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ENCODE data at the ENCODE portal.

Nucleic acids research | Jan 4, 2016

The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome. This phase of the project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements. To date, results for almost 5000 experiments have been released for use by the scientific community. These data are available for searching, visualization and download at the new ENCODE Portal (www.encodeproject.org). The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance. In addition, it is a flexible platform that allows integration of genomic data from multiple projects. The portal experience was designed to improve access to ENCODE data by relying on metadata that allow reusability and reproducibility of the experiments.

Pubmed ID: 26527727 RIS Download

Mesh terms: Animals | DNA | Databases, Genetic | Genes | Genome, Human | Genomics | Humans | Mice | Proteins | RNA

Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.

This is a list of tools and resources that we have found mentioned in this publication.


CHEBI

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

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Experimental Factor Ontology

An application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome.

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Cell Type Ontology

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

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Ontology for Biomedical Investigations

An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project.

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UBERON

An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.

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NCBI BioSample

Database containing descriptions of biological source materials used in experimental assays. Sources include: GenBank, Sequence Read Archive (SRA), Coriell, ATCC. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their samples. As the capacity and complexity of biological data sets expands, databases face new challenges in ensuring that the information is adequately organized and described. The NCBI BioSample database is being developed to help address the challenges by providing the means by which data generators can organize and describe a broad range of sample types, and link to corresponding sets of experimental data in archival databases.

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Roadmap Epigenomics Project

A public resource of human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. The Consortium expects to deliver a collection of normal epigenomes that will provide a framework or reference for comparison and integration within a broad array of future studies. The Consortium also aims to close the gap between data generation and its public dissemination by rapid release of raw sequence data, profiles of epigenomics features and higher-level integrated maps to the scientific community. The Consortium is also committed to the development, standardization and dissemination of protocols, reagents and analytical tools to enable the research community to utilize, integrate and expand upon this body of data. Epigenetics is an emerging frontier of science that involves the study of changes in the regulation of gene activity and expression that are not dependent on gene sequence. For purposes of this program, epigenetics refers to both heritable changes in gene activity and expression (in the progeny of cells or of individuals) and also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable. While epigenetics refers to the study of single genes or sets of genes, epigenomics refers to more global analyses of epigenetic changes across the entire genome. The overall hypothesis of the NIH Roadmap Epigenomics Program is that the origins of health and susceptibility to disease are, in part, the result of epigentic regulation of the genetic blueprint. Specifically, epigenetic mechanisms that control stem cell differentiation and organogensis contribute to the biological response to endogenous and exogenous forms of stimuli that result in disease. The Roadmap Epigenomics Program proposes to: (1) create an international committee; (2) develop standardized platforms, procedures, and reagents for epigenomics research; (3) conduct demonstration projects to evaluate how epigenomes change; (4) develop new technologies for single cell epigenomic analysis and in vivo imaging of epigenetic activity; and (5) create a public data resource to accelerate the application of epigenomics approaches. Transforming biomedical research in the following ways:* Develop comprehensive reference epigenome maps * Develop new technologies for comprehensive epigenomic analyses A series of five interrelated initiatives are currently being developed under this program.

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