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BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature

Fig 1

Overview of the BEST System.

The BEST system consists of two main parts: Indexing and Searching. (1) “Indexing” represents the indexing subsystem of BEST. For every document, BEST extracts all biomedical entities (1-a) and makes a paired posting (1-b). The basic structure of BEST’s index is similar to that of the inverted index of conventional search engines. However, BEST uses a different indexing unit, paired posting, which is a pair of a document ID and a list of entities that appear in the document. (2) “Searching” represents the search subsystem of BEST. All retrieved paired postings are aggregated to rank the entities (2-a). Ranking scores are computed using four subcomponents described in “Searching and Scoring” in the Methods section (2-b).

Fig 1