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# GeneLab Knowledge Graph: Assay Node Exploration ## Chat Transcript **Date:** December 11, 2025 **Topic:** Understanding the Assay node structure in the GeneLab SPARQL endpoint **Focus:** Space flight vs ground control comparisons --- ### User Query > Describe the Assay node and its properties in @genelab-remote-cypher, and include an example for a space flight vs ground control comparison. --- ### Claude's Investigation Process #### Step 1: Schema Discovery First, I retrieved the complete schema to understand the GeneLab knowledge graph structure. **Key Findings:** - **7 Classes** including Assay, Gene, Study, Mission, Anatomy, CellType, and MethylationRegion - **40 Predicates** defining relationships and properties - Assay class URI: `http://purl.obolibrary.org/obo/OBI_0000070` #### Step 2: Understanding Assay Properties The Assay node has the following property categories: **Experimental Design Properties:** - `factor_space_1`: Primary experimental grouping (e.g., "Space Flight") - `factor_space_2`: Secondary experimental grouping (e.g., "Ground Control") - `factors_1`: Primary experimental factors (array) - `factors_2`: Secondary experimental factors (array) **Biological Material Properties:** - `material_1` / `material_2`: Biological material names - `material_name_1` / `material_name_2`: Ontology-based material names - `material_id_1` / `material_id_2`: Controlled ontology identifiers (UBERON codes) **Methodology Properties:** - `measurement`: Type of data produced (e.g., "transcription profiling") - `technology`: Platform/method used (e.g., "RNA Sequencing (RNA-Seq)") **Organism Information:** - `organism`: NCBI scientific organism name - `taxonomy`: NCBI taxonomy ID #### Step 3: Exploring Relationships The Assay node connects to other entities through: 1. **INVESTIGATED_ASiA** → Anatomical entities 2. **INVESTIGATED_ASiCT** → Cell types 3. **MEASURED_DIFFERENTIAL_EXPRESSION_ASmMG** → Genes (with edge properties) 4. **MEASURED_DIFFERENTIAL_METHYLATION_ASmMR** → Methylation regions 5. **PERFORMED_SpAS** ← Studies (inverse relationship) #### Step 4: Finding Real Data I queried for actual space flight vs ground control comparisons and found multiple assays. --- ### Example Analysis: Space Flight Effects on Mouse Eye **Assay Details:** - **ID:** OSD-100-f1b7f0b93f8d28bc606c5c1127f2d7c9 - **Study:** OSD-100 - **Label:** OSD-100_transcription-profiling_rna-sequencing-(rna-seq) **Experimental Parameters:** ``` Organism: Mus musculus (mouse) Tissue: Left eye (UBERON:0004548) Technology: RNA Sequencing (RNA-Seq) Measurement Type: Transcription profiling Comparison: Space Flight vs Ground Control ``` **Differential Expression Results:** | Gene Symbol | Gene Name | Log2FC | Adj. P-value | Regulation | |-------------|-----------|--------|--------------|------------| | Apol9b | Apolipoprotein L9b | +1.83 | 0.011 | ↑ Up in space | | Apol9a | Apolipoprotein L9a | +1.79 | 0.002 | ↑ Up in space | | Oas2 | 2'-5'-oligoadenylate synthetase 2 | +1.74 | 0.002 | ↑ Up in space | | Oas3 | 2'-5'-oligoadenylate synthetase 3 | +1.56 | 0.006 | ↑ Up in space | | Sst | Somatostatin | +1.52 | 2.3×10⁻⁶ | ↑ Up in space | | Oas1a | 2'-5'-oligoadenylate synthetase 1A | +1.52 | 0.0006 | ↑ Up in space | | Fbp2 | Fructose-bisphosphatase 2 | -1.30 | 0.039 | ↓ Down in space | | Spink7 | Serine peptidase inhibitor, Kazal type 7 | +1.26 | 0.012 | ↑ Up in space | | Pln | Phospholamban | -1.16 | 0.003 | ↓ Down in space | | Colq | Collagen-like tail subunit | -1.15 | 0.039 | ↓ Down in space | **Biological Interpretation:** The differential expression pattern reveals several key responses to spaceflight in mouse eye tissue: 1. **Immune/Stress Response Activation:** - Multiple oligoadenylate synthetases (Oas1a, Oas2, Oas3) are significantly up-regulated - These enzymes are part of the interferon-mediated antiviral response - Suggests activation of innate immune pathways 2. **Lipid Metabolism Changes:** - Apolipoprotein L family members (Apol9a, Apol9b) show strong up-regulation - May indicate alterations in lipid transport or cellular stress responses 3. **Metabolic Adjustments:** - Fbp2 (gluconeogenesis enzyme) is down-regulated - Could reflect changes in energy metabolism under microgravity 4. **Regulatory Changes:** - Somatostatin (Sst) up-regulation suggests neuroendocrine signaling changes - Phospholamban (Pln) down-regulation may affect calcium handling --- ### Additional Example Assays Found The knowledge graph contains multiple comparative assays: 1. **OSD-100** (Eye tissue, RNA-Seq) - Space Flight vs Ground Control comparison - Ground Control vs Space Flight comparison (reciprocal) 2. **OSD-101** (Gastrocnemius muscle, RNA-Seq) - Multiple assays comparing Space Flight and Ground Control - Different tissues allow cross-tissue comparison of spaceflight effects --- ### Technical Notes on Data Structure **Edge Properties:** The differential expression data uses RDF reification, where properties like `log2fc` and `adj_p_value` are attached to the relationship (edge) between the Assay and Gene, not to the Gene node itself. **SPARQL Pattern for Querying Differential Expression:** ```sparql SELECT ?gene ?symbol ?log2fc ?adj_p_value WHERE { ?stmt a rdf:Statement . ?stmt rdf:subject <ASSAY_URI> . ?stmt rdf:predicate schema:MEASURED_DIFFERENTIAL_EXPRESSION_ASmMG . ?stmt rdf:object ?gene . ?stmt schema:log2fc ?log2fc . ?stmt schema:adj_p_value ?adj_p_value . ?gene schema:symbol ?symbol . } ``` --- ### Summary The GeneLab knowledge graph provides a rich, interconnected dataset for studying molecular responses to spaceflight. The Assay node serves as the central hub connecting: - Experimental design metadata - Biological samples and anatomical context - Molecular measurements (gene expression, methylation) - Statistical results (fold changes, significance values) - Study and mission context This structure enables systematic cross-study comparisons and meta-analyses of spaceflight biology. --- **End of Transcript**