Biomarker Ontology #2604
Comments
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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. You will be informed once your ontology is loaded in the OBO NOR Dashboard. Good luck! |
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Dear @pfabry thank you very much for the detailed information. I am looking forward to checking the Dashboard and proceeding with further steps. |
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@Astghik-S |
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@Astghik-S |
pfabry
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new ontology - reviewer response required
nlharris
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attn: OFOC call
Manual review of Biomarker Ontology1. Ontology scopeThe submitter describes Biomarker Ontology (BMO) as an ontology for classifying biomarkers, improving biomarker identification and facilitating tools used in machine learning and large language models. Upon closer inspection of the ontology, it looks like the ontology adds new terms and extends existing terms from CHEBI, CTO, CMO, OMIT, PR with additional axioms. The domain is 'health' which is consistent with the description and the terms defined within BMO. The submitter states that several domain experts from Fraunhofer SCAI were involved in the development of BMO. But it is not clear who they are. The terms in BMO do not have any attribution so as to who contributed it. In addition, there are 36 terms in the ontology that have 2. Terms with the new ontology prefix ❗Do the terms follow the OBO identifier scheme?❗The Base IRI for terms in BMO is Are there terms with the same meaning available in another OBO Foundry ontology? Yes❗Yes, after reviewing terms from BMO, there are cases where a term from another ontology could be used instead. Following are some of the terms that could be replaced with an existing term:
Is there another OBO Foundry ontology whose scope covers any of the new terms? ❗Yes, after reviewing terms from BMO, there are cases where another ontology would cover some of the new terms. Following are BMO terms that could be added to another OBO Foundry ontology: Clinical Measurement Ontology (CMO) CMO contains terms that are specific to clinical measurements and thus could cover the following terms defined within BMO:
Protein Ontology (PRO) PRO contains terms that represent proteins and thus could cover the following terms defined within BMO:
Ontology of Precision Medicine and Investigation (OPMI) OPMI already defines several biomarkers and thus could cover the following terms defined within BMO:
Ontology for Biomedical Investigations (OBI) OBI already defines several terms for devices and thus could cover the following terms defined in BMO:
Note: The ontology submitter must make efforts to coordinate and add these terms to the suggested ontologies. If the terms are rejected or deemed as out of scope by the target ontologies then an exception can be made for those terms. 3. Correct use of imported terms ❗If the ontology reuses terms from other OBO ontologies, are they used accurately? ✅The BMO ontology imports several terms from CHEBI, OBI, SIO, EFO, OMIT and extends these terms using object properties to indicate whether the terms are a predictive, prognostic, diagnostic biomarker for a disease (via OWL restrictions). The imported terms have sufficient metadata. Are imported terms in appropriate hierarchies, and do they preserve the term’s upper-level alignment? ❗There are certain cases where an imported term does not have the parent class from the upstream ontology as its parent. Rather it is an ancestral class which is ambiguous.
Are any additional axioms used for these terms correct in both a technical (e.g. passes reasoning) and substantive sense? ❗There are other cases where an imported term is defined as a subclass of a term from an entirely different ontology.
4. Basic review of axiomatic patterns ✅Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.) ✅The axioms are simply and appropriately constructed. Are existential restrictions used correctly? ✅Yes, existential restrictions are used correctly. 5. Appropriate use of object properties ✅BMO defines 7 BMO-specific object properties and they are used in a consistent manner throughout the ontology. One thing to note is that the object properties have a label but no additional information such as definition, domain or range that further describe these properties and their usage. BMO also re-uses object properties from RO and their usage are consistent as well. 6. Responsiveness to suggested changes ❔This is the first iteration of feedback. Will evaluate the responsiveness in the next iteration. Additional Questions/Suggestions
Lexical MatchingAfter running lexical match on term labels in BMO with terms from OBO Foundry ontologies (excluding NCIT), following are the results:
Note: The above list is a suggestion and it is up to the discretion of the ontology submitter to check for consistency before considering a term as a potential replacement. Robot ReportAfter running the java -jar robot.jar report --input BMO-merged.owlFollowing are BMO-specific issues as reported by Checklist
@Astghik-S Please take time to go through the above review and the subsequent checklist. You can use this issue thread to keep us up to date regarding progress. If you have any questions or concerns then please don't hesitate to reach out. |
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@deepakunni3 Thank you for the review and comments. I shall check all mentioned points, address all, and come back to you! |
addiehl
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new ontology - submitter action needed
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@deepakunni3 sorry for the late reply. We checked all comments and below I am addressing all of those.
