 at 11:59 pm

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