KBWS: an EMBOSS associated package for accessing bioinformatics web services

The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal)

Retrospective Analysis of Emergency Department Ultrasound for Acute Appendicitis

OBJECTIVES: To determine whether emergency physicians (EPs) who have skills in the other applications of ultrasound can apply these in appendicitis diagnosis. METHODS: EPs did not have focused training in bedside ultrasound for appendicitis. We identified patients receiving an ED bedside ultrasound evaluation for appendicitis from our ultrasound log. Criterion reference was radiology ultrasound (RUS), CT scan, or pathology report. RESULTS: We performed 155 ED ultrasounds for appendicitis. There were 27/155 cases where the ED ultrasound was true positive and agreed with pathology (sensitivity = 39%, 95% CI 28 – 52%). In 42/155 (27%) the ED ultrasound was non-diagnostic (false negative) with pathology positive. In 77 cases the ED ultrasound was true negative with non-visualization of the appendix in concert with non-visualization by RUS or CT scan (specificity = 90%, 95% CI 81-95%). In nine cases (6%), ED ultrasound was falsely positive, compared to CT scan with surgical consult. CONCLUSION: ED ultrasound by EPs prior to focused appendicitis ultrasound training is insufficiently accurate

A web server for interactive and zoomable Chaos Game Representation images

Chaos Game Representation (CGR) is a generalized scale-independent Markov transition table, which is useful for the visualization and comparative study of genomic signature, or for the study of characteristic sequence motifs. However, in order to fully utilize the scale-independent properties of CGR, it should be accessible through scale-independent user interface instead of static images. Here we describe a web server and Perl library for generating zoomable CGR images utilizing Google Maps API, which is also easily searchable for specific motifs. The web server is freely accessible at , and the Perl library as well as the source code is distributed with the G-language Genome Analysis Environment under GNU General Public License

Ultrasound in Emergency Medicine EMERGENCY BILIARY SONOGRAPHY: UTILITY OF COMMON BILE DUCT MEASUREMENT IN THE DIAGNOSIS OF CHOLECYSTITIS AND CHOLEDOCHOLITHIASIS

, Abstract-Background: Measurement of the common bile duct (CBD) has traditionally been considered an integral part of gallbladder sonography, but accurate identification of the CBD can be difficult for novice sonographers. Objective: To determine the prevalence of isolated sonographic CBD dilation in emergency department (ED) patients with cholecystitis or choledocholithiasis without laboratory abnormalities or other pathologic findings on biliary ultrasound. Methods: We conducted a retrospective chart review on two separate ED patient cohorts between June 2000 and June 2010. The first cohort comprised all ED patients undergoing a biliary ultrasound and subsequent cholecystectomy for presumed cholecystitis. The second cohort consisted of all ED patients receiving a biliary ultrasound who were ultimately diagnosed with choledocholithiasis. Ultrasound data and contemporaneous laboratory values were collected. Postoperative gallbladder pathology reports and endoscopic retrograde cholangiopancreatography (ERCP) reports were used as the criterion standard for final diagnosis. Results: Of 666 cases of cholecystitis, there were 251 (37.7%) with a dilated CBD > 6 mm and only 2 cases (0.3%; 95% confidence interval [CI] 0.0-0.7%) of isolated CBD dilation with an otherwise negative ultrasound and normal laboratory values. Of 111 cases of choledocholithiasis, there were 80 (72.0%) with a dilated CBD and only 1 case (0.9%; 95% CI 0.0-2.7%) with an otherwise negative ultrasound and normal laboratory values. Conclusion: The prevalence of isolated sonographic CBD dilation in cholecystitis and choledocholithiasis is <1%. Omission of CBD measurement is unlikely to result in missed cholecystitis or choledocholithiasis in the setting of a routine ED evaluation with an otherwise normal ultrasound and normal laboratory values. Ó 2013 Elsevier Inc

Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API

BACKGROUND: Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. METHODOLOGY/PRINCIPAL FINDINGS: We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. CONCLUSIONS/SIGNIFICANCE: Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/)

G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved]

With the availability of numerous curated databases, researchers are now able to efficiently use the multitude of biological data by integrating these resources via hyperlinks and cross-references. A large proportion of bioinformatics research tasks, however, may include labor-intensive tasks such as fetching, parsing, and merging datasets and functional annotations from distributed multi-domain databases. This data integration issue is one of the key challenges in bioinformatics. We aim to provide an identifier conversion and data aggregation system as a part of solution to solve this problem with a service named G-Links, 1) by gathering resource URI information from 130 databases and 30 web services in a gene-centric manner so that users can retrieve all available links about a given gene, 2) by providing RESTful API for easy retrieval of links including facet searching based on keywords and/or predicate types, and 3) by producing a variety of outputs as visual HTML page, tab-delimited text, and in Semantic Web formats such as Notation3 and RDF. G-Links as well as other relevant documentation are available at http://link.g-language.org