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http://www.pathbase.net/

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)

Proper citation: Pathbase (RRID:SCR_006141) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: MRB - Mouse Resource Browser (RRID:SCR_005961) Copy   

•   Source: SciCrunch Registry

http://www.perseus-framework.org

Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing.

Proper citation: Perseus (RRID:SCR_015753) Copy   

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https://www.mousephenotype.org/imits/

This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products.

Proper citation: iMITS (RRID:SCR_016552) Copy   

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http://www.proteomexchange.org

A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.

Proper citation: ProteomeXchange (RRID:SCR_004055) Copy   

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

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.

Proper citation: RNAmmer (RRID:SCR_017075) Copy   

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https://syngoportal.org/

Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.

Proper citation: SynGO (RRID:SCR_017330) Copy   

•   Source: SciCrunch Registry

http://project-dare.eu/

EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously.

Proper citation: Project DARE (RRID:SCR_017538) Copy   

•   Source: SciCrunch Registry

http://www.aneurist.org/

Project focused on cerebral aneurysms and provides integrated decision support system to assess risk of aneurysm rupture in patients and to optimize their treatments. IT infrastructure has been developeded for management and processing of vast amount of heterogeneous data acquired during diagnosis.

Proper citation: aneurIST (RRID:SCR_007427) Copy   

•   Source: SciCrunch Registry

http://fmf.igh.cnrs.fr/ISSAID/infevers

Registry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided.

Proper citation: INFEVERS (RRID:SCR_007738) Copy   

•   Source: SciCrunch Registry

http://www.interaction-proteome.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 28, 2013. (URL is no longer valid) A platform for high-throughput proteomic analysis. Major objectives of IPP include the establishment of a broadly applicable platform of routine methods for the analysis of protein interaction networks in bio-medical research. A multidisciplinary approach will address; * their validation by cell biological, biochemical and biophysical methods. * their collection in a new type of public database. * their exploitation and use for in silico simulations of protein-interaction networks. The innovations generated in IPP will provide the basis for an efficient analysis and systems modeling of fundamental biological processes in health and disease. It will develop novel technology, including a high-end mass spectrometer with extremely large dynamic range, high-density peptide arrays, and improved visualization technology for light and electron microscopy. Additionally, the novel technologies will be validated with selected model systems of high relevance to medicine and biotechnology. Extensive bioinformatics support is a key element in the project to cope with the massive increase in experimental data on protein interactions obtained using the novel technologies. In particular, the efficient integration of disparate data sets represents a key challenge in proteomics and functional genomics. Therefore, the consortium includes the creator of the only European protein-interactions database, MINT. The multi-disciplinary efforts required in the scientific program of IPP are organized into four sub-projects (SP): * SP1: Tools for interaction analysis - SP1 is dedicated to the development of innovative proteomics technology to map protein-interaction networks and their cellular topology for the interaction analyses in SP2 and SP3. * SP2: Identification of interaction partners for protein domains - SP2 will generate (high throughput) data for important protein-protein interactions defined by bioinformatics and biomedical interest and by SP3, utilizing technology developed in SP1. * SP3: Functional analysis of interactions - SP3 focuses on the validation of technologies and tools developed in SP1. It will perform functional analyses of protein-interactions in medically and biochemically relevant prokaryotic and eukaryotic (mammalian) model systems. * SP4: Interactome database and modelling - SP4 provides the required bioinformatics infrastructure for the project, comprising the improvement of the public MINT database for the collection and dissemination of the interactome data; modelling and simulation of protein-interaction networks characterised in SP2 and SP3; and the dissemination of the technology developments to the scientific community.

Proper citation: Interaction Proteome Project (RRID:SCR_008043) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

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http://www.imexconsortium.org/

Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data.

Proper citation: IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) Copy   

•   Source: SciCrunch Registry

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

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

Proper citation: FunSimMat (RRID:SCR_002729) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org

Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution.

Proper citation: GenePaint (RRID:SCR_003015) Copy   

•   Source: SciCrunch Registry

http://www.mged.org/Workgroups/MAGE/mage-ml.html

A language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms.

Proper citation: MicroArray and Gene Expression Markup Language (RRID:SCR_003023) Copy   

•   Source: SciCrunch Registry

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

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

Proper citation: ArrayExpress (RRID:SCR_002964) Copy   

•   Source: SciCrunch Registry

http://www.mugen-noe.org/database/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. MMdb is being developed within the context of the MUGEN network of Excellence, a consortium of 21 leading research institutes and universities, and currently holds all mutant mouse models that were developed within the consortium. Its primary aim is to enable information exchange between participating institutions on mouse strain characteristics and availability. More importantly, it aims to create a mouse-centric international forum on modelling of immunological diseases and pave the way to systems biology of the mouse by correlating various genotypic and phenotypic characteristics. The basic categorization of models is based on three major research application categories: * Model of Human Disease * Model of Immune Processes * Transgenic Tool Mutant strains carry detailed information on affected gene(s), mutant alleles and genetic background (DNA origin, targeted, host and backcrossing background). Each gene/transgene index also includes IDs and direct links to Ensembl (EBI��s genome browser), ArrayExpress (providing expression profiles), Eurexpress II (for embryonic expression patterns) and NCBI��s Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI��s mammalian phenotypic ontology terms, but also includes relevant images and references. Since version 2.1.0 MMdb is also utilizing PATO. Availability (in the form of live mice, cryopreserved embryos or sperm, as well as ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and JAX hyperlinks where available).

Proper citation: MUGEN Mouse Database (RRID:SCR_003243) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/

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.

Proper citation: DTU Center for Biological Sequence Analysis (RRID:SCR_003590) Copy   

•   Source: SciCrunch Registry

https://protein.mpiib-berlin.mpg.de/cgi-bin/pdbs/2d-page/extern/index.cgi

The Proteome 2D-PAGE Database system for microbial research is a curated database for storing and investigating proteomics data. Software tools are available and for data submission, please contact the Database Curator. Established at the Max Plank Institution for Infection Biology, this system contains four interconnected databases: i.) 2D-PAGE Database: Two dimensional electrophoresis (2-DE) and mass spectrometry of diverse microorganisms and other organisms. This database currently contains 4971 identified spots and 1228 mass peaklists in 44 reference maps representing experiments from 24 different organisms and strains. The data were submitted by 84 Submitters from 24 Institutes and 12 nations. It also contains various software tools that are important in formatting and analyzing gels and mass peaks; software include: *TopSpot: Scanning the gel, editing the spots and saving the information *Fragmentation: Fragmentation of the gel image into sections *MS-Screener: Perl script to compare the similarity of MALDI-PMF peaklists *MS-Screener update: MS-Screener can be used to compare mass spectra (MALDI-MS(/MS) as well as ESI-MS/MS spectra) on the basis of their peak lists (.dta, .pkm, .pkt, or .txt files), to recalibrate mass spectra, to determine and eliminate exogenous contaminant peaks, and to create matrices for cluster analyses. *GelCali: Online calibration of the Mr- and pI-axis of 2-DE gels with mathematical regression methods ii.)Isotope Coded Affinity Tag (ICAT)-LC/MS database: Isotope Coded Affinity Tag (ICAT)-LC/MS data for Mycobacterium tuberculosis strain BCG versus H37Rv. iii.) FUNC_CLASS database: Functional classification of diverse microorganism. This database also integrates genomic, proteomic, and metabolic data. iv.) DIFF database: Presentation of differently regulated proteins obtained by comparative proteomic experiments using computerized gel image analysis.

Proper citation: Proteome 2D-PAGE Database (RRID:SCR_001678) Copy   

•   Source: SciCrunch Registry