KG-RELATIONSHIPS.json

{
  "items": [
    {
      "subject_entity_id": "concept:dna-replication",
      "object_entity_id": "concept:central-dogma",
      "relationship_type": "EXAMPLE_OF",
      "confidence": 0.949999988079071,
      "data": {
        "subject": "concept:dna-replication",
        "predicate": "EXAMPLE_OF",
        "object": "concept:central-dogma",
        "confidence": 0.95,
        "provenance": {
          "source_document": "CHEM 373 W26 Syllabus (Chik)",
          "section_title": "Learning Objectives",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction",
          "raw_text": "central dogma, including replication, transcription, and translation"
        },
        "notes": "Replication is explicitly listed as included in the central dogma for this course."
      }
    },
    {
      "subject_entity_id": "concept:transcription",
      "object_entity_id": "concept:central-dogma",
      "relationship_type": "EXAMPLE_OF",
      "confidence": 0.949999988079071,
      "data": {
        "subject": "concept:transcription",
        "predicate": "EXAMPLE_OF",
        "object": "concept:central-dogma",
        "confidence": 0.95,
        "provenance": {
          "source_document": "CHEM 373 W26 Syllabus (Chik)",
          "section_title": "Learning Objectives",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction",
          "raw_text": "central dogma, including replication, transcription, and translation"
        },
        "notes": "Transcription is explicitly listed as included in the central dogma for this course."
      }
    },
    {
      "subject_entity_id": "concept:translation",
      "object_entity_id": "concept:central-dogma",
      "relationship_type": "EXAMPLE_OF",
      "confidence": 0.949999988079071,
      "data": {
        "subject": "concept:translation",
        "predicate": "EXAMPLE_OF",
        "object": "concept:central-dogma",
        "confidence": 0.95,
        "provenance": {
          "source_document": "CHEM 373 W26 Syllabus (Chik)",
          "section_title": "Learning Objectives",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction",
          "raw_text": "central dogma, including replication, transcription, and translation"
        },
        "notes": "Translation is explicitly listed as included in the central dogma for this course."
      }
    },
    {
      "subject_entity_id": "concept:nucleotide",
      "object_entity_id": "concept:nucleoside",
      "relationship_type": "CONTRASTS_WITH",
      "confidence": 0.9200000166893005,
      "data": {
        "subject": "concept:nucleotide",
        "predicate": "CONTRASTS_WITH",
        "object": "concept:nucleoside",
        "confidence": 0.92,
        "provenance": {
          "source_document": "CHEM 373 course handout/slides (provided text)",
          "section_title": "Nucleosides and nucleotides only differ by the presence of phosphate",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_text",
          "raw_text": "Nucleosides and nucleotides only differ by the presence of phosphate"
        },
        "notes": "Slide explicitly contrasts nucleosides vs nucleotides by phosphate presence."
      }
    },
    {
      "subject_entity_id": "concept:prokaryotic-systems",
      "object_entity_id": "concept:eukaryotic-systems",
      "relationship_type": "CONTRASTS_WITH",
      "confidence": 0.8999999761581421,
      "data": {
        "subject": "concept:prokaryotic-systems",
        "predicate": "CONTRASTS_WITH",
        "object": "concept:eukaryotic-systems",
        "confidence": 0.9,
        "provenance": {
          "source_document": "CHEM 373 W26 Syllabus (Chik)",
          "section_title": "Learning Objectives",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction",
          "raw_text": "Compare and contrast these processes in prokaryotic and eukaryotic systems"
        },
        "notes": "The syllabus explicitly frames prokaryotic vs eukaryotic as a compare/contrast pair."
      }
    },
    {
      "subject_entity_id": "concept:deoxyribose-2prime",
      "object_entity_id": "concept:ribose",
      "relationship_type": "CONTRASTS_WITH",
      "confidence": 0.8799999952316284,
      "data": {
        "subject": "concept:deoxyribose-2prime",
        "predicate": "CONTRASTS_WITH",
        "object": "concept:ribose",
        "confidence": 0.88,
        "provenance": {
          "source_document": "CHEM 373 course handout/slides (provided text)",
          "section_title": "The pentose sugar exists as ribose or 2\u2019-deoxyribose",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_text",
          "raw_text": "The pentose sugar exists as ribose or 2\u2019-deoxyribose"
        },
        "notes": "Bidirectional contrast captured explicitly."
