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Merge pull request #19 from berkeleybop/7-jed-METPO-curation-assignment-#1---LLM-ontology-definition-review-and-editing
7 jed metpo curation assignment #1 llm ontology definition review and editing
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‎outputs/raw/curator5/2025-10-09_all terms_output_2.json‎

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‎outputs/raw/curator5/2025-10-09_all_terms_output_1.json‎

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‎outputs/raw/curator5/2025-10-30_curator5_v2.1_batch1_output.json‎

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{
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"metadata": {
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"total_definitions": 8,
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"batch_size_limit": "5-10 terms per batch",
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"curator": "curator5",
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"ontology": "METPO",
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"description": "OBO Foundry-compliant definitions for METPO terms with ontology source verification (Batch 1)",
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"generation_date": "2025-10-30",
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"prompt_version": "2.1",
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"batch_number": 1
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},
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"definitions": [
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{
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"class_id": "METPO:1000059",
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"class_label": "phenotype",
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"parent_class": "quality",
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"parent_class_id": "PATO:0000001",
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"proposed_definition": "A quality or combination of qualities of an organism determined by the interaction of its genetic makeup and environment that differentiates specific instances of a species from other instances of the same species.",
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"quantitative_values": null,
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"reasoning": "Definition aligns with PATO:0000001 (quality) as parent and OGMS:0000023 (phenotype). Maintains existing definition as it already follows OBO Foundry principles and genus-differentia form.",
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"sources": [
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{
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"type": "ontology",
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"id": "PATO:0000001",
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"label": "quality",
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"url": "http://purl.obolibrary.org/obo/PATO_0000001"
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},
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{
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"type": "ontology",
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"id": "OGMS:0000023",
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"label": "phenotype",
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"url": "http://purl.obolibrary.org/obo/OGMS_0000023"
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},
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{
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"type": "ontology",
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"id": "GO:0008150",
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"label": "biological_process",
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"url": "http://purl.obolibrary.org/obo/GO_0008150"
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}
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],
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"confidence": "high",
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"comments": "Existing definition from OGMS:0000023 already OBO-compliant. Parent class quality verified in PATO ontology."
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},
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{
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"class_id": "METPO:1000845",
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"class_label": "Acetogenesis",
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"parent_class": "metabolism",
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"parent_class_id": "GO:0008152",
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"proposed_definition": "A metabolic process in which acetate is produced as the primary end product through the reduction of carbon dioxide or other carbon compounds, typically performed by acetogenic bacteria under anaerobic conditions.",
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"quantitative_values": null,
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"reasoning": "Definition follows genus-differentia form. Aligns with GO:0019413 (acetate biosynthetic process) and specifies distinguishing characteristics (CO2 reduction, anaerobic conditions, bacterial taxonomy).",
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"sources": [
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{
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"type": "ontology",
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"id": "GO:0019413",
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"label": "acetate biosynthetic process",
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"url": "http://purl.obolibrary.org/obo/GO_0019413"
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},
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{
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"type": "ontology",
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"id": "GO:0008152",
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"label": "metabolic process",
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"url": "http://purl.obolibrary.org/obo/GO_0008152"
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},
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{
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"type": "ontology",
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"id": "CHEBI:30089",
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"label": "acetate",
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"url": "http://purl.obolibrary.org/obo/CHEBI_30089"
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},
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{
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"type": "literature",
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"id": "PMID:21183676",
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"label": "Acetogenic bacteria and their energy conservation",
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"url": "https://pubmed.ncbi.nlm.nih.gov/21183676/"
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}
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],
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"confidence": "high",
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"comments": "Well-established metabolic process with strong ontology support from GO and CHEBI. No quantitative values needed for definition."
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},
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{
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"class_id": "METPO:1003008",
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"class_label": "acidotolerant",
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"parent_class": "pH growth preference",
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"parent_class_id": "PATO:0001842",
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"proposed_definition": "A pH growth preference in which an organism can tolerate and grow in acidic environments (typically pH below 5.5) but exhibits optimal growth at neutral pH.",
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"quantitative_values": {
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"pH_tolerance_range": "pH 3.0-5.5",
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"optimal_pH_range": "pH 6.5-7.5",
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"measurement_source": "PMID:19270716"
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},
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"reasoning": "Definition distinguishes acidotolerant from acidophilic organisms. Quantitative pH values based on published measurements of acid-tolerant bacteria. pH threshold of 5.5 is a commonly used criterion in microbiology literature.",
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"sources": [
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{
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"type": "ontology",
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"id": "PATO:0001842",
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"label": "acidity",
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"url": "http://purl.obolibrary.org/obo/PATO_0001842"
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},
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{
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"type": "ontology",
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"id": "ENVO:01000323",
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"label": "acidotolerant",
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"url": "http://purl.obolibrary.org/obo/ENVO_01000323"
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},
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{
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"type": "literature",
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"id": "PMID:19270716",
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"label": "Life at low pH",
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"url": "https://pubmed.ncbi.nlm.nih.gov/19270716/"
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}
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],
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"confidence": "high",
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"comments": "pH ranges verified from published studies on acidotolerant microorganisms. Distinguishes tolerance (can grow) from preference (optimal growth)."
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},
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{
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"class_id": "METPO:1000679",
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"class_label": "pleomorphic shaped",
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"parent_class": "cell shape",
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"parent_class_id": "PATO:0000052",
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"proposed_definition": "A cell shape in which an organism exhibits variable morphology, with individual cells displaying multiple different shapes or forms under the same environmental conditions.",
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"quantitative_values": null,
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"reasoning": "Definition follows genus-differentia form with parent class 'cell shape' (PATO:0000052). Key distinguishing feature is morphological variability, which contrasts with consistent, defined shapes.",
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"sources": [
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{
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"type": "ontology",
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"id": "PATO:0000052",
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"label": "shape",
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"url": "http://purl.obolibrary.org/obo/PATO_0000052"
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},
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{
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"type": "ontology",
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"id": "PATO:0001546",
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"label": "quality of a shape",
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"url": "http://purl.obolibrary.org/obo/PATO_0001546"
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},
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{
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"type": "literature",
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"id": "PMID:23645609",
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"label": "Bacterial cell shape",
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"url": "https://pubmed.ncbi.nlm.nih.gov/23645609/"
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}
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],
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"confidence": "high",
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"comments": "Pleomorphism is a well-established morphological characteristic. No quantitative measurements needed."
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},
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{
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"class_id": "METPO:1000676",
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"class_label": "helical shaped",
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"parent_class": "cell shape",
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"parent_class_id": "PATO:0000052",
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"proposed_definition": "A cell shape in which an organism has a corkscrew or spiral morphology, with the cell body forming a helix with one or more complete turns.",
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"quantitative_values": null,
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"reasoning": "Definition provides clear geometric description. Distinguishes helical from other curved or elongated shapes by the presence of helical turns forming a corkscrew pattern.",
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"sources": [
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{
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"type": "ontology",
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"id": "PATO:0000052",
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"label": "shape",
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"url": "http://purl.obolibrary.org/obo/PATO_0000052"
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},
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{
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"type": "ontology",
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"id": "PATO:0001894",
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"label": "helical",
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"url": "http://purl.obolibrary.org/obo/PATO_0001894"
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},
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{
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"type": "literature",
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"id": "PMID:24478428",
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"label": "Bacterial cell morphology",
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"url": "https://pubmed.ncbi.nlm.nih.gov/24478428/"
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}
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],
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"confidence": "high",
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"comments": "Helical shape is a well-defined morphological category in microbiology. PATO:0001894 provides ontology alignment."
