Add ToxCast 1.5m datapoint for 8K mol on 617 assay

data/toxcast/meta.yaml

@@ -0,0 +1,46 @@
+name: toxcast
+description: ToxCast includes qualitative results of over 600 experiments on 8k compounds.
+targets:
+- id: Toxicity
+  description: Presence of a compound toxicity in a specific assay.
+  units: ''
+  type: categorical
+  names:
+  - noun: Toxicity
+  - noun: Toxic compound
+  - noun: Toxicity in specific assay
+- id: Assay
+  description: Assay where the compound tested
+  units: ''
+  type: categorical
+  names:
+  - noun: Toxicity
+  - noun: Toxicity assay
+  - noun: Experimental assay
+  uris:
+  - https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C60819
+identifiers:
+- id: SMILES
+  type: SMILES
+  description: SMILES
+license: CC BY 4.0
+links:
+- url: https://doi.org/10.1021/acs.chemrestox.6b00135
+  description: corresponding publication
+- url: https://tdcommons.ai/single_pred_tasks/tox/#toxcast
+  description: data source
+num_points: 1533660
+bibtex:
+- |-
+  @article{Richard2016,
+                doi = {10.1021/acs.chemrestox.6b00135},
+                url = {https://doi.org/10.1021/acs.chemrestox.6b00135},
+                year = {2016},
+                month = jul,
+                publisher = {American Chemical Society (ACS)},
+                volume = {29},
+                number = {8},
+                pages = {1225--1251},
+                author = {Ann M. Richard and Richard S. Judson and Keith A. Houck and Christopher M. Grulke and Patra Volarath and Inthirany Thillainadarajah and Chihae Yang and James Rathman and Matthew T. Martin and John F. Wambaugh and Thomas B. Knudsen and Jayaram Kancherla and Kamel Mansouri and Grace Patlewicz and Antony J. Williams and Stephen B. Little and Kevin M. Crofton and Russell S. Thomas},
+                title = {ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology},
+                journal = {Chemical Research in Toxicology}

data/toxcast/transform.py

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+import pandas as pd
+import yaml
+from tdc.single_pred import Tox
+from tdc.utils import retrieve_label_name_list
+
+def get_and_transform_data():
+    label = 'ToxCast'
+
+    df_all = []
+    toxcast_list = retrieve_label_name_list('Toxcast')
+    for x in toxcast_list:
+        df = Tox(name = label, label_name = x).get_data(format = 'df')
+        df['Assay'] = x
+        df_all.append(df)
+
+    df_data = pd.concat(df_all)
+    fn_data_original = 'data_original.csv'
+    df_data.to_csv(fn_data_original, index=None)
+    df = pd.read_csv(fn_data_original, delimiter=",")
+    df = df.dropna()
+    fields_orig = df.columns.tolist()
+    assert fields_orig == ['Drug_ID', 'Drug', 'Y', 'Assay']
+    fields_clean = ['Drug_ID', 'SMILES', 'Toxicity', 'Assay']
+    df.columns = fields_clean
+    assert fields_orig != fields_clean
+    assert not df.duplicated().sum()
+    fn_data_csv = "data_clean.csv"
+    df.to_csv(fn_data_csv, index=False)
+
+    meta = {
+        "name": "toxcast",  # unique identifier, we will also use this for directory names
+        "description": """ToxCast includes qualitative results of over 600 experiments on 8k compounds.""",
+        "targets": [
+            {
+                "id": "Toxicity",  # name of the column in a tabular dataset
+                "description": "Presence of a compound toxicity in a specific assay.",  # description of what this column means
+                "units": "",  # units of the values in this column (leave empty if unitless)
+                "type": "categorical",  # can be "categorical", "ordinal", "continuous"
+                "names": [  # names for the property (to sample from for building the prompts)
+                    {"noun": "Toxicity"},
+                    {"noun": "Toxic compound"},
+                    {"noun": "Toxicity in specific assay"},
+                ],
+            },
+            {
+                "id": "Assay",  # name of the column in a tabular dataset
+                "description": "Assay where the compound tested",  # description of what this column means
+                "units": "",  # units of the values in this column (leave empty if unitless)
+                "type": "categorical",  # can be "categorical", "ordinal", "continuous"
+                "names": [  # names for the property (to sample from for building the prompts)
+                    {"noun": "Toxicity"},
+                    {"noun": "Toxicity assay"},
+                    {"noun": "Experimental assay"},
+
+                ],
+                      "uris":[
+            "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C60819",
+                    ],
+            },
+
+        ],
+        "identifiers": [
+            {
+                "id": "SMILES",  # column name
+                "type": "SMILES",  # can be "SMILES", "SELFIES", "IUPAC", "Other"
+                "description": "SMILES",  # description (optional, except for "Other")
+            },
+        ],
+        "license": "CC BY 4.0",  # license under which the original dataset was published
+        "links": [  # list of relevant links (original dataset, other uses, etc.)
+            {
+                "url": "https://doi.org/10.1021/acs.chemrestox.6b00135",
+                "description": "corresponding publication",
+            },
+            {
+                "url": "https://tdcommons.ai/single_pred_tasks/tox/#toxcast",
+                "description": "data source",
+            }
+        ],
+        "num_points": len(df),  # number of datapoints in this dataset   
+        "bibtex": [
+            """@article{Richard2016,
+              doi = {10.1021/acs.chemrestox.6b00135},
+              url = {https://doi.org/10.1021/acs.chemrestox.6b00135},
+              year = {2016},
+              month = jul,
+              publisher = {American Chemical Society (ACS)},
+              volume = {29},
+              number = {8},
+              pages = {1225--1251},
+              author = {Ann M. Richard and Richard S. Judson and Keith A. Houck and Christopher M. Grulke and Patra Volarath and Inthirany Thillainadarajah and Chihae Yang and James Rathman and Matthew T. Martin and John F. Wambaugh and Thomas B. Knudsen and Jayaram Kancherla and Kamel Mansouri and Grace Patlewicz and Antony J. Williams and Stephen B. Little and Kevin M. Crofton and Russell S. Thomas},
+              title = {ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology},
+              journal = {Chemical Research in Toxicology}""",
+        ],
+    }
+
+
+    def str_presenter(dumper, data):
+        """configures yaml for dumping multiline strings
+        Ref: https://stackoverflow.com/questions/8640959/how-can-i-control-what-scalar-form-pyyaml-uses-for-my-data
+        """
+        if data.count("\n") > 0:  # check for multiline string
+            return dumper.represent_scalar("tag:yaml.org,2002:str", data, style="|")
+        return dumper.represent_scalar("tag:yaml.org,2002:str", data)
+
+    yaml.add_representer(str, str_presenter)
+    yaml.representer.SafeRepresenter.add_representer(
+        str, str_presenter
+    )  # to use with safe_dum
+    fn_meta = "meta.yaml"
+    with open(fn_meta, "w") as f:
+        yaml.dump(meta, f, sort_keys=False)
+
+    print(f"Finished processing {meta['name']} dataset!")
+
+
+if __name__ == "__main__":
+    get_and_transform_data()