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Planteome 3.0 Release: Managing your crop data doesn’t have to be scary!

Are you feeling overwhelmed by massive amounts of crop data? 

Does it seem there is just too much to deal with?

Don't let your data turn into a Zombie Apocalypse!

Annotating your data with ontologies can make it Findable, Accessible, Interoperable and Reusable (FAIR)

 

Zombies

Source: https://letterpile.com/personal-essays/Zombie-apocalypse-scenario

Planteome Ontologies and Database- Release 3.0

The Planteome is pleased to announce the latest release of the database and ontology files. In this Planteome Version 3.0, there are 59,189 ontology terms, 2,057,205 data objects (bioentities) and 21,400,874 associations between bioetities and ontology terms. The Planteome database contains data from 95 plant taxa.

The Planteome Project (http://planteome.org/) is an international collaboration of plant scientists, ontology experts, crop data managers and domain experts. The Planteome hosts a centralized platform where reference ontologies for plants can be used to access data resources for plant traits, phenotypes, diseases, genomes, genetic diversity and gene expression data across a wide range of plant species. The Planteome team develops and maintains the suite of reference ontologies for plants; the Plant Ontology (PO), Plant Trait Ontology (TO) and the Plant Experimental Conditions Ontology (PECO), along with other reference ontologies for data annotation, such as the Gene Ontology (GO), Chemical Entities of Biological Interest (ChEBI), and the Phenotypic Qualities Ontology (PATO).

 

Integration of Crop-Specific Ontologies

The Planteome works closely with data managers and ontology experts from the Crop Ontology (http://www.cropontology.org/) to map crop plant trait ontology terms to the reference Plant Trait Ontology for data integration.  In this Release 3.0, two new Crop Ontology files have been added- for sorghum and yam, which along with rice, maize, wheat, cassava, soybean, sweet potato, pigeon pea and lentil, brings the total number of mapped CO files to ten. 

In the example below, four CO terms from the crop-specific trait dictionaries have been mapped to the reference Plant Trait Ontology term plant height (TO:0000207).  Data annotated to the crop-specific trait terms can be compared with data from other species annotated with TO plant height using the Planteome Ontology browser (http://browser.planteome.org/amigo). Annotations may be searched, filtered and downloaded for further analysis.  

Plant height

For further information, please see our recent publication: “The Planteome Database: An integrated resource for reference ontologies, plant genomics and phenomics” (https://academic.oup.com/nar/article/46/D1/D1168/4653531)

So, don’t let the data Zombie Apocalypse overwhelm you! Annotate your data with ontology terms and share with other researchers by contributing it to the Planteome database.

 

Planteome is an international collaborative effort and is supported by primary funding (IOS:1340112 award) from the National Science Foundation of USA.

 

 

Plant Height

Planteome 2.0 release

The Planteome project (www.planteome.org), an international collaborative effort, is pleased to announce their first full release of the database and ontology browser. This is a centralized portal where common reference ontologies (structured, controlled vocabularies) for plants are used to annotate gene expression, traits, phenotypes, genomes, and genetic diversity, across a wide range of plant taxa. Reference ontologies for plants, developed by the Planteome, include the Plant Ontology (PO), Plant Trait Ontology (TO), and the Plant Environment Ontology (EO), and the Planteome portal also provides reference ontologies developed by collaborating groups: the Gene Ontology (GO), the Phenotypic Qualities Ontology (PATO), the Chemical Entities of Biological Interest (ChEBI), and the NCBI taxonomy.

In the current Release 2.0, the Planteome database includes 67,272 ontology terms with links to approximately 2.0 million (M) bioentities (data objects) including proteins, genes, RNA transcripts and gene models, germplasm, and QTLs. Bioentities were often annotated to more than one ontology term, resulting in approximately 21.2M annotations. Annotated data was sourced from 24 unique database resources and covers 86 different plant taxa. Functional GO annotations are available for 62 species, which, for many of these species, the Planteome is a unique annotation resource. You can view or download a brochure about Planteome Project here: http://planteome.org/documents The Planteome browser can also be accessed by visiting our mirror site at CyVerse: http://draco.cyverse.org/amigo The Planteome Project (http://planteome.org/) is funded by the National Science Foundation (NSF Award #1340112), and is accessible for use from the Planteome project website.

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