https://github.com/nathanielng/research_tools

Coding Tools for Scientific Research
https://github.com/nathanielng/research_tools

Last synced: 25 days ago
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Coding Tools for Scientific Research

• Host: GitHub
• URL: https://github.com/nathanielng/research_tools
• Owner: nathanielng
• License: mit
• Created: 2019-08-22T12:37:05.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2020-05-20T12:01:30.000Z (over 4 years ago)
• Last Synced: 2024-11-08T13:12:23.350Z (3 months ago)
• Language: Python
• Homepage: https://nathanielng.github.io/research_tools
• Size: 44.9 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Coding Tools for Scientific Research

## 1. Background

This is a set of coding tools for scientific research.  The intention is to have at least three parts:

1. an article lookup / API client

2. a parsing and natural language processing engine

3. a bot linking to Twitter feeds and Discord

### 1.1 Article Lookup / API Client

Article lookup will be carried out using an API Client for scientific papers.

Initially, development will be prioritized towards the following

1. Open Citations API at [opencitations.net](http://opencitations.net/index/coci/api/v1)

2. [Crossref API](https://www.crossref.org/services/metadata-delivery/rest-api/) via [crossref_commons_py](https://gitlab.com/crossref/crossref_commons_py)

Tentative APIs currently under exploration:

1. Elsevier API at [dev.elsevier.com/](http://dev.elsevier.com/)

2. [CORE](https://core.ac.uk/services/api/)

3. [Microsoft Academic Services](https://docs.microsoft.com/en-us/academic-services/)

### 1.2 Parsing & Natural Language Processing Engine

For the NLP aspect, initial work will focus on on Materials Science,

via the [mat2vec](https://github.com/materialsintelligence/mat2vec) library

with a general direction to eventually cover at least the following 4 areas:

1. Materials Science

2. Engineering

3. Physics

4. Chemistry

For a start, the initial tool is `pdf_extract.py` which extracts the text of a `pdf` file.

The text is parsed for DOI (digital object identifier) data and arXiv IDs.

At a later stage, the text may be used as an input to the parsing & Natural Language Processing (NLP) engine.

## 2. Usage

### 2.1 Parser

#### 2.1.1 Extracting a DOI from a file

```bash

python src/pdf_extract.py --file $FILE

```

#### 2.1.2 Extracting multiple DOIs from a folder

```bash

python src/pdf_extract.py --path $FOLDER

```

### 2.2 Discord Bot

A bot based on some of the tools here will eventually be made available for testing at the following Discord: https://discord.gg/ZPnKCkU