manifests/gfp.json

{
  "citation": [
    {
      "text": "Sarkisyan et al. (2016), Local fitness landscape of the green fluorescent protein.",
      "url": "https://doi.org/10.1038/nature17995"
    }
  ],
  "context": [
    {
      "description": "Stable SHA-256-derived protein join identifier.",
      "name": "protein_id",
      "required": false
    },
    {
      "description": "Author substitution notation relative to avGFP.",
      "name": "aa_mutations",
      "required": false
    },
    {
      "description": "Number of amino-acid substitutions.",
      "name": "mutation_count",
      "required": false
    },
    {
      "description": "Barcodes supporting the protein aggregate.",
      "name": "unique_barcodes",
      "required": false
    },
    {
      "description": "Nullable author-reported barcode dispersion.",
      "name": "brightness_std",
      "required": false
    },
    {
      "description": "Aligned nucleotide substitution notations.",
      "name": "nucleotide_mutations",
      "required": false
    },
    {
      "description": "Aligned nucleotide substitution counts.",
      "name": "nucleotide_mutation_counts",
      "required": false
    },
    {
      "description": "Aligned nucleotide aggregate barcode counts.",
      "name": "nucleotide_unique_barcodes",
      "required": false
    },
    {
      "description": "Aligned nucleotide aggregate medians.",
      "name": "nucleotide_median_log10_brightness",
      "required": false
    },
    {
      "description": "Aligned nullable nucleotide dispersions.",
      "name": "nucleotide_brightness_std",
      "required": false
    },
    {
      "description": "Aligned author barcode identifiers for provenance.",
      "name": "source_barcode_ids",
      "required": false
    },
    {
      "description": "Aligned barcode nucleotide genotypes.",
      "name": "barcode_nucleotide_mutations",
      "required": false
    },
    {
      "description": "Aligned barcode mutation counts.",
      "name": "barcode_nucleotide_mutation_counts",
      "required": false
    },
    {
      "description": "Aligned filtered barcode brightness values.",
      "name": "barcode_log10_brightness",
      "required": false
    },
    {
      "description": "Aligned minimum genotype sequencing coverage.",
      "name": "barcode_min_coverage",
      "required": false
    },
    {
      "description": "Aligned mean genotype sequencing coverage.",
      "name": "barcode_mean_coverage",
      "required": false
    }
  ],
  "dataset_id": "design-bench/gfp",
  "default_split": "protein_genotypes",
  "description": "Canonical protein-level Sarkisyan GFP measurements with retained nucleotide and filtered-barcode source observations.",
  "inputs": [
    {
      "constraints": [
        {
          "kind": "alphabet",
          "symbols": [
            "A",
            "C",
            "D",
            "E",
            "F",
            "G",
            "H",
            "I",
            "K",
            "L",
            "M",
            "N",
            "P",
            "Q",
            "R",
            "S",
            "T",
            "V",
            "W",
            "Y"
          ]
        },
        {
          "kind": "length",
          "maximum": 237,
          "minimum": 237
        }
      ],
      "description": "Uppercase 237-residue avGFP variant sequence.",
      "name": "sequence"
    }
  ],
  "knowledge": {
    "aequorea_victoria_gfp_and_engineered_variants": {
      "description": "Experimentally established properties of avGFP and selected engineered GFP variants, with conventional residue numbering.",
      "media_type": "text/markdown",
      "path": "knowledge/design-bench/gfp/aequorea-victoria-gfp-and-engineered-variants.md",
      "title": "Aequorea victoria GFP and Engineered Variants"
    },
    "flow_cytometry_and_barcode_linked_fluorescence_measurement": {
      "description": "Single-cell fluorescence measurement, sorting bins, calibration, autofluorescence, barcode linkage, coverage, and aggregation.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/flow-cytometry-and-barcode-linked-fluorescence-measurement.md",
      "title": "Flow Cytometry and Barcode-Linked Fluorescence Measurement"
    },
    "fluorescence_photophysics_and_brightness": {
      "description": "Absorption, excitation, emission, extinction coefficient, quantum yield, molecular brightness, photobleaching, and environmental effects.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/fluorescence-photophysics-and-brightness.md",
      "title": "Fluorescence Photophysics and Brightness"
    },
    "gfp_structure_chromophore_and_maturation": {
      "description": "The GFP beta-barrel, central chromophore-forming residues, autocatalytic maturation, oxygen dependence, and protonation.",
      "media_type": "text/markdown",
      "path": "knowledge/design-bench/gfp/gfp-structure-chromophore-and-maturation.md",
      "title": "GFP Structure, Chromophore, and Maturation"
    },
    "mixcr_mutation_encoding": {
      "description": "Reference-relative substitution, deletion, and insertion notation, zero-based coordinates, validation, and amino-acid adaptation.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/mixcr-mutation-encoding.md",
      "title": "MiXCR Mutation Encoding"
    },
    "protein_fitness_landscapes_and_epistasis": {
      "description": "Genotype-to-phenotype landscapes, mutational neighborhoods, additive expectations, and magnitude and sign epistasis.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/protein-fitness-landscapes-and-epistasis.md",
      "title": "Protein Fitness Landscapes and Epistasis"
    },
    "protein_folding_stability_and_mutational_effects": {
      "description": "Folding thermodynamics and kinetics, structural environments, aggregation, and mechanisms by which substitutions alter proteins.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/protein-folding-stability-and-mutational-effects.md",
      "title": "Protein Folding, Stability, and Mutational Effects"
    },
    "protein_sequences_amino_acids_and_substitutions": {
      "description": "Protein sequence notation, amino-acid physicochemical classes, residue coordinates, and substitution semantics.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/protein-sequences-amino-acids-and-substitutions.md",
      "title": "Protein Sequences, Amino Acids, and Substitutions"
    }
  },
  "license": "CC-BY-4.0",
  "schema_version": 1,
  "source": [
    {
      "checksum": "sha256:5581230b9888f9960708a4769ce1c9b4453561f0b5f0374525445b4a984d54d5",
      "name": "Sarkisyan GFP Figshare data",
      "url": "https://doi.org/10.6084/m9.figshare.3102154.v1",
      "version": "v1"
    }
  ],
  "splits": [
    {
      "attributes": {
        "barcode_observations": 65678,
        "mutation_type": "substitution_only",
        "nucleotide_observations": 56086,
        "protein_length": 237,
        "reference": "avGFP",
        "target_aggregation": "author_protein_level_median"
      },
      "description": "All clean canonical protein-level measurements.",
      "name": "protein_genotypes",
      "num_rows": 51715
    }
  ],
  "targets": [
    {
      "constraints": [
        {
          "kind": "finite"
        }
      ],
      "description": "Author protein-level median log-brightness over accepted barcodes.",
      "name": "median_log10_brightness",
      "unit": "log10 fluorescence intensity"
    }
  ],
  "version": "1.0.0"
}