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. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorith

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. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profile

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Etude des croyances motivationnelles chez les adolescents à haut potentiel intellectuel : des représentations à dénouer

Schooling of intellectually gifted adolescents remains an essential issue. However, it conveys with it many clichés, from the young and gifted who can only experience great success in school, to the ones who cannot avoid difficulties in regular school education. These representations are fed by deep-rooted stereotypes about intelligence and academic achievement. Therefore, some points need to be clarified scientifically. For instance, do these students attribute less value than others to academic tasks? Do they feel equipped to succeed in school or on the contrary, do they perceive themselves as less efficient, because they have never really needed to study? In this research, we use a social cognitive motivation approach to make an inventory of the motivational beliefs of adolescents enrolled in regular education. The first part of this book also presents a synthetic theoretical model of giftedness based on a review of literature.La scolarité des adolescents à haut potentiel intellectuel (HPI) reste aujourd’hui une question incontournable. Or, cette thématique véhicule avec elle encore toute une série de clichés allant du jeune HPI, qui ne peut que réussir à l’école, à l’élève HPI qui, s’il est scolarisé en classe ordinaire, présentera des difficultés dans son parcours scolaire. Ces représentations sont nourries par des stéréotypes tenaces sur l’intelligence et la réussite scolaire. Une série de questions méritent ainsi d’être clarifiées scientifiquement. Par exemple, ces élèves attribuent-ils moins de valeur aux apprentissages scolaires que les autres? Se sentent-ils plus compétents pour faire face aux différents apprentissages scolaires, ou au contraire se perçoivent-ils comme moins efficients, faute de n’avoir jamais eu vraiment besoin de travailler? Et, dans ce contexte, comment se représentent-ils l’effort ? Par une approche sociale-cognitive de la motivation, ce travail de recherche tente de faire l’état des lieux des croyances motivationnelles de ces adolescents scolarisés dans le système d’enseignement ordinaire. Le début de cet ouvrage présente également un modèle théorique synthétique du haut potentiel intellectuel basé sur une large revue de la littérature.(PSYE - Sciences psychologiques et de l'éducation) -- UCL, 201

Quand l’intégration de jeunes à haut potentiel dans un groupe hétérogène peut profiter à tous. Quels les liens entre cette philosophie de travail et la formation des enseignants.

Cuche, C. & Goldschmidt, I. (2009) . Quand l’intégration de jeunes à haut potentiel dans un groupe hétérogène peut profiter à tous. Actes de la IXième journée d’étude des chercheurs belges francophones en éducation. Bruxelles