title: Finding Text-Supported Gene-to-Disease Co-appearances with MOPED-Digger.
abstract: Gene/disease associations are a critical part of exploring disease causes and ultimately cures, yet the publications that might provide such information are too numerous to be manually reviewed. We present a software utility, MOPED-Digger, that enables focused human assessment of literature by applying natural language processing (NLP) to search for customized lists of genes and diseases in titles and abstracts from biomedical publications. The results are ranked lists of gene/disease co-appearances and the publications that support them. Analysis of 18,159,237 PubMed title/abstracts yielded 1,796,799 gene/disease co-appearances that can be used to focus attention on the most promising publications for a possible gene/disease association. An integrated score is provided to enable assessment of broadly presented published evidence to capture more tenuous connections. MOPED-Digger is written in Java and uses Apache Lucene 5.0 library. The utility runs as a command-line program with a variety of user-options and is freely available for download from the MOPED 3.0 website (moped.proteinspire.org).
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.|4 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|5 Departments of Biomedical Informatics and Medical Education and Pediatrics, School of Medicine, University of Washington , Seattle, Washington.|6 Department of Chemistry and Chemical Biology, College of Science, Northeastern University , Boston, Massachusetts.
authors.forename: Eugene
authors.initials: E
authors.lastname: Kolker
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.
authors.forename: Imre
authors.initials: I
authors.lastname: Janko
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.|4 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Montague
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.|4 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: Roger
authors.initials: R
authors.lastname: Higdon
authors.affiliation: 2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.|4 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Stewart
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.|4 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: John
authors.initials: J
authors.lastname: Choiniere
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|4 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|7 University of Pennsylvania , School of Arts and Sciences, Philadelphia, Pennsylvania.
authors.forename: Aaron
authors.initials: A
authors.lastname: Lai
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|4 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|8 Northeastern University , College of Science, Boston, Massachusetts.
authors.forename: Mary
authors.initials: M
authors.lastname: Eckert
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.
authors.forename: William
authors.initials: W
authors.lastname: Broomall
authors.affiliation: 1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.|2 CDO Analytics, cdoanalytics.org , Seattle Children's Hospital , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA) , Seattle, Washington.
authors.forename: Natali
authors.initials: N
authors.lastname: Kolker
mesh_terms: D019295:Computational Biology / Q000379:methods*; D056726:Genetic Association Studies / Q000379:methods*; D020022:Genetic Predisposition to Disease; D006801:Humans; D012984:Software