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Add Toxcast with an assay description 90k datapoint for 158 assay #346

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Add Toxcast with an assay description 90k datapoint for 158 assay #346

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85 changes: 85 additions & 0 deletions data/toxcast_with_description/meta.yaml
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name: toxcast_with_description
description: ToxCast includes qualitative results of over 600 experiments on 8k compounds.
targets:
- id: Toxicity
description: Presence (1) or absence(0) 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
- id: assay_desc
description: Description of the Assay where the compound tested
units: ''
type: text
names:
- noun: Toxicity description
- noun: Toxicity assay description
- noun: Experimental assay description
- noun: Description of a given assay
uris:
- https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C60819
- id: Organism
description: cell origin for which assay is tested
units: ''
type: categorical
names:
- noun: The organism that the cell isolate from
- noun: For which organism cell related to
- noun: living that the cell isolate from
uris:
- http://purl.bioontology.org/ontology/CCON
- id: tissue
description: Tissue where cell isolated from
units: ''
type: categorical
names:
- noun: Tissue
- noun: body
- noun: Experimental assay description
uris:
- http://purl.obolibrary.org/obo/NCIT_C12801
- id: cell_format
description: cell format
units: ''
type: categorical
names:
- noun: cell format
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://doi.org/10.23645/epacomptox.6062623.v10
description: data source
- url: https://tdcommons.ai/single_pred_tasks/tox/#toxcast
description: data source
num_points: 90145
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}
195 changes: 195 additions & 0 deletions data/toxcast_with_description/transform.py
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import pandas as pd
import yaml
import requests

def get_and_transform_data():
target_folder = "toxcast_with_description"
url = "https://huggingface.co/datasets/phalem/awesome_chem_clean_data/resolve/main/Toxcast_with_description.csv.gz"
df = pd.read_csv(url, compression='gzip')
fn_data_original = 'data_original.csv'
df.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',
'Target',
'assay_desc',
'organism',
'tissue',
'cell_format']

fields_clean = ['Drug_ID',
'SMILES',
'Toxicity',
'Assay',
'assay_desc',
'organism',
'tissue',
'cell_format']

df.columns = fields_clean
assert fields_orig != fields_clean
df = df.drop_duplicates()
assert not df.duplicated().sum()
fn_data_csv = "data_clean.csv"
df.to_csv(fn_data_csv, index=False)

meta = {
"name": f"{target_folder}", # 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 (1) or absence(0) 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",
],
},
{
"id": "assay_desc", # name of the column in a tabular dataset
"description": "Description of the Assay where the compound tested", # description of what this column means
"units": "", # units of the values in this column (leave empty if unitless)
"type": "text", # can be "categorical", "ordinal", "continuous"
"names": [ # names for the property (to sample from for building the prompts)
{"noun": "Toxicity description"},
{"noun": "Toxicity assay description"},
{"noun": "Experimental assay description"},
{"noun": "Description of a given assay"},
],
"uris":[
"https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C60819",
],
},
{
"id": "Organism", # name of the column in a tabular dataset
"description": "cell origin for which assay is 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": "The organism that the cell isolate from"},
{"noun": "For which organism cell related to"},
{"noun": "living that the cell isolate from"},
],
"uris":[
"http://purl.bioontology.org/ontology/CCON", #organism
],
},
{
"id": "tissue", # name of the column in a tabular dataset
"description": "Tissue where cell isolated from", # 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": "Tissue"},
{"noun": "body"},
{"noun": "Experimental assay description"},
],
"uris":[
"http://purl.obolibrary.org/obo/NCIT_C12801"
],
},
{
"id": "cell_format", # name of the column in a tabular dataset
"description": "cell format", # 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": "cell format"},

],
},

],
"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://doi.org/10.23645/epacomptox.6062623.v10",
"description": "data source",
},

{
"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}""",
# """@misc{https://doi.org/10.23645/epacomptox.6062623.v8,
# doi = {10.23645/EPACOMPTOX.6062623.V8},
# url = {https://epa.figshare.com/articles/dataset/ToxCast_Database_invitroDB_/6062623/8},
# author = {Toxicology, EPA's National Center for Computational},
# keywords = {Toxicology (incl. clinical toxicology)},
# title = {ToxCast Database (invitroDB)},
# publisher = {The United States Environmental Protection Agency’s Center for Computational Toxicology and Exposure},
# year = {2022},
# copyright = {Creative Commons Zero v1.0 Universal}"""

]
}


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()