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The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen-Host Interactions Database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology and controlled vocabularies to curate pathogen-host interaction data (at the level of the host, pathogen, strain, gene and genotype). The concept of a multispecies genotype, the ‘metagenotype’, is introduced to facilitate capturing changes in the pathogens’ disease-causing abilities, and host resistance or susceptibility observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors.

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.

International audience; Arctic landscapes are experiencing intense warming and modification of precipitation regimes with climate change. Permafrost disturbances and climate change impacts on hydrology of Arctic watersheds are likely to modify the quantity and composition of exported dissolved organic matter (DOM). In July 2007, intense rainfall and active layer thickening caused widespread active layer detachments at Cape Bounty, Melville Island (Canada). This study investigates the impacts of seasonal hydrology and permafrost disturbance on DOM composition exported from High Arctic headwater catchments. In 2012, streams were sampled from three disturbed catchments and one undisturbed catchment. The composition of DOM was characterized using absorbance and fluorescence spectroscopy. DOM was mostly exported during the spring freshet. Throughout this period, the undisturbed catchment exported humified DOM with high humic-like fluorescence that likely originated from runoff through shallow organic rich soil. In contrast, DOM exported from disturbed catchments was fresher, less humified with a high proportion of low molecular weight humic acid. We demonstrate that disturbed catchments delivered likely more labile DOM derived from either thawed permafrost or enhanced microbial activity. If this labile DOM comes from an ancient pool, as indicated by other studies at this site, disturbances may strengthen the permafrost carbon feedback on climate change.; Avec le changement climatique, les paysages arctiques connaissent un réchauffe-ment intense et une modification des régimes de précipitation. Les impacts des perturbations du pergélisol et du changement climatique sur l'hydrologie des bassins hydrographiques arc-tiques vont probablement modifier la quantité et la composition de matière organique dis-soute (MOD) exportée. En juillet 2007, des averses intenses et l'épaississement de la couche active ont causé des décollements généralisés de la couche active à Cape Bounty, île Melville (Canada). Cette étude examine les impacts de l'hydrologie saisonnière et de la perturbation du pergélisol sur la composition de la MOD exportée des bassins versants d'amont du Haut-Arctique. En 2012, on a échantillonné des cours d'eau de trois bassins versants perturbés et d'un bassin versant non perturbé. La composition de la MOD a été analysée en utilisant la spectroscopie à fluorescence et l'absorptiométrie. La MOD a surtout été exportée pendant la crue printanière. Pendant cette période, le bassin versant non perturbé a exporté de la MOD humifiée à haute fluorescence telle humique qui provenait probablement de ruisselle-ment par sol riche organique mince. En revanche, la MOD exportée de bassins versants per-turbés était plus fraîche, moins humifiée avec une haute proportion d'acide humique à faible poids moléculaire. Nous démontrons que les bassins versants perturbés ont déversé de la MOD probablement plus labile provenant du pergélisol dégelé ou de l'activité microbienne améliorée. Si cette MOD labile vient d'un bassin ancien, tel que révélé par d'autres études à ce site, les perturbations peuvent renforcer la rétroaction du carbone du pergélisol sur le changement climatique.

The prenatal period is of critical importance in defining how individuals respond to their environment throughout life. Stress experienced by pregnant females has been shown to have detrimental effects on offspring biology in humans and a variety of other species. It also is becoming increasingly apparent that prenatal events can have important consequences for the behavior, health, and productivity of offspring in farmed species. Pregnant cattle may experience many potentially important stressors, for instance, relating to their social environment, housing system and physical environment, interactions with humans and husbandry procedures, and their state of health. We examined the available literature to provide a review of the implications of prenatal stress for offspring welfare in cattle. The long-term effects of dystocia on cattle offspring also are reviewed. To ensure a transparent and repeatable selection process, a systematic review approach was adopted. The research literature clearly demonstrates that prenatal stress and difficult births in beef and dairy cattle both have implications for offspring welfare and performance. Common husbandry practices, such as transport, were shown to influence offspring biology and the importance of environmental variables, including thermal stress and drought, also were highlighted. Maternal disease during pregnancy was shown to negatively impact offspring welfare. Moreover, dystocia-affected calves suffer increased mortality and morbidity, decreased transfer of passive immunity, and important physiological and behavioral changes. This review also identified considerable gaps in our knowledge and understanding of the effects of prenatal stress in cattle.

There is an increasing number of organic dairy farms in the UK. The aim of this study is to compare behaviour of dairy cows on organic and non-organic farms. Twenty organic and 20 non-organic farms throughout the UK were visited over two winters (2004/05 and 2005/06). Organic and non-organic farms were paired for housing type, herd size, milk production traits and location. The number of cows feeding was counted every fifteen minutes for 4.5 h after new feed was available post morning milking. Behaviour at the feed-face was recorded for 60 minutes and aggressive interactions between cows were quantified. Farm type had no effect on numbers of cows feeding. There were more interactions between cows feeding at open feed-faces compared to head-bale barriers. At open feed-faces, there were more interactions on organic farms than non-organic. It is possible that organic cows were hungrier than non-organic cows after the arrival of new feed.