Request for new ontology VVO

[edithlaszny]

Title

Vitis Vinifera Ontology

Short Description

A BFO 2020-aligned ontology formally describing the morphological structures, phenological development stages, quality parameters, dispositions, roles, and information entities of Vitis vinifera L., the common grapevine.

Description

The VVO (Vitis Vinifera Ontology) formally describes the domain of Vitis vinifera L., the common grapevine. Its scope encompasses six categories of entities:

1. Morphological structures — the physical parts of the grapevine (root system, trunk, shoots, leaves, inflorescences, berries, seeds, etc.)

2. Phenological development stages — the temporally ordered processes of the grapevine's annual growth cycle (dormancy, bud burst, shoot growth, flowering, fruit set, veraison, ripening, senescence), systematically aligned with the BBCH extended scale for grapevine

3. Quality parameters — measurable attributes of grapevine entities (sugar content, acidity, color, firmness, aroma compounds, phenolic content, etc.)

4. Dispositions — inherent capacities and tendencies (disease resistance, drought tolerance, cold hardiness, vigor, ripening timing, etc.)

5. Roles — context-dependent functions (rootstock, scion, clone, propagation material, training system roles, production system roles, etc.)

6. Information entities — designations, codes, descriptions, and data records used in viticulture (cultivar names, BBCH codes, ampelographic descriptors, geographic indications, genetic markers, quality analysis data, etc.)

VVO comprises 3,333 classes organized in a strict subsumption hierarchy under a single root class (Vitis_vinifera, aligned with BFO:entity). Every class carries a full set of IAO-compliant annotations: definition (genus-differentia, English), alternative terms (bilingual English/German), example of usage, editor note, curation status, definition source (peer-reviewed literature), and PO cross-reference where applicable.

VVO does NOT model other Vitis species, winemaking processes, vineyard management equipment, soil science, or general plant biology beyond the scope of V. vinifera.

Identifier Space

VVO

License

CC-BY 4.0

Domain

agriculture

Source Code Repository

https://github.com/edithlaszny/vvo

Homepage

https://github.com/edithlaszny/vvo

Issue Tracker

https://github.com/edithlaszny/vvo/issues

Contribution Guidelines

https://github.com/edithlaszny/vvo

Ontology Download Link

https://raw.githubusercontent.com/edithlaszny/vvo/main/vvo.owl

Contact Name

Dr Edit Hlaszny PhD

Contact Email

edithlaszny@gmail.com

Contact GitHub Username

edithlaszny

Contact ORCID Identifier

0009-0005-6549-9839

Formats

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

Dependencies

• bfo
• iao

Related

BFO (Basic Formal Ontology): VVO is fully aligned with BFO 2020. Every VVO class is traceable through its parent hierarchy to a BFO category (entity → continuant/occurrent → material entity, process, quality, disposition, role, or generically dependent continuant).

IAO (Information Artifact Ontology): VVO uses IAO annotation properties throughout (IAO_0000115 definition, IAO_0000118 alternative term, IAO_0000112 example of usage, IAO_0000116 editor note, IAO_0000114 curation status, IAO_0000119 definition source). VVO imports IAO.

PO (Plant Ontology): VVO cross-references PO terms via oboInOwl:hasDbXref where equivalent or related PO classes exist (e.g., VVO:Berry → PO:0009001). VVO does not import PO, as VVO deliberately provides grapevine-specific granularity beyond what PO covers. Where no PO equivalent exists, this is explicitly documented ("no direct PO equivalent").

PATO (Phenotypic Quality Ontology): VVO's Quality category covers grapevine-specific quality parameters. Future alignment with PATO is planned where applicable.

Usages

- user: https://bioportal.bioontology.org/ontologies/VVO/
  description: VVO is published on NCBO BioPortal as a publicly accessible ontology for grapevine biology
  examples:
    - url: https://bioportal.bioontology.org/ontologies/VVO/
      description: "BioPortal entry for VVO with 95 unique visitors within five days of publication"
- user: https://hlaszny.com/vvo/vvo_browser.html
  description: The VVO Browser provides an interactive web interface for exploring VVO classes and annotations
  examples:
    - url: https://hlaszny.com/vvo/vvo_browser.html
      description: "Static single-page application for browsing all 3,333 VVO classes with bilingual annotations"

Intended Use Cases and/or Related Projects

VVO serves multiple purposes:

1. PhD research foundation: VVO originated from the doctoral research of Dr Edit Hlaszny (PhD, plant biology/viticulture, 2012) and has been refined over nine years of systematic domain analysis.