-- We changed the ontology description as 10 years ago our colleagues created not an ontology but rather a terminology and we have only used it to extract relevant terms. The BMONT was built from scratch. I hope this resolves the ambiguity.
-- The mentioned terms that were mistakenly defined as new ones despite the fact they already exist are replaced.
-- Trying to guess which OBO ontology could include the suggested term is very demotivating and time consuming. If the term is not in other ontologies then simply we should define it as we are applying for OBO approval. Moreover, we do not think that "BMO:0000076 therapeutic biomarker", "BMO:0000075 parmacodynamic biomarker"
We would like to mention that, it is not ambiguous at all and we do not have to include all ancestral classes if it is not necessary otherwise we will include the whole CHEBI which is nonsense. “Triglyceride” is a “molecular entity” so “is a” relationship is there so no obligation or violation.
-As you mentioned there are terms in BMO that do not have a parent class. It would be clearer to give these an appropriate parent class: The mentioned classes do not have parent classes because they are for text mining purposes which also is given in their name to avoid confusions. |
bpeters42
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new ontology - reviewer response required
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@deepakunni3 just wondering if you've had a chance to circle back to this? |
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@pfabry Following the first round of reviews, the name of the ontology has been changed from BMO to BMONT. The repository location has also changed from https://github.com/Astghik-S/BMO/ to https://github.com/SCAI-BIO/BiomarkerOntology. It would be great if you could update the NOR Dashboard entry for BMO with the newer metadata. |
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@Astghik-S Thank you for the response to the comments in the review. After discussing about BMONT (née BMO) during the OBO Foundry Operations Committee meeting (2024-09-17), there were a few concerns raised with the scope of this ontology.
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@deepakunni3 Thank you for your comments and suggestions. We tried to address each of those: - Is the ontology specific to biomarkers in humans or all species? The ontology and the users of the ontology would benefit from this being specified via taxon constraints.
- The submitter describes BMONT as an ontology of biomarkers but it is not clear what the extent of this ontology is. Does it focus on particular area like cell biomarkers, diagnostic biomarkers, prognostic biomarkers, molecular biomarkers or all of them? It would be good to clarify in the ontology description.
- Additionally, it would be great if the submitter could clarify if BMONT is a reference ontology or an application ontology. The repository (https://github.com/SCAI-BIO/BiomarkerOntology) does not provide sufficient clarification.
