new term: bone marrow adipocyte

[pmaye1]

Please check that the term does not already exist by using the ontology search tool OLS:
https://www.ebi.ac.uk/ols4/ontologies/cl

My searches in OLS did not reveal any cell named "bone marrow adipocyte" or "marrow adipocyte"

Preferred term label == "bone marrow adipocyte"

Synonyms (add reference(s), please) "marrow adipocyte, adipocyte"

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)
PMID: 34912805 - "Bone Marrow Adipocytes: A Critical Player in the Bone Marrow Microenvironment" (2021, Frontiers) - We found this earlier, comprehensive overview. { PMID correct by @dosumis }
PMID: 31899563 - de Paula & Rosen (2020) "Marrow Adipocytes: Origin, Structure, and Function" Annual Review of Physiology - authoritative review
PMID: 32286228 - "Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment" (2020, eLife) - landmark scRNA-seq study defining marrow adipocyte populations

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)

parent cell type term = adipocyte CL:0000136

Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)

bone marrow of various skeletal bony elements....too many to detail

Your ORCID
0000-0003-0098-4399

Additional notes or concerns

bone marrow preadipocyte too ???

[dosumis]

@pmaye1 - Many thanks for your term request. We are trialling a new agentic-AI curator pipeline on this ticket. I hope you don't mind. Please bear with us while we work on tuning. Please let us know if too much email traffic. We will @ you again for more feedback when we are ready).

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Agentic research repot on generated for this term request
STATUS: IN PROGRESS

Curation Report: Bone Marrow Adipocyte

1. Term Identification

• Proposed Label: bone marrow adipocyte
• Status: New term request (NTR)
• Requester ORCID: 0000-0003-0098-4399

2. Verification - Term Does Not Exist

OLS Search Confirmed: No existing term "bone marrow adipocyte" or "marrow adipocyte" found in CL.

CL Ontology Grep Search: Confirmed absence. Only one mention of "marrow adipocytes" was found in a definition text (line 10194 of cl-edit.owl) but not as a distinct term.

3. Definition Validation

Proposed Definition (to be constructed from literature):
"An adipocyte located in the bone marrow that contributes to the bone marrow microenvironment. Bone marrow adipocytes are distinct from white and brown adipocytes and play important roles in hematopoiesis, bone homeostasis, and systemic metabolism."

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AFTER PROMPTING TO USE DEFINITION STRUCTURE GUIDE

Draft Definition Structure

(80-120 words, genus-differentia form):
"An adipocyte that is part of bone marrow [GENUS], characterized by [distinguishing structural/molecular features from PMID:31899563, PMID:32286228]. This cell plays critical roles in regulating the hematopoietic microenvironment [citation needed], bone homeostasis [citation needed], and systemic metabolism [citation needed]. It is distinct from subcutaneous and visceral white adipocytes by [specific distinguishing features from literature]. Development involves [lineage/transcription factors if available from PMID:32286228 scRNA-seq study]."

CRITICAL: The actual definition MUST be constructed by extracting specific text and inline citations from the verified PMIDs. The above is a structural template only.

Literature Support Provided:

1. PMID:31991541 - Listed but requires verification (appears to be incorrect PMID based on retrieval attempt)
2. PMID:31899563 - de Paula & Rosen (2020) "Marrow Adipocytes: Origin, Structure, and Function" Annual Review of Physiology - AUTHORITATIVE REVIEW
3. PMID:32286228 - "Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment" (2020, eLife) - LANDMARK scRNA-seq STUDY

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Validation Notes:

• PMID:31899563 (de Paula & Rosen, 2020) in Annual Reviews is an authoritative and comprehensive review that would provide excellent definitional support
• PMID:32286228 (2020, eLife) is a high-impact single-cell study that characterized bone marrow adipocyte populations at molecular level
• PMID:31991541 appears to need verification - my retrieval attempt returned a coronavirus paper, suggesting this may be an incorrect PMID
• Additional verification of PMIDs and extraction of specific definitional text from these papers is needed

4. Parent Term Validation

Proposed Parent: adipocyte (CL:0000136)

Current CL Definition of CL:0000136:
"A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides."

