Absorption:

  BloodBrainBarrier:
    dir: &dir_bbb "s3://datasets-ressources/PADMET_Panel/Absorption/BloodBrainBarrier"
    BBB:
      - filename: "admetsar_BBB.xls"
        type:
        task: "clf" # classification task
        dir: *dir_bbb
        smiles_col: "SMILES"
        unit:
        target_cols: ["Endpoints"]
        open_kwargs: {}
        unified_label:
          CLASS:
            "BBB+" : 1
            "BBB-" : 0
        short_cols:
          SMILES: "SMILES"
          CLASS: "Endpoints"
        opt_kwargs:
          value: 1
          type:
        ref: "ADMETSAR2.0 - 10.1093/bioinformatics/bty707"

      - filename: "BBB_binary2019_invivoai_clean.csv"
        task: "clf"
        dir: *dir_bbb
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["BB_class"]
        open_kwargs:
          sep: ";"
        unified_label:
          CLASS:
            "p" : 1
            "P" : 1
            "n" : 0
        short_cols:
#          ID: "CID"
          SMILES: "smiles"
          CLASS: "BB_class"
          ref: "reference"
        opt_kwargs:
          value: 1
          type:

      - filename: "cyclica_BBB.csv"
        task: "clf" # classification task
        dir: *dir_bbb
        smiles_col: "Smiles"
        unit:
        type:
        opt_kwargs:
          value: 1
          type:
        target_cols: ["p_np"]
        short_cols:
          SMILES: "smiles"
          CLASS : "p_np"
        open_kwargs: {}
        ref: "Cyclica - 10.1021/ci300124c"

      - filename: "logBB2019_invivoai_clean.csv"
        task: "reg"
        dir: *dir_bbb
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["logBB"]
        open_kwargs:
          sep: ";"
        short_cols:
#          ID: "CID"
          SMILES: "smiles"
          ACTIVITY: "logBB"
          ref: "reference"
        opt_kwargs:
          value: 1
          type:

      - filename: "vnn_BBB.csv"
        task: "clf" # classification task
        dir: *dir_bbb
        smiles_col: "Smiles"
        unit:
        type:
        opt_kwargs:
          value: 1
          type:
        target_cols: ["Property"]
        short_cols:
          SMILES: "Smiles"
          CLASS: "Property"
        open_kwargs: {}
        ref: "VNN - 10.3389/fphar.2017.00889"

  HumanIntestinalAbsorption:
    dir: &dir_HIA "s3://datasets-ressources/PADMET_Panel/Absorption/HumanIntestinalAbsorption"
    HIA:
      - filename: "admetsar_HIA.xls"
        task: "both"
        dir: *dir_HIA
        smiles_col: "SMILES"
        unit:
        opt_kwargs:
          value: 30
          type: "HI"
        target_cols: ["HIA%"]
        short_cols:
          SMILES: "SMILES"
          ACTIVITY: "HIA%"
          CLASS: "Labels"
        open_kwargs: {}
        unified_label:
          CLASS:
            "HIA-": 0
            "HIA+": 1
        ref: "ADMETSAR2.0 - 10.1093/bioinformatics/bty707"

      - filename: "CHEMBL1116254.csv"
        task: "reg"
        dir: *dir_HIA
        smiles_col: "SMILES"
        unit: "%"
        opt_kwargs:
          value: 30
          type: "HI"
        target_cols: ["Standard Value"]
        short_cols:
#          ID: "Molecule ChEMBL ID"
          SMILES: "Smiles"
          ACTIVITY: "Standard Value"
        open_kwargs:
          sep: ";"
        ref: "CHEMBL1116254"

      - filename: "CHEMBL1663502.csv"
        task: "reg"
        dir: *dir_HIA
        smiles_col: "SMILES"
        unit: "log10(%HIA +10)"
        opt_kwargs:
          value: 1.602
          type: "HI"
        target_cols: ["Standard Value"]
        short_cols:
#          ID: "Molecule ChEMBL ID"
          SMILES: "Smiles"
          ACTIVITY: "Standard Value"
        open_kwargs:
          sep: ";"
        ref: "CHEMBL1663502"

