SIBiLS

SIBiLS provides semantically enriched indexing and customizable information retrieval of biomedical literature to support literature triage and biocuration of genes and gene products.

Key Features:

• Customizable search engines: Executes searches using both keywords and mapped biomedical entities from standardized and legacy vocabularies.
• Semantic enrichment and entity mapping: Maps nearly 2 billion biomedical entities to annotate and semantically enrich literature content.
• Curation workflow support: Supplies personalized literature triage engines tailored for biocuration of genes and gene products.
• API access and scalability: Exposes services via RESTful APIs and supports scalable deployment with MongoDB and Elasticsearch.
• Literature coverage: Indexes MEDLINE and PubMed Central Open Access content for retrieval and analysis.
• Update frequency: Incorporates new content through daily updates.

Scientific Applications:

• Literature triage: Prioritizes and retrieves relevant publications for curation and review workflows.
• Gene and gene product curation: Supports identification and aggregation of literature evidence for genes and gene products.
• Entity-centric literature mining: Enables retrieval and analysis focused on biomedical entities mapped across literature.
• Large-scale literature integration: Facilitates integration of indexed literature into big-data projects using MongoDB and Elasticsearch.

Methodology:

Semantic enrichment by mapping biomedical entities from standardized and legacy vocabularies; indexing MEDLINE and PubMed Central Open Access; service access via RESTful APIs; storage and search scalability using MongoDB and Elasticsearch; daily update cadence.