Request for new ontology [EUPH]

[gsusanj]

Title

Pollinator Ontology

Short Description

A controlled vocabulary for pollinator related data maintained by Bee-life under the guidance of EFSA.

Description

The Pollinator Ontology of the EU Pollinator Hub Controlled Vocabulary (EUPH-CV) is an ontology for information and data about pollinators and their interaction with the abiotic and biotic environment, particularly humans. The scope of the Pollinator Ontology was to standardise and internationalise terms related to pollinators and facilitate the integration of experimental or modelling data into the risk assessment and risk management domain. The main field of interest of the Pollinator Ontology is therefore the formal representation of the knowledge on pollinators and their relationship with their abiotic and biotic environment, in particular with humans. The interaction with humans includes the economic exploitation of pollinators (in particular of the genus Apis), legislation (directly or indirectly) related to pollinators, concepts of veterinary medicine related to pollinators (currently restricted to Apis mellifera), the effect of plant protection products on pollinators, and, in particular, scientific studies related to pollinators. The Pollinator Ontology relates with the OBO Edition for most root terms and terms related to biological analysis, the Hymenoptera Anatomy Ontology (HAO), Uberon multi-species anatomy ontology, the Units of measurement ontology (UO), the Statistical Ontology (STATO) , the Environment Ontology, the Chemical Entities of Biological Interest Ontology (ChEBI), as well as some minor ontologies from the agricultural domain. Scientists, environmental risk assessors and risk managers, policymakers, veterinarians, technicians and beekeepers are supposed to be the adopters and drivers of this process, accessible through the EU Pollinator Hub.

Identifier Space

EUPH

License

CC-BY 4.0

Domain

environment

Source Code Repository

https://gitlab.com/bee-life/controlled-vocabulary

Homepage

https://app.pollinatorhub.eu/ontology

Issue Tracker

https://gitlab.com/bee-life/controlled-vocabulary/-/issues

Contribution Guidelines

https://gitlab.com/bee-life/controlled-vocabulary/-/blob/main/CONTRIBUTING.md

Ontology Download Link

https://gitlab.com/bee-life/controlled-vocabulary/-/blob/main/EUPH.owl

Contact Name

Gregor Sušanj

Contact Email

susanj@bee-life.eu

Contact GitHub Username

gsusanj

Contact ORCID Identifier

https://orcid.org/0009-0000-6519-9709

Formats

• OWL RDF/XML (.owl)
• OBO (.obo)
• OBO Graph JSON (.json)

Dependencies

• bfo
• chebi
• chmo
• envo
• ro
• ncit
• iao
• hao
• go
• pr
• uberon
• uo
• stato

Related

• envo

Usages

- user: https://app.pollinatorhub.eu/
  description: "Users use to standardise pollinator related datasets"
  examples:
    - url: https://app.pollinatorhub.eu/dataset-discovery/PLLNT11.0.0
      description: "Example dataset usage of the CV for defining columns and classes within columns"

Intended Use Cases and/or Related Projects

The EU Pollinator Hub platform is used as a interactive database of pollinator related data, aggregating datasets from various EU funded projects, supported and partially financed by European Food Safety Authority (EFSA).
Related publications:

• The EU Bee Partnership (EUBP) Prototype Platform: data model description
• The EU Pollinator Hub: Operationalisation of the EU Bee Partnership Platform for Harmonised Data Collection and Sharing Among Stakeholders on Bees and Pollinators
• Animal Welfare Data Hub template

Related projects:

• MUST-B EFSA article, dataset
• PollinEra official website
• PoshBee official website
• B-Good official website, datasets
• Animal Welfare Data Hub EFSA publication

Data Sources

1. Cazier J, Bruneau E. Standardizing data in bees and beekeeping. Bee Cult. 2020 ;November: 89.
2. Crane EE. Dictionary of Beekeeping Terms with Allied Scientific Terms. London: Bee Research Association Limited; 1951. Available: https://www.abebooks.com/Dictionary-Beekeeping-Terms-Allied-Scientific-Crane/31070175889/bd
3. Crane E. International Bee Research Association dictionary of beekeeping terms: with allied scientific terms. Giving translations from and into English-French-Italian-Spanish-Portuguese-Romanian with Latin index. London: published in collaboration with International Bee Research Association by Apimondia; 1979.
4. Crane EE, Kolisko G. Dictionary of beekeeping terms, with allied scientific terms. 7. Giving translations from and into English-German-Dutch-Danish-Norwegian-Swedish : with Latin index. London: Bee Research Association Limited; 1978. Available: https://bibsok.no/?tnr=5621943
5. B-Good official website, datasets
6. Darwin Core Maintenance Group. Darwin Core List of Terms. Biodiversity Information Standards (TDWG). 2023 [cited 24 Nov 2025]. Available: https://dwc.tdwg.org/list/2023-09-18.html
7. FAOSTAT. [cited 21 Mar 2025]. Available: https://www.fao.org/faostat/en/#home
8. EFSA. Harmonized terminology for scientific research. Zenodo; 2023. doi:10.5281/zenodo.7590216

Additional comments or remarks

No response

OBO Foundry Pre-registration Checklist

• I have read and understood the registration process instructions and the registration checklist.
• There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
• My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
• My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
  • We use w3id.org as basis for the identifiers (https://w3id.org/euph/{id})
• My term labels are in English and conform to the OBO Foundry Naming Conventions
• I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the IAO:0000115 property.
• For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
• For all relationship properties (Object and Data Property), I checked whether the Relation Ontology (RO) includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
• For the selection of appropriate annotation properties, I looked at OMO first. I understand that aligning ontology metadata and term-level metadata is essential for cross-integration of OBO ontologies.
• If I was not sure about the meaning of any of the checkboxes above, I have consulted with a member of the OBO Foundry for advice, e.g., through the obo-discuss Google Group.
• The requested ID space does not conflict with another ID space found in other registries such as the Bioregistry and BioPortal, see here for a complete list.

[pfabry]

Dear @gsusanj

Thank you for your submission. The review will be executed as a two stage process:

First, you will have to pass OBO NOR Dashboard. Pass means that no check apart from Users and Versioning may be red. In addition, a new check is currently implemented: it consists in a lexical match of your original terms with those already existing in OBO Foundry published ontologies. The goal is to prevent the duplication of terms with similar meanings (cf. Review SOP). A list of terms that are potential duplicates will be provided soon.

After you have successfully passed the Dashboard you will be assigned an OBO Operations committee member to review the ontology. The assigned reviewer is to be considered the final arbiter of requirements; look to that reviewer's guidance regarding which suggestions made by other reviewers must be done, which suggestions are simply good to do but not required, and which should not be done.

Usually, the review will result in an opportunity for you to improve the ontology. When the reviewer believes the ontology is ready for presentation to the OBO Operations Committee, they will present your ontology during an OBO Operations Call. This gives other members of the committee the opportunity to assess your work.

When a decision is reached by the committee you will be informed here on the issue tracker. The process can take any number of weeks or months, depending on the case at hand.
Please let us know about any reasons you might have for increased urgency.

You will be informed once your ontology is loaded in the OBO NOR Dashboard.

Good luck!