RESUMEN
Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.
Asunto(s)
Colaboración de las Masas/métodos , Ontología de Genes , Anotación de Secuencia Molecular/métodos , Biología Computacional , Bases de Datos Genéticas , Humanos , Proteínas/genética , Proteínas/fisiologíaRESUMEN
The Gene Ontology Normal Usage Tracking System (GONUTS) is a community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins. GONUTS uses wiki technology to allow registered users to share and edit notes on the use of each term in GO, and to contribute annotations for specific genes of interest. By providing a site for generation of third-party documentation at the granularity of individual terms, GONUTS complements the official documentation of the Gene Ontology Consortium. To provide examples for community users, GONUTS displays the complete GO annotations from seven model organisms: Saccharomyces cerevisiae, Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus and Arabidopsis thaliana. To support community annotation, GONUTS allows automated creation of gene pages for gene products in UniProt. GONUTS will improve the consistency of annotation efforts across genome projects, and should be useful in training new annotators and consumers in the production of GO annotations and the use of GO terms. GONUTS can be accessed at http://gowiki.tamu.edu. The source code for generating the content of GONUTS is available upon request.
Asunto(s)
Bases de Datos de Ácidos Nucleicos , Anotación de Secuencia Molecular , Proteínas/genética , Programas Informáticos , Vocabulario Controlado , Animales , Genes , Internet , RatonesRESUMEN
EcoliWiki is the community annotation component of the PortEco (http://porteco.org; formerly EcoliHub) project, an online data resource that integrates information on laboratory strains of Escherichia coli, its phages, plasmids and mobile genetic elements. As one of the early adopters of the wiki approach to model organism databases, EcoliWiki was designed to not only facilitate community-driven sharing of biological knowledge about E. coli as a model organism, but also to be interoperable with other data resources. EcoliWiki content currently covers genes from five laboratory E. coli strains, 21 bacteriophage genomes, F plasmid and eight transposons. EcoliWiki integrates the Mediawiki wiki platform with other open-source software tools and in-house software development to extend how wikis can be used for model organism databases. EcoliWiki can be accessed online at http://ecoliwiki.net.
Asunto(s)
Bases de Datos Genéticas , Escherichia coli/genética , Colifagos/genética , Genes Bacterianos , Internet , Secuencias Repetitivas Esparcidas , Anotación de Secuencia Molecular , Plásmidos/genética , Programas Informáticos , Integración de SistemasRESUMEN
Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.
Asunto(s)
Biología , Bases de Datos Factuales , Internet , Integración de SistemasRESUMEN
OBJECTIVE: To compare abduction angles of shoulders with medial instability and unaffected shoulders in the same dogs and in age- and breed-matched dogs. STUDY DESIGN: Case-control study. ANIMALS: Dogs with medial instability of the shoulder (n=33) and 26 control dogs. METHODS: Dogs were sedated and positioned in lateral recumbency with both scapulas parallel to the table. With the elbow and shoulder in extension, the non-recumbent limb was maximally abducted and the angle between the scapular spine and lateral aspect of the brachium measured with a goniometer; a digital image was taken from the cranial aspect. Both techniques were performed in triplicate by 2 examiners. Mean abduction angles for each shoulder were determined from goniometric measurements and image analysis. Data were analyzed for significant differences between affected and unaffected shoulders, measurement techniques, and examiners. Strength of correlation between measurement techniques was determined. RESULTS: Mean abduction angles for shoulders with instability (53.7+/-4.7 degrees goniometric, 51.2+/-4.9 degrees image) were significantly (P<.001) larger than for all unaffected shoulders (32.6+/-2.0 degrees goniometric, 30.9+/-2.3 degrees image). In dogs diagnosed with instability, affected shoulders had significantly (P<.001) larger abduction angles than the contralateral (unaffected) shoulders. No significant differences were identified between right and left shoulders for control dogs, measurement techniques, or examiners. A strong (r=0.90) significant (P<.001) positive correlation between measurement techniques was noted. CONCLUSIONS: Shoulder abduction angles measured under sedation provide objective data for diagnosis of shoulder instability in dogs. Shoulders with clinical and arthroscopic evidence of medial instability have significantly higher abduction angles than shoulders that are considered normal. CLINICAL RELEVANCE: Determination of shoulder abduction angles should be included in the diagnostic protocol for forelimb lameness assessment in dogs.