Welcome to PHENO’s documentation!
PHENO is a data portal for the submission, storage and sharing of metadata for plant phenotypic experiments.
In a Nutshell, PHENO:
Receives as input a MIAPPE compliant Excel file
Validates it according to the MIAPPE specifications
Makes your metadata and associated phenotypic data FAIRly available worldwide through BrAPI compatible search engines
Make your data FAIR using PHENO
FAIR data is increasingly more valued in research, with new projects tending to follow FAIR guidelines when working with their data.
PHENO is a tool that helps you make your data FAIR by providing a platform for the submission, storage and sharing of metadata for plant phenotypic experiments.
PHENO incorporates the FAIR principles in the sense that:
* Data is stored in a secure, open and accessible repository with version control.
* Enables data findability and reusability through descriptive metadata of phenotypic experiments using MIAPPE.
* It is interoplable with other data repositories (e.g., FAIDARE) through the use of the Breeding API (BRAPI).
Getting Started
To submit metadata in PHENO, users are required beforehand to deposit the actual phenotypic data (e.g., tables, images) in another data holder of choice, for example:
Google Drive / Microsoft OneDrive
Other specialized data repositories
*Dataverse is a database for any type of scientific data. For portuguese users, learn on how to submit your data in DMPortal, the portuguese Dataverse.
To use PHENO for the first time, please check the Getting started with PHENO section.
To get acquainted with the FAIR and MIAPPE standards, and terms such as BrAPI or FAIDARE, feel free to check the References section.
If you require additional assistance, feel free to contact us directly (hm.rodrigues@itqb.unl.pt).
PHENO in Detail
PHENO structure overview
PHENO ensures data FAIRness by integrating 3 main modules based on international standards:
Data submission (MIAPPE)
Data storage (RDF)
Data sharing (BrAPI)
1) In data submission, a Graphical User Interface (GUI) allows the conversion of MIAPPE compliant spreadsheets into n-triples format.
The GUI allows users to dynamically map the MIAPPE spreadsheet to the appropriate Plant Phenotype Experiment Ontology (PPEO)
in Javascript Object Notation (JSON). The user can use a predefined MIAPPE - PPEO mapping template available, or adjust any fields as
deemed necessary. The GUI uses the constraints of the ontology to validate the mapping.
2) PHENO relies on OpenLink Virtuoso to store the metadata in triples and create a database
management system for data curators to validate datasets and select which ones are ready for sharing.
3) PHENO serves as a BrAPI endpoint where the data stored is made available in JSON to BrAPI calls, in accordance with the BrAPI specifications.
To submit medata in PHENO, check the Submitting Metadata in PHENO section.
To learn how to browse PHENO for a specific project (meta)data, check the Getting started with PHENO section.