Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Motivation: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support efforts to study and predict functionally relevant interactions between protein sequences and structures and small molecule ligands.

Results: We structured the data model for cognate ligand binding site annotations in UniProtKB and performed a complete reannotation of all cognate ligand binding sites using stable unique identifiers from ChEBI, which we now use as the reference vocabulary for all such annotations. We developed improved search and query facilities for cognate ligands in the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that ChEBI provides.

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

Motivation: The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes.

HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes.

Background: Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation.

Enzyme annotation in UniProtKB using Rhea.

Motivation: To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical Entities of Biological Interest) ontology.

Results: We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB. We developed improved search and query facilities for the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that Rhea and ChEBI provide.

The UniProtKB guide to the human proteome.

Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB).

Higher HIV RNA Viral Load in Recent Patients with Symptomatic Acute HIV Infection in Lyon University Hospitals.

Introduction: Increased human immunodeficiency virus (HIV) virulence at infection has been suggested by a meta-analysis based on viral load and CD4 T lymphocytes (CD4) count during acute infection. This result was obtained after secondary analyses of large databases, facilitating the detection of differences. Similar finding in cohorts of more modest sample size would indicate that the effect could be more substantial.

HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins--available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences.

Pertussis vaccination coverage among adults in the Lyon area.

Background: The compliance with recommendations for Pertussis vaccination was assessed in the Lyon population through vaccination coverage (VC).

Methods: A cross-sectional study was conducted in collaboration with 10 private biological analysis laboratories between October 2010 and March 2012, on 1930 adults (>19 years of age) from the Lyon area. Proof of vaccination (PV) was requested to prove the current vaccination status.

HAMAP in 2013, new developments in the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences.

Evaluation of adult dTPaP vaccination coverage in France: experience in Lyon city, 2010-2011.

Background: Compliance with official recommendations can be assessed by evaluating vaccination coverage (VC) in populations. The main objective of our study was to assess VC of adults against diphtheria, tetanus, poliomyelitis and pertussis (dTPaP) according to age. The second objective was to explore if vaccination status could be confirmed by documentation.

ExPASy: SIB bioinformatics resource portal.

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics.

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.

The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline.

Effect of early initiation of highly active antiretroviral therapy on CD4 cell count and HIV-RNA viral load trends within 24 months of the onset of acute retroviral syndrome.

Objectives: The effect of starting highly active antiretroviral therapy (HAART) early after the onset of acute retroviral syndrome (ARS) on CD4 and HIV-RNA trends was studied over a 2-year follow-up period.

Methods: Four groups of HIV-infected patients stratified according to the time interval from ARS onset to HAART initiation and a control group of untreated patients were compared.

Results: The results indicated that the earlier the start of HAART, the faster was the rate of CD4 increase and HIV-RNA decrease.

Reduction of urinary tract infections acquired in an intensive care unit during a 10-year surveillance program.

Purpose: To describe trends of urinary catheter-related infections (UCRIs) acquired by patients hospitalized in intensive care units (ICU) in relation with an infection control program.

Materials And Methods: Prospective surveillance in one ICU of a university hospital in Lyon (France) between 1995 and 2004.

Results: A 66% reduction of urinary catheter-related infections (UCRIs) acquired by patients hospitalized was observed between 1995 and 2004 after adjustment on age, gender, antibiotic use at admission, and duration of exposure to urinary catheter.

Incidence of methicillin-resistant Staphylococcus aureus nosocomial infections in intensive care units in Lyon University hospitals, France, 2003-2006.

We describe the trends in the incidence of methicillin-resistant Staphylococcus aureus nosocomial infection in intensive care units in Lyon hospitals from January 1, 2003, through December 31, 2006. The incidence rate decreased from 1.77 cases per 100 ICU patients in 2003 to 1.

Pneumococcal pneumonia in HIV-infected patients by antiretroviral therapy periods.

Objective: To ascertain the relationship between periods of various antiretroviral therapies and the incidence of first community-acquired pneumococcal pneumonia (CAPP) among HIV-1 infected patients.

Methods: We analysed 4075 patients enrolled prospectively in the Lyon section of the French Hospital Database on HIV between 1993 and 2004, stratified into three groups. The first group (G1) included patients for whom enrolment and last follow-up were before the highly active antiretroviral therapy (HAART) period (beginning 1 July 1996); the second group (G2) comprised patients who were enrolled before HAART but had last follow-up in the HAART period; the third group (G3) included patients for whom both enrolment and last follow-up took place in the HAART period.

A recent increase in AIDS at Lyon University Hospitals: patient characteristics and comparisons with previous years.

Background: A 36% increase in the incidence of AIDS was observed in 2002/2003 compared with 2000/2001 at Lyon University Hospitals.

Objectives: We compared the characteristics of these patients with the characteristics of those diagnosed previously with AIDS.

Methods: Data for all patients with AIDS diagnosed at Lyon University Hospitals were analyzed.

Characteristics of patients diagnosed with AIDS shortly after first detection of HIV antibodies in Lyon University hospitals from 1985 to 2001.

A diagnosis of AIDS shortly after the detection of HIV antibodies suggests a long-lasting course of the disease without care. The factors associated with a short delay between the initial HIV-1-positive test and the first AIDS-defining event were identified in 1901 patients from 1985 to 2001 in Lyon University hospitals. A total of 576 individuals (30.

The AIDS epidemic in Lyon: patient characteristics and defining illnesses between 1985 and 2000.

Objectives: To define the characteristics of 1899 patients diagnosed with AIDS at Lyon University Hospitals (LUH) across four time periods corresponding to different antiretroviral eras, and to analyse the evolution of specific AIDS-defining illnesses (ADIs) with time.

Methods: All AIDS patients at LUH between 1 January 1985 and 31 December 2000 were included in the study. The data were compared using the chi(2) test and one-way analysis of variance.

Clinical features of acute retroviral syndrome differ by route of infection but not by gender and age.

The rate of HIV disease progression is associated with the severity of the acute retroviral syndrome (ARS). We explored the clinical features of ARS by gender, age and route of infection among 378 individuals with documented ARS enrolled in 5 prospective cohort studies with similar enrollment criteria. No major differences were detected by gender or by age.

TT virus. A review of the literature.

In 1997, a new DNA virus was cloned by a Japanese team and designated TT virus (TTV). This virus seemed to be associated with non-A, non-G post-transfusion hepatitis. It was isolated by polymerase chain reaction (PCR) and was presumed to be human Circoviridae.