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Thank you for taking the time to go through the comments above and for your response. Following are observations made after a second round of review: 1. Ontology scopeThe submitter states that BMONT contains only human-related biomarkers with the possibility of considering other species in the future. Similarly, the submitter states that the extent of the ontology is open-ended on purpose to allow for flexibility and incremental development of BMONT according to use cases. Thank you @Astghik-S for the clarification. It would be good to put this clarification in the description of the ontology so that it is clear to the users of BMONT. 2. Terms with the new ontology prefix ❗Do the terms follow the OBO identifier scheme? ✅
The ontology prefix and IRI has been updated. All terms now have IRIs that conform to the OBO identifier scheme. Are there terms with the same meaning available in another OBO Foundry ontology? ✅
The authors have replaced the terms for which there exists an exact replacement. Is there another OBO Foundry ontology whose scope covers any of the new terms? ❗Response from submitter:
The goal of this section is to promote discussion and cross-talk between existing OBO Foundry ontologies and a new prospective ontology. The objective is not to discourage or demotivate ontology developers, but rather to prevent the proliferation of terms with similar meaning across different OBO Foundry ontologies. To that end, the request is not to place all possible terms from BMONT into another ontology, but rather to see if the ontology submitter and maintainers are willing to engage in collaboration with other OBO Foundry ontologies. The relevance, scope, choice and decision of whether to add terms to an existing OBO Foundry ontology is left to discretion of the ontology maintainers. But we do want to see efforts made by the ontology maintainers. And if the target ontology does not respond to the ontology maintainers then we would like to know that as well. 3. Correct use of imported terms ❗Response from submitter:
Understood and thank you for the clarification. Response from submitter:
The explanation does not clarify why a new subClassOf axiom was injected. My previous observation was in regards to scenarios where a term from an ontology does not preserve its parent class after it is imported. One example was
These could be artifacts introduced by the ontology authoring tools. It would be good for the submitter to look into this. Note: When an ontology introduces a new parent for an imported term that is different from the original upstream ontology, this is called as axiom injection. The distinction of whether BMONT is a reference ontology or an application ontology matters here. If BMONT is a reference ontology then injecting new axioms to imported terms is discouraged. See the ongoing discussion regarding this topic. 4. Basic review of axiomatic patterns ❗Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.) ✅The axioms are simply and appropriately constructed. Are existential restrictions used correctly? ❗Yes, existential restrictions are used correctly. But there are scenarios where restrictions are added to imported terms from CHEBI, HP, MAXO, NCIT, OMIT, PR For example,
The distinction of whether BMONT is a reference ontology or an application ontology matters here. If BMONT is a reference ontology then injecting new axioms to imported terms is discouraged. See the ongoing discussion regarding this topic. 5. Appropriate use of object properties ✅6. Responsiveness to suggested changes ✅The submitter is response to suggested changes. Additional Questions/SuggestionsGreat to see BMONT moved to the https://github.com/SCAI-BIO organization. The renaming to BiomarkerOntology (BMONT) is appropriate and consistent. The base IRI, ontology IRI and prefix for all terms in the ontology looks correct. The submitted is encouraged to consider the distinction between a reference and an application ontology and decide what would suit best for BMONT. |
deepakunni3
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new ontology - submitter action needed
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Dear @deepakunni3 thank you for responses. I am sorry for the late reply.
The goal of this section is to promote discussion and cross-talk between existing OBO Foundry ontologies and a new prospective ontology. The objective is not to discourage or demotivate ontology developers, but rather to prevent the proliferation of terms with similar meaning across different OBO Foundry ontologies. To that end, the request is not to place all possible terms from BMONT into another ontology, but rather to see if the ontology submitter and maintainers are willing to engage in collaboration with other OBO Foundry ontologies. The relevance, scope, choice and decision of whether to add terms to an existing OBO Foundry ontology is left to discretion of the ontology maintainers. But we do want to see efforts made by the ontology maintainers. And if the target ontology does not respond to the ontology maintainers then we would like to know that as well.** - I am reaching out to the groups responsible for OBO Foundry ontologies to inquire whether BMONT terms can be incorporated into other OBO Foundry ontologies, such as CMO, PRO, and OBI. I am asking them to review these terms and let me know if they are willing to include them in their respective ontologies. Hopefully, we will receive responses in the coming days.
