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PubMed2005

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines?

An in-depth analysis of a multidimensional chromatography-mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument was carried out. A total of 3269 CID spectra were acquired. Through manual verification of database search results and de novo interpretation of spectra 2368 spectra could be confidently determined as predicted tryptic peptides. A detailed analysis of the non-matching spectra was also carried out, highlighting what the non-matching spectra in a database search typically are composed of. The results of this comprehensive dataset study demonstrate that QqTOF instruments produce information-rich data of which a high percentage of the data is readily interpretable.

Chromatography, Liquid↗

PubMed2001

HONselect: multilingual assistant search engine operated by a concept-based interface system to decentralized heterogeneous sources.

Any new user to the Internet will think that to retrieve the relevant document is an easy task especially with the wealth of sources available on this medium, but this is not the case. Even experienced users have difficulty formulating the right query for making the most of a search tool in order to efficiently obtain an accurate result. The goal of this work is to reduce the time and the energy necessary in searching and locating medical and health information. To reach this goal we have developed HONselect [1]. The aim of HONselect is not only to improve efficiency in retrieving documents but to respond to an increased need for obtaining a selection of relevant and accurate documents from a breadth of various knowledge databases including scientific bibliographical references, clinical trials, daily news, multimedia illustrations, conferences, forum, Web sites, clinical cases, and others. The authors based their approach on the knowledge representation using the National Library of Medicine's Medical Subject Headings (NLM, MeSH) vocabulary and classification [2,3]. The innovation is to propose a multilingual "one-stop searching" (one Web interface to databases currently in English, French and German) with full navigational and connectivity capabilities. The user may choose from a given selection of related terms the one that best suit his search, navigate in the term's hierarchical tree, and access directly to a selection of documents from high quality knowledge suppliers such as the MEDLINE database, the NLM's ClinicalTrials.gov server, the NewsPage's daily news, the HON's media gallery, conference listings and MedHunt's Web sites [4, 5, 6, 7, 8, 9]. HONselect, developed by HON, a non-profit organisation [10], is a free online available multilingual tool based on the MeSH thesaurus to index, select, retrieve and display accurate, up to date, high-level and quality documents.

Databases, Bibliographic↗

PubMed2004

WRAPIN: new generation health search engine using UMLS knowledge sources for MeSH term extraction from health documentation.

To realize the potential of the Internet as a source of valuable healthcare information, for the general public, patients or practitioners, it is imperative to establish a validation system based on standards of quality. The WRAPIN project (World-wide online Reliable Advice to Patients and Individuals) from the European Community has this ambitious goal. WRAPIN is a federating system for medical information with an editorial policy of intelligently sharing quality and professional information. The WRAPIN project has two main axes: the efficient and intelligent search of information and the assertion of the trustworthiness of content. This article presents the scientific challenges involved in extracting the knowledge from text-based information in order to better manage the knowledge and the rest of the retrieval proc-ess. Our innovative approach is to efficiently extract MeSH terms from the analyzed documents exploiting UMLS knowledge sources. A benefit has been measured when comparing extraction results. Even if the evaluation is made with a limited corpus, this research work proposes heuristics that can be validated to the whole biomedical domain, and possibly enhanced by the adjunction of other methods.

Abstracting and Indexing↗

PubMed2006

A combined strategy of "in silico" transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies.

Traditionally housekeeping genes have been employed as endogenous reference (internal control) genes for normalization in gene expression studies. Since the utilization of single housekeepers cannot assure an unbiased result, new normalization methods involving multiple housekeeping genes and normalizing using their mean expression have been recently proposed. Moreover, since a gold standard gene suitable for every experimental condition does not exist, it is also necessary to validate the expression stability of every putative control gene on the specific requirements of the planned experiment. As a consequence, finding a good set of reference genes is for sure a non-trivial problem requiring quite a lot of lab-based experimental testing. In this work we identified novel candidate barley reference genes suitable for normalization in gene expression studies. An advanced web search approach aimed to collect, from publicly available web resources, the most interesting information regarding the expression profiling of candidate housekeepers on a specific experimental basis has been set up and applied, as an example, on stress conditions. A complementary lab-based analysis has been carried out to verify the expression profile of the selected genes in different tissues and during heat shock response. This combined dry/wet approach can be applied to any species and physiological condition of interest and can be considered very helpful to identify putative reference genes to be shortlisted every time a new experimental design has to be set up.

Base Sequence↗

PubMed1998