Curator Dashboard

Service and open API to tag the people, places, facts and events in your content. You hand the Web Service unstructured text (like news articles, blog postings, your term paper, etc.) and it returns semantic metadata in RDF format. Using natural language processing and machine learning techniques, the Calais Web Service examines your text and locates the entities, facts, and events. Calais then processes the entities, facts and events extracted from the text and returns them to the caller in RDF format. * Calais Tagaroo: If you are on WordPress, this plug-in automatically tags content as you type. It can also fetch images from Flickr and videos from Google Video. * Calais Marmoset: To manipulate your search results appearance in Google and Yahoo!, which is simple javacode you embed in your site pages. It will collect the metadata from your page (in the form of RDFa) and hand it over to Google Rich Snippets> and Yahoo! Search Monkey so that you can customize the way your search results appear. * Semantic Proxy: If you want to extract metadata from Web pages using URLs * Calais Collection: For the open source platform Drupal, you can find a complete Calais Collection of modules for easy integration. * OpenPublish: for building a new site from the ground up, this free Content Management System is based on Drupal. OpenPublish bakes-in OpenCalais from the ground up to semantify your site and automate the creation of ''related reading'' widgets, ''topic hubs'' and more.

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• SciCrunch
• 15 years ago - by Anonymous

Database that gathers, generates, and shares taxa, images, videos, and sounds to freely provide knowledge about life on earth to increase awareness and understanding of living nature. Free EOL memberships are ranked so members have greater authority and editorial abilities based on their level of expertise.

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• SciCrunch
• 15 years ago - by Anonymous

The Global Biodiversity Information Facility (GBIF) was established by governments in 2001 to encourage free and open access to biodiversity data, via the Internet. Through a global network of countries and organizations, GBIF promotes and facilitates the mobilization, access, discovery and use of information about the occurrence of organisms over time and across the planet. GBIF provides three core services and products: # An information infrastructure an Internet-based index of a globally distributed network of interoperable databases that contain primary biodiversity data information on museum specimens, field observations of plants and animals in nature, and results from experiments so that data holders across the world can access and share them # Community-developed tools, standards and protocols the tools data providers need to format and share their data # Capacity-building the training, access to international experts and mentoring programs that national and regional institutions need to become part of a decentralized network of biodiversity information facilities. GBIF and its many partners work to mobilize the data, and to improve search mechanisms, data and metadata standards, web services, and the other components of an Internet-based information infrastructure for biodiversity. GBIF makes available data that are shared by hundreds of data publishers from around the world. These data are shared according to the GBIF Data Use Agreement, which includes the provision that users of any data accessed through or retrieved via the GBIF Portal will always give credit to the original data publishers. * Explore Species: Find data for a species or other group of organisms. Information on species and other groups of plants, animals, fungi and micro-organisms, including species occurrence records, as well as classifications and scientific and common names. * Explore Countries: Find data on the species recorded in a particular country, territory or island. Information on the species recorded in each country, including records shared by publishers from throughout the GBIF network. * Explore Datasets: Find data from a data publisher, dataset or data network. Information on the data publishers, datasets and data networks that share data through GBIF, including summary information on 10028 datasets from 419 data publishers.

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• SciCrunch
• 15 years ago - by Anonymous

Publisher that specializes in academic and professional book and journal publishing, mostly in the field of biodiversity science and natural history. They are academic publishers based in Eastern Europe with more than 600 books and e-books published so far. They largely perform their activities in English, with only a minor fraction of publications being in French, German, Russian and Bulgarian. Pensoft is also involved as a publisher in several European Union Fp5, FP6 and FP7 projects where they have specialized in dissemination, communication and publishing; as well as in creating and maintaining websites and Internal Communication Platforms (ICP), designing of logos, flyers, leaflets and posters. Open-access journals include ZooKeys, BioRisk, and PhytoKeys. ZooKeys is a journal in biodiversity science and has implemented several innovations in digital publishing and dissemination including developing and implementing an XML-based submission, editorial, publication and dissemination workflow. The TRIADA platform, for publishing, disseminating and marketing of printed books, e-books and open access journals, provides a linked environment for content, authors, reviewers, editors and customers through four independent classifications (taxonomic, subject, geographical, and geological time scale) as well through tagging and semantic mark-up. TRIADA uses a one-time registration process which allows users to submit, review or edit manuscripts, to subscribe for E-mail and RSS alerts, and to purchase Pensoft''s products. Web services: Metadata and journal content can be harvested.

