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modal_endpoint.py
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import json
import os
from typing import Dict
from fastapi import Depends, FastAPI, HTTPException, status
from fastapi.responses import Response
from fastapi.security import HTTPAuthorizationCredentials, HTTPBearer
from modal import Image, Secret, Stub, asgi_app
stub = Stub("drugcrow")
web_app = FastAPI()
auth_scheme = HTTPBearer()
image = (
Image.debian_slim(python_version="3.11")
.pip_install(
"langchain==0.1.16",
"langchain-openai",
"pandas",
"numpy",
"scipy",
"matplotlib",
"google-cloud-bigquery",
"db-dtypes",
"networkx"
)
)
with image.imports():
import os
from langchain.agents import AgentExecutor
from langchain.callbacks.streaming_stdout import StreamingStdOutCallbackHandler
from langchain_openai import ChatOpenAI
from google.cloud.bigquery.client import Client
from langchain.agents import OpenAIFunctionsAgent, ZeroShotAgent
import json
import os.path
from langchain_core.prompts import PromptTemplate
import json
import pickle
import networkx as nx
def find_shortest_path(graph, start, end):
try:
path = nx.shortest_path(graph, start, end)
out_path = [(n, graph.nodes[n]["node_type"]) for n in path]
return out_path
except nx.NetworkXNoPath:
return None
def format_query(start, end, path, schema):
query = f"Write a SQL query to find the relationship between the columns {start} and {end}. "
query += "Here is are the schema of some relevant tables:\n\n"
for node, node_type in path:
if node_type == "table":
table = next(t for t in schema if t["TableName"].upper() == node)
query += f'Table: {table["TableName"]}\n'
for column in table["Columns"]:
key = column["Keys"]
query += f'Column: {column["ColumnName"]}, Type: {column["DataType"]}, Key type: {key or "n/a"}\n'
query += "\n"
return query
with open("service-account.json", "w") as f:
f.write(json.dumps())
os.environ['GOOGLE_APPLICATION_CREDENTIALS'] = "service-account.json"
client = Client()
llm = ChatOpenAI(
temperature=0.1,
model="gpt-4-turbo",
openai_api_key="",
)
from langchain_core.messages import HumanMessage, SystemMessage
# tools = []
# agent_instance = AgentExecutor.from_agent_and_tools(
# tools=tools,
# agent=OpenAIFunctionsAgent.from_llm_and_tools(llm, tools),
# handle_parsing_errors=True,
# )
@stub.function(image=image, gpu="a100")
def answer(question:str):
found_columns = []
json_objects = [
{
"TableName": "ACTION_TYPE",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ACTION_TYPE",
"DataType": "VARCHAR2(50)",
"Noneable": "NOT None",
"Comment": "Primary key. Type of action of the drug e.g., agonist, antagonist"
},
{
"Keys": None,
"ColumnName": "DESCRIPTION",
"DataType": "VARCHAR2(200)",
"Noneable": "NOT None",
"Comment": "Description of how the action type is used"
},
{
"Keys": None,
"ColumnName": "PARENT_TYPE",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Higher-level grouping of action types e.g., positive vs negative action"
}
]
},
{
"TableName": "ACTIVITIES",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ACTIVITY_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Unique ID for the activity row"
},
{
"Keys": "FK",
"ColumnName": "ASSAY_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Foreign key to the assays table (containing the assay description)"
},
{
"Keys": "FK",
"ColumnName": "DOC_ID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Foreign key to documents table (for quick lookup of publication details - can also link to documents through compound_records or assays table)"
},
{
"Keys": "FK",
"ColumnName": "RECORD_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Foreign key to the compound_records table (containing information on the compound tested)"
},
{
"Keys": "FK",
"ColumnName": "MOLREGNO",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Foreign key to compounds table (for quick lookup of compound structure - can also link to compounds through compound_records table)"
},
{
"Keys": None,
"ColumnName": "STANDARD_RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Symbol constraining the activity value (e.g. >, <, =)"
},
{
"Keys": None,
"ColumnName": "STANDARD_VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Same as PUBLISHED_VALUE but transformed to common units: e.g. mM concentrations converted to nM."
