Ontology-based services for querying and mining plant genomic and phenomic data
Findingphenotypeassociationsacrossmultipleplantspecies, annotation strategies, and environments has become more di cult as the amount of annotated data has continued to increase. By associating annotations with ontologies as metadata, we can provide a structured, inferrable, and standardized context in which to improve our ability to mine data by more accurately defining our own data. To this end, the Planteome project (http://planteome.org) ingests over 20 database sources, 80 taxa, and 2 million bioentities (genes, germplasm, QTL). Over 17 million bioentities are annotated to defined ontology terms in a standardized manner. With this infrastructure in place, Planteome provides a browsable resource for multiple reference ontologies for plants such as Plant Ontology (PO) describing anatomy and growth and de- velopmental stages, Plant Trait Ontology (TO) describing phenotype traits, Gene Ontology (GO) describing molecular function, biological process and cellular components, Phenotype and Attribute Trait On- tology (PATO) and the Application ontologies that are species-specific Crop Ontology (CO). The database also allows for an ontology-based, faceted, cross-species search of plant phenomic and genomic data anno- tated with the reference ontologies. Data is denormalized using the GOlr infrastructure (http://wiki.geneontology.org/index.php/GOlr), built on top of the Solr search platform, providing quick and meaningful querying capabilities. Work is currently underway to allow adopt a standardized Biolink web- services API (https://github.com/biolink/biolink-api) that, with GOlr, has already been adopted by the Monarch Initiative (https://monarchinitiative.org), an ontology-based tool for search and aggregation service focused on hu- man disease through analysis of cross-species annotations.
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Ontology-based services for querying and mining plant genomic and phenomic data
- 2. Questions we ask our data • What genes are associated with a plant trait? • What are the effects of a gene on an organism? • Are there useful genes from another organism that affect these traits?
- 3. • What genes are associated with a plant trait? • What are the effects of a gene on an organism? • Are there useful genes from another organism that affect these traits? • Browse and search related terms • Cross-species analysis search • Search multiple terms and term types Questions we ask our answers Questions we ask our data
- 8. Annotate data with ontologies • Ontology: Logical, Interconnected Dictionary • Annotation: Associate data to ontology BioEntity (Data) ontology termannotation ontology term part_of ontology term ontology term is_a protein germplasm gene model mRNA QTL transcript annotation is_a
- 10. Planteome • 20+ database sources • 80+ taxa • 2+ million bioentities (genes, germplasm, QTL) • 17+ million standardized annotations • link BioEntities to ontology terms Ontol BioEntity (Data) Ontol BioEntity (Data) Ontol BioEntity (Data) Ontology Term BioEntity (Data)
- 12. Annotations modeled naturally by ontology INDO NO 7505 germplasm annotation annotation flag leaf angle leaf length leaf size flag leaf morphology trait adult leaf morphology trait vascular leaf morphology trait leaf morphology trait phyllome morphology trait Oryza sativa ns1 gene Zea mays FCL1 gene Medicago truncatula is_a is_a is_a is_a is_a is_a is_a
- 13. Genes annotated to “shrunken endosperm” http://browser.planteome.org/amigo/term/TO:0000100 Planteome
- 18. Parent term provides more results endosperm quality: http://browser.planteome.org/amigo/term/TO:0000587 • 139 total annotations • 13 direct annotations • 4 direct annotations
- 35. • Plant Ontology (PO): anatomy, growth and developmental stages • Plant Trait Ontology (TO): phenotype traits • Gene Ontology (GO): molecular function, biological process and cellular components • Phenotype and Attribute Trait Ontology (PATO) • Application ontologies: e.g., Crop Ontology (CO) Planteome Ontologies
- 36. Planteome: GOlr • Data is optimized for querying using GOlr • uses Solr / Lucene • very fast • denormalized • supports loose queries
- 43. Monarch Initiative • Similar ontology model for association • Humans, model organisms, non-model organisms • Supports BioLink API • Will be used to drive interface • Galaxy Toolshed Tool
- 56. LBNL Seth Carbon* Chris Mungall* Suzanna Lewis Monica Munoz-Torres Eric Douglass Jeremy Nguyen-Xuan Nathan Dunn* OHSU Planteome is an international collaborative effort and is supported by primary funding (IOS:1340112 award) from the National Science Foundation of USA Oregon State University • Searchable “plant database” • Annotation to ontologies defines and connects data • Ontologies organize high dimensional data • BioLink API enhances integration • Monarch shows additional possibilities of ontologies Justin Elser* Pankaj Jaiswal Laurel Cooper* Planteome http://planteome.org/ Melissa Haendel* Kent Shefchek Tom Conlin Dan Keith
- 59. Connect data via ontology logic Os03g0107300 annotation gene product Oryza sativa Ames 28933 germplasm Zea mays annotation • Connect arbitrary types across species