These could be artifacts introduced by the ontology authoring tools. It would be good for the submitter to look into this. Note: When an ontology introduces a new parent for an imported term that is different from the original upstream ontology, this is called as axiom injection. The distinction of whether BMONT is a reference ontology or an application ontology matters here. If BMONT is a reference ontology then injecting new axioms to imported terms is discouraged. See the #1443 regarding this topic.** - Let’s review the issue:
Yes, existential restrictions are used correctly. But there are scenarios where restrictions are added to imported terms from CHEBI, HP, MAXO, NCIT, OMIT, PR For example, The distinction of whether BMONT is a reference ontology or an application ontology matters here. If BMONT is a reference ontology then injecting new axioms to imported terms is discouraged. See the #1443 regarding this topic. - BMONT is both a reference and application ontology. Our primary goal is to consolidate all biomarker-related terms into a single ontology. However, this is a complex task that spans multiple fields. For instance, numerous diseases require descriptions using both established and candidate biomarkers, many of which are still under discussion. For preventive, transnational, and personalized medicine, it is crucial for clinicians to have tools that enable easy access to existing knowledge. To achieve satisfying results, we plan to implement our ontology within our SCAIView text mining machine. This is why we are also adding restrictions to the imported classes, allowing us to create text mining BINs. We have applied this approach to other OBO-approved ontologies, particularly the Epilepsy Ontology (see Epilepsy Ontology GitHub OBO Issue #1514). We aim to enhance BMONT by defining biomarkers for various diseases, fostering improved dialogue between clinicians and researchers. As we integrate classes from existing OBO ontologies, we must inject those axioms for practical application. |
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Dear @deepakunni3, I wanted to follow up regarding the current status. I recently responded to the comments provided addressing your suggestions. It has been about two weeks since my response so I wanted to check in to see if there is any further feedback or if there are additional steps I should take to move the process forward. |
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Hi @Astghik-S! Apologies for the late response. Took some time to circle back to this ticket. Response from submitter:
Fantastic! Glad to hear that the discussions are ongoing. If possible, please provide link(s) to the tickets/issues created at the respective OBO Foundry ontologies to make it easier to follow the discussion. Response from submitter:
Thank you for the detailed breakdown. My assumption is that if you are importing Later, when you import You do not have to specifically add all the parent (and ancestral) terms of an imported term. A tool like Robot would take care of this. In fact, if the term You can have both When you need to integrate another term that is a subclass of The Note: This scrutiny is applied because BMONT is stated to be a reference ontology. Instances of axiom injection are highly discouraged as it affects interoperability of BMONT with other ontologies. Also to clarify, the goal here is not to decide whether to import terms exclusively from MONDO or DOID. In the case of 'neurodegenerative disease', the choice of the term to import depends on your evaluation of which ontology gives you the right hierarchy of terms for your use-case. Response from submitter:
Given the stated goals, I would recommend looking into and coordinating efforts with OBCI (#2643). |
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Hi Astghik, By the way, OBCI and BMONT have very different approaches to biomarkers. BMONT appears to be an application ontology while OBCI is not. That being said, it might be quite difficult for us to get OBCI into the OBO Foundry without us changing something fundamental. Perhaps us three biomarker ontology developers can come up with something that will work! In that spirit, please let me know if you are able to join that rather informal meeting. |
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Hi Darren, Sure, we can meet and discuss. November 6 at 8 AM works for me. |
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@Astghik-S I need an email to send the meeting link. |
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Hi @deepakunni3 ,
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@Astghik-S Thank you for clarifying about BMONT as an application ontology. Glad to hear that the discussions are ongoing with CMO (rat-genome-database/CMO-Clinical-Measurement-Ontology#14), PRO (PROconsortium/PRoteinOntology#338), and OPMI (OPMI/opmi#15). We will discuss about BMONT on the next Operations Committee call (2024-11-26). |
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@pfabry I notice this ontology failed FP11 "Authority" despite having what appears to be proper contact information. Is it possible that the dashboard configuration file needs to be edited? I notice that the 'orcid' entry is given as 'https://orcid.org/0000-0001-9896-3531' instead of just '0000-0001-9896-3531'. Other NOR dashboard configurations lack the https...prefix. Can you fix, or, if you prefer, I can make a pull request to fix. |
