Request for new ontology [Compound Toxicity Ontology]

[zjy959354]

Title

Compound Toxicity Ontology

Short Description

An ontology that classifies chemical compounds according to their associated toxicity types.

Description

This ontology is an application ontology for representing chemical compounds and their associated toxicity effects. It supports standardized classification of toxicity types and enables integration of toxicological data. It reuses and aligns with existing ontologies, including NCI Thesaurus (NCIT), Experimental Factor Ontology (EFO), and eNanoMapper ontology (ENM), to ensure semantic interoperability.

Identifier Space

CTxO

License

CC0

Domain

health

Source Code Repository

https://github.com/zjy959354/Compound-Toxicity-Ontology

Homepage

https://github.com/zjy959354/Compound-Toxicity-Ontology

Issue Tracker

https://github.com/zjy959354/Compound-Toxicity-Ontology/issues

Contribution Guidelines

https://github.com/zjy959354/Compound-Toxicity-Ontology/blob/main/CONTRIBUTING.md

Ontology Download Link

https://github.com/zjy959354/Compound-Toxicity-Ontology

Contact Name

Zhang jiang yan

Contact Email

2968317207@qq.com

Contact GitHub Username

zjy959354

Contact ORCID Identifier

0009-0002-8957-5742

Formats

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

Dependencies

• ncit
• efo
• enm

Related

• ncit
• efo

Usages

Intended Use Cases and/or Related Projects

No response

Data Sources

No response

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
• 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 @zjy959354,
Thank you for your submission. The review process is as follows:
1. Technical review
You will first need to pass the technical review, which includes:

• Ensuring all pre-registration checklist items are satisfied
• Passing the OBO NOR Dashboard (a pass requires that no checks are red except for “Users”)
• Reviewing lexical alignment of your terms against existing OBO Foundry ontologies to avoid duplication of terms with similar meanings

2. Ontology review
Once the technical review is completed successfully, an OBO Operations Committee member will be assigned to review your ontology.
This review typically leads to iterative improvements. When the reviewer considers the ontology ready, it will be presented during an OBO Operations Call, allowing other committee members to provide feedback.

A final decision will then be made by the committee, and you will be notified through this issue tracker. The overall process may take several weeks or months, depending on the complexity of the case. If you anticipate any urgency, please let us know. Conversely, if additional time is needed to address issues, you may close this issue and reopen it when updates are ready.
You will be informed once your ontology has been loaded into the OBO NOR Dashboard.

[pfabry]

Dear @zjy959354,

Several pre-registration requirements have been checked and appear not to be satisfied.

• My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML: No
• My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy: No
• 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): No
• 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: No

Additionally, the imports declared in the main ontology cannot be retrieved.
Finally, most chemical compounds are modeled as instances rather than classes in this ontology. I would recommend reviewing CHEBI as an example of how molecular entities are typically modeled.