Update OWL file #142
Update OWL file #142
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WalkthroughThe pull request removes an owl:Class declaration for the entity Changes
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🧹 Nitpick comments (1)
pride_cv.owl (1)
393-399: Review hierarchical structure of PRIDE classes.All modified PRIDE classes are now direct subclasses of
BFO_0000001. While this change maintains consistency, please verify if this flat hierarchy is intentional, as these classes represent different types of entities (version numbers, experiment types, file properties, analysis parameters, and instrument properties).Consider if a more granular hierarchy using intermediate BFO classes would better represent the ontological relationships. For example:
- Experiment types might better align under a process-related BFO class
- Properties might better align under a quality-related BFO class
- Version numbers might better align under an information-related BFO class
Would you like me to help research appropriate BFO parent classes for each PRIDE class?
Also applies to: 8247-8253, 8530-8536, 8782-8788, 9882-9888
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pride_cv.owl(6 hunks)
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- GitHub Check: convert_and_validate_owl
🔇 Additional comments (2)
pride_cv.owl (2)
285-9888: Verify alignment with OBO file.Since this PR's objective is to update the OWL file to match the OBO file, please verify that these changes maintain consistency between the two formats.
285-291:✅ Verification successful
Verify BFO reference validity.
The change from
BF_0000001toBFO_0000001appears to be aligning with the Basic Formal Ontology (BFO) standard. Let's verify that this is the correct BFO entity.
🌐 Web query:
What is BFO_0000001 in Basic Formal Ontology (BFO)?💡 Result:
In Basic Formal Ontology (BFO),
BFO_0000001represents the most fundamental category: entity. This term serves as the root class in BFO’s hierarchical structure and encompasses everything that exists, has existed, or will exist[2][5][6].Key Details About
BFO_0000001:
- Definition: An entity is "anything that exists or has existed or will exist"[2][5]. This includes physical objects (e.g., a person), abstract qualities (e.g., color), processes (e.g., a chemical reaction), and spatial/temporal regions[2][6].
- Scope: As the top-level class in BFO, it subsumes all other categories in the ontology. Entities are divided into two disjoint categories:
- Continuants: Entities that persist through time without temporal parts (e.g., objects like cells or organs)[3][4].
- Occurrents: Entities extended through time with temporal parts (e.g., processes like digestion)[3][4].
- Examples: Julius Caesar, World War II, a body mass index measurement, and Verdi’s Requiem are all instances of entities[2][6].
Role in BFO’s Framework:
BFO_0000001provides a universal foundation for domain-specific ontologies by ensuring interoperability through shared high-level categorization[1][7]. For instance:
- Biomedical ontologies use
BFO_0000001to define entities like cells (continuants) or metabolic processes (occurrents)[1][3].- Industrial ontologies (e.g., supply chain models) extend this class to represent artifacts or logistics workflows[8][10].
This classification system underpins ISO/IEC standard 21838-2 (2021), which recognizes BFO as a top-level ontology for global information systems[7].
Citations:
- 1: https://en.wikipedia.org/wiki/Basic_Formal_Ontology
- 2: https://matportal.org/ontologies/MSEO?p=classes
- 3: https://ontology.buffalo.edu/smith/articles/Functions-in-BFO.pdf
- 4: https://basic-formal-ontology.org
- 5: https://mconlon17.github.io/organization-ontology/en/master/doc-BFO_0000001.html
- 6: https://www.virtualflybrain.org/blog/releases/ontologies/bfo/
- 7: https://www.buffalo.edu/cas/philosophy/news/latestnews/global-ontology.html
- 8: https://industryportal.enit.fr/ontologies/IOF-SCRO
- 9: https://groups.google.com/g/ontolog-forum/c/pq-4rA4CT8g/m/5cfQfM6_AgAJ
- 10: https://industryportal.enit.fr/ontologies/CCO
BFO Reference Verified
The update from
BF_0000001toBFO_0000001is correct. According to the Basic Formal Ontology,BFO_0000001represents the universal entity—the foundational class encompassing everything that exists. This change aligns with BFO standards and ensures that the ontology correctly extends from this top-level category.
- File: pride_cv.owl (Lines 285-291)
- Change: Update of superclass reference to
http://purl.obolibrary.org/obo/BFO_0000001No further modifications are necessary.
This automated PR updates the OWL file corresponding to the OBO file
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