Ontologies at iPlant

Ontologies at the iPlant Collaborativepresented by Ramona WallsPRO-PO-GO meeting, Buffalo, NYMay 16, 2013

http://www.iplantcollaborative.org/

http://user.iplantcollaborative.org/ 3

iPlant servicesAtmosphereBisqueCoGeDiscovery EnvironmentDNA SubwayIntegrated Breeding PlatformiPlant Data StoreMyPlantTarget (Tree Analysis of Related Genes and Transposons)TNRSPlus:APIsAccess to high performance computingSemantic web technologies (SSWAP)

iPlants interest in ontologies falls into three categories:Metadata for files and folders

Data tagging

Semantic web

Metadata for the iPlant Data Store and Data CommonsOrganize files within a group & track analyses;Find data within iPlant public domain;Synthesize data through a workflow;Manage, track, and preserve data from generation to publication;Reuse and repurposing of data for new experiments;Knowledge discovery and hypothesis generation

7iPlant metadata policyUnder developmentCombination of system and user-supplied metadataMust allow (but not require) use of ontologiesshould support sematic webUser-friendly interface for entering ontology tags

Ontologies for data annotationclassic use case for OBO Foundry ontologiesiPlant can:provide computer infrastructure support for community ontology development promote the use of shared ontologies fortagging plant trait dataincludes tagging of images (using BISQUE)

computer infrastructure support includes:data storage (Data Store, Data Commons)web-based analysis platform (Discovery Environment)free cloud computing (Atmosphere)Education, outreach and training (Learning Center)Semantic web support (SSWAP)Access to high Performance Computing (API/TACC)

Ontologies for web services at iPlantSimple Semantic Web Architecture and Protocol (sswap.info)Uses ontologies for in-flux, just-in-time semantic web servicesJust in Time (JIT) Ontology editorhttp://sswapmeet.sswap.info/jit/see sswap.info/wiki/jit

Combining semantic web services with ontology annotated dataCan use JIT for both web services and data or use other ontologies (such as OBO Foundry) for data.BioPortal ontology support via /modularize:sswap.info/modularize For any RDF/RDFS/OWL ontology term or set of terms (called a "signature"), return all axioms logically implied to be necessary and sufficient for complete reasoning over the signature. Currently, /modularize is stand-alonewill be incorporated it into SSWAP by Dec 2013

Ontology success story: TreeGenes and SSWAPSee: https://pods.iplantcollaborative.org/wiki/display/SemanticWeb/example

More info:iPlant home page http://www.iplantcollaborative.org/questions on iPlant tools and services:http://ask.iplantcollaborative.org/questions/