Towards BioDBcore: a community-defined information specification for biological databases

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological database

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference.

The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration's (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions with journals. The conference is an essential part of the ISB's goal to support exchanges among members of the biocuration community. Next year's conference will be held in Cambridge, UK, from 7 to 10 April 2013. In the meanwhile, the ISB website provides information about the society's activities (http://biocurator.org), as well as related events of interest

Cellular anatomy of the mouse primary motor cortex.

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture

A multimodal cell census and atlas of the mammalian primary motor cortex

ABSTRACT We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties

Between formal and enacted policy: changing the contours of boundaries

This study examines the strategies of the biomedical discourse vis-à-vis the growing public demand for alternative medicine by comparing formal and informal claims for jurisdiction. The analysis is based on two main sources of data from Israel: (a) two formal position statements, and (b) a series of participant observations and interviews with practitioners in clinical settings where biomedical and alternative practitioners collaborate. At the formal level, the biomedical discourse seeks to secure its dominant position by drawing strict cognitive and moral lines differentiating "proper biomedicine" from "improper alternative medicine." At this level alternative medicine appears morally "contaminated" and its knowledge-base delegitimized by extreme forms of boundary-work. At the informal level, the contour of boundaries change. In the hospital field where alternative and biomedical practitioners are collaborating, mutual respect was expressed even as social and symbolic boundaries were being demarcated. Modifying the forms of boundary-work appears to be biomedicine's reactive strategy in the field to changing environmental and market demands. It is a strategy that allows biomedical discourse to absorb its competitor within its professional jurisdiction with no battle, while retaining absolute epistemological hegemony and Institutional Control.Alternative medicine Biomedicine Boundary-work Israel

Entering the well-guarded fortress: alternative practitioners in hospital settings

There is a growing evidence that alternative health care practitioners and physicians are working together in collaborative patterns. The paper examines these collaborative patterns in hospital settings in Israel. On the theoretical level, the specific issues relate to theories concerning relationships between dominant institutional structures which enjoy the benefits of epistemological legitimacy as well as extensive, supportive social structures and groups of non-conformists who seek to attain many of the same goals by utilizing different methods based on other epistemologies. In the most general sense, the issues involved concern processes of accommodation and social change. Data were collected by means of semi-structured, qualitative interviews in four general hospitals in Jerusalem during 2000. Nineteen persons were interviewed including 10 alternative practitioners working in a variety of fields and nine biomedical practitioners who worked with them (six physicians and three nurses). Interviews focused on background and training, reasons for entry into the hospital, length of practice, status in the hospital system, mode of remuneration, content of work, modes of interaction with others in the hospital and problems encountered. The findings suggest a dual process of simultaneous acceptance and marginalization of alternative practitioners. While small numbers of alternative practitioners were found to be practicing in a wide variety of hospital departments and in a broad spectrum of specialties, they were in no way accepted as regular staff members and their marginality was made clear by a variety of visible structural, symbolic and geographical cues. There is a division of labour expressed by focusing on the biomedical practitioners on the diagnosis and treatment of specific disease entities, while the alternative practitioners work in the illness context, concentrating of feelings and affective states involving the alleviation of pain, suffering and efforts to improve the quality of life.Alternative medicine Complementary medicine Hospitals Israel

Novel Mutations In Alox12B In Patients With Autosomal Recessive Congenital Ichthyosis And Evidence For Genetic Heterogeneity On Chromosome 17P13

We report clinical and molecular findings in 20 patients from 11 families with autosomal recessive congenital ichthyosis (ARCI) linked to chromosome 17p13, and attributed to mutations in the ALOX gene cluster, which includes three lipoxygenase genes, ALOXE3, ALOX12B, and ALOX15B. We identified six novel missense mutations and one novel deletion leading to a premature stop codon in ALOX12B in only six out of the 11 familes which led us to investigate a possible implication of ALOX15B. Mutation analysis of this gene, as well as ALOXE3, which is known to be mutated in some cases of ARCI, failed to reveal causative mutations in the five remaining ARCI families, indicating that other genes on chromosome 17p13 may be involved in this disease. However, by adding new variants to the repertoire of ALOX12B mutations in non-bullous congenital ichthyosiform erythroderma, our data contribute to an enlargement of the spectrum of mutations for the development of efficient molecular genetic tests for analysis of at risk individuals whose carrier status is unknown.WoSScopu

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.

The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration\u27s (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions with journals. The conference is an essential part of the ISB\u27s goal to support exchanges among members of the biocuration community. Next year\u27s conference will be held in Cambridge, UK, from 7 to 10 April 2013. In the meanwhile, the ISB website provides information about the society\u27s activities (http://biocurator.org), as well as related events of interest