},
{
"Keys": None,
"ColumnName": "STANDARD_UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Selected 'Standard' units for data type: e.g. concentrations are in nM."
},
{
"Keys": None,
"ColumnName": "STANDARD_FLAG",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Shows whether the standardised columns have been curated/set (1) or just default to the published data (0)."
},
{
"Keys": None,
"ColumnName": "STANDARD_TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": None,
"Comment": "Standardised version of the published_activity_type (e.g. IC50 rather than Ic-50/Ic50/ic50/ic-50)"
},
{
"Keys": None,
"ColumnName": "ACTIVITY_COMMENT",
"DataType": "VARCHAR2(4000)",
"Noneable": None,
"Comment": "Previously used to report non-numeric activities i.e. 'Slighty active', 'Not determined'. STANDARD_TEXT_VALUE will be used for this in future, and this will be just for additional comments."
},
{
"Keys": "FK",
"ColumnName": "DATA_VALIDITY_COMMENT",
"DataType": "VARCHAR2(30)",
"Noneable": None,
"Comment": "Comment reflecting whether the values for this activity measurement are likely to be correct - one of 'Manually validated' (checked original paper and value is correct), 'Potential author error' (value looks incorrect but is as reported in the original paper), 'Outside typical range' (value seems too high/low to be correct e.g., negative IC50 value), 'Non standard unit type' (units look incorrect for this activity type)."
},
{
"Keys": None,
"ColumnName": "POTENTIAL_DUPLICATE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "When set to 1, indicates that the value is likely to be a repeat citation of a value reported in a previous ChEMBL paper, rather than a new, independent measurement. Note: value of zero does not guarantee that the measurement is novel/independent though"
},
{
"Keys": None,
"ColumnName": "PCHEMBL_VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Negative log of selected concentration-response activity values (IC50/EC50/XC50/AC50/Ki/Kd/Potency)"
},
{
"Keys": "FK",
"ColumnName": "BAO_ENDPOINT",
"DataType": "VARCHAR2(11)",
"Noneable": None,
"Comment": "ID for the corresponding result type in BioAssay Ontology (based on standard_type)"
},
{
"Keys": None,
"ColumnName": "UO_UNITS",
"DataType": "VARCHAR2(10)",
"Noneable": None,
"Comment": "ID for the corresponding unit in Unit Ontology (based on standard_units)"
},
{
"Keys": None,
"ColumnName": "QUDT_UNITS",
"DataType": "VARCHAR2(70)",
"Noneable": None,
"Comment": "ID for the corresponding unit in QUDT Ontology (based on standard_units)"
},
{
"Keys": None,
"ColumnName": "TOID",
"DataType": "INTEGER",
"Noneable": None,
"Comment": "The Test Occasion Identifier, used to group together related activity measurements"
},
{
"Keys": None,
"ColumnName": "UPPER_VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Where the activity is a range, this represents the highest value of the range (numerically), while the PUBLISHED_VALUE column represents the lower value"
},
{
"Keys": None,
"ColumnName": "STANDARD_UPPER_VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Where the activity is a range, this represents the standardised version of the highest value of the range (with the lower value represented by STANDARD_VALUE)"
},
{
"Keys": "FK",
"ColumnName": "SRC_ID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Foreign key to source table, indicating the source of the activity value"
},
{
"Keys": None,
"ColumnName": "TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": "NOT None",
"Comment": "Type of end-point measurement: e.g. IC50, LD50, %inhibition etc, as it appears in the original dataset"
},
{
"Keys": None,
"ColumnName": "RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Symbol constraining the activity value (e.g. >, <, =), as it appears in the original dataset"
},
{
"Keys": None,
"ColumnName": "VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Datapoint value as it appears in the original dataset."
},
{
"Keys": None,
"ColumnName": "UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Units of measurement as they appear in the original dataset"
},
{
"Keys": None,
"ColumnName": "TEXT_VALUE",
"DataType": "VARCHAR2(1000)",
"Noneable": None,
"Comment": "Additional information about the measurement"
},
{
"Keys": None,
"ColumnName": "STANDARD_TEXT_VALUE",
"DataType": "VARCHAR2(1000)",
"Noneable": None,
"Comment": "Standardized version of additional information about the measurement"
},
{
"Keys": "FK",
"ColumnName": "ACTION_TYPE",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Foreign key to action_type table; specifies the effect of the compound on its target."