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• SciCrunch
• 15 years ago - by Anonymous

Data Product Citation Policy of including a bibliographic citation for the products that were used in publications to acknowledge the scientists who have provided archived ORNL DAAC (Oak Ridge National Laboratory Distributed Active Archive Center) data products. Such citations will help others find the products and see how they have been used. Citation information is provided in the documentation that accompanies all data products. ORNL DAAC is operated by the ORNL Environmental Sciences Division and is responsible for data archival, product development and distribution, and user support for biogeochemical and ecological data and models. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemcial dynamics is one of the NASA Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project, which is responsible for providing scientific and other users access to data from NASA''s Earth Science Missions.

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• SciCrunch
• 15 years ago - by Anonymous

Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts.

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• SciCrunch
• 13 years ago - by Anonymous

A major university

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• SciCrunch
• 13 years ago - submitted by Stephen Larson

Immunomodulatory drugs in multiple sclerosis (IMSE) is a nation-wide pharmacoepidemiological and genetic study on persons treated with Tysabri. The study focuses on response to treatment and development of neutralizing antibodies, and to perform large-scale genetic studies. Sample types * EDTA whole blood * DNA * Plasma Number of sample donors: 1293 (June 2010)

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• SciCrunch
• 15 years ago - by Anonymous

A multi-center population based epidemiological investigation of risk factors for Multiple Sclerosis (MS), where lifestyle- and environmental factors are examined systematically with concurrent genetic information. Newly diagnosed cases of MS in a geographically defined population and randomly chosen controls are identified and asked to answer a questionnaire on lifestyle, previous exposures at work, home and during spare time activities. For both cases and controls blood samples are taken for analysis of putative risk genes since environmental exposures probably contributes to disease only in individuals with certain genotypes. Exposures of interest are different sociodemographic factors, smoking, sunlight exposure, oral contraceptives / hormonal factors, butyrophilin (a milk protein), vaccinations, infections, atopic disease, organic solvents, mineral oils and a number of different psychosocial factors, such as critical lifetime events. Data from more than 1600 cases and 3200 controls are currently collected. (August 2014) The intention is to continue with the data collection over several years in order to analyse how genes and environment interact. The study is a collaboration between different institutions at Karolinska Institutet and neurological centers from 38 different hospitals in Sweden. Sample types * EDTA whole blood * DNA * Plasma * Serum

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project creating a DNA biobank from persons admitted to the neurointensive care unit of the Karolinska University Hospital to study possible genetic influences in traumatic brain injuries (TBI). Serum and cerebrospinal fluid sampled during the subacute phase are also collected. Samples were collected prospectively from clinically well characterized patients to allow for studies of association between candidate genes and clinical outcome parameters or biomarkers for relevant disease processes. The aim is to collect samples from 200-400 individuals. Samples will be collected from TBI patients at up to three different occasions. At first sampling, whole blood, serum and liquor will be collected and at the second and third occasions only serum and liquor.

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• SciCrunch
• 15 years ago - by Anonymous

An Antibody supplier.

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• SciCrunch
• 14 years ago - by Anonymous

An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1����m^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download. ViBE-Z provides a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern. The ViBE-Z database, atlas and software are provided via a web interface.

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• SciCrunch
• 15 years ago - by Anonymous

XuvTools (pronounced ex-you-vee-tools) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). The goal of XuvTools is to provide tools, that combine multiple microscopic recordings to obtain a larger field of view (stitching) and a higher dynamic range (HDR recombination), or better resolution (multi view reconstruction), and to make these tools publicly available. What XuvTools can do: * Full 3D Stitching * Scaling, if the voxel sizes are known from image data * Fully automatic stitching modes * Manual pre-alignment modes * Arbitrary large datasets * Reads stage coordinates if available * free, no hidden costs * Reads many many input formats via LOCI Bio-Formats and Dmitry Fedorov''s BioImage. Limitations of XuvTools: (current limitations, we are working on it!) * No 2D Stitching: stacks need 4 Z-slices or more * No memory management: You need lots of RAM * No rotational alignment * The only supported output formats are: Imaris, HDF5 (No TIFF output support)

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• SciCrunch
• 15 years ago - by Anonymous

The study subjects invited to participate is chosen from the Swedish national Multiple Sclerosis registry and will number around 10 000 individuals to be included during two to three years. The same number of matched controls will also be included in the study. A pilot study with around 100 participants was performed during 2009, and the large scale study started in November 2009. Multiple sclerosis (MS) is a neurological disease that affects the central nervous system. It affects young people and the debut age is between 20 and 40 years. The disease comes with exacerbations but further on leads to disability. The incidence in Sweden is around 5 per 100 000 per year and the prevalence is 125 per 100 000 inhabitants. In total there are estimated around 13000 cases in Sweden and today 9000 of them are registered in the Swedish National Multiple Sclerosis register. Sample types * EDTA whole blood * DNA * Plasma Number of sample donors: 5592 (June 2010)

