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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NEXTDB Resource Report Resource Website 10+ mentions |
NEXTDB (RRID:SCR_004480) | NextDB | data analysis service, expression atlas, analysis service resource, data or information resource, production service resource, atlas, service resource, database | Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae | rnai phenotype, homology, blast, fasta, chromosome map, cosmid, gene, cdna clone, genome, in situ hybridization, expressed sequence tag, developmental stage, sequence, embryonic caenorhabditis elegans, chromosome, phenotype, blastx, clone, sequence tag, yac, predicted gene, protein, development, larval caenorhabditis elegans, image collection, experimental protocol, FASEB list |
is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: Expression Patterns for C. elegans promoter GFP fusions has parent organization: National Institute of Genetics; Shizuoka; Japan |
Core Research for Evolutional Science and Technology ; Japan Science and Technology Corporation ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
Permission required, Acknowledgement required | nlx_46406 | SCR_004480 | Nematode Expression Pattern DataBase | 2026-02-14 02:00:41 | 35 | ||||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | data repository, storage service resource, analysis service resource, data set, data or information resource, production service resource, source code, service resource, software resource, database | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-02-14 02:00:43 | 2 | ||||
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems https://doi.org/10.17616/R31K80 |
SCR_004690 | BioSystems Database, NCBI BioSystems | 2026-02-14 02:00:59 | 118 | |||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | 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. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
EMBL member states ; European Union ; NIH ; Wellcome Trust ; UK Research Councils ; Industry Programme partners ; BBSRC |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-02-14 02:00:46 | 3696 | ||||||
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PR Resource Report Resource Website |
PR (RRID:SCR_004964) | PR | data or information resource, ontology, controlled vocabulary | An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563). | database, obo, protein |
is listed by: BioPortal has parent organization: Protein Information Resource has parent organization: Georgetown University; Washington D.C.; USA |
NIH ; NIGMS GM080646-01 |
nlx_92849 | SCR_004964 | PRO, Protein Ontology | 2026-02-14 02:01:02 | 0 | |||||||
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Gene Map Annotator and Pathway Profiler Resource Report Resource Website 100+ mentions |
Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) | software resource, data visualization software, data processing software, software application | GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options. | expression, gene, analysis, biological, mapping, microarray, network, pathway, protein, visualization, ontology, proteomics, FASEB list |
has parent organization: University of California at San Francisco; California; USA is parent organization of: MAPPFinder |
Agilent Foundation ; BayGenomics ; NIGMS |
PMID:17588266 | nif-0000-00244 | SCR_005094 | GenMAPP | 2026-02-14 02:01:04 | 211 | |||||||
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SNPdbe Resource Report Resource Website 1+ mentions |
SNPdbe (RRID:SCR_005190) | SNPdbe | data repository, storage service resource, data or information resource, service resource, database | A database to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. It currently covers over 155,000 protein sequences which come from more than 2,600 organisms. Overall more than one million single amino acid substitutions (SAASs) are referenced consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts. SNPdbe offers the following pieces of information (if available) on each SAAS: * Experimentally derived functional and structural impact * Predicted functional effect * Associated disease * Average heterozygosity * Experimental evidence of the nsSNP * Evolutionary conservation of wildtype and mutant amino acid * Link-outs to external databases A convenient webinterface to query SAASs on the following levels is offered: * Protein and gene identifiers and keywords * Disease keywords * Protein sequence on different sequence identity thresholds * Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence They offer the possibility to submit protein sequences along with experimentally substantiated mutations in order to predict their functional effect and inclusion into our database. | single amino acid substitution, protein variant, protein, variant, protein sequence, natural variant, mutagenesis, sequencing, mutation |
is listed by: OMICtools has parent organization: ROSTLAB |
PMID:22210871 | Free for academic use, Non-commercial, Commercial use with permission, The community can contribute to this resource | OMICS_00185 | SCR_005190 | SNPdbe - nsSNP database of functional effects, nsSNP database of functional effects | 2026-02-14 02:00:52 | 4 | ||||||
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PiMS Resource Report Resource Website 100+ mentions |
PiMS (RRID:SCR_011816) | PiMS | software resource | Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes. | protein | is listed by: OMICtools | BBSRC ; CCP4 ; Instruct |
PMID:21385349 | Free for academic use | OMICS_01010 | SCR_011816 | Protein Information Management System | 2026-02-14 02:02:27 | 188 | |||||