}
]
},
{
"TableName": "ACTIVITY_PROPERTIES",
"Columns": [
{
"Keys": "PK",
"ColumnName": "AP_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Unique ID for each record."
},
{
"Keys": "FK,UK",
"ColumnName": "ACTIVITY_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "FK to ACTIVITY_ID in ACTIVITIES table."
},
{
"Keys": "UK",
"ColumnName": "TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": "NOT None",
"Comment": "The parameter or property type"
},
{
"Keys": None,
"ColumnName": "RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Symbol constraining the value (e.g. >, <, =)"
},
{
"Keys": None,
"ColumnName": "VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Numberical value for the parameter or property"
},
{
"Keys": None,
"ColumnName": "UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Units of measurement"
},
{
"Keys": None,
"ColumnName": "TEXT_VALUE",
"DataType": "VARCHAR2(2000)",
"Noneable": None,
"Comment": "Non-numerical value of the parameter or property"
},
{
"Keys": None,
"ColumnName": "STANDARD_TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": None,
"Comment": "Standardised form of the TYPE"
},
{
"Keys": None,
"ColumnName": "STANDARD_RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Standardised form of the RELATION"
},
{
"Keys": None,
"ColumnName": "STANDARD_VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Standardised form of the VALUE"
},
{
"Keys": None,
"ColumnName": "STANDARD_UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Standardised form of the UNITS"
},
{
"Keys": None,
"ColumnName": "STANDARD_TEXT_VALUE",
"DataType": "VARCHAR2(2000)",
"Noneable": None,
"Comment": "Standardised form of the TEXT_VALUE"
},
{
"Keys": None,
"ColumnName": "COMMENTS",
"DataType": "VARCHAR2(2000)",
"Noneable": None,
"Comment": "A Comment."
},
{
"Keys": None,
"ColumnName": "RESULT_FLAG",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "A flag to indicate, if set to 1, that this type is a dependent variable/result (e.g., slope) rather than an independent variable/parameter (0, the default)."
}
]
},
{
"TableName": "ACTIVITY_SMID",
"Columns": [
{
"Keys": "PK",
"ColumnName": "SMID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "FK to SMID in ACTIVITY_SUPP_MAP, and a FK to SMID in ACTIVITY_SUPP"
}
]
},
{
"TableName": "ACTIVITY_STDS_LOOKUP",
"Columns": [
{
"Keys": "PK",
"ColumnName": "STD_ACT_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Primary key."
},
{
"Keys": "UK",
"ColumnName": "STANDARD_TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": "NOT None",
"Comment": "The standard_type that other published_types in the activities table have been converted to."
},
{
"Keys": None,
"ColumnName": "DEFINITION",
"DataType": "VARCHAR2(500)",
"Noneable": None,
"Comment": "A description/definition of the standard_type."
},
{
"Keys": "UK",
"ColumnName": "STANDARD_UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": "NOT None",
"Comment": "The units that are applied to this standard_type and to which other published_units are converted. Note a standard_type may have more than one allowable standard_unit and therefore multiple rows in this table."
},
{
"Keys": None,
"ColumnName": "NORMAL_RANGE_MIN",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "The lowest value for this activity type that is likely to be genuine. This is only an approximation, so lower genuine values may exist, but it may be desirable to validate these before using them. For a given standard_type/units, values in the activities table below this threshold are flagged with a data_validity_comment of 'Outside typical range'."
},
{
"Keys": None,
"ColumnName": "NORMAL_RANGE_MAX",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "The highest value for this activity type that is likely to be genuine. This is only an approximation, so higher genuine values may exist, but it may be desirable to validate these before using them. For a given standard_type/units, values in the activities table above this threshold are flagged with a data_validity_comment of 'Outside typical range'."