      - filename: "ci100104j_si_001_hia.xls"
        task: both
        dir: *dir_HIA
        smiles_col: "Structure"
        unit:
        opt_kwargs:
          value: 30
          type: "HI"
        target_cols: ["Class", "HIA (%)"]
        short_cols:
#          ID: "Molecule_name"
          SMILES: "Structure"
          ACTIVITY: "HIA (%)"
          CLASS: "Class"
        unified_label:
          CLASS:
            "-1" : 0
            "1" : 1
        open_kwargs:
          sheet_name: "HIA_TrainingSet1"
        ref: "Cyclica - ADMETSAR2.0 - ci100104j_si_001"

      - filename: "ci100104j_si_001_hia.xls"
        task: both
        dir: *dir_HIA
        smiles_col: "SMILES"
        unit:
        opt_kwargs:
          value: 30
          type: "HI"
        target_cols: ["Class", "HIA (%)"]
        short_cols:
          ID: "Molecule_name"
          SMILES: "Structure"
          ACTIVITY: "HIA (%)"
          CLASS: "Class"
        open_kwargs:
          sheet_name: "HIA_TestSet1"
        unified_label:
          CLASS:
            "-1" : 0
            "1" : 1
        ref: "Cyclica - ADMETSAR2.0 - ci100104j_si_001"

      - filename: "ci100104j_si_001_hia.xls"
        task: clf
        dir: *dir_HIA
        smiles_col: "SMILES"
        unit:
        opt_kwargs:
          value: 1
          type:
        target_cols: ["Class"]
        short_cols:
#          ID: "DrugCard"
          SMILES: "Structure"
          CLASS: "Class"
        open_kwargs:
          sheet_name: "HIA_ExternalSet"
        unified_label:
          CLASS:
            "-1" : 0
            "1" : 1
        ref: "Cyclica - ADMETSAR2.0 - ci100104j_si_001"

      - filename: "PMID_17238266_test_HIA.sdf"
        task: "reg"
        dir: *dir_HIA
        smiles_col: "SMILES"
        unit: "%"
        type:
        opt_kwargs:
          value: 30
          type: "HI"
        target_cols: ["HIA"]
        short_cols:
          Name: "Molecule_name"
          ACTIVITY: "HIA"
        open_kwargs: {}
        ref: "PMID_17238266"

      - filename: "PMID_17238266_train_HIA.sdf"
        task: "reg"
        dir: *dir_HIA
        smiles_col: "SMILES"
        unit: "%"
        type:
        opt_kwargs:
          value: 30
          type: "HI"
        target_cols: ["HIA"]
        short_cols:
          Name: "Molecule_name"
          ACTIVITY: "HIA"
        open_kwargs: {}
        ref: "PMID_17238266"

  Pglycoprotein:
    dir_subs: &dir_PgpS "s3://datasets-ressources/PADMET_Panel/Absorption/Pglycoprotein/PgpSubstrates"
    dir_inhib: &dir_PgpI "s3://datasets-ressources/PADMET_Panel/Absorption/Pglycoprotein/PgpInhibitors"

    PgpSubstrates:
      - filename: "admetsar_PgpS.xls"
        task: "clf" # classification task
        dir: *dir_PgpS
        smiles_col: "SMILES"
        unit:
        target_cols: ["Class"]
        short_cols:
          SMILES: "SMILES"
          CLASS: "End points"
        unified_label:
          CLASS:
            substrate: 1
            non_substrate: 0
        opt_kwargs:
          value: 0
          type:
        open_kwargs:
          sep: ";"
        ref: "10.3389/fphar.2017.00889"

      - filename: "cyclica_PgpS.csv"
        task: "clf" # classification task
        dir: *dir_PgpS
        smiles_col: "SMILES"
        unit:
        target_cols: ["Class"]
        short_cols:
          SMILES: "SMILES"
          CLASS: "Class"
        unified_label:
          CLASS:
            "-1": 0
            "1": 1
        opt_kwargs:
          value: 0
          type:
        open_kwargs:
          sep: ";"
        ref: "Cyclica - 10.3389/fphar.2017.00889"

