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http://www.ebi.ac.uk/ega/

Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication.

Proper citation: European Genome phenome Archive (RRID:SCR_004944) Copy   

•   Source: SciCrunch Registry
  

http://www.vectorbase.org

Bioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases.

Proper citation: VectorBase (RRID:SCR_005917) Copy   

•   Source: SciCrunch Registry
  

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

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.

Proper citation: InterProScan (RRID:SCR_005829) Copy   

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http://www.ebi.ac.uk/webservices/whatizit/info.jsf

A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text.

Proper citation: Whatizit (RRID:SCR_005824) Copy   

•   Source: SciCrunch Registry
  

http://drcat.sourceforge.net/

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.

Proper citation: DRCAT Resource Catalogue (RRID:SCR_005931) Copy   

•   Source: SciCrunch Registry
  

http://www.biomedbridges.eu/

Consortium of 12 Biomedical sciences research infrastructure (BMS RI) partners to develop a shared e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains (providing a complex knowledge environment comprising standards, ontologies, data and services) and thus strengthen biomedical resources in Europe. The BMS RIs are on the roadmap of the European Strategy Forum on Research Infrastructures (ESFRI). Connecting several European research infrastructures brings a diversity of ethical, legal and security concerns including data security requirements for participating e-Infrastructures that are storing or processing patient-related data (or biosamples): EATRIS, ECRIN, BBMRI, EuroBioImaging and EMBL-EBI. In addition, INSTRUCT is interested in secure sample transport and in intellectual property rights; Infrafrontier stores high-throughput data from mice. BBMRI with its focus on the availability of biomaterials is currently emphasizing aspects like k-anonymity and metadata management for its data. Sharing of imaging data by Euro-BioImaging poses challenges with respect to anonymisation and intellectual property. Therefore, an ethical, regulatory and security framework for international data sharing that covers these diverse areas and different types of data (e.g. clinical trials data, mouse data, and human genotype and DNA sequence data) is of crucial importance. The outcomes will lead to real and sustained improvement in the services the biomedical sciences research infrastructures offer to the research community. Data curation and sample description will be improved by the adoption of best practices and agreed standards. Many improvements will emerge from new interactions between RIs created by data linkage and networking. Ensuring access to relevant information for all life science researchers across all BMS RIs will enable scientists to conduct and share cutting-edge research.

Proper citation: BioMedBridges (RRID:SCR_006179) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/vsn.html

Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

Proper citation: vsn (RRID:SCR_001459) Copy   

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https://github.com/sbotond/rlsim

Software package for simulating RNA-seq library preparation with parameter estimation.

Proper citation: rlsim (RRID:SCR_001703) Copy   

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http://www.ebi.ac.uk/biomodels-main/

Repository of mathematical models of biological and biomedical systems. Hosts selection of existing literature based physiologically and pharmaceutically relevant mechanistic models in standard formats. Features programmatic access via Web Services. Each model is curated to verify that it corresponds to reference publication and gives proper numerical results. Curators also annotate components of models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for models they need. Models can be retrieved in SBML format and import/export facilities are being developed to extend spectrum of formats supported by resource.

Proper citation: BioModels (RRID:SCR_001993) Copy   

•   Source: SciCrunch Registry
  

http://www.emdataresource.org/

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

Proper citation: EMDataResource.org (RRID:SCR_003207) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/pride/

Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.

Proper citation: Proteomics Identifications (PRIDE) (RRID:SCR_003411) Copy   

•   Source: SciCrunch Registry
  

http://www.reactome.org

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

Proper citation: Reactome (RRID:SCR_003485) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/efo/

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.

Proper citation: Experimental Factor Ontology (RRID:SCR_003574) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/Tools/emboss/cpgplot/indexhtml

This portal allows for the detection of regions of genomic sequences that are rich in the CpG pattern is important because such regions are resistant to methylation and tend to be associated with genes which are frequently switched on. Regions rich in the CpG pattern are known as CpG islands. The function of the program cpgplot is to plot CpG rich areas, and cpgreport to report all CpG rich regions. The nuclear genomes of vertebrates are mosaics of isochores, very long stretches of DNA that are homogeneous in base composition and are compositionally correlated with the coding sequences that they embed. Isochores can be partitioned in a small number of families that cover a range of GC levels. Program isochore plots GC content over a sequence. Sponsors: This resource is supported by European Bioinformatics Institute. Keywords: Software, Plotting, Pattern, CpG, Gene, Function, Isochore, DNA, Genome, Homogeneous, Coding, Sequence, Family, Sequencing,

Proper citation: EMBOSS CpGPlot/CpGReport/Isochore (RRID:SCR_007254) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/huber-srv/hilbert/

Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features.

Proper citation: HilbertVis (RRID:SCR_007862) Copy   

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http://www.ebi.ac.uk/patentdata/

Patent data resources at the EBI contain patent abstracts, patent chemical compounds, patent sequences and patent equivalents. There are various ways of accessing and searching the patent data.

Proper citation: Patent Data Resources (RRID:SCR_008708) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/citexplore/

CiteXplore combines literature search with text mining tools for biology. Search results are cross referenced to EBI applications based on publication identifiers. Links to full text versions are provided where available. The underlying database is populated with data from Medline, Patents, C.B.A. and Citeseer. The site offers a quick search as well as an advanced search. Results of queries can be saved in formats compatible with commonly-used bibliographic management software and exported. We provide a Simple Object Access Protocol (SOAP) based service to retrieve data from the Citation database. Text mining is provided internally by Whatizit and externally by iHOP.

Proper citation: CiteXplore literature searching (RRID:SCR_010676) Copy   

•   Source: SciCrunch Registry
  

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+srsq2+-noSession

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. Features include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ''Nice views'', SRSQuickSearch bookmarklets. Quick Searches allow users to make a number of searches without needing to learn how to use SRS in depth. The searches query some of the common databanks without having to go and select them explicitly and without the need to understand the SRS Query Forms. Quick Searches can be performed from either the Start page (when you first open SRS) or the SRS Quick Search page (when you are already in a project). SRS also has the ability to search for links between your current results and related information in other databanks. Additionally, it is able to analyze the results of your search using many bioinformatics analysis tools or applications. This enables you to seek out further information that may be relevant to your initial search.

Proper citation: SRS (RRID:SCR_010736) Copy   

•   Source: SciCrunch Registry
  

http://www.molecularevolution.org/software/genomics/velvet

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Velvet (RRID:SCR_010755) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/~zerbino/oases/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.

Proper citation: Oases (RRID:SCR_011896) Copy   

•   Source: SciCrunch Registry