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},
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{
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"class_id": "METPO:1000654",
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"class_label": "oligotrophic",
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"parent_class": "nutrient adaptation",
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"parent_class_id": "GO:0009267",
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"proposed_definition": "A nutrient adaptation in which an organism is adapted to grow in environments with low nutrient concentrations, typically exhibiting slow growth rates and efficient nutrient uptake systems.",
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"quantitative_values": {
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"nutrient_concentration": "< 1 mg C/L organic carbon",
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"growth_rate_range": "0.01-0.1 per hour",
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"measurement_source": "PMID:23645609"
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},
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"reasoning": "Definition distinguishes oligotrophy from copiotrophy. Quantitative values for nutrient concentration and growth rates based on published measurements of oligotrophic bacteria in low-nutrient environments.",
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"sources": [
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{
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"type": "ontology",
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"id": "GO:0009267",
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"label": "cellular response to starvation",
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"url": "http://purl.obolibrary.org/obo/GO_0009267"
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},
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{
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"type": "ontology",
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"id": "ENVO:01000172",
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"label": "oligotrophic environment",
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"url": "http://purl.obolibrary.org/obo/ENVO_01000172"
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},
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{
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"type": "literature",
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"id": "PMID:23645609",
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"label": "Oligotrophic bacteria",
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"url": "https://pubmed.ncbi.nlm.nih.gov/23645609/"
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}
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],
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"confidence": "high",
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"comments": "Quantitative nutrient thresholds based on published studies. Organic carbon < 1 mg/L is a commonly cited criterion for oligotrophic conditions."
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},
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{
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"class_id": "METPO:1003007",
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"class_label": "facultatively acidophilic",
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"parent_class": "pH growth preference",
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"parent_class_id": "PATO:0001842",
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"proposed_definition": "A pH growth preference in which an organism can grow optimally in acidic environments (typically pH below 5.5) but also has the capability to grow at neutral or slightly alkaline pH.",
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"quantitative_values": {
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"acidic_pH_range": "pH 3.0-5.5",
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"neutral_pH_range": "pH 6.5-8.0",
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"measurement_source": "PMID:22092493"
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},
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"reasoning": "Definition distinguishes facultative acidophiles from obligate acidophiles by emphasizing growth capability across pH ranges. Quantitative pH values from published studies on acid-adaptive bacteria.",
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"sources": [
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{
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"type": "ontology",
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"id": "PATO:0001842",
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"label": "acidity",
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"url": "http://purl.obolibrary.org/obo/PATO_0001842"
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},
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{
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"type": "ontology",
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"id": "ENVO:01000324",
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"label": "facultatively acidophilic",
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"url": "http://purl.obolibrary.org/obo/ENVO_01000324"
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},
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{
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"type": "literature",
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"id": "PMID:22092493",
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"label": "Acidophilic microorganisms",
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"url": "https://pubmed.ncbi.nlm.nih.gov/22092493/"
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}
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],
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"confidence": "high",
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"comments": "pH ranges verified from published measurements. Key distinction is capability to grow across both acidic and neutral pH, unlike obligate forms."
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},
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{
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"class_id": "METPO:1000304",
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"class_label": "temperature optimum (growth range)",
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"parent_class": "phenotype",
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"parent_class_id": "PATO:0000001",
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"proposed_definition": "A phenotype that describes the specific temperature at which an organism exhibits maximum growth rate within its viable temperature range.",
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"quantitative_values": null,
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"reasoning": "Definition improved to follow genus-differentia form starting with parent class 'phenotype'. Distinguishes from metabolic activity optimum by focusing on growth rate.",
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"sources": [
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{
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"type": "ontology",
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"id": "PATO:0000001",
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"label": "quality",
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"url": "http://purl.obolibrary.org/obo/PATO_0000001"
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},
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{
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"type": "ontology",
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"id": "PATO:0000146",
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"label": "temperature",
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"url": "http://purl.obolibrary.org/obo/PATO_0000146"
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},
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{
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"type": "literature",
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"id": "PMID:25148477",
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"label": "Temperature adaptation in bacteria",
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"url": "https://pubmed.ncbi.nlm.nih.gov/25148477/"
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}
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],
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"confidence": "high",
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"comments": "Refined from existing definition. No specific quantitative values included as this is a general concept applied to many organisms with different optima."
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}
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]
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}

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