}
]
},
{
"TableName": "ACTIVITY_SUPP",
"Columns": [
{
"Keys": "PK",
"ColumnName": "AS_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Unique ID for each record."
},
{
"Keys": "UK",
"ColumnName": "RGID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Record Grouping ID, used to group together related data points in this table"
},
{
"Keys": "FK",
"ColumnName": "SMID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "FK to SMID in ACTIVITY_SMID."
},
{
"Keys": "UK",
"ColumnName": "TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": "NOT None",
"Comment": "Type of end-point measurement: e.g. IC50, LD50, %inhibition etc, as it appears in the original dataset"
},
{
"Keys": None,
"ColumnName": "RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Symbol constraining the activity value (e.g. >, <, =), as it appears in the original dataset"
},
{
"Keys": None,
"ColumnName": "VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Datapoint value as it appears in the original dataset."
},
{
"Keys": None,
"ColumnName": "UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Units of measurement as they appear in the original dataset"
},
{
"Keys": None,
"ColumnName": "TEXT_VALUE",
"DataType": "VARCHAR2(1000)",
"Noneable": None,
"Comment": "Non-numeric value for measurement as in original dataset"
},
{
"Keys": None,
"ColumnName": "STANDARD_TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": None,
"Comment": "Standardised form of the TYPE"
},
{
"Keys": None,
"ColumnName": "STANDARD_RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Standardised form of the RELATION"
},
{
"Keys": None,
"ColumnName": "STANDARD_VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Standardised form of the VALUE"
},
{
"Keys": None,
"ColumnName": "STANDARD_UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Standardised form of the UNITS"
},
{
"Keys": None,
"ColumnName": "STANDARD_TEXT_VALUE",
"DataType": "VARCHAR2(1000)",
"Noneable": None,
"Comment": "Standardised form of the TEXT_VALUE"
},
{
"Keys": None,
"ColumnName": "COMMENTS",
"DataType": "VARCHAR2(4000)",
"Noneable": None,
"Comment": "A Comment."
}
]
},
{
"TableName": "ACTIVITY_SUPP_MAP",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ACTSM_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Primary key"
},
{
"Keys": "FK",
"ColumnName": "ACTIVITY_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "FK to ACTIVITY_ID in ACTIVITIES table."
},
{
"Keys": "FK",
"ColumnName": "SMID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "FK to SMID in ACTIVITY_SMID."
}
]
},
{
"TableName": "ASSAY_CLASS_MAP",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ASS_CLS_MAP_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Primary key."
},
{
"Keys": "FK,UK",
"ColumnName": "ASSAY_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Foreign key that maps to the ASSAYS table"
},
{
"Keys": "FK,UK",
"ColumnName": "ASSAY_CLASS_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Foreign key that maps to the ASSAY_CLASSIFICATION table"
}
]
},
{
"TableName": "ASSAY_CLASSIFICATION",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ASSAY_CLASS_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Primary key"
},
{
"Keys": None,
"ColumnName": "L1",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "High level classification e.g., by anatomical/therapeutic area"
},
{
"Keys": None,
"ColumnName": "L2",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Mid-level classification e.g., by phenotype/biological process"
},
{
"Keys": "UK",
"ColumnName": "L3",
"DataType": "VARCHAR2(1000)",
"Noneable": None,
"Comment": "Fine-grained classification e.g., by assay type"
},
{
"Keys": None,
"ColumnName": "CLASS_TYPE",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "The type of assay being classified e.g., in vivo efficacy"
},
{
"Keys": None,
"ColumnName": "SOURCE",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Source from which the assay class was obtained"
}
]
},
{
"TableName": "ASSAY_PARAMETERS",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ASSAY_PARAM_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Numeric primary key"
},
{
"Keys": "FK,UK",
"ColumnName": "ASSAY_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Foreign key to assays table. The assay to which this parameter belongs"
},
{
"Keys": "UK",