      }
    },
    {
      "subject_entity_id": "concept:ribose",
      "object_entity_id": "concept:deoxyribose-2prime",
      "relationship_type": "CONTRASTS_WITH",
      "confidence": 0.8799999952316284,
      "data": {
        "subject": "concept:ribose",
        "predicate": "CONTRASTS_WITH",
        "object": "concept:deoxyribose-2prime",
        "confidence": 0.88,
        "provenance": {
          "source_document": "CHEM 373 course handout/slides (provided text)",
          "section_title": "The pentose sugar exists as ribose or 2\u2019-deoxyribose",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_text",
          "raw_text": "The pentose sugar exists as ribose or 2\u2019-deoxyribose"
        },
        "notes": "Presented as two forms of pentose sugar."
      }
    },
    {
      "subject_entity_id": "concept:purine-biosynthesis",
      "object_entity_id": "concept:pyrimidine-biosynthesis",
      "relationship_type": "CONTRASTS_WITH",
      "confidence": 0.8600000143051147,
      "data": {
        "subject": "concept:purine-biosynthesis",
        "predicate": "CONTRASTS_WITH",
        "object": "concept:pyrimidine-biosynthesis",
        "confidence": 0.86,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Learning Objectives / Major differences from purine biosynthesis",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Identify the differences between purine and pyrimidine synthesis \npathways.\n...\nMajor differences from purine biosynthesis:\n\n\u2022 Fewer precursors\n\n\u2022 Base built first, then condensed with PRPP"
        },
        "notes": "Slides explicitly prompt identification of differences and list major differences."
      }
    },
    {
      "subject_entity_id": "method:thymidylate-synthase",
      "object_entity_id": "concept:dtmp",
      "relationship_type": "PRODUCES",
      "confidence": 0.8600000143051147,
      "data": {
        "subject": "method:thymidylate-synthase",
        "predicate": "PRODUCES",
        "object": "concept:dtmp",
        "confidence": 0.86,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "We cannot allow dUTP to accumulate in the cell / dTMP is synthesized from dUMP",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "thymidylate\nsynthase\n\ndTMP\n\n...\n\ndTMP is synthesized from dUMP"
        },
        "notes": "Stated that dTMP is synthesized from dUMP by thymidylate synthase."
      }
    },
    {
      "subject_entity_id": "method:thymidylate-synthase",
      "object_entity_id": "concept:dump",
      "relationship_type": "CONSUMES",
      "confidence": 0.8600000143051147,
      "data": {
        "subject": "method:thymidylate-synthase",
        "predicate": "CONSUMES",
        "object": "concept:dump",
        "confidence": 0.86,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "We cannot allow dUTP to accumulate in the cell / dTMP is synthesized from dUMP",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "thymidylate\nsynthase\n\ndTMP\n\n...\n\ndTMP is synthesized from dUMP"
        },
        "notes": "Stated that dTMP is synthesized from dUMP by thymidylate synthase."
      }
    },
    {
      "subject_entity_id": "concept:prpp",
      "object_entity_id": "concept:purine-biosynthesis",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.8500000238418579,
      "data": {
        "subject": "concept:prpp",
        "predicate": "APPLIES_TO",
        "object": "concept:purine-biosynthesis",
        "confidence": 0.85,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Purine biosynthesis requires components from many sources",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Purine biosynthesis requires components from many \nsources\n\nBuilt directly onto PRPP"
        },
        "notes": "Purine ring stated to be built directly onto PRPP."
