test.jsonld

{
  "@context": {
    "@version": 1.1,
    "marr": "http://bbqs-project.org/ontology/marr#",
    "uberon": "http://purl.obolibrary.org/obo/UBERON_",
    "cl": "http://purl.obolibrary.org/obo/CL_",
    "go": "http://purl.obolibrary.org/obo/GO_",
    "ncit": "http://purl.obolibrary.org/obo/NCIT_",
    "prov": "http://www.w3.org/ns/prov#"
  },
  "@type": "marr:NeuroscienceExtraction",
  "marr:paper_id": "DOI:10.xxxx/xxxxx",
  "marr:paper_title": "Extracted Paper Title",
  "marr:extraction_date": "2025-12-21T13:51:04.869884",
  "marr:schema_version": "2.0",
  "marr:entities_by_level": {
    "L1_computational": [
      {
        "entity": "photoreceptor cell maintenance",
        "label": "biological process",
        "marr_level": "L1",
        "ontology_id": "GO:0042463",
        "ontology_label": "photoreceptor cell maintenance",
        "marr_rationale": "The entity 'photoreceptor cell maintenance' refers to the process of maintaining photoreceptor cells, which is a computational goal. It describes what is being computed, which is the maintenance of photoreceptor cells.",
        "context_sentences": [
          "The photoreceptor cell maintenance is crucial for vision."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the computational level."
          ]
        }
      },
      {
        "entity": "color sensitivity",
        "label": "biological process",
        "marr_level": "L1",
        "ontology_id": "GO:0050908",
        "ontology_label": "detection of visual stimuli",
        "marr_rationale": "The entity 'color sensitivity' refers to the ability to detect different colors, which is a computational goal. It describes what is being computed, which is the detection of colors.",
        "context_sentences": [
          "The color sensitivity is an important aspect of vision."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.8
          ],
          "remarks": [
            "The entity is relevant to the computational level, but the definition could be more specific."
          ]
        }
      },
      {
        "entity": "vision",
        "label": "biological process",
        "marr_level": "L1",
        "ontology_id": "GO:0007601",
        "ontology_label": "visual perception",
        "marr_rationale": "The entity 'vision' refers to the ability to see, which is a computational goal. It describes what is being computed, which is the interpretation of visual information.",
        "context_sentences": [
          "The vision is a complex process that involves multiple stages."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.8
          ],
          "remarks": [
            "The entity is relevant to the computational level, but the definition could be more specific."
          ]
        }
      },
      {
        "entity": "photopic spectral sensitivity",
        "label": "biological process",
        "marr_level": "L1",
        "ontology_id": "GO:0050911",
        "ontology_label": "detection of light intensity",
        "marr_rationale": "The entity 'photopic spectral sensitivity' refers to the sensitivity of photoreceptors to different wavelengths of light, which is a computational goal. It describes what is being computed, which is the sensitivity of photoreceptors to light.",
        "context_sentences": [
          "The photopic spectral sensitivity is important for color vision."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.8
          ],
          "remarks": [
            "The entity is relevant to the computational level, but the definition could be more specific."
          ]
        }
      }
    ],
    "L2_algorithmic": [
      {
        "entity": "electroretinogram (ERG)",
        "label": "method",
        "marr_level": "L2",
        "ontology_id": "EFO:0004157",
        "ontology_label": "electroretinogram",
        "marr_rationale": "The entity 'electroretinogram (ERG)' refers to a method for measuring the electrical activity of the retina, which is an algorithmic level. It describes how the electrical activity is being measured, which is through the use of an electroretinogram.",
        "context_sentences": [
          "The electroretinogram is a useful tool for diagnosing retinal disorders."
        ],
        "paper_location": [
          "Methods"
        ],
        "provenance": {
          "judge_score": [
            0.8
          ],
          "remarks": [
            "The entity is relevant to the algorithmic level, but the definition could be more specific."
          ]
        }
      },
      {
        "entity": "scotopic ERG",
        "label": "method",
        "marr_level": "L2",
        "ontology_id": "EFO:0004160",
        "ontology_label": "scotopic electroretinogram",
        "marr_rationale": "The entity 'scotopic ERG' refers to a method for measuring the electrical activity of the retina under low-light conditions, which is an algorithmic level. It describes how the electrical activity is being measured, which is through the use of a scotopic electroretinogram.",
        "context_sentences": [
          "The scotopic ERG is used to measure the rod cell function."
        ],
        "paper_location": [
          "Methods"
        ],
        "provenance": {
          "judge_score": [
            0.8
          ],
          "remarks": [
            "The entity is relevant to the algorithmic level, but the definition could be more specific."