2. VVO Browser: A publicly accessible web-based browser for exploring the VVO hierarchy and annotations is hosted at https://hlaszny.com/vvo/vvo_browser.html — this serves as the primary user interface for domain experts who are not ontology specialists.

3. NCBO BioPortal publication: VVO has been published on BioPortal (https://bioportal.bioontology.org/ontologies/VVO/) and attracted 95 unique visitors within five days of publication, indicating community interest.

4. Viticulture research: VVO provides a formal vocabulary for annotating grapevine phenotypic data, enabling integration across viticultural research datasets. Potential applications include phenological modeling, cultivar characterization, precision viticulture, and climate adaptation studies.

5. Teaching: VVO an be used in university-level biology education courses for demonstrating ontological modeling of plant biology domains.

6. Methodological reference: The accompanying "Building Domain Ontology" (BDO - https://www.researchgate.net/publication/397833683_Building_Domain_Ontology) guide documents the VVO development methodology for use by other ontology developers.

Data Sources

VVO's 3,333 class annotations are derived from the following primary sources:

1. Keller M (2020) The Science of Grapevines: Anatomy and Physiology, 3rd Ed, Academic Press

2. Mullins MG, Bouquet A, Williams LE (1992) Biology of the Grapevine, Cambridge University Press

3. Lorenz DH, Eichhorn KW, Bleiholder H, Klose R, Meier U, Weber E (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera) — Codes and descriptions according to the extended BBCH scale, Australian Journal of Grape and Wine Research 1(2): 100-103

4. Coombe BG (1995) Growth Stages of the Grapevine, Australian Journal of Grape and Wine Research 1(1): 100-110

5. OIV (International Organisation of Vine and Wine) descriptor lists and focus publications

6. Hlaszny E (2012) PhD dissertation on grapevine phenology and climate adaptation

7. Hlaszny E, Szilassy B (2017) SysML-based modeling of grapevine morphology (conference paper)

Additional comments or remarks

Technical details:

1. VVO uses OBO Foundry-compliant numeric identifiers (VVO_0000001 through VVO_0003333) with a stable prefix map ensuring identifier persistence independent of label changes.

2. All annotations are bilingual (English definitions and examples; English and German alternative terms).

3. VVO contains no object properties or data properties — it is a pure class taxonomy with rich annotations, following the pattern of several established OBO ontologies.

4. VVO does not define new annotation properties; it reuses IAO properties exclusively.

5. The ontology is maintained by two developers: Dr Edit Hlaszny (domain expert, editor) and Dr Christopher Johann Müller (data modeler, IT architect, programmer), with a combined experience of over 40 years in systems development and ontology engineering.

6. The ontology has also been tested with HermiT 1.4.3.456 and ELK 0.5.0 reasoners in Protégé 5.6.3 without errors.

The VVO fills a genuine gap: no comprehensive formal ontology for Vitis vinifera currently exists in OBO Foundry or elsewhere. The Plant Ontology covers plant structures generically but lacks the species-specific depth required for viticultural research. VVO provides this depth while maintaining full cross-referencing to PO where applicable.
We look forward to the review process and to contributing VVO to the OBO Foundry community.

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.

[cmungall]

how does this compare to https://cropontology.org/term/CO_356:ROOT?

[pfabry]

Dear @edithlaszny ,

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.
• 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.

Typically, the review will provide an opportunity for you to enhance 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 allows other committee members to assess your work.

When the committee reaches a decision, you will be informed here on the issue tracker. The process can take any number of weeks or months, depending on the specific case.
Please let us know if there are any reasons you have for increased urgency.

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

Good luck!

