iHOP WS

iHOP WS exposes a web-service interface to the Information Hyperlinked over Proteins (iHOP) system, transforming PubMed literature into a navigable gene/protein-centered knowledge network.

Key Features:

• Gene/protein-centered network: Connects ∼30,000 genes across multiple organisms into a literature-anchored network.
• Sentence-based hyperlinks: Uses genes and proteins as hyperlinks between sentences extracted directly from publications to enable stepwise traversal of molecular relationships.
• Indexed corpus: Indexes >500,000 curated sentences derived from >10 million PubMed abstracts.
• Controlled synonym handling: Links gene mentions using controlled synonym handling with 87–99% precision depending on organism.
• Evidential provenance: Preserves provenance by presenting sentence fragments taken verbatim from the literature.
• Programmatic access: Exposes the iHOP infrastructure via a web-service interface for integration into computational pipelines.
• Integration with experimental data: Enables simultaneous mapping of literature-derived associations onto experimental interaction datasets (e.g., yeast-two-hybrid).
• Cross-domain semantic links: Supports controlled exploration of semantic bridges across medical and biological concepts.

Scientific Applications:

• Literature-derived association integration: Incorporate literature-derived gene–gene associations into downstream computational and analytical pipelines.
• Experimental interaction mapping: Map and compare literature links against experimental interaction datasets such as yeast-two-hybrid results.
• Semantic bridge exploration: Explore connections between medical and biological concepts through literature-anchored sentence fragments.

Methodology:

Extraction of sentences from PubMed abstracts, linking sentences via gene/protein mentions with controlled synonym handling (87–99% precision), and indexing the resulting curated sentence network (∼30,000 genes; >500,000 sentences).