Skip to main content

A tool for extractor patent literature in drug discovery

Project description

PEMT: A tool for extracting patent literature in drug discovery
Documentation Status PEMT on PyPI MIT

Table of Contents

General Info

PEMT is a patent extractor tool that enables users to retrieve patents relevant to drug discovery. The overall workflow of the tool can be seen in the figure below:

Installation

$ pip install PEMT

The most recent code can be installed from the source on GitHub with:

$ pip install git+https://github.com/Fraunhofer-ITMP/PEMT.git

Alternatively, for developer the tool can be installed in an editable mode as shown below:

$ git clone https://github.com/Fraunhofer-ITMP/PEMT.git
$ conda create --name pemt python=3.8
$ conda activate pemt
$ cd PEMT
$ pip install pemt

For developers, the repository can be cloned from GitHub and installed in editable mode with:

$ git clone https://github.com/Fraunhofer-ITMP/PEMT.git
$ cd PEMT
$ pip install -e .

Documentation

Read the official docs for more information.

Input Data Formats

Data

For running PEMT from the gene level, you need the input file with the following structure:

symbol uniprot
HGNC_Symbol_1 Uniprot_ID_1
HGNC_Symbol_2 Uniprot_ID_2
HGNC_Symbol_3 Uniprot_ID_3

For running PEMT from the chemical level, you need the input file with the following structure:

chembl
ChEMBL_ID_1
ChEMBL_ID_2
ChEMBL_ID_3

Note: The data must be in a comma or tab separated file format. If not so, the file should have at least one of the columns shown above.

Usage

In-order to use PEMT, an installation of chromedriver is required.

As mentioned above, the tool has a two-step approach. Each of these steps can be run individually as well as together as show belwo:

  1. Chemical enrichment The following command links chemicals to genes of interest based on causality. In this command it is necessary to indicate whether the file contains uniprot ids or not with the --uniprot or --no-uniprot parameter.
$ pemt run-chemical-extractor --name=<ANALYSIS NAME> --data=<DATA FILE PATH> --input-type=<DATA FILE SEPARATOR> --uniprot
  1. Patent enrichment The following command interlinks chemicals to patent literature publicly available.
$ pemt run-patent-extractor --name=<ANALYSIS NAME> --chromedriver-path=<PATH TO CHROMEDRIVER> --os=<OS NAME> --no-chemical

We also allow the flexibility to start the pipeline from this step, if the user has list of chemicals in the right format as indicated above. The user then has to use the tag --chemical and provide a respective --chemical-data path.

  1. PEMT workflow The following command generates the patent enrichment on the gene data where the gene data file is a TSV file containing uniprot identifiers.
$ pemt run-pemt --name=<ANALYSIS NAME> --data=<DATA FILE PATH> --input-type=<DATA FILE SEPARATOR> --chromedriver-path=<PATH TO CHROMEDRIVER> --os=<OS NAME>

Issues

If you have difficulties using PEMT, please open an issue at our GitHub repository.

Disclaimer

PET is a scientific tool that has been developed in an academic capacity, and thus comes with no warranty or guarantee of maintenance, support, or back-up of data.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

PEMT-0.0.2.tar.gz (60.1 kB view details)

Uploaded Source

File details

Details for the file PEMT-0.0.2.tar.gz.

File metadata

  • Download URL: PEMT-0.0.2.tar.gz
  • Upload date:
  • Size: 60.1 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.8.13

File hashes

Hashes for PEMT-0.0.2.tar.gz
Algorithm Hash digest
SHA256 11c5c1f2d2f931a5dab36557b2a4b3e9be91a4a2fccd64712d9dba16d78b1b0e
MD5 55a783da0ea9a2c22e39ca53751e9b2e
BLAKE2b-256 0faf9d0835cc98bd329683c924483ae7f280c2d289970b80c068c9cac1971839

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page