Planteome: A resource for common reference ontologies and applications for plant biology
Around the world, a small number of plant species serve as the primary source of food for the human population, yet these crops are vulnerable to multiple stressors, such as diseases, nutrient deficiencies and unfavorable environmental conditions. Traditional breeding methods for plant improvement m...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Conference Paper |
| Language: | Inglés |
| Published: |
2016
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/78564 |
| _version_ | 1855531743996542976 |
|---|---|
| author | Jaiswal, P. Cooper, Laurel D. Elser, J.L. Meier, A. Laporte, Marie-Angélique Mungall, C. Smith, B. Johnson, E.K.S. Seymour, M. Preece, J. Xu, X. Kitchen, R.S. Qu, B. Zhang, E. Arnaud, Elizabeth Carbon, S. Todorovic, S. Stevenson, D.W. |
| author_browse | Arnaud, Elizabeth Carbon, S. Cooper, Laurel D. Elser, J.L. Jaiswal, P. Johnson, E.K.S. Kitchen, R.S. Laporte, Marie-Angélique Meier, A. Mungall, C. Preece, J. Qu, B. Seymour, M. Smith, B. Stevenson, D.W. Todorovic, S. Xu, X. Zhang, E. |
| author_facet | Jaiswal, P. Cooper, Laurel D. Elser, J.L. Meier, A. Laporte, Marie-Angélique Mungall, C. Smith, B. Johnson, E.K.S. Seymour, M. Preece, J. Xu, X. Kitchen, R.S. Qu, B. Zhang, E. Arnaud, Elizabeth Carbon, S. Todorovic, S. Stevenson, D.W. |
| author_sort | Jaiswal, P. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Around the world, a small number of plant species serve as the primary source of food for the human population, yet these crops are vulnerable to multiple stressors, such as diseases, nutrient deficiencies and unfavorable environmental conditions. Traditional breeding methods for plant improvement may be combined with next-generation methods such as automated scoring of traits and phenotypes to develop improved varieties. Linking these analyses to the growing corpus of genomics data generated by high-throughput sequencing, transcriptomics, proteomics, phenomics and genome annotation projects requires common, interoperable, reference vocabularies (ontologies) for the description of the data. The Planteome initiative (www.planteome.org) is developing the needed suite of common reference ontologies that describe anatomy and development in Plant Ontology (PO), Plant Trait Ontology (TO), and Plant Environment Ontology (EO) and the Plant Stress Ontology (PSO) for describing the abiotic and biotic stresses. The project will also host ontologies such as Gene Ontology (GO), Chemical Entities of Biological Interest (ChEBI), Protein Ontology (PRO) and the Phenotypic Qualities Ontology (PATO) developed by collaborators. The project database and the online resources will provide researchers tools to search and browse and remote access via APIs for semantic integration in annotation tools and data repositories providing resources for plant traits, phenotypes, diseases, genomes, gene expression and genetic diversity data across a wide range of plant species. |
| format | Conference Paper |
| id | CGSpace78564 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| record_format | dspace |
| spelling | CGSpace785642024-03-06T10:16:43Z Planteome: A resource for common reference ontologies and applications for plant biology Jaiswal, P. Cooper, Laurel D. Elser, J.L. Meier, A. Laporte, Marie-Angélique Mungall, C. Smith, B. Johnson, E.K.S. Seymour, M. Preece, J. Xu, X. Kitchen, R.S. Qu, B. Zhang, E. Arnaud, Elizabeth Carbon, S. Todorovic, S. Stevenson, D.W. crops ontology data genomics information systems Around the world, a small number of plant species serve as the primary source of food for the human population, yet these crops are vulnerable to multiple stressors, such as diseases, nutrient deficiencies and unfavorable environmental conditions. Traditional breeding methods for plant improvement may be combined with next-generation methods such as automated scoring of traits and phenotypes to develop improved varieties. Linking these analyses to the growing corpus of genomics data generated by high-throughput sequencing, transcriptomics, proteomics, phenomics and genome annotation projects requires common, interoperable, reference vocabularies (ontologies) for the description of the data. The Planteome initiative (www.planteome.org) is developing the needed suite of common reference ontologies that describe anatomy and development in Plant Ontology (PO), Plant Trait Ontology (TO), and Plant Environment Ontology (EO) and the Plant Stress Ontology (PSO) for describing the abiotic and biotic stresses. The project will also host ontologies such as Gene Ontology (GO), Chemical Entities of Biological Interest (ChEBI), Protein Ontology (PRO) and the Phenotypic Qualities Ontology (PATO) developed by collaborators. The project database and the online resources will provide researchers tools to search and browse and remote access via APIs for semantic integration in annotation tools and data repositories providing resources for plant traits, phenotypes, diseases, genomes, gene expression and genetic diversity data across a wide range of plant species. 2016 2016-12-30T10:41:59Z 2016-12-30T10:41:59Z Conference Paper https://hdl.handle.net/10568/78564 en Open Access Jaiswal, P.; Cooper, L.; Elser, J.L.; Meier, A.; Laporte, M-A.; Mungall, C.; Smith, B.; Johnson, E.K.S.; Seymour, M.; Preece, J.; Xu, X.; Kitchen, R.S.; Qu, B.; Zhang, E.; Arnaud, E.; Carbon, S.; Todorovic, S.; Stevenson, D.W. (2016) Planteome: A resource for common reference ontologies and applications for plant biology. [Abstract] presented at XXIV Plant and Animal Genome Conference. San Diego, CA (USA) 9-13 Jan 2016. 1 p. |
| spellingShingle | crops ontology data genomics information systems Jaiswal, P. Cooper, Laurel D. Elser, J.L. Meier, A. Laporte, Marie-Angélique Mungall, C. Smith, B. Johnson, E.K.S. Seymour, M. Preece, J. Xu, X. Kitchen, R.S. Qu, B. Zhang, E. Arnaud, Elizabeth Carbon, S. Todorovic, S. Stevenson, D.W. Planteome: A resource for common reference ontologies and applications for plant biology |
| title | Planteome: A resource for common reference ontologies and applications for plant biology |
| title_full | Planteome: A resource for common reference ontologies and applications for plant biology |
| title_fullStr | Planteome: A resource for common reference ontologies and applications for plant biology |
| title_full_unstemmed | Planteome: A resource for common reference ontologies and applications for plant biology |
| title_short | Planteome: A resource for common reference ontologies and applications for plant biology |
| title_sort | planteome a resource for common reference ontologies and applications for plant biology |
| topic | crops ontology data genomics information systems |
| url | https://hdl.handle.net/10568/78564 |
| work_keys_str_mv | AT jaiswalp planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT cooperlaureld planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT elserjl planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT meiera planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT laportemarieangelique planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT mungallc planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT smithb planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT johnsoneks planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT seymourm planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT preecej planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT xux planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT kitchenrs planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT qub planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT zhange planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT arnaudelizabeth planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT carbons planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT todorovics planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology AT stevensondw planteomearesourceforcommonreferenceontologiesandapplicationsforplantbiology |