FlyBase: enhancing Drosophila Gene Ontology annotations

FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. This article describes recent changes to the FlyBase GO annotation strategy that are improving the quality of the GO annotation data. Many of these changes stem from our participation in the GO Reference Genome Annotation Project—a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species

Crystal chemistry and electronic properties of the n=2 Ruddlesden-Popper manganates: unconventional CMR materials

The crystallography and electronic properties of the Ln[sub 2- x]Sr[sub 1+x]Mn[sub 2]O[sub 7] manganese oxides adopting the n=2 Ruddlesden-Popper (RP) structure are discussed, focusing on the structural phase diagrams and electronic properties in the vicinity of the Mn +3.5 oxidation state and in particular the ease of synthesis of single phases of these materials

Interplay of spin and orbital ordering in the layered colossal magnetoresistance manganite La2-2xSr1+2xMn2O7 (0.5<=x<=1.0)

The crystallographic and magnetic phase diagram of the n=2 layered manganite La2-2xSr1+2xMn2O7 in the region x=>0.5 has been studied using temperature dependent neutron powder diffraction. The magnetic phase diagram reveals a progression of ordered magnetic structures generally paralleling that of 3-D perovskites with similar electronic doping: A (0.5 C (0.75 G (0.90<=x<=1.0). However, the quasi-2-D structure amplifies this progression to expose features of manganite physics uniquely accessible in the layered systems: (a) a "frustrated" region between the A and C regimes where no long-range magnetic order is observed; (b) magnetic polytypism arising from weak inter-bilayer magnetic exchange in the Type-C regime; and (c) a tetragonal to orthorhombic phase transition whose temperature evolution directly measures ordering of d3y2-r2 orbitals in the a-b plane. This orbital-ordering transition is precursory to Type-C magnetic ordering, where ferromagnetic rods lie parallel to the b-axis. These observations support the notion that eg orbital polarisation is the driving force behind magnetic spin ordering. Finally, in the crossover region between Type-C and Type-G states, we see some evidence for the development of local Type-C clusters embedded in a Type-G framework, directly addressing proposals of similar short-range magnetic ordering in highly-doped La1-xCaxMnO3 perovskites.Comment: 32 pages, 13 figures, submitted to Phys. Rev.

Expansion of the Gene Ontology knowledgebase and 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/.National Institutes of Health/National Human Genome Research Institute [HG002273] awarded to the PI group formed by (alphabetically) Judith A. Blake, J. Michael Cherry, Suzanna E. Lewis, Paul W. Sternberg and Paul D. Thomas, as well as additional funding awarded to each participating institution. For more details please visit: http://geneontology.org/page/go-consortium-contributors-list. Funding for open access charge: National Institutes of Health/National Human Genome Research Institute [HG002273]

Ageing and Long-Term Care Planning Perceptions of Hispanics in the USA: Evidence from a Case Study in New London, Connecticut

This paper explores the ageing attitudes and long-term care planning behavior of adult Hispanics in New London, Connecticut, a town with 30 thousand inhabitants that is rapidly ageing. We conducted six focus groups and had 37 participants share their ageing perceptions and long-term care needs. Our main findings suggest that informal care arrangements are vulnerable and unsustainable especially since women have historically and disproportionately provided most family eldercare even at their own personal and financial expense. Though male participants expected their female relatives to care for them when they age and need personal assistance, female participants did not necessarily expect the same from their relatives including their daughters. Also, both formal and government long-term care systems lack cultural competence and can be prohibitively costly. Therefore, Hispanics plan for ageing within their circles of family care and their resilience in a context of cultural exclusion and socio-economic disadvantage epitomizes strong intergenerational values. These support networks may help explain why may outlive whites (the Hispanic paradox ) who, on average, have higher wealth and education levels. Long-term care planning is a complex process that cannot be relayed to families only. Adequate training for family members from other relatives, and from private and government entities to appropriately convey this type of planning is vital to ensure that Hispanic families understand their options

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource