The pemt from fraunhofer-itmp

chembl to surechembl mapping file source and mapping method question

Hello,

The chembl to surechembl mapping file used in the patent_chemical_harmonizer.py file from the Fraunhofer-ITMP/PEMT Github repository, as mentioned in the paper, seems to have been created based on cross-reference information between the SureChEMBL database and the ChEMBL database.
(https://github.com/Fraunhofer-ITMP/PEMT/blob/main/src/pemt/patent_extractor/patent_chemical_harmonizer.py#:~:text=https%3A//raw.githubusercontent.com/Fraunhofer%2DITMP/PEMT/main/data/mapper/chemical_mapper.json)

However, neither Chebml nor surechembl can find a connection to each other.

If you have used crawling or used other DBs or APIs, please let me know the URL link of the database or API you used.
Also, it would be appreciated if you could tell us the mapping method.

Using this, if what I test produces good results,
I plan to publish it as a paper.
Then, the PEMT papers you published can also benefit from being cited.

thank you

[BUG]: Missing data in PyPI package

Describe the bug
The chemical extractor fails due to a missing chembl_uniprot_mapping.txt file. It seems installing from PyPI omits the data directory.
After manually copying data files from the github repo to the expected directory, the error is gone (and the tool runs into a probably unrelated 500 internal server error by ebi.ac.uk).

To Reproduce
Steps to reproduce the behavior:

conda create --prefix /tmp/pemt python=3.8
conda activate /tmp/pemt
pip install PEMT
pemt run-chemical-extractor --name=symbol --data=/tmp/symbol.tsv  --uniprot

Expected behavior
Program run with exit code 0.

Error

Starting the chemical extractor pipeline for symbol
Traceback (most recent call last):
  File "/tmp/pemt/bin/pemt", line 8, in <module>
    sys.exit(main())
  File "/tmp/pemt/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/tmp/pemt/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/tmp/pemt/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/tmp/pemt/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/tmp/pemt/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/tmp/pemt/lib/python3.8/site-packages/pemt/cli.py", line 98, in run_chemical_extractor
    gene_chemical_dict = extract_chemicals(
  File "/tmp/pemt/lib/python3.8/site-packages/pemt/chemical_extractor/experimental_data_extraction.py", line 138, in extract_chemicals
    chembl_mapper = pd.read_csv(
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 482, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 811, in __init__
    self._engine = self._make_engine(self.engine)
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in __init__
    self._open_handles(src, kwds)
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/io/parsers/base_parser.py", line 222, in _open_handles
    self.handles = get_handle(
  File "/tmp/pemt/lib/python3.8/site-packages/pandas/io/common.py", line 702, in get_handle
    handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pemt/lib/python3.8/site-packages/pemt/../../data/mapper/chembl_uniprot_mapping.txt'

Desktop (please complete the following information):

OS: Ubuntu 22.04

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chembl to surechembl mapping file source and mapping method question

[BUG]: Missing data in PyPI package

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