Pubmed Parser: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

Pubmed Parser is a Python library for parsing the PubMed Open-Access (OA) subset and MEDLINE XML repositories. It uses lxml library to parse this information into a Python dictionary which can be easily used for research such in text mining and natural language processing pipelines. See our Wiki page or this documentation on how to download and process dataset using the repository.

About the dataset

PubMed Open-Access (OA) subset contains XMLs of a full submitted papers which has information that you might get from a regular PDF article file but in a more structured format. MEDLINE XML contains about 30M biomedical articles published until now. We can access information until abstracts from a compressed XML file. Other information such as number of citations of an article can be query through Entrez Programming Utilities (E-utils) which can be obtained in XML format.

To work with the data, normally, you have to write an XML to parse these XMLs which can take time and effort. Pubmed Parser aims to reduce those development by giving a high level functionalities so that researchers can obtain the dataset to analyze fast. It is also developed by researchers who use these data so that we always keep it up-to-date.

Contents

• Installation
• API Documentation
• Resources
• Setting up Pubmed Parser with PySpark

Questions / Contributions / Bugs

We provide an information for you for all above in our Contribution Guidelines.