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Enhancing Plant Data Management with Ontologies: Insights from iPlant Collaborative

At the PRO-PO-GO meeting held in Buffalo, NY on May 16, 2013, Ramona Walls presented the pivotal role of ontologies in the iPlant Collaborative. This presentation emphasized three main categories of ontological applications: metadata for files, data tagging, and semantic web metadata. It explored how iPlant fosters community ontology development and supports researchers in managing, tracking, and preserving plant data efficiently. Key initiatives include the use of the iPlant Data Store, collaborative tools like BISQUE, and semantic web technologies to enhance accessibility and usability of plant datasets.

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Enhancing Plant Data Management with Ontologies: Insights from 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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