Biomarker Ontology - Githubissues

Astghik-S commented 1 month ago

Title

Biomarker Ontology

Short Description

The Biomarker Ontolody comprises a comprehensive knowledge involving a variety of fields of medical and biological aspects.

Description

The Biomarker Ontology (BMO) is a comprehensive knowledge representation involving a variety of fields of medical and biological aspects. BMO is built in line with Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) principles. Entities and definitions are added by reviewing the biomarker ontology (created by Fraunhofer SCAI 10 years ago and used for the validation of the companion biomarker for a anticancer drug), as well as collected from scientific publications and books from different fields capturing various diseases.

The ontology is proposed to be used for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM).

Identifier Space

BMO

License

CC-BY 4.0

Domain

health

Source Code Repository

OBOFoundry.github.io

Contact Name

Alpha Tom Kodamullil

Contact Email

alpha.tom.kodamullil@scai.fraunhofer.de

Contact GitHub Username

akodamullil

Contact ORCID Identifier

https://orcid.org/0000-0001-9896-3531

Formats

[X] OWL RDF/XML (.owl)
[ ] OBO (.obo)
[ ] OBO Graph JSON (.json)

Dependencies

-doid -chebi -mondo -cto -efo

Usages

No response

Intended Use Cases and/or Related Projects

A biomedical ontology to classify biomarkers and apply semantic technologies in the domain of various diseases, analyse biomarker discovery workflows. Annotation of medical texts.

Data Sources

Several sources from domain experts assembled by Fraunhofer SCAI.

Additional comments or remarks

No response

OBO Foundry Pre-registration Checklist

[X] I have read and understood the registration process instructions and the registration checklist.
[X] 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.
[X] My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
[X] My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
[X] My term labels are in English and conform to the OBO Foundry Naming Conventions
[X] 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.
[X] 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).
[X] 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!
[X] 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.
[X] 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.
[X] 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.

nlharris commented 3 weeks ago

@matentzn @pfabry did you see this New Ontology request?

pfabry commented 3 weeks ago

Dear @Astghik-S ,

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!

Astghik-S commented 3 weeks ago

Dear @pfabry thank you very much for the detailed information. I am looking forward to checking the Dashboard and proceeding with further steps.

pfabry commented 2 weeks ago

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