      }
    },
    {
      "subject_entity_id": "concept:prpp",
      "object_entity_id": "concept:pyrimidine-biosynthesis",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.8399999737739563,
      "data": {
        "subject": "concept:prpp",
        "predicate": "APPLIES_TO",
        "object": "concept:pyrimidine-biosynthesis",
        "confidence": 0.84,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Pyrimidine biosynthesis only requires input from two precursor molecules",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Base is built first, then condensed with PRPP"
        },
        "notes": "Pyrimidine base is condensed with PRPP."
      }
    },
    {
      "subject_entity_id": "method:aspartate-transcarbamoylase",
      "object_entity_id": "concept:feedback-inhibition",
      "relationship_type": "EXAMPLE_OF",
      "confidence": 0.8399999737739563,
      "data": {
        "subject": "method:aspartate-transcarbamoylase",
        "predicate": "EXAMPLE_OF",
        "object": "concept:feedback-inhibition",
        "confidence": 0.84,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Feedback inhibition is an important regulator of nucleotide synthesis",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Aspartate transcarbamoylase is inhibited \nby CTP"
        },
        "notes": "ATCase inhibition by CTP is presented as an instance of feedback inhibition."
      }
    },
    {
      "subject_entity_id": "concept:air",
      "object_entity_id": "concept:inosinate-imp",
      "relationship_type": "PREREQUISITE_OF",
      "confidence": 0.8299999833106995,
      "data": {
        "subject": "concept:air",
        "predicate": "PREREQUISITE_OF",
        "object": "concept:inosinate-imp",
        "confidence": 0.83,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Part II: Generating the 6-membered ring",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "AIR + CO2 + Aspartate \n+ Formate + ATP \u2192 \nInosinate (IMP)"
        },
        "notes": "AIR is an input for the reaction producing IMP."
      }
    },
    {
      "subject_entity_id": "concept:folate",
      "object_entity_id": "concept:purine-biosynthesis",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.8199999928474426,
      "data": {
        "subject": "concept:folate",
        "predicate": "APPLIES_TO",
        "object": "concept:purine-biosynthesis",
        "confidence": 0.82,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Glutamine and folate are other common players in purine and pyrimidine synthesis",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Glutamine and folate are other common players in purine \nand pyrimidine synthesis"
        },
        "notes": "Folate is described as common to purine and pyrimidine synthesis."
      }
    },
    {
      "subject_entity_id": "concept:folate",
      "object_entity_id": "concept:pyrimidine-biosynthesis",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.8199999928474426,
      "data": {
        "subject": "concept:folate",
        "predicate": "APPLIES_TO",
        "object": "concept:pyrimidine-biosynthesis",
        "confidence": 0.82,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Glutamine and folate are other common players in purine and pyrimidine synthesis",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Glutamine and folate are other common players in purine \nand pyrimidine synthesis"
        },
        "notes": "Folate is described as common to purine and pyrimidine synthesis."
      }
    },
    {
      "subject_entity_id": "concept:glutamine",
      "object_entity_id": "concept:purine-biosynthesis",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.8199999928474426,
      "data": {
        "subject": "concept:glutamine",
        "predicate": "APPLIES_TO",
        "object": "concept:purine-biosynthesis",
        "confidence": 0.82,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Glutamine and folate are other common players in purine and pyrimidine synthesis",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Glutamine and folate are other common players in purine \nand pyrimidine synthesis"
        },
        "notes": "Glutamine is described as common to purine and pyrimidine synthesis."
      }
    },
    {
      "subject_entity_id": "concept:glutamine",
      "object_entity_id": "concept:pyrimidine-biosynthesis",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.8199999928474426,
      "data": {
        "subject": "concept:glutamine",
        "predicate": "APPLIES_TO",
        "object": "concept:pyrimidine-biosynthesis",
        "confidence": 0.82,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Glutamine and folate are other common players in purine and pyrimidine synthesis",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Glutamine and folate are other common players in purine \nand pyrimidine synthesis"
        },
        "notes": "Glutamine is described as common to purine and pyrimidine synthesis."
