A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records.

ABSTRACT:

Objective

The metadata reflecting the location of the infected host (LOIH) of virus sequences in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases.

Materials and methods

We developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, bas

SUBMITTER: Tahsin T 

PROVIDER: S-EPMC4997033 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature