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Data Source

• Pubmed is a public repository of abstract and metadata for literature in the medical and biological field. Entries have a pubmed id (pmid). Query terms are matched against title, keywords and abstract text.

• Pubmed Central is a public repository containing literature fulltext in the medical and biological field. Entries have a pubmed central id (pmcid) and are not to be confused with the pubmed id. Query terms are matched against the full text of the document and therefore often returns more results than Pubmed. Will also return results if keyword matches to reference titles which may need need to be filtered out.

API's

• Ebot generates perl scripts to fetch data from both PubMed and PubMed Central. The tool is hosted at NCBI.

• RISmed is an R package that fetches data from PubMed. I have not found functionality for PubMed Central but please contact me if some one has more info on this.

Graph Analysis

• Mango Graph Studio is a multi-network visualization and analysis environment. The tool provides a graph exploration language (GEL) and multi-graph mathematics to combine/compare graphs and their attributes.

• iGraph is a C package although API's exist in R and python. Provides graph centrality measures and other network statistics. I was hoping to use these measures to identify multi-tool authors but did not finish.

Pipeline