          ]
        }
      },
      {
        "entity": "photopic ERG",
        "label": "method",
        "marr_level": "L2",
        "ontology_id": "EFO:0004159",
        "ontology_label": "photopic electroretinogram",
        "marr_rationale": "The entity 'photopic ERG' refers to a method for measuring the electrical activity of the retina under high-light conditions, which is an algorithmic level. It describes how the electrical activity is being measured, which is through the use of a photopic electroretinogram.",
        "context_sentences": [
          "The photopic ERG is used to measure the cone cell function."
        ],
        "paper_location": [
          "Methods"
        ],
        "provenance": {
          "judge_score": [
            0.8
          ],
          "remarks": [
            "The entity is relevant to the algorithmic level, but the definition could be more specific."
          ]
        }
      }
    ],
    "L3_implementational": [
      {
        "entity": "retina",
        "label": "anatomical structure",
        "marr_level": "L3",
        "ontology_id": "UBERON:0000970",
        "ontology_label": "retina",
        "marr_rationale": "The entity 'retina' refers to the physical structure of the retina, which is an implementational level. It describes the physical substrate where the computation is taking place.",
        "context_sentences": [
          "The retina is a complex tissue that consists of multiple layers."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      },
      {
        "entity": "rods",
        "label": "cell type",
        "marr_level": "L3",
        "ontology_id": "CL:0000572",
        "ontology_label": "rod cell",
        "marr_rationale": "The entity 'rods' refers to a type of photoreceptor cell in the retina, which is an implementational level. It describes the physical components that are responsible for detecting light.",
        "context_sentences": [
          "The rods are sensitive to low light levels and are responsible for peripheral vision."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      },
      {
        "entity": "cones",
        "label": "cell type",
        "marr_level": "L3",
        "ontology_id": "CL:0000573",
        "ontology_label": "cone cell",
        "marr_rationale": "The entity 'cones' refers to a type of photoreceptor cell in the retina, which is an implementational level. It describes the physical components that are responsible for detecting color.",
        "context_sentences": [
          "The cones are sensitive to different wavelengths of light and are responsible for color vision."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      },
      {
        "entity": "photoreceptors",
        "label": "cell type",
        "marr_level": "L3",
        "ontology_id": "CL:0000066",
        "ontology_label": "photoreceptor cell",
        "marr_rationale": "The entity 'photoreceptors' refers to the cells in the retina that are responsible for detecting light, which is an implementational level. It describes the physical components that are responsible for detecting light.",
        "context_sentences": [
          "The photoreceptors are specialized cells that convert light into electrical signals."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      },
      {
        "entity": "rhodopsin",
        "label": "protein",
        "marr_level": "L3",
        "ontology_id": "PR:000021534",
        "ontology_label": "rhodopsin",
        "marr_rationale": "The entity 'rhodopsin' refers to a protein in photoreceptor cells that is responsible for detecting light, which is an implementational level. It describes the physical components that are responsible for detecting light.",
        "context_sentences": [
          "The rhodopsin is a crucial protein for vision and is found in rod cells."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      },
      {
        "entity": "UV cones",
        "label": "cell type",
        "marr_level": "L3",
        "ontology_id": "CL:0001034",
        "ontology_label": "ultraviolet-sensitive cone cell",
        "marr_rationale": "The entity 'UV cones' refers to a type of cone cell in the retina that is sensitive to ultraviolet light, which is an implementational level. It describes the physical components that are responsible for detecting ultraviolet light.",
        "context_sentences": [
          "The UV cones are found in some species and are responsible for detecting ultraviolet light."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      },
      {
        "entity": "M cones",
        "label": "cell type",
        "marr_level": "L3",
        "ontology_id": "CL:0001035",
        "ontology_label": "medium-wavelength-sensitive cone cell",
        "marr_rationale": "The entity 'M cones' refers to a type of cone cell in the retina that is sensitive to medium-wavelength light, which is an implementational level. It describes the physical components that are responsible for detecting medium-wavelength light.",
        "context_sentences": [
          "The M cones are found in the human retina and are responsible for detecting green light."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      },
      {
        "entity": "brain",
        "label": "anatomical structure",
        "marr_level": "L3",
        "ontology_id": "UBERON:0000955",
        "ontology_label": "brain",
        "marr_rationale": "The entity 'brain' refers to the physical structure of the brain, which is an implementational level. It describes the physical substrate where the computation is taking place.",
        "context_sentences": [
          "The brain is a complex organ that consists of multiple regions."
        ],
        "paper_location": [
          "Introduction"
        ],
        "provenance": {
          "judge_score": [
            0.9
          ],
          "remarks": [
            "The entity is well-defined and relevant to the implementational level."
          ]
        }
      }
    ]
  }
}