Flexible Object

[GAOChengzhan]

Changes Made

• Support a more flexible way to show the object view, namely detect the built-in property called _object_spec, where the specification of the object's properties is defined, it must follow

  {
      ...
      
      _object_spec: {
          property_name: {
              view: typeName
          }
          ...
      }
  }
  

Test

The following two objects can be used for test

Object 1

const dataObject = {
    "name": "RAS and Apoptosis - Run 5-analyst_anthropic_o1-mini-h2",
    "short_text_editable": "Test short text",
    "text_long_editable": "## Hypothesis:\nRASSF7 acts as a critical host factor that facilitates dengue virus (DENV) replication by modulating the RAS signaling pathway. Upon DENV infection, the downregulation of RASSF7 disrupts normal RAS pathway regulation, thereby enhancing viral replication. Targeting RASSF7-RAS interactions may inhibit DENV replication, presenting a novel therapeutic strategy.\n\n## Reasoning:\n**Connection of Experimental Perturbations with Observed Outcomes:**\n- **siRNA Screening:** RASSF7 knockdown inhibits DENV infection (knockdown_inhibits=1), indicating that RASSF7 supports viral replication.\n- **RNAseq Data:** RASSF7 exhibits a significant downregulation of mRNA levels at 48 hours post-infection (log2FC = -2.061), suggesting that DENV infection modulates its expression.\n- **Protein-Protein Interactions:** Although not explicitly provided, integrating Shah et al.’s PPI dataset likely reveals interactions between RASSF7 and DENV proteins.\n\n**Intermediate Steps Hypothesized:**\n- **RAS Signaling Pathway Modulation:** RASSF7 is known to interact with members of the RAS family (e.g., HRAS), which play roles in cell proliferation and survival. DENV may manipulate RASSF7 to alter RAS signaling, creating a cellular environment conducive to viral replication.\n- **Feedback Mechanisms:** The downregulation of RASSF7 could lead to dysregulation of RAS activity, potentially affecting downstream effectors like RSK (RPS6KA1), which is also identified as a pro-viral factor in the study.\n\n**Specific, Quantifiable Predictions:**\n1. **Reduction in Viral Load:** Knockdown of RASSF7 will result in a measurable decrease in DENV replication compared to control.\n2. **RAS Pathway Activity:** Altered RASSF7 levels will correlate with changes in RAS pathway activity markers (e.g., phosphorylated ERK levels).\n3. **Protein Interactions:** Disruption of RASSF7-RAS interactions will impair DENV replication efficiency.\n\n**Potential Experiments to Test the Hypothesis:**\n- **Knockdown and Overexpression Studies:** Assess DENV replication rates in cells with RASSF7 knockdown versus overexpression.\n- **RAS Pathway Analysis:** Measure activity levels of key RAS pathway components following DENV infection and RASSF7 modulation.\n- **Co-Immunoprecipitation:** Validate physical interactions between RASSF7 and RAS proteins during DENV infection.\n- **Inhibitor Studies:** Use small molecule inhibitors targeting RASSF7-RAS interactions to evaluate their effect on viral replication.\n\n**Possible Alternative Outcomes and Their Interpretations:**\n- **No Change in Viral Load with RASSF7 Manipulation:** Suggests that RASSF7 may not be directly involved in DENV replication, indicating the need to explore other pathways or compensatory mechanisms.\n- **Altered RAS Activity Without Impact on Viral Replication:** Implies that RASSF7’s role in RAS signaling is independent of its pro-viral function, necessitating investigation into alternative mechanisms by which RASSF7 supports DENV.\n\n## Limitations:\n- **Correlation vs. Causation:** The observed association between RASSF7 modulation and DENV replication does not confirm a direct causal relationship without further experimental validation.\n- **Complexity of Host-Virus Interactions:** Host factors often participate in multiple pathways; thus, the specific mechanism by which RASSF7 influences DENV replication may involve additional, unidentified factors.\n- **Dataset Scope:** The provided data snippet is limited; comprehensive analysis of the entire dataset may reveal additional insights or contradict the proposed hypothesis.",
    "data": [
      ["GeneSymbol", "GeneID", "knockdown_inhibits", "rna_log2FC_48h"],
      ["BRAP", "8315.00", "1.00", ""],
      ["RASSF7", "8045.00", "1.00", "-2.06"],
      ["RASSF5", "83593.00", "1.00", ""],
      ["RCE1", "9986.00", "1.00", ""],
      ["RGL1", "23179.00", "1.00", "2.20"],
      ["RGL4", "266747.00", "1.00", ""],
      ["RPS6KA1", "6195.00", "1.00", ""],
      ["MOAP1", "64112.00", "0.00", ""],
      ["HRAS", "3265.00", "0.00", "-2.36"],
      ["RASAL1", "8437.00", "0.00", "-2.31"]
    ],
    "object_id": "agent_9e1ff1ca-4c90-40da-ba85-7adebb9c34e0",
    "object_link": "agent_9e1ff1ca-4c90-40da-ba85-7adebb9c34e0",
    "created": "09.28.2024 08:27:02",
    "list_of_text": [
      "IMPACT",
      "RPS6KA1",
      "CD44",
      "MAPK1",
      "CELP",
      "SPARC",
      "PCYT2",
      "UBE3A",
      "PODXL2",
      "NR4A2",
      "SOD1",
      "HRAS",
      "SPI1",
      "RASSF7"
    ],
    "_object_spec": {
      "documentation": "Hypotheses are the product of the analysis process. Each hypothesis object is self-contained meaning that all the information necessary to reproduce the hypothesis is stored within it. Hypotheses are importable and exportable as a JSON file.",
      "properties": {
        "name": {
          "type": "string",
          "input_type": "text",
          "view": "text"
        },
        "short_text_editable": {
          "type": "string",
          "input_type": "text",
          "view": "text"
        },
        "text_long_editable": {
          "type": "string",
          "label": "long editable text",
          "input_type": "textarea",
          "view": "text"
        },
        "data": {
          "type": "list_of_csv_rows",
          "view": "scrolling_table"
        },
        "object_id": {
          "type": "string",
          "view": "text"
        },
        "object_link": {
          "type": "string",
          "label": "object link example",
          "view": "object_link"
        },
        "list_of_text": {
          "type": "list_of_text",
          "view": "json_tree"
        }
      }
    }
  }

Object 2

const dataObject = {
  "name": "RAS and Apoptosis - Run 5-analyst_anthropic_o1-mini-h2",
  "object_id": "agent_9e1ff1ca-4c90-40da-ba85-7adebb9c34e0",
  "created": "09.28.2024 08:27:02",
  "svg": "<svg xmlns=\"http://www.w3.org/2000/svg\" width=\"100\" height=\"100\">\n  <rect width=\"100\" height=\"100\" fill=\"blue\" />\n  <text x=\"50\" y=\"50\" fill=\"white\" text-anchor=\"middle\" dominant-baseline=\"middle\">Hello!</text>\n</svg>",
  "_object_spec": {
    "documentation": "Hypotheses are the product of the analysis process. Each hypothesis object is self-contained meaning that all the information necessary to reproduce the hypothesis is stored within it. Hypotheses are importable and exportable as a JSON file.",
    "properties": {
      "name": {
        "type": "string",
        "input_type": "text",
        "view": "text"
      },
      "svg":{
          "view": "svg"
      }
    }
  }
}