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Request for new ontology OBCI #2643
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@nataled OBCI is in the NOR dashboard. Is there a plan to bring the owl file to the github? We could discuss the reviewer at the next OFOC call. |
@pfabry that's the hope at least. We need a better indication of how large OBCI might get, as I'm aware of size limitations for github (I already cannot have the Protein Ontology there for that reason). I believe I'll have a better assessment of potential size within the next few months. |
@pfabry I checked the NOR results and it appears there was some processing error on my part that caused a duplication of term identifiers. I fixed that and have re-uploaded a new version for testing. |
I have made a few updates and reviewed various errors. To ensure that the version that will be reviewed will be the same as the version tested, I will not upload a new version prior to review, so this update is just for information.
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@balhoff has been assigned to review this ontology. |
What's the relationship to terms in OBA? Cc @matentzn |
@cmungall currently no relation. It is possible that some terms in OBCI could be composed using terms from OBA. For example, one possible biomarker could be something like elevated blood glucose, which could refer to the OBA term 'blood glucose amount'. A potential complication for doing so is the way that OBA terms are defined. Continuing with the above example, 'blood glucose amount' is equivalent to: instead of something more direct like: So it is unclear to me how that extra layer would be interpreted in the context of biomarkers. I suspect it reflects the difference between a biomarker (a perturbation away from whatever is normal for a given person) and a phenotype (the normal for a given person). |
yes, OBA=traits (e.g. |
I think you mean that hyperglycemia would go in a phenotype ontology. Elevated blood glucose is one biomarker of that condition. |
From the uPheno perspective, this is how things are separated:
We have never quite thought the "biomarker" problem all the way to the very end. So far, biomarker for us is mostly a role that a phenotype takes in a certain context; If you are interested, read up on our way of thinking on phenotype here (our recent course on phenotype data). Relevant docs:
I understand that the precise way of doing phenotype data is a bit contentious, some people do not like the idea of representing them as precoordinated at all - but for the sake of evolving as a community I would recommend for the review of OBCI to take this way of thinking into account while doing the review. (I personally have not looked at OBCI and cant at the moment) |
One word of caution from my end - I would not use an ontology submission to challenge the way we do phenotype modelling in dozens of OBO ontologies for more than 12 years: https://www.biorxiv.org/content/10.1101/2024.09.18.613276v1 The EQ model is widely established since 2009, we have hundreds of design patterns, for example, the one for "increased level of glucose" is https://raw.githubusercontent.com/obophenotype/upheno/master/src/patterns/dosdp-dev/abnormallyIncreasedLevelOfChemicalEntityInLocation.yaml. This has been reviewed by many members of the phenotype ontology community (meetings are biweekly and ongoing if you like to join), and the logical modelling is, while not ideal in all cases (especially when it comes to "absence"), pretty much set in stone now.. |
Both. Most phenotype ontologies treat these as synonyms or distinctions of
degree eg
https://www.ebi.ac.uk/ols4/ontologies/mp/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMP_0005559
…On Sun, Nov 3, 2024 at 3:51 PM Darren A. Natale ***@***.***> wrote:
I think you mean that hyperglycemia would go in a phenotype ontology.
Elevated blood glucose is one biomarker of that condition.
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It is not clear to me what the status of this is. Are we waiting for the reviewer to do something, or the submitter to do something? |
@nlharris we are waiting for the reviewer (me) to do something. Sorry for the delay, I am actually looking at it right now. |
Ok, thanks! I didn't mean to suggest that you should work on this on a Sunday!🙂 |
Here is my submission review: Review criteria
Technically I don't find any issues with the ontology. The developers are already active in OBO and make correct use of identifiers as well as imported content. The axioms are created using consistent modeling patterns. One thing that would be nice, but I don't think is part of the review criteria, is to provide the production workflow source code (e.g., on GitHub), if there is anything besides Protege. The one criterion I left un-checked above has to do with scope. As demonstrated in the discussion above, I think there are some differences of opinion on what a biomarker is as compared to a phenotype (or possibly concepts broader than just phenotype that follow the same EQ model). It seems to me that these are all basically the same kinds of structures, just differing in their choice of relations and model. I think biomarkers may sometimes include more information about how they were measured, rather than just the state of things, but maybe this could be done in a way that meshes with EQ? @nataled @cmungall @matentzn is there any way to come to an alignment? |
The result of the lexical matching is available here: OBCI lexmatch 20241125.txt |
Title
Ontology for Biomarkers of Clinical Interest
Short Description
The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.
Description
OBCI is a reference ontology for biomarkers that formalizes biomarker-centric knowledge (terms, definitions, synonyms) under a unified framework, enriched with objects imported from related reference ontologies and designed to aid clinicians seeking to identify biomarkers useful to their purpose. Construction of OBCI observes recommendations concerning accurate formal representation of biomarkers as proposed by the FDA-NIH Biomarker Working Group and in accordance with the principles of the Open Biomedical and Biological Ontologies (OBO) Foundry to ensure ontological rigor and interoperability.
Identifier Space
OBCI
License
CC-BY 4.0
Domain
health
Source Code Repository
https://github.com/clinical-biomarkers/OBCI
Homepage
https://github.com/clinical-biomarkers/OBCI
Issue Tracker
https://github.com/clinical-biomarkers/OBCI/issues
Contribution Guidelines
https://github.com/clinical-biomarkers/OBCI/blob/main/CONTRIBUTING.md
Ontology Download Link
https://proteininformationresource.org/staff/nataled/OBCI/obci.owl
Contact Name
Darren A. Natale
Contact Email
[email protected]
Contact GitHub Username
nataled
Contact ORCID Identifier
0000-0001-5809-9523
Formats
Dependencies
Related
There is currently no active OBO Foundry ontology that covers the same domain. There is, however, a newly-submitted ontology (BMONT) that is being considered for inclusion, and we are aware of at least one other group developing a biomarker ontology. We have looked at BMONT and determined that the approach taken by the developers is inconsistent with our approach. It can best be described as an application ontology (it makes use of axiom injection). OBCI is purely a reference ontology. Indeed, by our criteria, BMONT contains mostly what we term 'biomarker assessed entities', nearly all of which (in OBCI) are imported terms. Thus, OBCI could not fit under the umbrella of BMONT without radically changing that ontology. It is unclear as yet how OBCI and the other not-yet-submitted ontology relate in terms of scope or approach, but our two groups will be initiating discussions in the near future.
Usages
No response
Intended Use Cases and/or Related Projects
The NIH CFDE funded BiomarkerKB (https://glygen.ccrc.uga.edu/frontend/home/) was built using early versions of OBCI as a guide for approach and organization. In turn, OBCI will largely--but not solely--ontologically represent many of the biomarkers collected there.
Data Sources
The main definition source for upper level terms in OBCI is the FDA-NIH Biomarker Working Group (see NCBI:books/NBK402285 and PMID:29405771). Many of the specific biomarkers in OBCI will derive from the collected data found in the aforementioned BiomarkerKB.
Additional comments or remarks
OBO Foundry Pre-registration Checklist
dc:license
annotation, serialised in RDF/XML.The text was updated successfully, but these errors were encountered: