[
{
"id": "GERG-CIDM-001",
"source_question_id": "UQG-006",
"question": "Why is the Influenza / respiratory viruses × Whole-genome sequencing relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "SUBSTANTIALLY_RESOLVED_GLOBALLY",
"resolution": "Influenza whole-genome/genomic sequencing is an established global surveillance capability; the remaining iCIDM issue is representation/capability-history calibration rather than whether the relationship exists scientifically.",
"next_state": "U1_REPRESENTATION_UNKNOWN",
"next_action": "Return to classification/detector calibration; reformulate as CIDM adoption/capability-history question if useful.",
"public_sources": [
{
"label": "CDC influenza genetic characterization",
"url": "https://www.cdc.gov/flu/php/viruses/genetic-characterization.html"
},
{
"label": "WHO/GISRS genomics context",
"url": "https://www.who.int/initiatives/global-influenza-surveillance-and-response-system"
}
]
},
{
"id": "GERG-CIDM-002",
"source_question_id": "UQG-008",
"question": "Why is the Influenza / respiratory viruses × Bioinformatics / modelling relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "SUBSTANTIALLY_RESOLVED_GLOBALLY",
"resolution": "Bioinformatics and modelling are long-established components of influenza surveillance, evolution analysis and vaccine-strain work. The stronger remaining question is how CIDM's documented capability compares with global practice.",
"next_state": "U1_U4_REFORMULATE",
"next_action": "Reformulate from existence question to comparative institutional capability/adoption question.",
"public_sources": [
{
"label": "PubMed: bioinformatics/computational biology in influenza",
"url": "https://pubmed.ncbi.nlm.nih.gov/12686090/"
},
{
"label": "WHO GISRS bioinformatics workshop",
"url": "https://www.who.int/news-room/events/detail/2024/09/27/default-calendar/who-bioinformatics-workshop-to-strengthen-the-global-influenza-surveillance-and-response-system-%28gisrs%29-in-collaboration-with-gisaid-and-who-collaborating-centre-for-influenza-in-australia"
}
]
},
{
"id": "GERG-CIDM-003",
"source_question_id": "UQG-009",
"question": "The Streptococcus pneumoniae × PCR / molecular diagnostics relationship was recurrent but has not appeared recently in the corpus. Is the capability obsolete, absorbed into newer methods, dormant, or simply relabelled?",
"global_status": "SUBSTANTIALLY_RESOLVED_GLOBALLY",
"resolution": "PCR-based pneumococcal detection/serotyping is an established global diagnostic/surveillance capability. The iCIDM question should focus on local historical continuity, relabelling, replacement or documentation rather than whether the method is scientifically established.",
"next_state": "U1_U4_REFORMULATE",
"next_action": "Trace CIDM historical method labels and later replacement technologies; do not promote original existence-gap question.",
"public_sources": [
{
"label": "CDC pneumococcal PCR and serotyping",
"url": "https://www.cdc.gov/strep-lab/php/pneumococcus/serotyping-using-pcr.html"
},
{
"label": "PubMed pneumococcal PCR clinical study",
"url": "https://pubmed.ncbi.nlm.nih.gov/10639531/"
}
]
},
{
"id": "GERG-CIDM-004",
"source_question_id": "UQG-001",
"question": "Why is the Cryptococcus × Whole-genome sequencing relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "SUBSTANTIALLY_RESOLVED_GLOBALLY",
"resolution": "Whole-genome/population genomics is well established for clinical Cryptococcus isolates and global population structure. The original existence-gap question should close; the useful CIDM question is local adoption, contribution, coverage, or representation.",
"next_state": "U1_REPRESENTATION_OR_LOCAL_CAPABILITY_HISTORY",
"next_action": "Reformulate toward CIDM historical contribution/adoption and inspect local classification coverage.",
"public_sources": [
{
"label": "PubMed: 372 clinical Cryptococcus isolates, WGS/population genetics",
"url": "https://pubmed.ncbi.nlm.nih.gov/37952096/"
},
{
"label": "PubMed: Cryptococcus population genomics, Brazil",
"url": "https://pubmed.ncbi.nlm.nih.gov/33822048/"
},
{
"label": "PubMed: C. gattii phylogenomics/WGS",
"url": "https://pubmed.ncbi.nlm.nih.gov/36014098/"
}
]
},
{
"id": "GERG-CIDM-005",
"source_question_id": "UQG-002",
"question": "Why is the Arboviruses × Clinical trial / therapy relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "PARTIALLY_RESOLVED_GLOBALLY_AND_TOO_BROAD",
"resolution": "Clinical management and therapeutic research clearly exist globally across arboviral diseases, but 'arboviruses' mixes distinct diseases with different evidence, vaccines and treatment gaps. The broad relationship question is not a useful U5 question.",
"next_state": "U2_MIXED_REALITY_PLUS_U4_REFORMULATE",