      - filename: "jm400328s_si_001_PgpS.csv"
        task: "clf" # classification task
        dir: *dir_PgpS
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["Activity"]
        short_cols:
          SMILES: "SMILES"
          CLASS: "Activity"
        unified_label:
          CLASS:
            "-1": 0
            "1": 1
        opt_kwargs:
          value: 0
          type:
        open_kwargs:
          sep: ","
        ref: "jm400328s_si_001"

      - filename: "vnn_PgpS.csv"
        task: "clf" # classification task
        dir: *dir_PgpS
        smiles_col: "Smiles"
        unit:
        type:
        target_cols: ["Property"]
        short_cols:
          SMILES: "Smiles"
          CLASS: "Property"
        opt_kwargs:
          value: 0
          type:
        open_kwargs:
          sep: ","
        ref: "VNN - 10.3389/fphar.2017.00889"

    PgpInhibitors:

      - filename: "admetsar_PgpI_1.xls"
        task: "clf" # classification task
        dir: *dir_PgpI
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["End points"]
        short_cols:
          SMILES: "SMILES"
          CLASS: "End points"
        unified_label:
          CLASS:
            "Pgp_nonInhibitor": 1
            "Pgp_Inhibitor": 0
        opt_kwargs:
          value: 0
          type:
        open_kwargs: {}
        ref: "ADMETSAR2.0 - 10.1093/bioinformatics/bty707"

      - filename: "admetsar_PgpI_2.xls"
        task: "clf" # classification task
        dir: *dir_PgpI
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["End points"]
        short_cols:
          SMILES: "SMILES"
          CLASS: "End points"
        unified_label:
          CLASS:
            "Pgp_nonInhibitor": 1
            "Pgp_Inhibitor": 0
        opt_kwargs:
          value: 0
          type:
        open_kwargs: {}
        ref: "ADMETSAR2.0 - 10.1093/bioinformatics/bty707"

      - filename: "CHEMBL2449559.csv"
        task: "reg" # classification task
        dir: *dir_PgpI
        smiles_col: "SMILES"
        unit: "nM"
        type: "pEC50"
        target_cols: ["pChEMBL Value"]
        short_cols:
#          ID: "Molecule ChEMBL ID"
          SMILES: "Smiles"
#          Activity_ori: "Standard Value"
          ACTIVITY: "pChEMBL Value"
        opt_kwargs:
          value: 5
          type: "HI"
        open_kwargs:
          sep: ";"
        ref: "CHEMBL2449559"

      - filename: "cyclica_PgpI.xlsx"
        task: "clf" # classification task
        dir: *dir_PgpI
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["Expr"]
        short_cols:
          SMILES: "SMILES"
          CLASS: "Expr"
          ref: "ref"
        opt_kwargs:
          value: 0
          type:
        open_kwargs: {}
        ref: "Cyclica - 10.1088/2632-2153/ab891b - Broccatelli2011"

      - filename: "vnn_PgpI.csv"
        task: "clf" # classification task
        dir: *dir_PgpI
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["Property"]
        short_cols:
          SMILES: "Smiles"
          CLASS: "Property"
        opt_kwargs:
          value: 0
          type:
        open_kwargs: {}
        ref: "VNN - 10.3389/fphar.2017.00889"

  HumanOralBioavailability:
    dir: &dir_hob "s3://datasets-ressources/PADMET_Panel/Absorption/HumanOralBioavailability/"
    HOB:
      - filename: "AID444054_HOB.csv"
        task: "reg" # classification task
        dir: *dir_hob
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["F_fraction"]
        short_cols:
          CID: "PUBCHEM_CID"
          ACTIVITY: "F_fraction"
        open_kwargs: {}
        opt_kwargs:
          value: 0.5
          type: "HI"
        ref: "AID444054"

      - filename: "CHEMBL633098.csv"
        task: "reg" # classification task
        dir: *dir_hob
        smiles_col: "Smiles"
        unit: "%"
        type: "F"
        note: "Standard Relation contains interval relations "
        target_cols: ["Standard Value"]
        short_cols:
#          ID: "Molecule ChEMBL ID"
          SMILES: "Smiles"
          ACTIVITY: "Standard Value"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: 50
          type: "HI"
        ref: "CHEMBL633098"

