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Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.

Accepted version
Peer-reviewed

Change log

Authors

Urbano, Jose M 
Marygold, Steven J 
Millburn, Gillian H 
Brown, Nicholas H 

Abstract

Brief summaries describing the function of each gene's product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene's product, which we edited for consistency to produce a 'gene snapshot'. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature. Database URL: https://flybase.org/.

Description

Keywords

Animals, Data Collection, Databases, Genetic, Drosophila melanogaster, Genome, Insect, Software

Journal Title

Database (Oxford)

Conference Name

Journal ISSN

1758-0463
1758-0463

Volume Title

2020

Publisher

Oxford University Press (OUP)

Rights

All rights reserved
Sponsorship
Medical Research Council (G1000968)
Medical Research Council (MR/N030117/1)
National Institutes of Health (NIH) (via Harvard School of Public Health) (132685-5104589)
National Institutes of Health (NIH) (via Harvard University) (132685-5104589)
National Institutes of Health (NIH) (via Harvard University) (132626-5085854)
Medical Research Council (UK) [G1000968 and MR/N030117/1] National Human Genome Research Institute at the National Institutes of Health [U41 HG00739]