PosMed: Ranking genes and bioresources based on Semantic Web Association Study.

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.

A new species of the genus Rimicaris (Alvinocarididae: Caridea: Decapoda) from the active hydrothermal vent field, "Kairei Field," on the Central Indian Ridge, the Indian Ocean.

Rimicaris kairei new species (Alvinocarididae: Caridea: Decapoda) is described based on materials, from the active hydrothermal vent field, "Kairei Field," on the Central Indian Ridge, the Indian Ocean. The new species is clearly distinguishable from the unique congener, R. exoculata Williams & Rona, 1986, which is known from the Atlantic Ocean. The following morphological differences were identified: (1) all punctations on carapace strongly ornamented by tufts of short stiff setae in R. exoculata, whereas without any setae in R. kairei; (2) antennal flagella in R. exoculata shorter than in R. kairei; (3) walking legs in R. exoculata more robust than in R. kairei.