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@nataled Yes, this is a problem in the config file. I will fix it. Thanks! |
nlharris
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new ontology - reviewer response required
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Final review of BMONT 1. Ontology scopeThe submitter describes Biomarker Ontology (BMONT) as an ontology for classifying biomarkers, improving biomarker identification and facilitating tools used in machine learning and large language models. Upon closer inspection of the ontology, it looks like the ontology adds new terms and extends existing terms from CHEBI, CTO, CMO, OMIT, PR with additional axioms. The submitter states that BMONT contains only human-related biomarkers with the possibility of considering other species in the future. Similarly, the submitter also states that the extent of the ontology is open-ended on purpose to allow for flexibility and incremental development of BMONT according to use cases. 2. Terms with the new ontology prefix ✅Do the terms follow the OBO identifier scheme? ✅The name of the ontology was changed from BMO to BMONT. The ontology prefix and IRI has been updated to account for this change. All terms now have IRIs that conform to the OBO identifier scheme. Are there terms with the same meaning available in another OBO Foundry ontology? ✅After review, the authors have replaced the terms for which there exists an exact replacement. Is there another OBO Foundry ontology whose scope covers any of the new terms? ✅After reviewing terms from BMO, there are cases where another ontology would cover some of the new terms. The submitter has made new term requests for CMO (rat-genome-database/CMO-Clinical-Measurement-Ontology#14), PRO (PROconsortium/PRoteinOntology#338), and OPMI (OPMI/opmi#15). 3. Correct use of imported terms ✅If the ontology reuses terms from other OBO ontologies, are they used accurately? ✅The BMO ontology imports several terms from CHEBI, OBI, SIO, EFO, OMIT and extends these terms using object properties to indicate whether the terms are a predictive, prognostic, diagnostic biomarker for a disease (via OWL restrictions). The imported terms have sufficient metadata. Are imported terms in appropriate hierarchies, and do they preserve the term’s upper-level alignment? ✅Yes, the imported terms are in appropriate hierarchies and preserve the term's upper-level alignment. 4. Basic review of axiomatic patterns ✅Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.) ✅The axioms are simply and appropriately constructed. Are existential restrictions used correctly? ✅Yes, existential restrictions are used correctly. But there are scenarios where restrictions are added to imported terms from CHEBI, HP, MAXO, NCIT, OMIT, PR. Given that BMONT is an application ontology, the addition of such restrictions are expected and does not negatively impact the review. 5. Appropriate use of object properties ✅BMO defines 7 BMO-specific object properties and they are used in a consistent manner throughout the ontology. BMO also re-uses object properties from RO and their usage are consistent as well. 6. Responsiveness to suggested changes ✅The submitter is response to suggested changes. |
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Dear @deepakunni3 thank you very much for the final review of the BMONT. |
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@Astghik-S The above final review was mostly for the benefit of the OBO Foundry Operations Committee. The review for BMONT is still under discussion. We will be bringing it up again on the next call on 10.12.2024 |
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We decided to resume discussions about this on Jan 7th, 2025 due to the low attendance at the meeting in the holiday season. |
Title
Biomarker Ontology
Short Description
The Biomarker Ontology comprises a comprehensive knowledge involving a variety of fields of medical and biological aspects.
Description
The Biomarker Ontology (BMONT) is a comprehensive knowledge representation involving a variety of fields of medical and biological aspects. BMONT 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 old biomarker terminology that was created by Fraunhofer SCAI 10 years ago and was used for mining biomarker information in biomedical literature. In addition, related terms were collected from scientific publications and books capturing various disease fields.
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
Homepage
https://github.com/SCAI-BIO/BiomarkerOntology
Issue Tracker
https://github.com/SCAI-BIO/BiomarkerOntology/issues
Contribution Guidelines
https://github.com/SCAI-BIO/BiomarkerOntology/blob/main/CONTRIBUTING.md
Ontology Download Link
https://github.com/SCAI-BIO/BiomarkerOntology
Contact Name
Alpha Tom Kodamullil
Contact Email
[email protected]
Contact GitHub Username
akodamullil
Contact ORCID Identifier
https://orcid.org/0000-0001-9896-3531
Formats
Dependencies
-doid -chebi -mondo -cto -efo
Related
DOID
MONDO
CHEBI
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
dc:licenseannotation, serialised in RDF/XML.The text was updated successfully, but these errors were encountered: