workshops

Integrate Phenotypic and Experimental Data and Metadatato Predict Biomass Properties from Genotypestrong communication ties with resource developers are major undertakings that most likelywill require the attention of a full-time scientist working as a liaison. Such an individual wouldneed in-depth knowledge of the current status of plant semantics within Kbase and havesufficient authority to initiate collaborative projects and terminate or redirect Kbase projectsredundant (with respect to function or information content) with external resources.TasksTask 1. Develop a semantic infrastructure for representing concepts related to plantphenotype, chemotype, genotype, and growing environment.1A. Use and extend existing controlled vocabularies and develop new ones that applyto plant phenotype, chemotype, genotype, and growing environment.In addition, define the relationships between terms in controlled vocabularies.This task will require working with appropriate existing infrastructure such as theGene Ontology (GO) project (www.geneontology.org), Protein Ontology (PRO)project (pir.georgetown.edu/pro/pro.shtml), and the Phenotypic QualitiesOntology (PATO; obofoundry.org/wiki/index.php/PATO:Main_Page)(GO/PO/PATO). Collaboration with these projects will help support curation ofcontrolled vocabularies, identify gaps in them that prevent implementation ofrequirements, and extend the ontologies through relationship-building withexisting plant ontology efforts. Existing software (both commercial and freeware)will be evaluated for the task of managing controlled vocabularies. Protégé or asimilar tool often will suffice and has the extra benefit of being an open-sourceproject with an active base. Also, the Protégé-OWL editor enables users to buildontologies for the semantic web, in particular in the World Wide WebConsortium’s Web Ontology Language (OWL).The creation of a semantic infrastructure will require an interdisciplinary effortthat consists of staff with computer science and biology skills. The computerscience–related skills would be in the area of semantic data representation,likely requiring someone with experience using extensible markup language(XML), Resource Description Framework (RDF), and OWL. The development ofreasonable metamodels for plant phenotypes, chemotypes, genotypes, andgrowing environments will involve the effort of two full-time staff. Various XMLbasedstandards already exist or are under development for a variety of datatypes listed here. The work involved in assessing these data models is going to belarge. The duration of this task will depend on the effort required to get somecommunity consensus on standardized vocabularies and the relationships amongterms in those vocabularies. For this, a third part-time person is needed to solicitinput from professional societies and experts, coordinate and plan meetingsused to select or develop standards, and advertise the standards.Chapter 3Plant 1DOE Systems Biology Knowledgebase Implementation Plan • September 201041