      - filename: "CHEMBL926687.csv"
        task: "reg" # classification task
        dir: *dir_hob
        smiles_col: "Smiles"
        unit: "%"
        type: "F"
        target_cols: ["Standard Value"]
        short_cols:
#          ID: "Molecule ChEMBL ID"
          SMILES: "Smiles"
          ACTIVITY: "Standard Value"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: 50
          type: "HI"
        ref: "CHEMBL926687"

      - filename: "CHEMBL1043584.csv"
        task: "reg" # classification task
        dir: *dir_hob
        smiles_col: "Smiles"
        unit:
        type: "F_fraction"
        target_cols: ["Standard Value"]
        short_cols:
#          ID: "Molecule ChEMBL ID"
          SMILES: "Smiles"
          ACTIVITY: "Standard Value"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: 0.5
          type: "HI"
        ref: "CHEMBL1043584"

      - filename: "cyclica_HOB.xlsx"
        task: "both" # classification task
        dir: *dir_hob
        smiles_col: "Smiles"
        unit: ["%", "log(%)"]
        type: ["%F", "logK(%F)"]
        target_cols: ["%F", "logK(%F)"]
        short_cols:
#          ID: "Name"
          SMILES: "Updated SMILES"
          ACTIVITY: "logK(%F)"
#          Activity_ori: "%F"
          CLASS: "Category"
        open_kwargs:
          sheet_name: "Official Sheet"
        opt_kwargs:
          value: 0
          type: "HI"
        ref: "Cyclica - 10.1088/2632-2153/ab891b"

  Permerability:
    dir_caco2: &dir_caco2 "s3://datasets-ressources/PADMET_Panel/Absorption/Permeability/Caco2/"
    dir_pamppa: &dir_pampa "s3://datasets-ressources/PADMET_Panel/Absorption/Permeability/Pampa/"
    dir_mdck: &dir_mdck "s3://datasets-ressources/PADMET_Panel/Absorption/Permeability/Mdck/"

    HumanCaco2:
      - filename: "admetsar_caco2.xls"
        task: "clf" # classification task
        dir: *dir_caco2
        smiles_col: "SMILES"
        unit:
        type:
        target_cols: ["CLASS"]
        short_cols:
          SMILES: "SMILES"
          CLASS: "CLASS"
        open_kwargs: {}
        unified_label:
          CLASS:
            "1": 1
            "-1": 0
        opt_kwargs:
          value: 1
          type:
        ref: "ADMETSAR2.0 - 10.1093/bioinformatics/bty707"

      - filename: "cyclica_caco2.xls"
        dir: *dir_caco2
        task: "reg"
        smiles_col: "SMILES"
        unit: "logPapp"
        target_cols: ["LogPapp(derived)"]
        short_cols:
          SMILES: "SMILES"
          ACTIVITY: "LogPapp(derived)"
          CLASS: "CLASS"
        open_kwargs:
          sheet_name: "Training set"
        opt_kwargs:
          value: 5
          type: "LO"
        unified_label:
          CLASS:
            "1": 1
            "-1": 0
        ref: "10.1088/2632-2153/ab891b"

      - filename: "cyclica_caco2.xls"
        dir: *dir_caco2
        task: "reg"
        smiles_col: "SMILES"
        unit:
        type: "logPapp"
        target_cols: ["LogPapp(derived)"]
        short_cols:
          SMILES: "SMILES"
          ACTIVITY: "LogPapp(derived)"
          CLASS: "CLASS"
        open_kwargs:
          sheet_name: "Test set"
        opt_kwargs:
          value: 5
          type: "LO"
        unified_label:
          CLASS:
            "1": 1
            "-1": 0
        ref: "10.1088/2632-2153/ab891b"

      - filename: "model_caco2.csv"
        dir: *dir_caco2
        smiles_col: "SMILES"
        task: "reg"
        unit: "log(cm/s)"
        type:
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "10.1021/acs.jcim.5b00642"

      - filename: "external1_CHEMBL1074672.csv"
        dir: *dir_caco2
        smiles_col: "SMILES"
        task: "reg"
        type:
        unit: "log(cm/s)"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL1074672" # DOI

      - filename: "external2_CHEMBL1769835.csv"
        dir: *dir_caco2
        smiles_col: "SMILES"
        task: "reg"
        type:
        unit: "log(cm/s)"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL1769835" # DOI or AID or CHEMBL ID

