PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net

JC virus and its possible role in oncogenesis

No abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34652/1/3_ftp.pd

The Quest for a Satisfactory Definition of Terrorism: R v Gul

The UK Supreme Court judgment in R v Gul presented a unique opportunity for a judicial appraisal of the definition of terrorism contained in section 1 of the Terrorism Act 2000. While the applicant was ultimately unsuccessful in his challenge, the Supreme Court's rejection of the state's argument that reliance on prosecutorial discretion could mitigate certain absurd applications of the section 1 definition of terrorism, eg the labelling of acts of UK or other military forces as terrorist, has potentially wide-raging implications for the UK's counter-terrorism measures. In addition, the powerful obiter dictum arguing in favour of a reform of this definition and a ‘root-and-branch’ review of counter-terrorism legislation is a strong rebuke of recent high profile misapplications of such powers

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net