"ColumnName": "TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": "NOT None",
"Comment": "The type of parameter being described, according to the original data source"
},
{
"Keys": None,
"ColumnName": "RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "The relation symbol for the parameter being described, according to the original data source"
},
{
"Keys": None,
"ColumnName": "VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "The value of the parameter being described, according to the original data source. Used for numeric data"
},
{
"Keys": None,
"ColumnName": "UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "The units for the parameter being described, according to the original data source"
},
{
"Keys": None,
"ColumnName": "TEXT_VALUE",
"DataType": "VARCHAR2(4000)",
"Noneable": None,
"Comment": "The text value of the parameter being described, according to the original data source. Used for non-numeric/qualitative data"
},
{
"Keys": None,
"ColumnName": "STANDARD_TYPE",
"DataType": "VARCHAR2(250)",
"Noneable": None,
"Comment": "Standardized form of the TYPE"
},
{
"Keys": None,
"ColumnName": "STANDARD_RELATION",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Standardized form of the RELATION"
},
{
"Keys": None,
"ColumnName": "STANDARD_VALUE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Standardized form of the VALUE"
},
{
"Keys": None,
"ColumnName": "STANDARD_UNITS",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Standardized form of the UNITS"
},
{
"Keys": None,
"ColumnName": "STANDARD_TEXT_VALUE",
"DataType": "VARCHAR2(4000)",
"Noneable": None,
"Comment": "Standardized form of the TEXT_VALUE"
},
{
"Keys": None,
"ColumnName": "COMMENTS",
"DataType": "VARCHAR2(4000)",
"Noneable": None,
"Comment": "Additional comments describing the parameter"
}
]
},
{
"TableName": "ASSAY_TYPE",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ASSAY_TYPE",
"DataType": "VARCHAR2(1)",
"Noneable": "NOT None",
"Comment": "Single character representing assay type"
},
{
"Keys": None,
"ColumnName": "ASSAY_DESC",
"DataType": "VARCHAR2(250)",
"Noneable": None,
"Comment": "Description of assay type"
}
]
},
{
"TableName": "ASSAYS",
"Columns": [
{
"Keys": "PK",
"ColumnName": "ASSAY_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Unique ID for the assay"
},
{
"Keys": "FK",
"ColumnName": "DOC_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Foreign key to documents table"
},
{
"Keys": None,
"ColumnName": "DESCRIPTION",
"DataType": "VARCHAR2(4000)",
"Noneable": None,
"Comment": "Description of the reported assay"
},
{
"Keys": "FK",
"ColumnName": "ASSAY_TYPE",
"DataType": "VARCHAR2(1)",
"Noneable": None,
"Comment": "Assay classification, e.g. B=Binding assay, A=ADME assay, F=Functional assay"
},
{
"Keys": None,
"ColumnName": "ASSAY_TEST_TYPE",
"DataType": "VARCHAR2(20)",
"Noneable": None,
"Comment": "Type of assay system (i.e., in vivo or in vitro)"
},
{
"Keys": None,
"ColumnName": "ASSAY_CATEGORY",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "screening, confirmatory (ie: dose-response), summary, panel, other,Thermal shift assay QC liability, Thermal shift assay, Affinity biochemical assay, Incucyte cell viability, Affinity phenotypic cellular assay, HTRF assay, Selectivity assay, Cell health data, NanoBRET assay, Alphascreen assay, Affinity on-target cellular assay, ITC assay, GPCR beta-arrestin recruitment assay"
},
{
"Keys": None,
"ColumnName": "ASSAY_ORGANISM",
"DataType": "VARCHAR2(250)",
"Noneable": None,
"Comment": "Name of the organism for the assay system (e.g., the organism, tissue or cell line in which an assay was performed). May differ from the target organism (e.g., for a human protein expressed in non-human cells, or pathogen-infected human cells)."
},
{
"Keys": None,
"ColumnName": "ASSAY_TAX_ID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "NCBI tax ID for the assay organism."
},
{
"Keys": None,
"ColumnName": "ASSAY_STRAIN",
"DataType": "VARCHAR2(200)",
"Noneable": None,
"Comment": "Name of specific strain of the assay organism used (where known)"
},
{
"Keys": None,
"ColumnName": "ASSAY_TISSUE",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Name of tissue used in the assay system (e.g., for tissue-based assays) or from which the assay system was derived (e.g., for cell/subcellular fraction-based assays)."
