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The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: # published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) # data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped # the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. Users can query the database by diseases, SNPs or genes. No matter which of the three query modes was used, an intermediate page will be shown listing all the studies that matched the search with a link to the corresponding publication. The user can select either all studies related to a certain disease or one specific study for which to view the related LD blocks. The DistiLD resource integrates information on: * Associations between Single Nucleotide Polymorphisms (SNPs) and diseases from genome-wide association studies (GWAS) * Links between SNPs and genes based on linkage disequilibrium (LD) data from HapMap For convenience, we provide the complete datasets as two (zipped) tab-delimited files. The first file contains GWAS results mapped to LD blocks. The second file contains all SNPs and genes assigned to each LD block.

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• SciCrunch
• 15 years ago - by Anonymous

Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\<br/>\\\\\\<br/>An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

Software tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+ and runs on any system that supports this toolkit (Linux, Windows, Mac OS X, etc.). The program incorporates automatic non-orthogonal data reslicing, allowing multiple data set to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library.

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• SciCrunch
• 16 years ago - by Anonymous

Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment.

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• SciCrunch
• 15 years ago - by Anonymous

Working group to support the widespread publication and use of provenance information of Web documents, data, and resources. The Working Group will publish W3C Recommendations that define a language for exchanging provenance information among applications. The Working Group is based on an extensive review and roadmap developed by a prior incubator group. Specifications: * PROV Primer * PROV Ontology * PROV Data Model * PROV Notation * PROV Constraints * PROV Access and Query

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• SciCrunch
• 15 years ago - by Anonymous

A lightweight provenance vocabulary to provide terms to enable practitioners of data publishing to publish their data responsibly. It is closely based on the community provenance data model, the Open Provenance Model (OPM). Since release 1.0 OPMV becomes a profile of OPM. OPMV can be used together with other provenance-related RDF/OWL vocabularies/ontologies, such as Dublin Core, FOAF, the Changeset Vocabulary, and the Provenance Vocabulary. As being grounded on OPM, the OPMV aims to assist the interoperability between provenance information on the Semantic Web. The Open Provenance Model Vocabulary is defined as an OWL-DL ontology and it is partitioned into a core ontology and supplementary modules. In order to avoid making the core ontology too complex, the core module only implements structures defined in OPM and the supplementary modules provide less frequently used terms and a broad range of specializations of the core terms. * Classes: Agent, Artifact, Process * Properties: used, wasControlledBy, wasDerivedFrom, wasEncodedBy, wasEndedAt, wasGeneratedAt, wasGeneratedBy, wasPerformedAt, wasPerformedBy, wasStartedAt, wasTriggeredBy, wasUsedAt

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• SciCrunch
• 15 years ago - by Anonymous

Database of biomedical literature citations, harvested from the reference lists of all open access articles in PubMed Central that reference ~20% of all PubMed Central papers (approx. 3.4 million papers), including all the highly cited papers in every biomedical field. All the data are freely available for download and reuse. The web site allows these bibliographic records and citations to be browsed, individual articles to be selected, and its citation network to be visualized in a variety of displays. Details of each selected reference, and the data and diagrams for its citation network, may be downloaded in a variety of formats, while the entire Open Citations Corpus can be downloaded from our source data page in several formats including RDF and BibJSON. Their aim for the future is to work with publishers to make available the reference lists from many more current and recent journal articles, starting with the biomedical literature, and to make the citations contained within them available as Open Linked Data in the manner demonstrated by the existing exemplar data available here.

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• SciCrunch
• 15 years ago - by Anonymous

Public research university in Denton, Texas.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of the study is to estimate the importance of genetic (primary) and environmental factors for economic behavior by conducting a series of standard behavioral economics experiments on a sample of twins from the Swedish Twin Registry.

