GeoBoost

GeoBoost extracts, integrates, and normalizes geographic location of infected hosts (LOIH) metadata from GenBank viral sequence records and related full-text publications to improve geospatial and epidemiological analyses by enabling probabilistic assignment of location scores.

Key Features:

• Geographic extraction: Extracts geographic information from GenBank sequence records and related full-text publications, including LOIH details.
• Integration and normalization: Integrates and normalizes geographic data to standardize LOIH values across records.
• Accession-based processing: Accepts sets of GenBank accession numbers corresponding to virus sequences and processes them to produce a refined dataset reflecting LOIH.
• Probabilistic geospatial modeling: Assigns probability scores to each potential location of infected hosts to support probabilistic geospatial analyses.
• Implementation: Implemented in Java 1.8.

Scientific Applications:

• Virology studies: Improves geographic metadata for viral sequences to support analyses of virus distribution and diversity.
• Epidemiological analysis: Enables geospatial and epidemiological analyses of virus transmission dynamics using refined LOIH data.
• Outbreak source tracking: Facilitates identification and tracking of outbreak sources through more complete and normalized location metadata.
• Public health interventions: Informs public health decision-making by providing probabilistic location assignments from sequence metadata.

Methodology:

Accepts GenBank accession numbers and programmatically extracts geographic information from sequence records and related full-text publications, integrates and normalizes LOIH data, and assigns probability scores to potential locations; implemented in Java 1.8.