DOI-Extractor-OEG

Description

DOI-Extractor-OEG is a tool for extracting all paper's name and DOI from OEG publications.

They are extracted from two main resources:

1. https://portalcientifico.upm.es/es/ipublic/entity/16247 , corresponding to all papers from OEG.

2. ExistingPapers/ Papers.csv with already extracted data from some OEG papers.

The resulting information is placed in Outputs folder, which include:

• A dois.txt containing, for each paper, the URL to the pdf if it was founded or if not the doi

• A results.csv, containing the title and the doi of every paper found, in addition to OpenAlex primary location attribute

• A results.json, containing the same information as results.csv but in a json format

Project Structure

DOI-Extractor-OEG
├───doiExtractor
|   ├───ExistingPapers
|   |   ├───name_doi_papers.csv
|   |   └───Papers.csv
|   ├───Outputs
|   |   ├───dois.csv
|   |   |───results.csv
|   |   └───results.json
|   ├───__init__.py
|   ├───doiExtractor.py
|   ├───main.py
|   └───openAlex.py
├───.gitignore
├───LICENSE.txt
├───README.MD
└───setup.py

doiExtractor.py - Contains the functions to extract the name and doi from portalcientifico.upm.es and to merge that information with the existing papers.

openAlex.py - Contains the functions to extract the primary location from openAlex and if the DOI was not found with doiExtractor.py, it tries to extract it using Open Alex.

Installation

1. Clone the repository:

git clone https://github.com/ptorija/DOI-Extractor-OEG.git

2. Change to the DOI-Extractor-OEG directory:

cd DOI-Extractor-OEG

3. Create a virtual environment:

python -m venv .env

4. Activate the virtual environment:

(Linux)

source .env/bin/activate

(Windows)

.env\Scripts\activate

5. Install the package dependencies:

pip install -e .

Usage

Download the package from Pypi or install the tool from Github:

pip install DataExtractorOEG

The tool can be used from the command line with the following argument:

• --start - To start the doi extraction

The script will execute and extract DOIs from the specified webpage and then merge them with the ones from ExistingPapers.

Options:

• --url <path> - Specify the webpage of the group you want to extract the information. Default: Ontology Engieneering Group
• --output <path> - Specify the path for the output files. Default: Outputs

Example

1. Install the tool from Pypi ( https://pypi.org/project/DataExtractorOEG/ )

pip install DataExtractorOEG

2. Start the execution

DataExtractorOEG --start

When the execution ends, the following files will be saved in doiExtractor/Outputs folder:

• dois.txt

• results.csv

• results.json

If you want to use RSEF with the output provided by this tool, follow the following steps

1. Clone RSEF repository:

git clone https://github.com/SoftwareUnderstanding/RSEF.git

2. Install the required dependencies by running:

pip install -e .

4. Use RSEF with the extracted results.json from DOI-Extractor-OEG, this will create a downloaded_metadata.json and a processed_metadata.json:

rsef process -j <path to results.json>

If you didn't execute DOI-Extractor-OEG previously, you can also execute DataExtractorOEG --start and then the previous command

5. To check the implementations of the papers use:

rsef asses -i <path to processed_metadata.json>

-U flag to check Unidirectionality

-B flag to check Bidirectionality