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• SciCrunch
• 15 years ago - by Anonymous

Format for creating, finding, using and citing nanopublications. A nanopublication has two basic elements: * The Assertion: An assertion is a minimal unit of thought, expressing a relationship between two concepts (called the Subject and the Object) using a third concept (called the Predicate). * The Provenance: This is metadata providing some context about the assertion. Provenance means, ''''how this came to be'''' and includes Supporting metadata (like methods) and Attribution metadata (such as authors, institutions, time-stamps, grants, links to DOIs, URLs). Nanopublications can be serialized using existing ontologies and RDF, allowing nanopublications to be machine readable and opening the door to universal interoperability. In turn, this allows extremely large, heterogeneous and decentralized data to be analyzed for the discovery of new associations that would otherwise be beyond the capacity of human reasoning. Nanopublication infrastructure is administered by the Concept Web Alliance, and are based on open standards. They anticipate the community-driven evolution of nanopublication formats to fit the changing needs of authors and publishers.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The study Genetic Regulation of the End-Stage Clotting Process that leads to Thrombotic Stroke (EuroClot) aims specifically to identify the major genes involved in variations of the end-stage clotting process and investigate the role of these novel genes (and existing candidate genes) in the pathogenesis of stroke across Europe. EuroClot will study stroke intermediate phenotypes in 4500 twins from GenomEUtwin project involving 8 countries and 1000 subjects from extended families from the GAIT2 (Spain) and EuroHead (Finland) studies. Types of samples * EDTA whole blood * DNA * Plasma * Serum Number of sample donors: 601 (sample collection completed)

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• SciCrunch
• 15 years ago - by Anonymous

Data resource catalog that collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. An entry includes information such as resource identifier(s), name, description and URL. ''''Query'''' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL). DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including ''''Query'''' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts.

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• SciCrunch
• 15 years ago - by Anonymous

Shuttleworth Foundation is supporting exceptional people to change the world. We provide funding for dynamic leaders who are at the forefront of social change. We identify amazing people, give them a fellowship grant, and multiply the money they put into their projects by a factor of ten or more. We are looking for social innovators who are helping to change the world for the better and are looking for some support through an innovative social investment model.

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• SciCrunch
• 15 years ago - by Anonymous

An ontology to describe Dictyostelium where the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle is defined. There are two main goals for this new tool: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes (already in use), and in the future, of gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning. To this end, all terms are defined. The complete ontology can be browsed using EBI''s ontology browser tool. (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=DDANAT)

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• SciCrunch
• 16 years ago - by Anonymous

Distributed repository of anatomo-functional data and of simulation algorithms, fully integrated into a seamless simulation environment and directly accessible. This infrastructure will be used to create the physiome of the human musculo-skeletal system.

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• SciCrunch
• 14 years ago - by Anonymous

Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.

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• SciCrunch
• 17 years ago - by Anonymous

Catalogue to: 1, centralize community-developed bioscience standards, linking to policies, other portals, open access resources and lists of tools and databases implementing the standards; 2. develop and maintain a set of criteria for assessing the usability and popularity of the standards, also the interoperability and relations among them; 3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems. Research community, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated. Similar trends in both the regulatory arena and commercial science. The BioSharing catalogue classifies standards into three types: * reporting requirements (minimal information checklists to report of the same core set of information) * terminological artifacts (such as controlled vocabularies and ontologies to describe the information) * exchange formats (to communicate the information) You can sort columns and browse the reporting guidelines content, or you can view all the standards, or reporting guidelines, or terminological artifacts or exchange formats only. Contribute and help build the catalogue.

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• SciCrunch
• 15 years ago - by Anonymous

An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.

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• SciCrunch
• 12 years ago - by Anonymous

The Database of Immunoglobulins and Integrated Tools (DIG IT) is an integrated resource storing sequences of annotated immunoglobulin variable domains of NCBI database and enriched with tools for searching and analyzing them. It contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type) with assigned canonical structures for the hypervariable loops and the data on the type of antigen as well as the pairing information of immunoglobulin heavy and light chains (9672 total pairs). The user can input the immunoglobulin variable domain sequence (amino acid or nucleotide) of interest (heavy chain variable domain sequence; light chain variable domain sequence or both) to retrieve the closest sequences (sorted according to e-value) with complete annotation. The user can also directly query the database by antigen type, canonical structure, germline family in accordance to the requirements.

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• SciCrunch
• 15 years ago - by Anonymous