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on page 1 showing 10 out of 10 results

Cite this (Biocatalogue - The Life Science Web Services Registry, RRID:SCR_001679)

URL: http://www.biocatalogue.org/

Resource Type: Resource, web service, software resource, data or information resource, data access protocol, database

Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services.

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Cite this (DTU Center for Biological Sequence Analysis, RRID:SCR_003590)

URL: http://www.cbs.dtu.dk/index.shtml

Resource Type: Resource, topical portal, data access protocol, production service resource, analysis service resource, training resource, data analysis service, data set, web service, service resource, portal, software resource, data or information resource

The Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.

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Cite this (Ensembl Genomes, RRID:SCR_006773)

URL: http://www.ensemblgenomes.org/

Resource Type: Resource, web service, software resource, data or information resource, data access protocol, database

Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

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    Ensembl

Cite this (Ensembl, RRID:SCR_002344)

URL: http://www.ensembl.org/

Resource Type: Resource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, catalog, service resource, software resource, data or information resource

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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Cite this (FunSimMat, RRID:SCR_002729)

URL: http://funsimmat.bioinf.mpi-inf.mpg.de

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resource

FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online tool

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Cite this (InterProScan, RRID:SCR_005829)

URL: http://www.ebi.ac.uk/Tools/pfa/iprscan/

Resource Type: Resource, data analysis service, data analysis software, data processing software, data access protocol, production service resource, analysis service resource, software application, web service, service resource, software resource

Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service.

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Cite this (MRB - Mouse Resource Browser, RRID:SCR_005961)

URL: http://bioit.fleming.gr/mrb/

Resource Type: Resource, source code, data access protocol, database, web service, registry, software resource, data or information resource

Dynamic and interactive view of 222 world wide available mouse resources, classified in 22 categories. The massive generation of data has led to the propagation of mouse resources and databases and the concomitant need for formalized experimental descriptions, data standardization and database interoperability and integration. In this context and with these goals, information is collected through an online questionnaire and/or manual curation. All mouse resource data in MRB are broken up in four sections and presented in four tabs: * The General section/tab contains information such as URL(s), contact information, database description and categorization and related links. * The Ontologies & Standards tab indicates controlled vocabularies and data representation standards adopted by each resource, such as ontologies and minimum information standards. A hyperlink to an index of OBO and non-OBO ontologies can be found here; an index of minimum information standards can be found here. * The Technical tab holds technical information for each resource such as the server technology used, relational database management system(s) utilized, programming language(s) of implementation, schema descriptive documents or actual database dumps and most importantly information on each resource''s programmatic access, the integration and interoperability services. Additionally and through the integration with Molgenis, MRB is capable of generating a SOAP API for hosted resources. * The final section on Database Description Framework (DDF) Criteria, describes the compliance of each resource to the CASIMIR database criteria, which aim to capture key technical data about a database in a formal framework. All data in MRB are freely available to interested users through downloadable weekly database dumps. Programmatic access to some of MRB''s data is feasible via MRB''s SOAP web service. MRB is the front end of a relational, fully normalized PostgreSQL database. The source code is available under the GNU general public license (GPL) as a binary download and via cvs.

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    Pathbase

Cite this (Pathbase, RRID:SCR_006141)

URL: http://www.pathbase.net/

Resource Type: Resource, ontology, data access protocol, database, web service, image collection, service resource, storage service resource, software resource, image repository, data repository, controlled vocabulary, data or information resource

Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)

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    RNAmmer

Cite this (RNAmmer, RRID:SCR_017075)

URL: http://www.cbs.dtu.dk/services/RNAmmer/

Resource Type: Resource, data analysis service, standalone software, data processing software, data access protocol, production service resource, web service, software application, analysis service resource, service resource, data analysis software, software resource

Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.

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    SMART

Cite this (SMART, RRID:SCR_005026)

URL: http://smart.embl.de/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resource

Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

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