Dataset Information

SNPdbe: constructing an nsSNP functional impacts database.

ABSTRACT: UNLABELLED: Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; 'human' being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs. AVAILABILITY: http://www.rostlab.org/services/snpdbe.

SUBMITTER: Schaefer C

PROVIDER: S-EPMC3278761 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

SNPdbe: constructing an nsSNP functional impacts database.

Schaefer Christian C Meier Alice A Rost Burkhard B Bromberg Yana Y

Bioinformatics (Oxford, England) 20111230 4

<h4>Unlabelled</h4>Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional imp ...[more]

PMID: 22210871

Similar Datasets

Project description:Summary The Human Impacts Database (www.anthroponumbers.org) is a curated, searchable resource housing quantitative data relating to the diverse anthropogenic impacts on our planet, with topics ranging from sea-level rise to livestock populations, greenhouse gas emissions, fertilizer use, and beyond. Each entry in the database reports a quantitative value (or a time series of values) along with clear referencing of the primary source, the method of measurement or estimation, an assessment of uncertainty, and links to the underlying data, as well as a permanent identifier called a Human Impacts ID (HuID). While there are other databases that house some of these values, they are typically focused on a single topic area, like energy usage or greenhouse gas emissions. The Human Impacts Database facilitates access to carefully curated data, acting as a quantitative resource pertaining to the myriad ways in which humans have an impact on the Earth, for practicing scientists, the general public, and those involved in education for sustainable development alike. We outline the structure of the database, describe our curation procedures, and use this database to generate a graphical summary of the current state of human impacts on the Earth, illustrating both their numerical values and their intimate interconnections. Graphical abstract Highlights • We present a holistic view of the many ways humans alter Earth at a global scale• We consider how these global quantities vary across geography• We further explore the time- and population-dependent dynamics of these impacts• We enumerate and describe key properties associated with each entry in the database The bigger picture Over the last 10,000 years, human activities have transformed Earth through farming, forestry, mining, and industry. The complex results of these activities are now observed and quantified as “human impacts” on Earth’s atmosphere, oceans, biosphere, and geochemistry. While myriad studies have explored facets of human impacts on the planet, they are necessarily technical and often highly focused. Thus, finding reliable quantitative information requires a significant investment of time to assess each quantity and associated uncertainty. We present the Human Impacts Database (www.anthroponumbers.org), which houses a diverse array of such quantities. We review a subset of these values and how they help build intuition for understanding the Earth-human system. While collation alone does not tell us how to best ameliorate human impacts, we contend that any future plans should be made in light of a quantitative understanding of the interconnected ways in which humans influence the planet. The environmental impacts of human action on Earth are being felt on many fronts. Despite our deep knowledge of these impacts, finding reliable quantitative information is burdensome, often requiring domain expertise and programmatic acumen. We present the Human Impacts Database, which houses a diverse array of quantities regarding human impacts, making them easily accessible and searchable. We use this database to present a broad view of the Anthropocene, exploring the global magnitudes, spatial dependence, and temporal dynamics of human impacts.

Dataset Information

SNPdbe: constructing an nsSNP functional impacts database.

Publications

SNPdbe: constructing an nsSNP functional impacts database.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets