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Ephesis, GNpIS and Ontologies needs

Ephesis, GNpIS and Ontologies needs. Cyril Pommier Bio informatician Ephesis project leader Seek standards, advices and best practice for Ephesis community which: Is willing to contribute to ontologies Has specific needs not clearly addressed by existing standards and ontologies.

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Ephesis, GNpIS and Ontologies needs

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  1. Ephesis, GNpIS and Ontologies needs • Cyril Pommier • Bio informatician • Ephesis project leader • Seek standards, advices and best practice for Ephesis community which: • Is willing to contribute to ontologies • Has specific needs not clearly addressed by existing standards and ontologies.

  2. International Databases Environmental Information Systems Phenotyping Growth chambers Controlled environment Whole field phenotyping Climatic data Ground Aerial imaging URGI GnpIS GnpProt GnpArray GnpSNP GnpSeq Data Integration GnpMap Siregal Ephesis GnpGenome Web interface Data extractionAnalysis Data interoperability exchangeCross references exchange International visibility GnpIS and EphesisEnvironment Phenotype Information System Expression Polymorphism Maps Field, hand data acquisition Phenotypes Genomes

  3. OntologiesWhy • Data standardization • Inside species groups • Help new project • Recommended for international collaboration and publications. • Ease data interoperability and reusability. • Phenotype Variable / descriptor • Simple : plant height • Not so simple : Young leaf: color of the upper side of blade (4th leaf) • Tracked in time : protein content during seed developement • Value (numeric, list of notations, triplets, …) • Date • Unit • Protocol • Species specific • Might change from one group to another • Cross references to existing vocabularies (OIV, Bioversity, …) • Optionally allow to carry synonyms and / or French translations

  4. Ontologiesneeds • Evaluation of existing ontologies and standards (biologists and informaticians). • Pros • Enthusiast for EQV approach (Mungallet al, Integratingphenotype ontologies acrossmultiple species Genome Biology 2010, 11:R2) • Ready to contribute • Cons • No unit, protocols, allowed values, date, … • Could be stored in a database alongside ontologies but • What belong to ontologies and to the database • What are the best practice (chado and apollo example) • Standard schema ? • Existing ontologies are huge : used to a few hundred terms list: • Track a subset of ontologies : • Favorites • Species tag • Specialized Trait ontologies strongly linked to international references. In this case we might a repository for publication.

  5. Tools • Need of edit tool, • Ideally concurrent . • Biologist will need to easily and quickly add (not edit?) new terms • No need of annotation tools. • User will pick there variables in the right ontology before doing field or high throughput phenotyping.

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