BioGPS and MyGene.info: organizing online, gene-centric information

By Chunlei Wu, Ian MacLeod, Andrew I. Su. Nucleic Acids Res., 2012

378 citations recorded by the source corpus.

Fast-evolving technologies have enabled researchers to easily generate data at genome scale, and using these technologies to compare biological states typically results in a list of candidate genes. Researchers are then faced with the daunting task of prioritizing these candidate genes for follow-up studies. There are hundreds, possibly even thousands, of web-based gene annotation resources available, but it quickly becomes impractical to manually access and review all of these sites for each gene in a candidate gene list. BioGPS (http://biogps.org) was created as a centralized gene portal for aggregating distributed gene annotation resources, emphasizing community extensibility and user customizability. BioGPS serves as a convenient tool for users to access known gene-centric resources, as well as a mechanism to discover new resources that were previously unknown to the user. This article describes updates to BioGPS made after its initial release in 2008. We summarize recent additions of features and data, as well as the robust user activity that underlies this community intelligence application. Finally, we describe MyGene.info (http://mygene.info) and related web services that provide programmatic access to BioGPS.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ffff41b245657ee779758fe17d2bd1b2fa2a6e93

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In Molecular Biology

Citations in the corpus

BioGPS: building your own mash-up of gene annotations and expression profiles (2015, background): “info provides up-to-date gene annotations and a rich query syntax to perform gene-based queries (2).”
Genenames.org: the HGNC resources in 2015 (2014, background): “We have also added a new ‘Other databases’ link to BioGPS (30) which is a gene annotation portal that allows the user to ‘plugin’ resources into the application for a gene.”
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations (2014, background): “…levels for a large number of human tissues, cancers and cell lines (16); BioGPS (http://biogps.org/) for tissue-specific pattern of mRNA expression (17); Wikipedia pages include information about protein function, RNA expression, interactions, clinical significance, references and further reading…”
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, background): “Achilles Cell Line Gene Essentiality Profiles (22–24) BioGPS Cell Line Gene Expression Profiles (1, 25, 26)”
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse (2016, background): “info (11) project organizes these Wikipedia pages and MGI links to these pages only for genes that have a one-to-one mouse/human orthology relationship.”
Massive mining of publicly available RNA-seq data from human and mouse (2017, background): “Such data can complement tissue and cell line expression resources such as BioGPS (43) and GTEx (14) as well as resources that provide accumulated knowledge about genes and proteins such as GeneCards, the Harmonizome and the NCBI gene database (44–46).”