"computational prediction"

[jimdavis1]

On the genome landing page "Computational Prediction" (bottom left of the image) should never mask panel data.

Here is an example of a CDC ARBank genome that has gold standard panel data, but on the landing page is says we only have a computational prediction.

[nconrad]

We probably need @mshukla1's input on how to address. I don't think the genome meta mentions anything about having panel data. Should it? antimicrobial_resistance_evidence is currently just a string with "Computational Prediction":

"{
    "completion_date": "2018-06-22T00:00:00Z",
    "genbank_accessions": "QHCM01000000",
    "contig_n50": 2182264,
    "taxon_id": 1280,
    "cds_ratio": 0.98,
    "mlst": "MLST.Staphylococcus_aureus.5",
    "species": "Staphylococcus aureus",
    "cell_shape": "",
    "oxygen_requirement": "",
    "gram_stain": "",
    "sequencing_depth": "25.41x",
    "strain": "AR_0224",
    "genome_quality": "Good",
    "owner": "PATRIC@patricbrc.org",
    "trna": 60,
    "contig_l50": 1,
    "genome_status": "WGS",
    "gc_content": 32.858315,
    "cds": 2881,
    "rrna": 16,
    "genome_id": "1280.16760",
    "hypothetical_cds_ratio": 0.19,
    "comments": [
        "The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels."
    ],
    "common_name": "Staphylococcus_aureus",
    "partial_cds_ratio": 0,
    "public": true,
    "taxon_lineage_ids": [
        "131567",
        "2",
        "1783272",
        "1239",
        "91061",
        "1385",
        "90964",
        "1279",
        "1280"
    ],
    "class": "Bacilli",
    "assembly_method": "canu v. 1.4",
    "bioproject_accession": "PRJNA316321",
    "kingdom": "Bacteria",
    "biosample_accession": "SAMN04901614",
    "taxon_lineage_names": [
        "cellular organisms",
        "Bacteria",
        "Terrabacteria group",
        "Firmicutes",
        "Bacilli",
        "Bacillales",
        "Staphylococcaceae",
        "Staphylococcus",
        "Staphylococcus aureus"
    ],
    "genome_length": 2940373,
    "order": "Bacillales",
    "habitat": "",
    "contigs": 3,
    "genome_name": "Staphylococcus aureus strain AR_0224",
    "refseq_cds": 2834,
    "hypothetical_cds": 557,
    "sequencing_centers": "FDA/CDC",
    "plfam_cds": 2825,
    "antimicrobial_resistance_evidence": "Computational Prediction",
    "motility": "",
    "phylum": "Firmicutes",
    "family": "Staphylococcaceae",
    "assembly_accession": "GCA_003260475.1",
    "sequencing_platform": "Pacbio; Illumina",
    "partial_cds": 0,
    "patric_cds": 2881,
    "plfam_cds_ratio": 0.98,
    "antimicrobial_resistance": [
        "Resistant",
        "Susceptible",
        "Nonsusceptible"
    ],
    "temperature_range": "",
    "publication": "",
    "genus": "Staphylococcus",
    "date_inserted": "2018-07-16T09:21:25.980Z",
    "date_modified": "2018-07-16T09:21:25.980Z",
    "coarse_consistency": 100,
    "fine_consistency": 99.9,
    "checkm_completeness": 100,
    "checkm_contamination": 0.6,
    "_version_": 1616513373528129500
}"

[nconrad]

I discussed this with @jimdavis1 and we decided to change the "Computational Prediction" link to "AMR phenotypes" as a short term solution.

[mshukla1]

This needs to be addressed at the data level. I will update the corresponding records in the database.

[mshukla1]

Done. I have cleaned up data for all public genomes in the database. Now, any genome that has AMR data from laboratory method has antimicrobial_resistance_envidence = AMR Panel.