Justification for Parent:

• Bone marrow adipocytes are functionally and morphologically adipocytes
• They store lipids as triglycerides
• They express adipocyte markers
• The genus-differentia pattern supports this: "An adipocyte that [is located in bone marrow]"

Hierarchical Context:

CL:0000136 (adipocyte)
├── CL:0000448 (white fat cell)
├── CL:0000449 (brown fat cell)  
├── CL:0002521 (subcutaneous adipocyte)
├── CL:0002615 (visceral adipocyte)
└── **PROPOSED: bone marrow adipocyte**

Note: Bone marrow adipocytes are considered a distinct depot with unique properties, similar to how subcutaneous and visceral adipocytes are distinguished by location.

5. Anatomical Location Validation

Proposed Location: bone marrow (UBERON:0002371)

Verification Needed: Search UBERON for "bone marrow" term

Notes from Requestor: "bone marrow of various skeletal bony elements....too many to detail"

Recommendation: Use generic "bone marrow" (UBERON:0002371) for the part_of relationship rather than listing specific bones. This is consistent with how CL handles anatomical specificity.

6. Synonyms

Proposed Synonyms:

• "marrow adipocyte" - EXACT SYNONYM (commonly used, found in PMID:31899563 title)
• "adipocyte" - NEEDS CLARIFICATION - this is too broad and is already the parent term label; should be REMOVED

Validation Notes:

• "marrow adipocyte" is well-supported and appears in the de Paula & Rosen review title
• "adipocyte" alone is not an appropriate synonym - it's the parent class
• May want to search literature for additional synonyms such as:
  • "bone marrow fat cell" (potential)
  • "BMAT cell" (bone marrow adipose tissue cell - potential abbreviation)
  • "MAT adipocyte" (marrow adipose tissue adipocyte - potential)

7. Logical Relationships

Primary Relationships:

• is_a: CL:0000136 (adipocyte) - implicit via logical definition
• part_of: UBERON:0002371 (bone marrow) - definitional criterion

Logical Definition (Proposed):

EquivalentClasses(CL:XXXXXXX ObjectIntersectionOf(CL:0000136 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON:0002371)))

This follows the pattern used in CL for location-specific adipocytes (see CL:0002521 subcutaneous adipocyte, CL:0002615 visceral adipocyte).

Additional Relationships (Literature-Supported):

Based on known biology, bone marrow adipocytes may have additional relationships:

• capable_of: GO terms related to lipid storage, hematopoietic support
• has_plasma_membrane_part: Markers such as perilipin, adiponectin receptors
• These would require specific PMID support from the provided references

8. Ontology Placement Recommendation

✓ RECOMMENDED: Create in CL

Reasoning:

1. Cell Type: Bone marrow adipocytes are a naturally occurring cell type in healthy organisms
2. Not Pathological: These are normal constituents of bone marrow, not disease-associated
3. Not Cultured/Engineered: These are primary cells found in vivo
4. Precedent: CL already includes anatomically-defined adipocyte subtypes (subcutaneous, visceral)
5. Scope Alignment: Fits CL's mission to represent cell types across anatomical locations

Not CLO because:

• CLO (Cell Line Ontology) is for immortalized/cultured cell lines
• Bone marrow adipocytes are primary cells, not cell lines

9. Additional Metadata Requirements

Required for CL Integration:

• term_tracker_item: Link to GitHub issue
• date created: Current ISO 8601 timestamp
• creator: "GitHub Copilot" (for NTR terms only)
• contributor: https://orcid.org/0000-0003-0098-4399 (requester ORCID)

Cross-references:

• Research community may have existing database IDs that should be added as xrefs

10. Additional Research Needed

CRITICAL - PMID Verification:

1. PMID:31991541 - Verification attempt returned wrong article (coronavirus paper). MUST VERIFY correct PMID or remove
2. PMID:31899563 - High confidence, authoritative Annual Reviews paper
3. PMID:32286228 - High confidence, eLife single-cell study

Recommended Next Steps:

1. Verify PMIDs - Confirm all three PMIDs actually discuss bone marrow adipocytes
2. Extract definitions - Get exact text from PMID:31899563 and PMID:32286228 to construct precise definition
3. Check for subtypes - The requester mentioned "bone marrow preadipocyte too???" - investigate if this should be a separate term
4. Marker genes - Extract key marker genes/proteins from scRNA-seq study (PMID:32286228) for potential has_plasma_membrane_part relationships
5. Functional capabilities - Determine GO terms for capable_of relationships

11. Confidence Assessment

• Term novelty: High (confirmed not in CL)
• Parent term: High (adipocyte is appropriate)
• Anatomical location: High (bone marrow is well-defined)
• Cross-references/PMIDs: MEDIUM-LOW (PMID:31991541 needs verification)
• Definition quality: Medium (needs extraction from verified sources)
• Synonym validation: Medium ("adipocyte" synonym should be removed)
• Overall: MEDIUM - Good foundation but requires PMID verification and definition construction

12. Questions for Requester/Editor

1. PMID:31991541 - Can you verify this PMID? My retrieval returned a coronavirus paper, not bone marrow adipocytes
2. Bone marrow preadipocyte - You mentioned this in "Additional notes". Should this be a separate NTR? If so, this would be a precursor cell (progenitor) rather than the mature adipocyte
3. Functional properties - Are there specific functional capabilities or markers you'd like included in the definition beyond general lipid storage?

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RECOMMENDATION

STATUS: ADDITIONAL RESEARCH NEEDED - NOT YET READY FOR INTEGRATION

Action Items:

1. VERIFY PMID:31991541 - Critical blocker
2. EXTRACT DEFINITIONS from verified PMIDs (31899563, 32286228)
3. REMOVE "adipocyte" from synonym list
4. CLARIFY bone marrow preadipocyte question
5. CONSTRUCT final definition with inline citations

Once PMIDs are verified and definition is constructed from primary sources, this term will be READY FOR CL INTEGRATION by the @CL-ontologist agent.

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Report prepared by: @CL-curator
Date: 19 December 2025

[dosumis]

Curation Report: Bone Marrow Adipocyte

1. Term Identification

• Proposed Label: bone marrow adipocyte
• Status: New term request (NTR)
• Requester ORCID: 0000-0003-0098-4399

2. Verification - Term Does Not Exist

OLS Search Confirmed: No existing term "bone marrow adipocyte" or "marrow adipocyte" found in CL.

CL Ontology Grep Search: Confirmed absence. Only one mention of "marrow adipocytes" was found in a definition text (line 10194 of cl-edit.owl) but not as a distinct term.

3. Definition Validation

Proposed Definition (following CL definition guidelines):

Note: This definition requires extraction of specific text from verified PMIDs to include proper inline citations. The structure below follows the CL definition guidelines from docs/LLM_prompt_guidelines_for_CL_definitions.md:

Draft Definition Structure (80-120 words, genus-differentia form):
"An adipocyte that is part of bone marrow [GENUS], characterized by [distinguishing structural/molecular features from PMID:31899563, PMID:32286228]. This cell plays critical roles in regulating the hematopoietic microenvironment [citation needed], bone homeostasis [citation needed], and systemic metabolism [citation needed]. It is distinct from subcutaneous and visceral white adipocytes by [specific distinguishing features from literature]. Development involves [lineage/transcription factors if available from PMID:32286228 scRNA-seq study]."

CRITICAL: The actual definition MUST be constructed by extracting specific text and inline citations from the verified PMIDs. The above is a structural template only.

Literature Support Provided:

1. PMID:31991541 - Listed but requires verification (appears to be incorrect PMID based on retrieval attempt)
2. PMID:31899563 - de Paula & Rosen (2020) "Marrow Adipocytes: Origin, Structure, and Function" Annual Review of Physiology - AUTHORITATIVE REVIEW
3. PMID:32286228 - "Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment" (2020, eLife) - LANDMARK scRNA-seq STUDY

Validation Notes:

• PMID:31899563 (de Paula & Rosen, 2020) in Annual Reviews is an authoritative and comprehensive review that would provide excellent definitional support
• PMID:32286228 (2020, eLife) is a high-impact single-cell study that characterized bone marrow adipocyte populations at molecular level
• PMID:31991541 appears to need verification - my retrieval attempt returned a coronavirus paper, suggesting this may be an incorrect PMID
• Additional verification of PMIDs and extraction of specific definitional text from these papers is needed

4. Parent Term Validation

Proposed Parent: adipocyte (CL:0000136)

Current CL Definition of CL:0000136:
"A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides."

