Enrich AMR Task

[j2whiting]

@pascaleproulx

I have a working GoLLM task for AMR enrichment. We need to integrate it with the rest of the task runner architecture @kbirk. Example outputs below.

---

BIOMD0000000024

{
  "initials": {
    "protein": {
      "description": "Relative concentration of the effective protein, which is in the molecular state capable of inhibiting mRNA production.",
      "unit": "dimensionless"
    },
    "mRNA": {
      "description": "Relative concentration of mRNA, which is involved in the production of the effective protein.",
      "unit": "dimensionless"
    }
  },
  "parameters": {
    "k": {
      "description": "Scaling constant used in the nonlinear term of the mRNA production rate equation.",
      "unit": "dimensionless"
    },
    "n": {
      "description": "Hill coefficient representing the cooperativity in the negative feedback loop of protein on mRNA production.",
      "unit": "dimensionless"
    },
    "rM": {
      "description": "Scaled mRNA production rate constant.",
      "unit": "hr^-1"
    },
    "m": {
      "description": "Exponent representing the nonlinearity in the protein production cascade.",
      "unit": "dimensionless"
    },
    "parameter_0000009": {
      "description": "Not explicitly described in the provided text.",
      "unit": "N/A"
    },
    "rP": {
      "description": "Protein production rate constant.",
      "unit": "hr^-1"
    },
    "qM": {
      "description": "mRNA degradation rate constant.",
      "unit": "hr^-1"
    },
    "qP": {
      "description": "Protein degradation rate constant.",
      "unit": "hr^-1"
    },
    "compartment_0000004": {
      "description": "Not explicitly described in the provided text.",
      "unit": "N/A"
    }
  }
}

---

BIOMD0000001048

{
  "initials": {
    "Ttum": {
      "description": "Cell concentration of the original tumor",
      "unit": "cells/ml"
    },
    "Tplas": {
      "description": "Cancer cell concentration in the plasma",
      "unit": "cells/ml"
    },
    "Tnew": {
      "description": "Cell concentration of new and developing tumor",
      "unit": "cells/ml"
    }
  },
  "parameters": {
    "b": {
      "description": "Relative drug efficacy factor for specific growth rate",
      "unit": "dimensionless"
    },
    "kf1": {
      "description": "Rate constant for cell release from the original tumor to plasma",
      "unit": "day^-1"
    },
    "kr1": {
      "description": "Rate constant for cell attachment from plasma to the original tumor",
      "unit": "day^-1"
    },
    "c": {
      "description": "Rate constant for plasma clearance",
      "unit": "day^-1"
    },
    "d": {
      "description": "Relative drug efficacy factor for plasma clearance",
      "unit": "dimensionless"
    },
    "kf2": {
      "description": "Rate constant for cell release from plasma to new tumor",
      "unit": "day^-1"
    },
    "kr2": {
      "description": "Rate constant for cell attachment from new tumor to plasma",
      "unit": "day^-1"
    },
    "T0": {
      "description": "Equilibrium tumor cell concentration in the tumor",
      "unit": "cells/ml"
    },
    "a": {
      "description": "Relative drug efficacy factor for cell release rate",
      "unit": "dimensionless"
    },
    "r": {
      "description": "Specific growth rate of tumor cells",
      "unit": "day^-1"
    },
    "n": {
      "description": "Number of new tumors being developed simultaneously",
      "unit": "dimensionless"
    },
    "Tumor": {
      "description": "General term for tumor cell concentration",
      "unit": "cells/ml"
    }
  }
}

---

Using MathML for units

MODEL8262229752

{
  "initials": {},
  "parameters": {
    "b_reac_r": {
      "description": "Bio-reaction rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "AdoMet_r": {
      "description": "Methionine adenosyl transfer rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "Methy_trans": {
      "description": "Methyl transfer rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "SAM_Dec": {
      "description": "SAM decarboxylation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "Spermi_uti": {
      "description": "Spermidine utilization rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "MTR_e": {
      "description": "MTR excretion rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "Polyamine_uti": {
      "description": "Polyamine utilization rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "Pfs_prot_d": {
      "description": "Pfs protein degradation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "pfs_transl": {
      "description": "Pfs translation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "pfs_mRNA_d": {
      "description": "Pfs mRNA degradation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "pfs_transc": {
      "description": "Pfs transcription rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "Met_recov": {
      "description": "Methionine recovery rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "DPD_deg_r": {
      "description": "DPD degradation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "LuxS_prot_d": {
      "description": "LuxS protein degradation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "LuxS_transl": {
      "description": "LuxS translation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "LuxS_mRNA_d": {
      "description": "LuxS mRNA degradation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "LuxS_transc": {
      "description": "LuxS transcription rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "AI2_syn_r": {
      "description": "AI-2 synthesis rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "AI2_excret_r": {
      "description": "AI-2 excretion rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "AI2_trans_r": {
      "description": "AI-2 transport rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "AI2_phos_r": {
      "description": "AI-2 phosphorylation rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "MTR_syn_r": {
      "description": "MTR synthesis rate constant",
      "units": {
        "expression": "1/min",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
      }
    },
    "SAH_Hydro_r": {
      "description": "SAH hydrolysis rate constant",
      "units": {
        "expression": "1/(M*min)",
        "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>M</ci><ci>min</ci></apply></apply>"
      }
    },
    "SRH_cleav": {
      "description": "SRH cleavage rate constant",
      "units": {
        "expression": "1/(M*min)",
        "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>M</ci><ci>min</ci></apply></apply>"
      }
    },
    "SpeE_syn_r": {
      "description": "Spermidine synthesis rate constant",
      "units": {
        "expression": "1/(M*min)",
        "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>M</ci><ci>min</ci></apply></apply>"
      }
    },
    "compartment": {
      "description": "Compartment for the reactions",
      "units": {
        "expression": "n/a",
        "expression_mathml": "<ci>n/a</ci>"
      }
    }
  }
}

---

MODEL9086926384

{  "initials": {},
  "parameters": {
    "kb": {
      "description": "Rate constant for the backward reaction in the model.",
      "units": {
        "expression": "1/s",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
      }
    },
    "kf": {
      "description": "Rate constant for the forward reaction in the model.",
      "units": {
        "expression": "1/s",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
      }
    },
    "default_compartment": {
      "description": "The default compartment where the reactions take place, typically representing the synaptic or cytosolic volume.",
      "units": {
        "expression": "fl",
        "expression_mathml": "<ci>fl</ci>"
      }
    },
    "geometry": {
      "description": "The geometric configuration of the synaptic and cytosolic compartments, including their volumes.",
      "units": {
        "expression": "fl",
        "expression_mathml": "<ci>fl</ci>"
      }
    },
    "geometry_sbo_1_sbc_": {
      "description": "Specific geometric parameter related to the synaptic and cytosolic compartments, possibly a scaling factor or specific volume.",
      "units": {
        "expression": "fl",
        "expression_mathml": "<ci>fl</ci>"
      }
    },
    "k1": {
      "description": "Rate constant for a specific reaction involving AMPAR or CaMKII in the model.",
      "units": {
        "expression": "1/s",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
      }
    },
    "k2": {
      "description": "Rate constant for another specific reaction involving AMPAR or CaMKII in the model.",
      "units": {
        "expression": "1/s",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
      }
    },
    "k3": {
      "description": "Rate constant for yet another specific reaction involving AMPAR or CaMKII in the model.",
      "units": {
        "expression": "1/s",
        "expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
      }
    }
  }
}

[j2whiting]

@kbirk this is ready to be integrated with the task runner