Biomedical Harvesters

This repository contains indepentent projects for harvesting knowledge from different biomedical resources into colletions of MongoDB in a form of relations between concepts.

In particular three harvesters are available:

1. The Litrature Harvester to retrieve online articles relevant to a MeSH term from PubMed and PMC through the Entrez Programming Utilities.
2. The OBO Harvester to process the OBO files of biomedical ontologies.
3. The DrugBank Harvester to process the XML file of DrugBank.

Nentidis, A., Bougiatiotis, K., Krithara, A., & Paliouras, G. (2019). Semantic integration of disease-specific knowledge, 1–8. Retrieved from http://arxiv.org/abs/1912.08633