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Ontologies at the iPlant Collaborative

Ontologies at the iPlant Collaborative. presented by Ramona Walls PRO-PO-GO meeting, Buffalo, NY May 16, 2013. http://www.iplantcollaborative.org /. http://user.iplantcollaborative.org /. iPlant services. Atmosphere Bisque CoGe Discovery Environment DNA Subway

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Ontologies at the iPlant Collaborative

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  1. Ontologies at the iPlant Collaborative presented by Ramona Walls PRO-PO-GO meeting, Buffalo, NY May 16, 2013

  2. http://www.iplantcollaborative.org/

  3. http://user.iplantcollaborative.org/

  4. iPlantservices • Atmosphere • Bisque • CoGe • Discovery Environment • DNA Subway • Integrated Breeding Platform • iPlant Data Store • MyPlant • Target (Tree Analysis of Related Genes and Transposons) • TNRS Plus: • APIs • Access to high performance computing • Semantic web technologies (SSWAP)

  5. iPlant’s interest in ontologies falls into three categories: • Metadata for files and folders • Data tagging • Semantic web

  6. Metadata for the iPlant Data Store and “Data Commons” • Organize 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

  7. iPlant metadata policy • Under development • Combination of system and user-supplied metadata • Must allow (but not require) use of ontologies • should support sematic web • User-friendly interface for entering ontology tags

  8. Ontologies for data annotation • classic use case for OBO Foundry ontologies • iPlant can: • provide computer infrastructure support for community ontology development • promote the use of shared ontologies fortagging plant trait data • includes tagging of images (using BISQUE)

  9. “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)

  10. Ontologies for web services at iPlant • Simple Semantic Web Architecture and Protocol (sswap.info) • Uses ontologies for in-flux, just-in-time semantic web services • Just in Time (JIT) Ontology editor • http://sswapmeet.sswap.info/jit/ • see sswap.info/wiki/jit

  11. Combining semantic web services with ontology annotated data • Can 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-alone • will be incorporated it into SSWAP by Dec 2013

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

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

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