title: PosMed: Ranking genes and bioresources based on Semantic Web Association Study.
abstract: Positional MEDLINE (PosMed; http://biolod.org/PosMed) is a powerful Semantic Web Association Study engine that ranks biomedical resources such as genes, metabolites, diseases and drugs, based on the statistical significance of associations between user-specified phenotypic keywords and resources connected directly or inferentially through a Semantic Web of biological databases such as MEDLINE, OMIM, pathways, co-expressions, molecular interactions and ontology terms. Since 2005, PosMed has long been used for in silico positional cloning studies to infer candidate disease-responsible genes existing within chromosomal intervals. PosMed is redesigned as a workbench to discover possible functional interpretations for numerous genetic variants found from exome sequencing of human disease samples. We also show that the association search engine enhances the value of mouse bioresources because most knockout mouse resources have no phenotypic annotation, but can be associated inferentially to phenotypes via genes and biomedical documents. For this purpose, we established text-mining rules to the biomedical documents by careful human curation work, and created a huge amount of correct linking between genes and documents. PosMed associates any phenotypic keyword to mouse resources with 20 public databases and four original data sets as of May 2013.
authors.affiliation: Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Makita
authors.forename: Norio
authors.initials: N
authors.lastname: Kobayashi
authors.forename: Yuko
authors.initials: Y
authors.lastname: Yoshida
authors.forename: Koji
authors.initials: K
authors.lastname: Doi
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Mochizuki
authors.forename: Koro
authors.initials: K
authors.lastname: Nishikata
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsushima
authors.forename: Satoshi
authors.initials: S
authors.lastname: Takahashi
authors.forename: Manabu
authors.initials: M
authors.lastname: Ishii
authors.forename: Terue
authors.initials: T
authors.lastname: Takatsuki
authors.forename: Rinki
authors.initials: R
authors.lastname: Bhatia
authors.forename: Zolzaya
authors.initials: Z
authors.lastname: Khadbaatar
authors.forename: Hajime
authors.initials: H
authors.lastname: Watabe
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Masuya
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D059472:Exome; D005796:Genes; D056726:Genetic Association Studies; D014644:Genetic Variation; D006801:Humans; D020407:Internet; D051379:Mice; D018345:Mice, Knockout; D010641:Phenotype; D012984:Software