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Identifying, naming and interoperating data in a Phenotyping platform network : the good, the bad and

the ugly

Romain David, Jean-Eudes Hollebecq, Llorenç Cabrera Bosquet, Francois Tardieu, Pascal Neveu

To cite this version:

Romain David, Jean-Eudes Hollebecq, Llorenç Cabrera Bosquet, Francois Tardieu, Pascal Neveu.

Identifying, naming and interoperating data in a Phenotyping platform network : the good, the bad and the ugly. 2. Open Science FAIR Conference: “ Synergies for Sustainable, Open and Responsible Research ”, Sep 2019, Porto, Portugal. 2019. �hal-02164160�

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RDA's 14th Plenary - Helsinki, Finland. Data Makes the Difference - 23-25 October 2019

Identifying, naming and interoperating data in a phenotyping platform network:

the Good , the Bad and the Ugly .

Romain David1, Jean-Eudes Hollebecq1, Llorenç Cabrera-Bosquet2, Hanna Ćwiek-Kupczyńska3, François Tardieu2 and Pascal Neveu1; Contact: romain.david@inra.fr

1 MISTEA, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France 2 LEPSE, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France, 3Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland

Reference: Pascal Neveu, Anne Tireau, Nadine Hilgert, Vincent Nègre, Jonathan MineauCesari, Nicolas Brichet, Romain Chapuis et al. "Dealing with multisource and multiscale information in plant phenomics: the

ontologydriven Phenotyping Hybrid Information System." New Phytologist (2018). DOI : 10.1111/nph.15385

The Good

● Use non ambiguous and persistent identifier

● Use minimal information, get rid of everything that may change.

● Require external identifier (B2HANDLE, e-PIC...) if your authority is not persistent enough.

● Provide multiple output format (.txt, .html, .csv, etc.) and link them together, so the user will have the choice.

● Integrate/upgrade already existing identifiers in a URI.

● Use persistent-URL with 303 redirect status.

● Associate creation date to help understanding.

The EPPN2020 is a research project funded by Horizon 2020 Programme of the EU that will provide European public and private scientific sectors with access to a wide range of state-of-the-art plant phenotyping installations, techniques and methods. Specifically, EPPN2020 includes access to 31 plant phenotyping installations, and joint research activities to develop novel technologies and methods for environmental and plant measurements.

Here we present the results of the discussions of the 2019 annual project meeting to adopt community-approved architectural choices. It focuses on persistent identification of data and real objects, the naming of variables and the priorities for increasing interoperability among phenotyping installations. We describe the main elements to prioritize (the good) in order to enhance Findable, Accessible, Interoperable and Reusable (FAIR) quality for each data management system with a pragmatic concern for all partners.

Acknowledgements

This work was supported by EPPN2020 project (H2020 grant agreement

No 731013) & PHENOME-EMPHASIS project (ANR-11-INBS-0012) funded by the National Research Agency and the ‘Programme d’Investissements d’Avenir’ (PIA) & EMPHASIS ESFRI.

The Bad

● Unnecessary metadata in the identifier

● Ownership and other information that are likely to change over time, prefer nature of the resource

● Unnecessary long identifiers with too much semantic

● Entirely opaque identifier

● Files extension in the URI (no .extension in the URI)

● Query (no ”?” in the URI)

● Misleading characters such as O and 0 or I and l, etc.

● URI that are not the best way to

identify the object you are looking at

The plant phenotyping

community gathers different actors with various means and practices. Among all the

recommendations, the

community requests identification methods (including the use of

ontologies) compatible with the

‘local’ pre-existing ones. The identification scheme being adopted is based on Uniform

Resource Identifiers (URIs) with independant left and right parts for each identifier. (based on ePID recommendations)

https://www.pidconsortium.eu/?page_id=122

Focus on identification...

The Good

● Look for “reference ontologies”, first in the dataweb stacks

● Be careful of needs and implementation capacities to manage ontology links on the long term

● Look for concepts related to your phenotyping experiments available in “application

ontologies” in your disciplinary domain first, before creating new ones.

● Ontologies should never be developed isolated.

Use SKOS to link as much data as possible to

reference ontologies first, and to trade/application ontologies with “exact match” then “close match”

SKOS predicates

● If you need a new concept, try to do it in

concertation with the larger community (as far as possible)

The Bad

● To create an ontology before prospecting an existing one

● To create an ontology without a community approving process

● To give a URI for an ontology with date or version in the persistent link

● To use first a species specific ontology before considering concepts from

general and recommended plant ontologies

● To use approximated data type

● To refer to approximated data concept in your specialized ontology

Naming variables need to share a community approved

vocabulary, and to build or reuse appropriate ontologies.

Some questions like how to

choose them, how to implement and update them and with which means are recurrent challenges in the EPPN

2020

Phenotyping

network. First work focuses on the associated objects and

variables common to all

EPPN

2020

members, namely the scientific object (which can be a plant in a pot or a plot),

sensors and variables.

Focus on naming...

Next challenges that need to be addressed by the EPPN

2020

community are related to:

● the partial reuse of pre-existing ontologies,

● the persistence of long-term access to data,

● interoperation between all potential users of the phenotyping data.

The Ugly

A common architecture for identifiers and variable names is being built in order to enable a first level of

interoperation between Phenotyping Hybrid Informations Systems (PHIS).

All instances are connected to a PHIS Resource center using

ontologies and enabling sharing between each instance of PHIS.

RDA P14

poster session WINNER

AWARD

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