Request for new ontology [PREFER]

[txellext]

Title

Precision Fermentation Ontology

Short Description

An ontology for PREcision FERmentation

Description

PREFER is an ontology designed to integrate high-throughput bioprocess data, covering operational, environmental and process parameters across different scales of a precision fermentation process, to accelerate the development and scaling of biosustainable production processes.

Identifier Space

PREFER

License

CC-BY 4.0

Domain

investigations

Source Code Repository

https://github.com/Multiomics-Analytics-Group/prefer_ontology

Homepage

https://github.com/Multiomics-Analytics-Group/prefer_ontology

Issue Tracker

https://github.com/Multiomics-Analytics-Group/prefer_ontology/issues

Contribution Guidelines

https://github.com/Multiomics-Analytics-Group/prefer_ontology/blob/main/CONTRIBUTING.md

Ontology Download Link

https://github.com/Multiomics-Analytics-Group/prefer_ontology/releases/latest/download/prefer.owl

Contact Name

Txell Amigó

Contact Email

txellmgsol@gmail.com

Contact GitHub Username

txellext

Contact ORCID Identifier

0009-0009-0018-4253

Formats

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

Dependencies

• id: iao
• id: cl
• id: omo
• id: ro
• id: chebi
• id: bao
• id: pato
• id: go

Related

FoodOn

Usages

- user: https://novonordiskfonden.dk/en/projects/bright/
  description: BRIGHT uses PREFER to integrate data from fermentation projects 
  examples:
    - currently being implemented

Intended Use Cases and/or Related Projects

Despite the increase in velocity, veracity, and variety of data generated by bioprocessing technologies, our ability to extract actionable information for improving biomanufacturing remains limited. Comprehensive analysis and visualization tools are largely proprietary, and we are still unable to fully leverage emerging omics due to challenges in integrating omics data to bioprocessing data. As we sought a general solution applicable to fermentation experiments across scales and operational modes, it became clear that a core barrier was the absence of an open, community-driven standard for bioprocess data.
To address this need, BRIGHT is looking to analyze data across multiple fermentation projects. PREFER ontology was developed as an open standard designed to facilitate the integration of heterogeneous data sources and enhance the ability to process large volumes of bioprocess information automatically.

Data Sources

PREFER was built in close collaboration with domain experts to ensure accurate representation of bioprocess concepts and workflows.

Additional comments or remarks

• The ontology is managed by @txellext @albsantosdel and @shawntanzk
• NNF Center for Biosustainability is rebranding as BRIGHT, and hence the URL for the website will be changed. The current website is "https://www.biosustain.dtu.dk/technologies/biofoundry"

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
• 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 @txellext,

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!