},
{
"Keys": None,
"ColumnName": "ASSAY_CELL_TYPE",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Name of cell type or cell line used in the assay system (e.g., for cell-based assays)."
},
{
"Keys": None,
"ColumnName": "ASSAY_SUBCELLULAR_FRACTION",
"DataType": "VARCHAR2(100)",
"Noneable": None,
"Comment": "Name of subcellular fraction used in the assay system (e.g., microsomes, mitochondria)."
},
{
"Keys": "FK",
"ColumnName": "TID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Target identifier to which this assay has been mapped. Foreign key to target_dictionary. From ChEMBL_15 onwards, an assay will have only a single target assigned."
},
{
"Keys": "FK",
"ColumnName": "RELATIONSHIP_TYPE",
"DataType": "VARCHAR2(1)",
"Noneable": None,
"Comment": "Flag indicating of the relationship between the reported target in the source document and the assigned target from TARGET_DICTIONARY. Foreign key to RELATIONSHIP_TYPE table."
},
{
"Keys": "FK",
"ColumnName": "CONFIDENCE_SCORE",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Confidence score, indicating how accurately the assigned target(s) represents the actually assay target. Foreign key to CONFIDENCE_SCORE table. 0 means uncurated/unassigned, 1 = low confidence to 9 = high confidence."
},
{
"Keys": "FK",
"ColumnName": "CURATED_BY",
"DataType": "VARCHAR2(32)",
"Noneable": None,
"Comment": "Indicates the level of curation of the target assignment. Foreign key to curation_lookup table."
},
{
"Keys": "FK",
"ColumnName": "SRC_ID",
"DataType": "NUMBER",
"Noneable": "NOT None",
"Comment": "Foreign key to source table"
},
{
"Keys": None,
"ColumnName": "SRC_ASSAY_ID",
"DataType": "VARCHAR2(50)",
"Noneable": None,
"Comment": "Identifier for the assay in the source database/deposition (e.g., pubchem AID)"
},
{
"Keys": "FK,UK",
"ColumnName": "CHEMBL_ID",
"DataType": "VARCHAR2(20)",
"Noneable": "NOT None",
"Comment": "ChEMBL identifier for this assay (for use on web interface etc)"
},
{
"Keys": "FK",
"ColumnName": "CELL_ID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Foreign key to cell dictionary. The cell type or cell line used in the assay"
},
{
"Keys": "FK",
"ColumnName": "BAO_FORMAT",
"DataType": "VARCHAR2(11)",
"Noneable": None,
"Comment": "ID for the corresponding format type in BioAssay Ontology (e.g., cell-based, biochemical, organism-based etc)"
},
{
"Keys": "FK",
"ColumnName": "TISSUE_ID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "ID for the corresponding tissue/anatomy in Uberon. Foreign key to tissue_dictionary"
},
{
"Keys": "FK",
"ColumnName": "VARIANT_ID",
"DataType": "NUMBER",
"Noneable": None,
"Comment": "Foreign key to variant_sequences table. Indicates the mutant/variant version of the target used in the assay (where known/applicable)"
},
{
"Keys": None,
"ColumnName": "AIDX",
"DataType": "VARCHAR2(200)",
"Noneable": "NOT None",
"Comment": "The Depositor Defined Assay Identifier"
}
]
},
{
"TableName": "ATC_CLASSIFICATION",
"Columns": [
{
"Keys": None,
"ColumnName": "WHO_NAME",
"DataType": "VARCHAR2(2000)",
"Noneable": None,
"Comment": "WHO/INN name for the compound"
},
{
"Keys": None,
"ColumnName": "LEVEL1",
"DataType": "VARCHAR2(10)",
"Noneable": None,
"Comment": "First level of classification"
},
{
"Keys": None,
"ColumnName": "LEVEL2",
"DataType": "VARCHAR2(10)",
"Noneable": None,
"Comment": "Second level of classification"
},
{
"Keys": None,
"ColumnName": "LEVEL3",
"DataType": "VARCHAR2(10)",
"Noneable": None,
"Comment": "Third level of classification"
},
{
"Keys": None,