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• SciCrunch
• 15 years ago - by Anonymous

A virtual database that indexes both BioNOT for negation data, and the Resource Discovery Pipeline: an automated resource discovery and semi-automated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. This virtual database currently indexes the following resources: * BioNOT, http://snake.ims.uwm.edu/bionot/index.php?searchterm=mecp2+autism&submit=Search * Resource Discovery Pipeline, http://lucene1.neuinfo.org/nif_resource/current/

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• SciCrunch
• 14 years ago - by Anonymous

The BLASTatlas is a tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms using either blastp, blastn, tblastn, or blastx. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots. The tool is SOAP compliant and WSDL (web services description language) files are available with programming examples available in Perl. The resolution is per-residue or per nucleotide depending on the regime of the blast search: For each annotation in the reference genome, the best hit in the database genome is found using one of the above algorithms. Each matching or mismatching residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the genome sequence, using the coordinates provided in the annotations. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set.

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• SciCrunch
• 16 years ago - by Anonymous

A manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker's yeast and Brewer's yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers and spirits. YMDB currently contains 2027 small molecules with 857 associated enzymes and 138 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties and links to spectral and chemical databases. Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein. Users may search through the YMDB using a variety of database-specific tools. The simple text query supports general text queries of the textual component of the database. By selecting either metabolites or proteins in the search for field it is possible to restrict the search and the returned results to only those data associated with metabolites or with proteins. Clicking on the Browse button generates a tabular synopsis of YMDB's content. This browser view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. A complete explanation of all the YMDB fields and sources is available. Under the Search link users will find a number of search options listed in a pull-down menu. The Chem Query option allows users to draw (using MarvinSketch applet or a ChemSketch applet) or to type (SMILES string) a chemical compound and to search the YMDB for chemicals similar or identical to the query compound. The Advanced Search option supports a more sophisticated text search of the text portion of YMDB. The Sequence Search button allows users to conduct BLASTP (protein) sequence searches of all sequences contained in YMDB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. YMDB also supports a Data Extractor option that allows specific data fields or combinations of data fields to be searched and/or extracted. Spectral searches of YMDB's reference compound NMR and MS spectral data are also supported through its MS, MS/MS, GC/MS and NMR Spectra Search links. Users may download YMDB's complete textual data, chemical structures and sequence data by clicking on the Download button.

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• SciCrunch
• 15 years ago - by Anonymous

A software tool designed to aid researchers in browsing through scientific literature. As one reads an online article and encounters a citation that looks important, CSIBS creates a preview summary of the cited document. The key innovation is the contextual tailoring of the automatically generated summaries using the citation and its surrounding text. As this context changes, so too does the citation-specific summary portion of the preview, which contains contextually-relevant sentences extracted from the cited document. The CSIBS preview presents relevant information required to appraise the citation, containing meta-data about the reference, the abstract and the citation-specific summary. Thus, CSIBS, alleviates information overload by enabling the reader to determine whether or not to invest time in exploring the cited article further. Reference, http://www.sciencedirect.com/science/article/pii/S1570826810000181

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• SciCrunch
• 15 years ago - by Anonymous

CSIRO''s hub for innovative information and communication technologies applied across the breadth of CSIRO''s engagement with industry and society. Our Labs * Autonomous systems - CSIRO is developing autonomous technologies to monitor the environment and infrastructure and improve safety and operating efficiency in the mining, manufacturing and agricultural industries. * Information engineering - Science and technology for finding, integrating, managing and delivering services and information in a trusted and secure way. * Wireless & networking - CSIRO is working on enabling technologies for future mobile and wireless communications networks and developing next generation imaging and sensing systems. CSIRO is developing improved communications systems and sensors for innovative medical and industrial applications. * Australia e-Health Research Centre - Through the Australian e-Health Research Centre, CSIRO invests significantly in using information and communication technologies to improve healthcare and clinical treatment for all Australians. * Tasmanian ICT Centre - The Tasmanian ICT Centre has developed a world-class ICT research capacity and conducts innovative applied research in the areas of sensor networks and data management.

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• SciCrunch
• 15 years ago - by Anonymous

A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability.

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• SciCrunch
• 15 years ago - by Anonymous