manifests/tfbind8.json

{
  "citation": [
    {
      "text": "Barrera et al. (2016), Survey of variation in human transcription factors reveals prevalent DNA binding changes.",
      "url": "https://doi.org/10.1126/science.aad2257"
    },
    {
      "text": "Trabucco et al. (2022), Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization.",
      "url": "https://arxiv.org/abs/2202.08450"
    }
  ],
  "context": [],
  "dataset_id": "design-bench/tfbind8",
  "default_split": "six6_ref_r1",
  "description": "Complete canonical DNA 8-mer binding landscape for the SIX6 reference allele, PBM replicate 1.",
  "inputs": [
    {
      "constraints": [
        {
          "kind": "alphabet",
          "symbols": [
            "A",
            "C",
            "G",
            "T"
          ]
        },
        {
          "kind": "length",
          "maximum": 8,
          "minimum": 8
        }
      ],
      "description": "DNA sequence of exactly eight nucleotides.",
      "name": "sequence"
    }
  ],
  "knowledge": {
    "binding_affinity_and_thermodynamics": {
      "description": "Equilibrium association and dissociation constants, occupancy, binding Gibbs energy, and kinetic rate constants.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/binding-affinity-and-thermodynamics.md",
      "title": "Binding Affinity and Thermodynamics"
    },
    "binding_sites_motifs_and_sequence_context": {
      "description": "Binding sites, consensus sequences, PFM/PWM representations, strand orientation, and nucleotide dependencies.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/binding-sites-motifs-and-sequence-context.md",
      "title": "Binding Sites, Motifs, and Sequence Context"
    },
    "dna_structure_and_base_pairing": {
      "description": "DNA strand direction, complementarity, canonical base pairing, grooves, and sequence-dependent duplex structure.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/dna-structure-and-base-pairing.md",
      "title": "DNA Structure and Base Pairing"
    },
    "protein_binding_microarrays": {
      "description": "Universal PBM assay principles, word-level measurements, E-score calculation, and interpretive limitations.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/protein-binding-microarrays.md",
      "title": "Protein-Binding Microarrays"
    },
    "six_family_and_six6": {
      "description": "SIX-family protein architecture and bounded biochemical evidence about SIX6 DNA recognition.",
      "media_type": "text/markdown",
      "path": "knowledge/design-bench/tfbind8/six-family-and-six6.md",
      "title": "The SIX Family and SIX6"
    },
    "transcription_factor_dna_binding": {
      "description": "Physical modes of DNA recognition and the distinctions among affinity, specificity, occupancy, and regulatory activity.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/transcription-factor-dna-binding.md",
      "title": "Transcription Factor\u2013DNA Binding"
    }
  },
  "license": "other",
  "schema_version": 1,
  "source": [
    {
      "checksum": "sha256:30778471f1c5167698ac3d2b18fb54098ddaddbaa0550448afb25567e5075231",
      "name": "Barrera et al. PBM TF binding landscapes",
      "notes": "Published contiguous 8-mer landscape; redistribution terms are described in the dataset card.",
      "url": "https://drive.google.com/file/d/1xS6N5qSwyFLC-ZPTADYrxZuPHjBkZCrj/view",
      "version": "BAR15A"
    },
    {
      "name": "Design-Bench TFBind8 preprocessing",
      "revision": "e52939588421b5433f6f2e9b359cf013c542bd89",
      "url": "https://github.com/brandontrabucco/design-bench/blob/e52939588421b5433f6f2e9b359cf013c542bd89/process/process_raw_tf_bind_8.py"
    }
  ],
  "splits": [
    {
      "attributes": {
        "allele": "REF",
        "assay": "universal protein-binding microarray",
        "replicate": 1,
        "transcription_factor": "SIX6"
      },
      "description": "SIX6 reference allele, PBM replicate 1.",
      "name": "six6_ref_r1",
      "num_rows": 65536
    }
  ],
  "targets": [
    {
      "constraints": [
        {
          "kind": "finite"
        },
        {
          "kind": "range",
          "maximum": 0.5,
          "minimum": -0.5
        }
      ],
      "description": "Published PBM enrichment score for the SIX6_REF_R1 condition.",
      "name": "e_score"
    },
    {
      "constraints": [
        {
          "kind": "finite"
        },
        {
          "kind": "range",
          "maximum": 1.0,
          "minimum": 0.0
        }
      ],
      "description": "Condition-level min-max normalization of the published E-score.",
      "name": "normalized_e_score"
    }
  ],
  "version": "1.0.0"
}