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JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | data analysis service, analysis service resource, production service resource, service resource, software application, software resource, simulation software | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-02-14 02:02:07 | 1 | ||||||
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Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | 2026-02-14 02:02:33 | 0 | |||||||
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Abgent Resource Report Resource Website 50+ mentions |
Abgent (RRID:SCR_008393) | commercial organization | Antibody supplier. | antibody, peptide, synthesis, protein, primary antibody, reagent, peptide synthesis, cell signaling, post-translational modification, stem cell, neuronal development, neurodegenerative disease, gene regulation, development, autophagy, apoptosis, stem cell, phosphorylation, cell function, gene, regulation, research, library, human, kinome, cdna clone, rnai, tissue, cell | is listed by: ScienceExchange | nif-0000-30051, SciEx_4353 | https://www.abcepta.com/ | SCR_008393 | Abgent Antibodies and Peptides, Abcepta | 2026-02-14 02:01:33 | 67 | ||||||||
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MODELLER Resource Report Resource Website 5000+ mentions |
MODELLER (RRID:SCR_008395) | portal, data or information resource, software application, software resource, simulation software, topical portal | Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms. | comparative, protein, structure, modelling, satisfaction, spatial, restrain, homology, 3D, alignment, sequence, hydrogen, atom, cluster |
is listed by: SoftCite has parent organization: University of California at San Francisco; California; USA |
Sandler Family Supporting Foundation ; NIGMS R01 GM54762; NIGMS P01 GM71790; NIH P01 A135707; NIGMS U54 GM62529; IBM ; Intel |
Restricted | nif-0000-30054 | SCR_008395 | 2026-02-14 02:01:40 | 5736 | ||||||||
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Distributed Annotation System Resource Report Resource Website 10+ mentions |
Distributed Annotation System (RRID:SCR_008427) | data or information resource, software resource, narrative resource, standard specification | The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center. | annotation, database, software, genomic, protein, sequence, visualization, data, client-server, integration, bioinformatics, genome, structure, data integration |
is listed by: 3DVC has parent organization: Uppsala University; Uppsala; Sweden |
Howard Hughes Medical Institute ; NHGRI 2-P01-HG00956 |
nif-0000-30177 | SCR_008427 | BioDAS | 2026-02-14 02:01:38 | 11 | ||||||||
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MoonProt Resource Report Resource Website 10+ mentions |
MoonProt (RRID:SCR_008803) | laboratory portal, data or information resource, organization portal, portal | The moonlighting protein database is not yet available publicly. Stay tuned. Moonlighting proteins have multiple, seemingly unrelated functions not due to gene fusions or alternative splicing. Like PGI, which is a cytosolic enzyme and an extracellular cytokine, dozens of other proteins have been found to moonlight. Connie coined the term moonlighting proteins and has written several review articles that develop the idea of moonlighting proteins and describe additional moonlighting proteins from the literature, how they switch between functions, how they might have evolved, and how they might benefit the cell. She is currently writing two additional invited articles and planning computational studies of the sequences and structures of known moonlighting proteins. | protein, multifunctional protein, double functional protein, protein database | has parent organization: University of Illinois at Chicago; Illinois; USA | PMID:12902157 | nlx_144357 | SCR_008803 | Moonlighting proteins database | 2026-02-14 02:01:47 | 27 | ||||||||
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Agile Protein Interactomes DataServer Resource Report Resource Website 10+ mentions |
Agile Protein Interactomes DataServer (RRID:SCR_008871) | APID | web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | 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. | protein, protein interaction, interactions, ppi, interactomes, analysis, gene, ontology, functional, environment, data, network, graphic, visualize |
is listed by: Gene Ontology Tools is related to: PSICQUIC Registry is related to: Gene Ontology is related to: BIND is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Database of Interacting Proteins (DIP) is related to: HPRD - Human Protein Reference Database is related to: IntAct is related to: MINT has parent organization: University of Salamanca; Salamanca; Spain |
Spanish Ministerio de Sanidad y Consumo ; Junta de Castilla y Leon |
PMID:27131791 PMID:30715274 |
Free for academic use | r3d100012339, nlx_149321 | https://doi.org/10.17616/R3407P https://doi.org/10.17616/R3407P |
SCR_008871 | Agile Protein Interactomes DataServer, APID, APID Interactomes, Agile Protein Interactomes DataServer (APID), APID (Agile Protein Interactomes DataServer) | 2026-02-14 02:01:47 | 14 | ||||
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TopFIND Resource Report Resource Website 10+ mentions |
