Request for new ontology [Data Modality]

[rsc3]

Title

Data Modality Ontology

Short Description

Biological nature of information from an experimental activity, independent of method.

Description

Data modality describes the biological nature of information gathered as the result of an experimental activity, independent of the technology or methods used to produce the information.

This ontology attempts to characterize entities in terms of the channel or mode of biological investigation. For example, activities that produce such results include assays, analysis pipelines, lab tests, and medical imaging -- x-ray, CT-scan, or microscopy as well as the data these activities generate.

Identifier Space

MODAL

License

CC0

Domain

biological systems

Source Code Repository

https://github.com/broadinstitute/modal

Homepage

https://github.com/broadinstitute/modal

Issue Tracker

https://github.com/broadinstitute/modal/issues

Contribution Guidelines

https://github.com/broadinstitute/modal/CONTRIBUTING.md

Ontology Download Link

https://github.com/broadinstitute/modal/blob/main/DataModality.owx

Contact Name

Robert Sidney Cox, III, Ph.D.

Contact Email

sidcox@broadinstitute.org

Contact GitHub Username

rsc3

Contact ORCID Identifier

0000-0002-2009-6236

Formats

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

Dependencies

No response

Related

Gene Ontology
chebi

Usages

- user: https://www.broadinstitute.org/
  description: The Broad Institute uses Data Modality to label datasets in the Data Use and Oversight System
- user: https://anvilproject.org/
  description: The AnVIL project uses Data Modality to label datasets in the AnVIL project for search via the AnVIL Data Explorer

Intended Use Cases and/or Related Projects

This ontology is intended for labeling biomedical datasets, and to capture the object of inquiry of a given experiment. While there are many attempts to catalog various molecular assay methods, there is no clear system for organizing studies by the subject of their inquiry.

Data Sources

AnVIL Project Data
CFoS Project Data
ENCODE Project Data

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 @rsc3,

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!

[pfabry]

Dear @rsc3,

Your ontology has been added to the OBO NOR Dashboard.
The result of the lexical matching is available here: MODAL - lexmatch 20250210.txt

There are however several points that need to be adressed before going further in the review process:

• The license annotation in the ontology does not match the OBO Foundry requirement (cf. Principle 1). It should be "https://creativecommons.org/publicdomain/zero/1.0/" if the proposed license is CC0 1.0
• The file format must be a syntactically valid OWL file using the RDF-XML syntax (cf. Principle 2). Actually the ontology uses a XML serialization format (.owx)
• The ontology IRI, and all terms IRI must follow the OBO Foundry format (cf. Principle 3).
• The ontology must have a unique version IRI (cf. Principle 4).
• There is a mismatch between the submitted ID_space (MODAL) and the one used in the ontology (BioCoreTerms) (cf. Principle 3).
• Textual definitions should be identified using the annotation property: ‘definition’ http://purl.obolibrary.org/obo/IAO_0000115 (cf. Principle 6).
• Concerning the scope of the ontology there are proposed terms that alreay exist in current ontologies such as GO (cf. lexical match file attached). In addition there are some very broad terms, such as "whole genome", "proteomic", "metabolomic" whose scope need to be precised in their definition.
• The ontology is a taxonomy without any object properties, is there a plan to add transversal relations?

[pfabry]

Dear @rsc3,

If you still intend to submit this ontology to OBO, please let us know how you plan to address the comment above. Otherwise, this issue will be closed.

[rays22]

Dear @rsc3 ,
If you wish to re-submit your request, please let us know.