pubchem's Introduction

Bio2BEL PubChem

This repository has multiple goals, most importantly: mapping between MeSH, PubChem, and standard chemical identifiers. Currently, this information is scattered and incredibly difficult to access. First the following resources are available:

Data

ftp://ftp.ncbi.nih.gov/pubchem/Compound/Extras/README-Extras
- Map to MeSH with ftp://ftp.ncbi.nih.gov/pubchem/Compound/Extras/CID-MeSH
- Map to Substance with ftp://ftp.ncbi.nih.gov/pubchem/Compound/Extras/CID-SID.gz
- Map to InChI with ftp://ftp.ncbi.nih.gov/pubchem/Compound/Extras/CID-InChI-Key.gz
ftp://ftp.ncbi.nih.gov/pubchem/Substance/Extras/README-Extras
- Map to MeSH with ftp://ftp.ncbi.nih.gov/pubchem/Substance/Extras/SID-MeSH
- Map to other databases with ftp://ftp.ncbi.nih.gov/pubchem/Substance/Extras/SID-Map.gz

Installation

bio2bel_pubchem can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_pubchem

or from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/pubchem.git@master

Setup

PubChem can be downloaded and populated from either the Python REPL or the automatically installed command line utility.

Python REPL

>>> import bio2bel_pubchem
>>> pubchem_manager = bio2bel_pubchem.Manager()
>>> pubchem_manager.populate()

Command Line Utility

bio2bel_pubchem populate

pubchem's People

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pubchem's Issues

How to map MESHC to MeSH terms?

Population of SID-Map

Make authors list

Population of SID-MeSH

sqlalchemy library changed - import statement throws error

Dear creators of pubchem,
I tried to run your code, and it throws the following error:

_/opt/conda/lib/python3.9/site-packages/bio2bel/manager/abstract_manager.py in
12 import click
13 from more_click import verbose_option
---> 14 from sqlalchemy.ext.declarative.api import DeclarativeMeta
15
16 from .cli_manager import CliMixin

ModuleNotFoundError: No module named 'sqlalchemy.ext.declarative.api'_

It would appear that the structure of the sqlalchemy library has changed in the meantime, which messed up your import statement:

https://docs.sqlalchemy.org/en/14/orm/mapping_api.html#sqlalchemy.orm.declarative_base

Changed in version 1.4: The declarative_base() function is now a specialization of the more generic registry class. The function also moves to the sqlalchemy.orm package from the declarative.ext package.

It would be great if you could have a look.
Thanks a lot!
Jesko