BeeSpace Navigator: Exploratory Analysis of gene function using semantic indexing of biological literature

Moushumi Sen Sarma
David Arcoleo
Radhika S. Khetani
Brant Chee
Xu Ling
Xin He
Jing JIANG, Singapore Management University
Qiaozhu MEI
ChengXiang ZHAI
Bruce Schatz


With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments can be analyzed to extract concepts that are computational equivalents of a classification such as Gene Ontology, yielding discriminating concepts that differentiate gene mentions from other mentions. The functions of individual genes can be summarized from sentences in biological literature, to produce results resembling a model organism database entry that is automatically computed. Statistical frequency analysis based on literature phrase extraction generates offline semantic indexes to support these gene function services. The website with BeeSpace Navigator is free and open to all; there is no login requirement at for version 4. Materials from the 2010 BeeSpace Software Training Workshop are available