Justification for Parent:

• Bone marrow adipocytes are functionally and morphologically adipocytes
• They store lipids as triglycerides
• They express adipocyte markers
• The genus-differentia pattern supports this: "An adipocyte that [is located in bone marrow]"

Hierarchical Context:

CL:0000136 (adipocyte)
├── CL:0000448 (white fat cell)
├── CL:0000449 (brown fat cell)  
├── CL:0002521 (subcutaneous adipocyte)
├── CL:0002615 (visceral adipocyte)
└── **PROPOSED: bone marrow adipocyte**

Note: Bone marrow adipocytes are considered a distinct depot with unique properties, similar to how subcutaneous and visceral adipocytes are distinguished by location.

5. Anatomical Location Validation

Proposed Location: bone marrow (UBERON:0002371)

Verification Needed: Search UBERON for "bone marrow" term

Notes from Requestor: "bone marrow of various skeletal bony elements....too many to detail"

Recommendation: Use generic "bone marrow" (UBERON:0002371) for the part_of relationship rather than listing specific bones. This is consistent with how CL handles anatomical specificity.

6. Synonyms

Proposed Synonyms:

• "marrow adipocyte" - EXACT SYNONYM (commonly used, found in PMID:31899563 title)
• "adipocyte" - NEEDS CLARIFICATION - this is too broad and is already the parent term label; should be REMOVED

Validation Notes:

• "marrow adipocyte" is well-supported and appears in the de Paula & Rosen review title
• "adipocyte" alone is not an appropriate synonym - it's the parent class
• May want to search literature for additional synonyms such as:
  • "bone marrow fat cell" (potential)
  • "BMAT cell" (bone marrow adipose tissue cell - potential abbreviation)
  • "MAT adipocyte" (marrow adipose tissue adipocyte - potential)

7. Logical Relationships

Primary Relationships:

• is_a: CL:0000136 (adipocyte) - implicit via logical definition
• part_of: UBERON:0002371 (bone marrow) - definitional criterion

Logical Definition (Proposed):

EquivalentClasses(CL:XXXXXXX ObjectIntersectionOf(CL:0000136 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON:0002371)))

This follows the pattern used in CL for location-specific adipocytes (see CL:0002521 subcutaneous adipocyte, CL:0002615 visceral adipocyte).

Additional Relationships (Literature-Supported):

Based on known biology, bone marrow adipocytes may have additional relationships:

• capable_of: GO terms related to lipid storage, hematopoietic support
• has_plasma_membrane_part: Markers such as perilipin, adiponectin receptors
• These would require specific PMID support from the provided references

8. Ontology Placement Recommendation

✓ RECOMMENDED: Create in CL

Reasoning:

1. Cell Type: Bone marrow adipocytes are a naturally occurring cell type in healthy organisms
2. Not Pathological: These are normal constituents of bone marrow, not disease-associated
3. Not Cultured/Engineered: These are primary cells found in vivo
4. Precedent: CL already includes anatomically-defined adipocyte subtypes (subcutaneous, visceral)
5. Scope Alignment: Fits CL's mission to represent cell types across anatomical locations

Not CLO because:

• CLO (Cell Line Ontology) is for immortalized/cultured cell lines
• Bone marrow adipocytes are primary cells, not cell lines

9. Additional Metadata Requirements

Required for CL Integration:

• term_tracker_item: Link to GitHub issue
• date created: Current ISO 8601 timestamp
• creator: "GitHub Copilot" (for NTR terms only)
• contributor: https://orcid.org/0000-0003-0098-4399 (requester ORCID)

Cross-references:

• Research community may have existing database IDs that should be added as xrefs

10. Additional Research Needed

CRITICAL - PMID Verification:

1. PMID:31991541 - Verification attempt returned wrong article (coronavirus paper). MUST VERIFY correct PMID or remove
2. PMID:31899563 - High confidence, authoritative Annual Reviews paper
3. PMID:32286228 - High confidence, eLife single-cell study