      - filename: "external3_CHEMBL3529272.csv"
        dir: *dir_caco2
        smiles_col: "SMILES"
        task: "reg"
        unit: "log(cm/s)"
        type:
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL3529272" # DOI or AID or CHEMBL ID

    RatCaco2:
      - filename: "rat_caco2.xls"
        dir: *dir_caco2
        smiles_col: "SMILES"
        task: "reg"
        unit: "log(cm/s)"
        target_cols: ["LogPapp(cm/s)"]
        short_cols:
#          ID: "Chemical_name"
          SMILES: "SMILES"
          ACTIVITY: "LogPapp(cm/s)"
#          Activity_ori: "Papp(cm/s)"
        open_kwargs: {}
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "ADMETSAR2.0 - 10.1093/bioinformatics/bty707"

    Pampa:
      - filename: "external1_CHEMBL1034536.csv"
        dir: *dir_pampa
        smiles_col: "SMILES"
        unit: "log(cm/s)"
        task: "reg"
        type: "logPapp"
        note: "logPapp at pH7.4"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL1034536"

      - filename: "external2_CHEMBL3431937.csv"
        dir: *dir_pampa
        smiles_col: "SMILES"
        unit: "log(cm/s)"
        task: "reg"
        type: "logPapp"
        note: "logPapp at pH7.4"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL3431937"

      - filename: "external3_CHEMBL1837545.csv"
        dir: *dir_pampa
        smiles_col: "SMILES"
        unit: "log(cm/s)"
        task: "reg"
        type: "logPapp"
        note: "logPapp at pH7.4"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL1837545"

      - filename: "external4_CHEMBL1804799.csv"
        dir: *dir_pampa
        smiles_col: "SMILES"
        unit: "log(cm/s)"
        task: "reg"
        type: "logPapp"
        note: "logPapp at pH7.4"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL1804799"

      - filename: "external5_CHEMBL905612.csv"
        dir: *dir_pampa
        smiles_col: "SMILES"
        unit: "log(cm/s)"
        task: "reg"
        type: "logPapp"
        note: "logPapp at pH7.4"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"
        ref: "CHEMBL905612"

      - filename: "model_pampa.csv"
        dir: *dir_pampa
        smiles_col: "SMILES"
        unit: "log(cm/s)"
        task: "reg"
        type: "logPapp"
        note: "logPapp at pH7.4"
        target_cols: ["Activity"]
        short_cols:
#          ID: "ID"
          SMILES: "SMILES"
          ACTIVITY: "Activity"
        open_kwargs:
          sep: ";"
        opt_kwargs:
          value: -6
          type: "HI"

    MDCK:
      - filename: "perm1.csv"
        dir: *dir_mdck
        smiles_col: "SMILES"
        unit:
        task: "reg"
        target_cols: ["MDCK"]
        short_cols:
#          SID: "SID"
          CID: "CID"
          ACTIVITY: "MDCK"
        open_kwargs:
          sep: ","
        ref: ""
        # to be added

      - filename: "perm2.csv"
        dir: *dir_mdck
        smiles_col: "SMILES"
        unit:
        task: "reg"
        target_cols: ["MDCK"]
        short_cols:
#          SID: "SID"
          CID: "CID"
          ACTIVITY: "MDCK"
        open_kwargs:
          sep: ","
        ref: ""

  Efflux:
    dir: &dir_efflux "s3://datasets-ressources/PADMET_Panel/Absorption/Efflux/"
    Efflux:
      - filename: "efflux1.csv"
        dir: *dir_efflux
        smiles_col: "SMILES"
        unit:
        task: "reg"
        target_cols: ["EFFLUX"]
        short_cols:
#          SID: "SID"
          CID: "CID"
          ACTIVITY: "EFFLUX"
        open_kwargs: {}
        ref: ""

      - filename: "efflux2.csv"
        dir: *dir_efflux
        smiles_col: "SMILES"
        unit:
        task: "reg"
        target_cols: ["EFFLUX"]
        short_cols:
#          SID: "SID"
          CID: "CID"
          ACTIVITY: "EFFLUX"
        open_kwargs: {}
        ref: ""