      }
    },
    {
      "subject_entity_id": "concept:ctp",
      "object_entity_id": "method:aspartate-transcarbamoylase",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.800000011920929,
      "data": {
        "subject": "concept:ctp",
        "predicate": "APPLIES_TO",
        "object": "method:aspartate-transcarbamoylase",
        "confidence": 0.8,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Feedback inhibition is an important regulator of nucleotide synthesis",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Aspartate transcarbamoylase is inhibited \nby CTP"
        },
        "notes": "CTP is stated as inhibiting ATCase (modeled as applies_to due to limited predicate set)."
      }
    },
    {
      "subject_entity_id": "concept:inosinate-imp",
      "object_entity_id": "concept:amp",
      "relationship_type": "PREREQUISITE_OF",
      "confidence": 0.7799999713897705,
      "data": {
        "subject": "concept:inosinate-imp",
        "predicate": "PREREQUISITE_OF",
        "object": "concept:amp",
        "confidence": 0.78,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Part II: Generating the 6-membered ring",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Inosine \u2013 \nour precursor to AMP and GMP"
        },
        "notes": "IMP stated as precursor to AMP."
      }
    },
    {
      "subject_entity_id": "concept:inosinate-imp",
      "object_entity_id": "concept:gmp",
      "relationship_type": "PREREQUISITE_OF",
      "confidence": 0.7799999713897705,
      "data": {
        "subject": "concept:inosinate-imp",
        "predicate": "PREREQUISITE_OF",
        "object": "concept:gmp",
        "confidence": 0.78,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Part II: Generating the 6-membered ring",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Inosine \u2013 \nour precursor to AMP and GMP"
        },
        "notes": "IMP stated as precursor to GMP."
      }
    },
    {
      "subject_entity_id": "method:nanodrop",
      "object_entity_id": "concept:uv-absorbance-260nm",
      "relationship_type": "APPLIES_TO",
      "confidence": 0.7799999713897705,
      "data": {
        "subject": "method:nanodrop",
        "predicate": "APPLIES_TO",
        "object": "concept:uv-absorbance-260nm",
        "confidence": 0.78,
        "provenance": {
          "source_document": "CHEM 373 course handout/slides (provided text)",
          "section_title": "Nucleotide bases absorb UV light at 260 nm",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_text",
          "raw_text": "Nucleotide bases absorb UV light at 260 nm ... Useful for quantification and analysis of purity for nucleic acids (NanoDrop)"
        },
        "notes": "NanoDrop mentioned in context of using A260 for quantification/purity."
      }
    },
    {
      "subject_entity_id": "concept:dutp",
      "object_entity_id": "concept:dump",
      "relationship_type": "CONTRASTS_WITH",
      "confidence": 0.7400000095367432,
      "data": {
        "subject": "concept:dutp",
        "predicate": "CONTRASTS_WITH",
        "object": "concept:dump",
        "confidence": 0.74,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "We cannot allow dUTP to accumulate in the cell",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "We cannot allow dUTP to accumulate in the cell\n...\ndUTPase\n\n... dUMP"
        },
        "notes": "Slides emphasize preventing dUTP accumulation and show diversion to dUMP; modeled as contrast in outcomes."
      }
    },
    {
      "subject_entity_id": "method:ribonucleotide-reductase",
      "object_entity_id": "concept:dctp",
      "relationship_type": "PRODUCES",
      "confidence": 0.699999988079071,
      "data": {
        "subject": "method:ribonucleotide-reductase",
        "predicate": "PRODUCES",
        "object": "concept:dctp",
        "confidence": 0.7,
        "provenance": {
          "source_document": "Nucleotide Biosynthesis (slides text provided by user)",
          "section_title": "Making dCTP",
          "page_number": null,
          "extraction_timestamp": "2026-02-22T00:00:00Z",
          "extraction_method": "manual_extraction_from_user_provided_text",
          "raw_text": "Making dCTP\n...\n... dCDP\n\ndCTP\n\n... ribonucleotide \nreductase ..."
        },
        "notes": "Diagram places ribonucleotide reductase in the pathway leading to dCTP (via dCDP)."
      }
    }
  ],
  "total": 24,
  "limit": 1000,
  "offset": 0
}