TopFIND (RRID:SCR_008918) | TopFIND | data repository, storage service resource, data or information resource, service resource, database | An integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases. It lists more than 120,000 N- and C-termini and almost 10,000 cleavages. TopFIND is a resource for comprehensive coverage of protein N- and C-termini discovered by all available in silico, in vitro as well as in vivo methodologies. It makes use of existing knowledge by seamless integration of data from UniProt and MEROPS and provides access to new data from community submission and manual literature curating. It renders modifications of protein termini, such as acetylation and citrulination, easily accessible and searchable and provides the means to identify and analyse extend and distribution of terminal modifications across a protein. The data is presented to the user with a strong emphasis on the relation to curated background information and underlying evidence that led to the observation of a terminus, its modification or proteolytic cleavage. In brief the protein information, its domain structure, protein termini, terminus modifications and proteolytic processing of and by other proteins is listed. All information is accompanied by metadata like its original source, method of identification, confidence measurement or related publication. A positional cross correlation evaluation matches termini and cleavage sites with protein features (such as amino acid variants) and domains to highlight potential effects and dependencies in a unique way. Also, a network view of all proteins showing their functional dependency as protease, substrate or protease inhibitor tied in with protein interactions is provided for the easy evaluation of network wide effects. A powerful yet user friendly filtering mechanism allows the presented data to be filtered based on parameters like methodology used, in vivo relevance, confidence or data source (e.g. limited to a single laboratory or publication). This provides means to assess physiological relevant data and to deduce functional information and hypotheses relevant to the bench scientist. TopFIND PROVIDES: * Integration of protein termini with proteolytic processing and protein features * Displays proteases and substrates within their protease web including detailed evidence information * Fully supports the Human Proteome Project through search by chromosome location CONTRIBUTE * Submit your N- or C-termini datasets * Contribute information on protein cleavages * Provide detailed experimental description, sample information and raw data | protein, n-termini, c-termini, protease, protein cleavage, proteomics, cleavage site, terminus, modification, proteolytic processing, protein function, domain structure, protein termini, terminus modification, protease, substrate, protease inhibitor, protein interaction, protein-protein interaction, interaction, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProtKB is related to: PSICQUIC Registry is related to: MEROPS has parent organization: University of British Columbia; British Columbia; Canada |
Canadian Institutes of Health Research ; Cancer Research Society ; British Columbia Proteomics Network ; Metalloproteinase Proteomics and Systems Biology ; Michael Smith Foundation for Health Research ; Breast Cancer Society of Canada ; Alexander von Humboldt-Stiftung ; BMBF ; German Academic Exchange Service |
PMID:22102574 PMID:21822272 |
Public, Acknowledgement requested | biotools:topfind, r3d100012721, nlx_151607 | https://bio.tools/topfind https://doi.org/10.17616/R3KB8J https://doi.org/10.17616/R3KB8J |
SCR_008918 | Termini oriented protein Function Inferred Database | 2026-02-14 02:01:48 | 29 | ||||
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PDBj - Protein Data Bank Japan Resource Report Resource Website 10+ mentions |
PDBj - Protein Data Bank Japan (RRID:SCR_008912) | PDBj | data repository, storage service resource, data or information resource, service resource, database | PDBj (Protein Data Bank Japan) maintains a centralized PDB archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. | protein, macromolecule, structure, sequence, ligand, binding site, nmr, molecule, gold standard |
is recommended by: NIDDK Information Network (dkNET) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBe - Protein Data Bank in Europe is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Osaka University; Osaka; Japan |
Japan Science and Technology Agency ; NBDC - National Bioscience Database Center |
PDB data, Text and images are free of all copyright restrictions. You can use them free of charge. When you reprint or cite them, Please also cite us as follows: Protein Data Bank Japan (PDBj) Please also see Terms of Use page. | nlx_151484, r3d100010910 | https://doi.org/10.17616/R3RP75 https://doi.org/10.17616/R3RP75 |
SCR_008912 | PDBj, Protein Data Bank Japan | 2026-02-14 02:01:49 | 39 | |||||
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BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2026-02-14 02:00:53 | 11 | ||||||
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Synergizer Resource Report Resource Website 1+ mentions |
Synergizer (RRID:SCR_005308) | Synergizer | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a namespace) to another. The Synergizer is a service for translating between sets of biological identifiers. It can, for example, translate Ensembl Gene IDs to Entrez Gene IDs, or IPI IDs to HGNC gene symbols, and much more. Unlike some other tools for this purpose, The Synergizer is simple and easy to learn. The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access). | gene, protein, json | has parent organization: University of Toronto; Ontario; Canada | nlx_144380 | SCR_005308 | The Synergizer | 2026-02-14 02:00:54 | 9 | ||||||||
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FaBox Resource Report Resource Website 100+ mentions |
FaBox (RRID:SCR_005350) | FaBox | software resource | Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER. | fasta, dna, protein sequence, dna sequence, protein, sequence, php |
is listed by: OMICtools has parent organization: Aarhus University; Aarhus; Denmark |
Acknowledgement requested | OMICS_01165 | SCR_005350 | FaBox - an online fasta sequence toolbox | 2026-02-14 02:01:06 | 116 |
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