[edithlaszny]

Dear Dr Mundall, Regarding Crop Ontology (CO) — a comparison with VVO: I have to be upfront: I was not previously aware of this ontology, so my comparison can only be partial. Here is what I found: 1) https://cropontology.org/term/CO_356:ROOT The website lists 106 morphological classes (concept details include: term_id, ontology_id, trait_name, language). No subclass hierarchy is defined. A separate section lists 13 phenological classes (concept details: term_id, ontology_id, ontology_name, language). Again, no subclasses are defined. 2) https://bioportal.bioontology.org/ontologies/CO I did not find substantive information about CO on NCBO BioPortal, although the ontology is hosted there. No metrics have been calculated yet, no views are available, and the visit count has not exceeded 65 since February 2025. 3) https://bigdata.cgiar.org/gardian-tool/the-crop-ntology-co/ This platform is led by IFPRI (International Food Policy Research Institute). No substantive ontological information was found here either. Summary: CO_356 appears to be a trait/descriptor vocabulary with a flat structure rather than a formally axiomatised ontology. VVO, by contrast, is BFO 2020-aligned, OWL-DL compliant, and covers 3,333 classes across six BFO top-level categories with full IAO annotations and reasoner validation. The overlap with CO_356 may exist at the trait/quality level, but the scope, depth, and formal rigour differ substantially. You've probably already seen the VVO browser: https://bioportal.bioontology.org/projects/VVO :) Best regards Edit Hlaszny

…

On Tue, Mar 10, 2026 at 12:13 AM Chris Mungall ***@***.***> wrote: *cmungall* left a comment (OBOFoundry/OBOFoundry.github.io#2857) <#2857 (comment)> how does this compare to https://cropontology.org/term/CO_356:ROOT? — Reply to this email directly, view it on GitHub <#2857 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK3A3RRLS5HDS54CS2QRSOL4P5F2BAVCNFSM6AAAAACWMDASAOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DAMRXGUZDGNRVGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ddooley]

In a preliminary look (and this is not the OBO review process, but rather my personal peek at vvo.owl), The VVO hierarchy is non-conformant to the OBO / BFO / COB vision. It would be a great specialist resource for Vitis, but a number of things will probably have to be revised content wise:

• One cannot have a material entity, Vitis vinifera, be the parent term of information, process, quality. This suggests a basic misunderstanding of what OBO Foundry ontologies look like.
• As well, OBO looks to term definitions to reflect just the basic Aristotelian genus / differentia natural language statement(s) - which might be axiomatized logically - rather than the much more lengthy definitions given for most terms. Were the definitions automatically generated by AI?
• There was a claim that the ontology provides numeric identifiers for terms but I couldn't find any such [ONTO_prefix][1234567] numeric codes? There is no VVO_0000001 or VVO_00.... anything in the ontology. While it is claimed above "My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy", that page clearly shows
  "Format of Foundry-compliant URIs" FOUNDRY_OBO_URI ::= "http://purl.obolibrary.org/obo/" IDSPACE "" LOCALID
  where IDSPACE is say "VVO" and LOCALID is recommended to be numeric and of a certain digit count, say 7 or 8 digits.
• It seems little effort has been made to position new terms or register new term requests with appropriate ontologies such as the Plant Trait Ontology, e.g. "shoot" http://purl.obolibrary.org/obo/vvo.owl#Shoot

[edithlaszny]

Dear Damion,

Thank you for your preliminary review and constructive feedback. We have addressed your points as follows:

Point 1 (hierarchy vision): Fully understood. VVO was conceived as a specialist domain resource for Vitis vinifera — we appreciate the acknowledgment of its value in that role.

Point 2 (BFO alignment): Corrected in v2-002. Vitis_vinifera is now formally declared as subClassOf BFO_0000040 (material entity). The six top-level categories root directly under their respective BFO parents.

Point 3 (definition style / AI question): The definitions were not AI-generated. They represent nine years of my manual curation — Vitis vinifera was the subject of my PhD thesis — based exclusively on peer-reviewed literature, each with explicit source citations. We acknowledge they exceed OBO's preferred genus-differentia length and propose retaining the current text as IAO_0000116 (editor note), while adding concise Aristotelian genus-differentia statements as IAO_0000115 (definition) — incrementally, beginning with top-level classes.

Point 4 (OBO IRIs): Corrected. The initial upload contained fragment IRIs (#ClassName) due to a serialization error. v2-002 uses OBO Foundry-compliant numeric IRIs (VVO_0000001 through VVO_0003333) throughout.

Point 5 (PO term alignment): Acknowledged. VVO's annotation structure already contains 772 PO_reference fields identifying Plant Ontology correspondences — the result of nine years of parallel mapping work. We will systematically upgrade these to skos:exactMatch or skos:relatedMatch as appropriate.

We remain committed to bringing VVO into full OBO conformance.

With kind regards,
Edit