SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context-specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query string (PubMed Entrez search) or a list of PubMed Unique Identifiers (PMIDs) as input.

• Scans biomedical literature of your interest for any molecular target (gene or protein) entities.
• Finds significant enrichments in your set of papers. Enrichment tests are supported on:
  • Target (gene) list
  • Gene Ontology
  • MeSH (Medical Subject Headings)
  • Pathways
  • PPI (Protein-Protein Interaction) Network
• Allows users to compare multiple different search (query) results.
• Provides EndNote citations for any retrieved documents.

Download the SciMiner User Manual (PDF)

• Query #1: "Amyotrophic lateral sclerosis"[MeSH] AND "Reactive Oxygen Species"[MeSH]
• Query #2: "Amyotrophic lateral sclerosis"[MeSH] AND Inflammation
• Analysis results: Query #1 vs Query #2