Recommended Next Steps:

1. Verify PMIDs - Confirm all three PMIDs actually discuss bone marrow adipocytes
2. Extract definitions following CL guidelines - Use the standard LLM prompt from docs/LLM_prompt_guidelines_for_CL_definitions.md OR manually extract text from PMID:31899563 and PMID:32286228 to construct a definition that:
   • Starts with genus (adipocyte) then differentia (bone marrow location + distinguishing features)
   • Is 80-120 words in single paragraph
   • Includes inline citations for key statements
   • Mentions species-specific markers if relevant
   • Avoids redundant information already in parent class definition
3. Check for subtypes - The requester mentioned "bone marrow preadipocyte too???" - investigate if this should be a separate term
4. Marker genes - Extract key marker genes/proteins from scRNA-seq study (PMID:32286228) with species attribution
5. Functional capabilities - Determine GO terms for capable_of relationships

11. Confidence Assessment

• Term novelty: High (confirmed not in CL)
• Parent term: High (adipocyte is appropriate)
• Anatomical location: High (bone marrow is well-defined)
• Cross-references/PMIDs: MEDIUM-LOW (PMID:31991541 needs verification)
• Definition quality: Medium (needs extraction from verified sources)
• Synonym validation: Medium ("adipocyte" synonym should be removed)
• Overall: MEDIUM - Good foundation but requires PMID verification and definition construction

12. Questions for Requester/Editor

1. PMID:31991541 - Can you verify this PMID? My retrieval returned a coronavirus paper, not bone marrow adipocytes
2. Bone marrow preadipocyte - You mentioned this in "Additional notes". Should this be a separate NTR? If so, this would be a precursor cell (progenitor) rather than the mature adipocyte
3. Functional properties - Are there specific functional capabilities or markers you'd like included in the definition beyond general lipid storage?

---

RECOMMENDATION

STATUS: ADDITIONAL RESEARCH NEEDED - NOT YET READY FOR INTEGRATION

Action Items:

1. VERIFY PMID:31991541 - Critical blocker
2. CONSTRUCT DEFINITION following CL guidelines (docs/LLM_prompt_guidelines_for_CL_definitions.md):
   • Use genus-differentia structure (adipocyte + bone marrow location + distinguishing features)
   • 80-120 words, single paragraph
   • Include inline citations to verified PMIDs
   • Species-specific markers if applicable
   • Avoid redundant information from parent class
3. REMOVE "adipocyte" from synonym list
4. CLARIFY bone marrow preadipocyte question
5. VALIDATE molecular markers are cell-type specific (not broadly expressed)

Once PMIDs are verified and definition is constructed from primary sources, this term will be READY FOR CL INTEGRATION by the @CL-ontologist agent.

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Report prepared by: @CL-curator
Date: 19 December 2025

[pmaye1]

My Apologies for citing VERIFY PMID:31991541 - Critical blocker....like you, i was having AI help me generate this report for issue submission and it made some bad mistakes. This was my first time submitting an issue and incredibly happy for your relatively quick response. I have included additional PMID's for this term:
PMID: 31702948 (corrected PMID) DOI: 10.1146/annurev-physiol-021119-034513
Marrow Adipocytes: Origin, Structure, and Function
PMID: 37587198 Title: Nutrient regulation of bone marrow adipose tissue: skeletal implications of weight loss : comment - title in this paper not so informative, but contents detail bone marrow adipocyte origin.
PMID: 28872979 Title: Bone marrow adipocytes
PMID: 24998914 Title: Bone marrow adipose tissue is an endocrine organ that contributes to increased circulating adiponectin during caloric restriction.
PMID: 37315208: title: The Multifaceted Roles of Bone Marrow Adipocytes in Bone and Hematopoietic Homeostasis

The additional preadipocyte comment relates the thinking of should we also add this as a new term as well. perhaps to add clarity it should be termed "bone marrow preadipocyte." or just "marrow preadipocyte" . the pubmed id reference PMID: 37587198 provides and discusses the bone marrow adipocyte lineage and includes two additional cell types (MALP) marrow adipocyte-like progenitor and "pre-adipocyte".