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

Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.

Proper citation: IntAct (RRID:SCR_006944) Copy   

•   Source: SciCrunch Registry

http://www.innatedb.com

Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.

Proper citation: InnateDB (RRID:SCR_006714) Copy   

•   Source: SciCrunch Registry

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

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy   

•   Source: SciCrunch Registry

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://www.flymine.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

Proper citation: FlyMine (RRID:SCR_002694) Copy   

•   Source: SciCrunch Registry

http://ophid.utoronto.ca/i2d

Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available.

Proper citation: I2D (RRID:SCR_002957) Copy   

•   Source: SciCrunch Registry

http://www.pathwaycommons.org/pc

Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)

Proper citation: Pathway Commons (RRID:SCR_002103) Copy   

•   Source: SciCrunch Registry

http://psidev.sourceforge.net/mi/xml/doc/user/index.html

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. As a first step, the PSI is developing standards for two key areas of proteomics: mass spectrometry and protein-protein interaction data. The document describes the molecular interaction data exchange format. PSI is following a leveled approach to building this specification. Level 1 will describe protein interactions at a basic level that covers a large amount of currently available data. Subsequent levels will add capability to represent new molecular interaction information that the community wishes to exchange. The scope of PSI MI is currently limited to protein-protein interactions. Other molecules, such as small molecules, DNA and RNA maybe taken into account in the future. The PSI MI format is a data exchange format for protein-protein interactions. It is not a proposed database structure. The purpose of the document is to describe the general structure of the PSI MI XML specification in a more user-friendly manner than the specification does itself. PSI MI was designed by a group of people including representatives from database providers and users in both academia and industry. PSI MI is supported by the DIP, MINT, IntAct, BIND and HPRD databases.

Proper citation: PSI-MI (RRID:SCR_010710) Copy   

•   Source: SciCrunch Registry

https://www.niddk.nih.gov/

Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country.

Proper citation: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) Copy   

•   Source: SciCrunch Registry

http://apid.dep.usal.es

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

Proper citation: Agile Protein Interactomes DataServer (RRID:SCR_008871) Copy   

•   Source: SciCrunch Registry

http://mint.bio.uniroma2.it/

A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.

Proper citation: MINT (RRID:SCR_001523) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry

http://cpdb.molgen.mpg.de

An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.

Proper citation: ConsensusPathDB (RRID:SCR_002231) Copy   

•   Source: SciCrunch Registry

http://channelpedia.epfl.ch/

An information management framework for comprehensive ion channel information. It is a knowledge base system centered on genetically expressed ion channel models and it encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models (September 2014). Channelepdia provides an ideal platform to collectively build ion channel knowledge base by accommodating both structured and unstructured data. The current version of Channelpedia contains the following sections : Introduction, Genes, Ontologies, Interactions, Structure, Expression, Distribution, Function, Kinetics and Models. Newly published literature related to ion channels is automatically queried every week from PubMed and added to respective categories. Currently, Channelpedia contains ~180,000 abstracts related to ion channels from Pubmed.

Proper citation: ChannelPedia (RRID:SCR_003807) Copy   

•   Source: SciCrunch Registry

http://www.re3data.org/

Global registry of research data repositories from all academic disciplines that allows the easy identification of appropriate research data repositories, both for data producers and users. Information icons display principal attributes of a repository that can be used for multi-faceted searches. Repository operators can suggest their infrastructures to be listed via a simple application form. A repository is indexed when the minimum requirements are met, i.e. mode of access to the data and repository, as well as the terms of use.

Proper citation: re3data.org (RRID:SCR_006782) Copy   

•   Source: SciCrunch Registry

http://www.agbase.msstate.edu/

A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase provides tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO. Additional tools for sequence analysis are also provided. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO. We appreciate any and all questions, comments, and suggestions. AgBase uses the NCBI Blast program for searches for similar sequences. And the Taxonomy Browser allows users to find the NCBI defined taxon ID for or taxon name for different organisms.

Proper citation: AgBase (RRID:SCR_007547) Copy   

•   Source: SciCrunch Registry

http://www.patika.org/

The human pathway database which contains different biological entities and reactions and software tools for analysis. PATIKA Database integrates data from several sources, including Entrez Gene, UniProt, PubChem, GO, IntAct, HPRD, and Reactome. Users can query and access this data using the PATIKAweb query interface. Users can also save their results in XML or export to common picture formats. The BioPAX and SBML exporters can be used as part of this Web service.

Proper citation: Pathway Analysis Tool for Integration and Knowledge Acquisition (RRID:SCR_002100) Copy   

•   Source: SciCrunch Registry

http://biodev.extra.cea.fr/interoporc/

Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

Proper citation: InteroPorc (RRID:SCR_002067) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resolver/SCR_002250

THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

Proper citation: OMICtools (RRID:SCR_002250) Copy   

•   Source: SciCrunch Registry

http://www.mechanobio.info/

Portal that deals with the process of mechanotransduction, providing in-depth, regularly updated reviews on the mechanics of cellular and molecular function. Each review is written by scientists and subsequently peer reviewed by experts in the field to ensure the content is accurate, reliable and up to date. Each review emphasizes the functional and mechanical aspects of a process, rather than the genetic aspects, with the aim of making this resource accessible to a wider audience. MBInfo is an ideal resource for scientists working in alternative fields, individuals working in industries where products are based on biological principles or students seeking a reliable introduction to a given cellular process. Each topic is written in a pyramid structure. The top of the pyramid is represented by an overview page, providing a basic description of a given function or process. These pages target a broad spectrum of readers and assume only a basic understanding of biology. Further down the pyramid, the reader will encounter the steps involved in the process described and functional modules that address specific mechanical aspects. These pages outline the protein complexes involved and the mechanisms by which they achieve the given process or function. These pages assume the readers have a more in-depth knowledge of scientific terms and principles. For every topic, a series of graphics and/or animations are available. These supplement the reviews, clarify information and guide the reader through complex processes pictorially. This makes MBInfo an ideal teaching resource, whether in the classroom or for clients trying to understand your product. All images and text are copyright protected and are for personal use only. Current Topics include: * Cellular Structures in Mechanosensing and Cell Motility * Methods in the Study of Mechanobiology * Nuclear Mechanotransduction Almost 100 stand alone Glossary Terms are now available. These include short definitions or summaries of proteins and processes that relate to broader topics discussed within the site. Browse an extensive range of figures, tables and videos in our resources section. New quizzes and other interactive content can also be found.

Proper citation: MBInfo (RRID:SCR_006768) Copy   

•   Source: SciCrunch Registry