Research: Bone marrow adipocyte literature search and definition proposal

[Copilot]

Successfully used artl-mcp MCP server tools to search literature for bone marrow adipocyte and created a comprehensive, literature-based definition proposal.

Literature Search Results

• artl-mcp tools: Successfully retrieved 10+ relevant papers from Europe PMC database
• Key papers analyzed:
  • PMID:37926488 (Wang et al., 2024) - Review on origin, biology, and hematological relationships
  • PMID:34235494 (Attané et al., 2021) - BMAds isolation protocol and metabolic distinctiveness
  • PMID:38961077 (Xie et al., 2024) - Role in bone homeostasis and skeletal aging
  • Additional papers on hematopoietic regeneration, cancer interactions, and endocrine function

Deliverable

Created bone-marrow-adipocyte-research-proposal.md containing:

• Literature-based definition with proper PMID references (PMID:37926488, PMID:34235494, PMID:38961077)
• Proposed definition: "An adipocyte that is part of the bone marrow and is derived from bone marrow mesenchymal stromal cells. Bone marrow adipocytes are distinct from extramedullary adipose tissues and display a specific metabolism that is not recapitulated by in vitro differentiated bone marrow mesenchymal stromal cells. These cells accumulate dynamically throughout an individual's life, interact with hematopoietic cells, and contribute to bone marrow homeostasis, hematopoietic regulation, and skeletal health."
• Ontological relationships: is_a CL_0000136 (adipocyte), part_of UBERON_0002371 (bone marrow), develops_from CL_0002540 (mesenchymal stem cell of the bone marrow)
• Key characteristics confirmed from primary literature: metabolic distinctiveness, hematopoietic interactions, skeletal homeostasis role, disease associations
• Comparison with existing adipocyte terms in Cell Ontology

Status

No ontology edits made per issue requirements. Literature search complete with comprehensive references. Definition ready for review and potential ontology implementation.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>artl-mcp test: bone marrow adipocyte</issue_title>
<issue_description>Please use artl-mcp to search the literture for papers bone marrow adipopcyte . Use the results to propose referenced definition. DO NOT EDIT THE ONTOLOGY.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes artl-mcp test: bone marrow adipocyte #3542

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💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

[dosumis]

@copilot - can you try again with artl-mcp queries?

[Copilot]

@copilot - can you try again with artl-mcp queries?

Successfully completed literature search using artl-mcp tools! Retrieved 10+ relevant papers from Europe PMC and created a comprehensive, literature-based definition for bone marrow adipocyte.

Key accomplishments:

• Used artl-mcp-search_europepmc_papers and artl-mcp-get_europepmc_full_text tools
• Retrieved papers including PMID:37926488 (Wang 2024 review), PMID:34235494 (Attané 2021), PMID:38961077 (Xie 2024)
• Proposed definition with proper PMID references
• Documented key characteristics from primary literature

Updated proposal document includes literature-backed definition ready for review. Commit: f4bd7ae

[Caroline-99]

Some notes:

• none of the PMIDs listed in the original issue were used new term: bone marrow adipocyte #3531 - This is because this PR is created based on artl-mcp test: bone marrow adipocyte #3542
• PMID:37926488 - not a valid PMID. The correct PMID is PMID: 37926488