Request for new ontology MEMON

[DominikMartinat]

Title

Membrane Ontology

Short Description

Cell membranes and membrane models

Description

Membrane Ontology aims to provide a structured, unified vocabulary for the annotation of biological data pertaining to cell membranes and their experimental and computational models. This should allow not only thorough membrane descriptions but also integration between datasets, where similar membranes or models approximating the same type of biological membrane can be identified.

Terms on ontology are supposed to cover different types of biological membrane models used in membrane research and components that are needed for their description. We also plan to add terms useful for connecting models to types of biological membranes which are approximated by them.

Identifier Space

MEMON

License

CC0

Domain

biochemistry

Source Code Repository

https://github.com/DominikMartinat/membrane_ontology

Homepage

https://github.com/DominikMartinat/membrane_ontology

Issue Tracker

https://github.com/DominikMartinat/membrane_ontology/issues

Contribution Guidelines

https://github.com/DominikMartinat/membrane_ontology/blob/main/CONTRIBUTING.md

Ontology Download Link

https://github.com/DominikMartinat/membrane_ontology/blob/main/memon.owl

Contact Name

Dominik Martinát

Contact Email

[email protected]

Contact GitHub Username

dominikmartinat

Contact ORCID Identifier

0000-0001-6611-7883

Formats

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

Dependencies

• go
• bfo

Related

• go
• chebi
• pr

Usages

No response

Intended Use Cases and/or Related Projects

The first intended application of this ontology is for the description of membranes in the MolMeDB database, mainly for categorization and connection to membrane components (mainly phospholipids) in other databases. The next step would be using Membrane Ontology to annotate membranes in WikiPathways and thus link pathways to relevant data in MolMeDB. We hope for the involvement of the membrane expert community and the adoption of the ontology in other projects so we can build a more interconnected world of membrane knowledge.

Data Sources

Membrane experts from University of Chemistry and Technology, Prague were consulted at start of the project. They will be involved with further development and involvement of other membrane experts is expected.

Additional comments or remarks

Hello everyone. I am completely new to building ontologies. I tried to do my best to follow OBO academy tutorials but I will be glad for any feedback what to change or fix.

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]

I put some comments here: https://github.com/DominikMartinat/membrane_ontology/issues

[pfabry]

Dear @DominikMartinat,

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]

@DominikMartinat
Your ontology has been added to the OBO NOR Dashboard.
In addition, the lexical matching hasn't find any duplicate in your ontology.

[pfabry]

@DominikMartinat

Your ontology has passed the dashboard. I'm assigned for the review.