mesh-term-massager 💆

Turn MeSH-terms xml file into tabular format (JSON or DataFrame)

Introduction

Mesh-term-massager is used to convert MeSH terms list downloaded from NCBI in XML format into a Pandas DataFrame or json format which could be readily used in down-stream applications.

Requirements

• Python > 3.5
• MeSH XML file downloaded from NCBI

Note: code was tested on the 2019, 2020 xml version

Usage

Please see the attached Jupyter notebook for an example on how to run the parser.

Basix steps:

1. Initiate a new instance of the class MeshTermMassager with and include the path to the .xml file downloaded from NCBI
2. Invoke the parse_terms function to parse the data
3. Use either the get_processed_df or save_json to view/export the processed data

Output

The out is a DataFrame or json file with the following structure

Unique_ID	MeSH_heading	tree_num	term_concepts	entry_terms
D000001	Calcimycin	[D03.633.100.221.173]	[Calcimycin, A-23187]	[A-23187, A23187, Antibiotic A23187]
D000002	Temefos	[D02.705.400.625.800, D02.705.539.345.800, D02...	[Temefos, Abate, Difos]	[Temephos, Abate, Difos]
D000003	Abattoirs	[J01.576.423.200.700.100, J03.540.020]	[Abattoirs]	[Slaughter Houses, Slaughter House, Slaughterh...
D000004	Abbreviations as Topic	[L01.559.598.400.556.131]	[Abbreviations as Topic, Acronyms as Topic]	[Acronyms as Topic]