"next_action": "Split by dengue/chikungunya/Zika/yellow fever and by supportive care, antiviral therapy, vaccine, severe-disease management, then search each narrower question.",
"public_sources": [
{
"label": "WHO 2025 integrated arboviral clinical management guideline",
"url": "https://www.who.int/publications/i/item/9789240111110"
},
{
"label": "NCBI Bookshelf: WHO arboviral guideline",
"url": "https://www.ncbi.nlm.nih.gov/books/NBK616307/"
}
]
},
{
"id": "GERG-CIDM-006",
"source_question_id": "UQG-003",
"question": "Why is the Aspergillus × Whole-genome sequencing relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "SUBSTANTIALLY_RESOLVED_GLOBALLY",
"resolution": "Whole-genome and population genomic approaches are well established for Aspergillus, including clinical/environmental A. fumigatus isolates, azole resistance, species identification and population structure.",
"next_state": "U1_REPRESENTATION_OR_LOCAL_CAPABILITY_HISTORY",
"next_action": "Close the global existence question; reformulate around CIDM/Australian contribution, clinical translation, resistance prediction or corpus representation.",
"public_sources": [
{
"label": "PubMed: A. fumigatus population genomics and azole resistance",
"url": "https://pubmed.ncbi.nlm.nih.gov/35469019/"
},
{
"label": "PubMed: clinical/environmental A. fumigatus WGS",
"url": "https://pubmed.ncbi.nlm.nih.gov/31551947/"
},
{
"label": "PubMed: fungal WGS clinical identification",
"url": "https://pubmed.ncbi.nlm.nih.gov/36836298/"
}
]
},
{
"id": "GERG-CIDM-007",
"source_question_id": "UQG-004",
"question": "Why is the Staphylococcus aureus / MRSA × Serology / immunology relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "PARTIALLY_RESOLVED_GLOBALLY_REFORMULATE",
"resolution": "Serologic/antibody approaches to S. aureus infection have a long literature, so the relationship itself is not globally absent. However, routine modern diagnostic value and the exact MRSA-specific role are narrower questions and may differ from historical immunology research.",
"next_state": "U4_PARTIAL_GLOBAL_RESOLUTION",
"next_action": "Reformulate to a precise use-case: historical serodiagnosis, immune correlates, vaccine/antibody research, or current clinical diagnostic utility.",
"public_sources": [
{
"label": "PubMed: S. aureus serological assays",
"url": "https://pubmed.ncbi.nlm.nih.gov/3922051/"
},
{
"label": "PubMed: antibody diagnosis of S. aureus endocarditis",
"url": "https://pubmed.ncbi.nlm.nih.gov/1995726/"
},
{
"label": "PubMed: teichoic-acid antibody ELISA",
"url": "https://pubmed.ncbi.nlm.nih.gov/6863509/"
}
]
},
{
"id": "GERG-CIDM-008",
"source_question_id": "UQG-005",
"question": "Why is the Bordetella pertussis × Clinical trial / therapy relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "SUBSTANTIALLY_RESOLVED_GLOBALLY",
"resolution": "Pertussis treatment and prophylaxis are globally established, with randomized antibiotic trials, systematic-review evidence and current clinical guidance. Remaining questions concern timing, resistance, severe disease and improved therapies rather than whether a therapy relationship exists.",
"next_state": "U1_U4_REFORMULATE",
"next_action": "Close original existence-gap question; reformulate toward resistance, treatment timing, clinical outcomes or local CIDM role.",
"public_sources": [
{
"label": "CDC pertussis treatment guidance",
"url": "https://www.cdc.gov/pertussis/hcp/clinical-care/"
},
{
"label": "PubMed: antibiotics for pertussis trials/review",
"url": "https://pubmed.ncbi.nlm.nih.gov/15674946/"
},
{
"label": "PubMed: randomized clarithromycin vs erythromycin trial",
"url": "https://pubmed.ncbi.nlm.nih.gov/11740322/"
}
]
},
{
"id": "GERG-CIDM-009",
"source_question_id": "UQG-007",
"question": "Why is the Streptococcus pneumoniae × Bioinformatics / modelling relationship sparse in the publication corpus, and is this a true capability gap, a terminology/classification gap, or simply an unrepresented relationship?",
"global_status": "SUBSTANTIALLY_RESOLVED_GLOBALLY",
"resolution": "Pneumococcal bioinformatics, pan-genomics, population genomics and epidemiological modelling are mature global research areas. The original existence-gap question should close.",
"next_state": "U1_REPRESENTATION_OR_LOCAL_CAPABILITY_HISTORY",
"next_action": "Reformulate to CIDM-specific adoption, distinctive contribution, local datasets or missing computational capability documentation.",
"public_sources": [
{
"label": "PubMed: 26,306 pneumococcal genomes and clustering/bioinformatics",
"url": "https://pubmed.ncbi.nlm.nih.gov/39196267/"
},
{
"label": "PubMed: pneumococcal pan-genome/population genetics review",
"url": "https://pubmed.ncbi.nlm.nih.gov/22000739/"
},
{
"label": "PubMed: Pneumo Wiki pan-genome database",
"url": "https://pubmed.ncbi.nlm.nih.gov/41860230/"
}
]
}
]