Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Morpholino Database Resource Report Resource Website 1+ mentions |
Morpholino Database (RRID:SCR_001378) | MODB | data repository, service resource, storage service resource, database, data or information resource | Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password. | morpholino, target mrna, embryonic zebrafish, sequence, target, blast, phenotype, anatomy, development, behavior, morphology, pigmentation, toxicity, pax2 expression, craniofacial structure, eye, kidney, pituitary, skin, name, target name, target sequence, gene target, genetic, mortality, toxicity, defect, function, gene annotation, genome, data analysis service |
uses: Zebrafish Information Network (ZFIN) uses: PATO has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
NIGMS GM63904; NIA CA65493 |
PMID:18179718 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152566 | SCR_001378 | MODB (MOprholino DataBase) | 2026-02-12 09:43:08 | 1 | |||||
|
FusionGDB2 Resource Report Resource Website 1+ mentions |
FusionGDB2 (RRID:SCR_025299) | data or information resource, database | Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level. | Functional annotation database, human fusion genes, fusion gene breakage tendency score, | NIGMS R35GM138184; University of Texas |
PMID:34755868 | Free, Freely available | SCR_025299 | FusionGDB 2.0 | 2026-02-11 11:01:03 | 2 | ||||||||
|
MAP Database Guide for Membrane Protein Solubilization Resource Report Resource Website 1+ mentions |
MAP Database Guide for Membrane Protein Solubilization (RRID:SCR_025656) | data or information resource, database | Open access web app that allows users to search for optimal condition for extraction of membrane proteins into membrane active polymers which allows for retention of native membrane environment around target protein. | optimal condition for extraction of membrane proteins, membrane active polymers, retention of native membrane environment, target protein, | has parent organization: Yale University; Connecticut; USA | NIGMS RM1GM149406; NIGMS R01GM141192; NIGMS R35GM147095; Michael J. Fox Foundation |
PMID:38405833 | Free, Freely available | SCR_025656 | Membrane Active Polymers Database Guide for Membrane Protein Solubilization | 2026-02-11 11:01:02 | 1 | |||||||
|
BioModels Resource Report Resource Website 100+ mentions |
BioModels (RRID:SCR_001993) | BIOMD | data repository, service resource, topical portal, storage service resource, database, data or information resource, portal | 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. | FAIR sharing, mathematical model, computational model, simulation, kinetic model, annotation, web service, data analysis service, systems biology, biological model, biology, molecular biology, nucleotide sequence, gene expression, protein, gene, dna, rna, genetics, gold standard |
is listed by: 3DVC is listed by: re3data.org is listed by: DataCite is related to: SBML is related to: PathCase Pathways Database System has parent organization: European Bioinformatics Institute is parent organization of: Kinetic Simulation Algorithm Ontology |
BBSRC BB/F010516/1; NIGMS R01 GM070923 |
PMID:20587024 PMID:16381960 |
CC0, Public Domain Dedication, Cf. our terms of use. | nif-0000-02609 | http://www.ebi.ac.uk/biomodels/ | SCR_001993 | BioModels Database - A Database of Annotated Published Models, BioModels Database, BioModels | 2026-02-12 09:43:17 | 249 | ||||
|
Pathway Commons Resource Report Resource Website 10+ mentions |
Pathway Commons (RRID:SCR_002103) | PC | data access protocol, software resource, web service, database, data or information resource | 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) | biological pathway, pathway, molecule, biopax, standard exchange format, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: cPath is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Reactome is related to: MINT is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Cancer Cell Map is related to: HPRD - Human Protein Reference Database is related to: Integrated Molecular Interaction Database is related to: Pathway Interaction Database is related to: CHEBI is related to: UniProt is related to: PANTHER is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of Toronto; Ontario; Canada |
NHGRI P41HG004118; NIGMS 2R01GM070743-06; NIGMS 1T32 GM083937; Cancer Biomedical Informatics Grid |
PMID:21071392 | Free, Freely available | nif-0000-20884, biotools:PathwayCommons_web_service_API | https://bio.tools/PathwayCommons_web_service_API | SCR_002103 | 2026-02-12 09:43:18 | 14 | |||||
|
GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | data repository, service resource, storage service resource, database, data or information resource | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NIGMS R01 GM123489; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIAAA U01 AA014425; NIA R01 AG043930; NIDA P20 DA21131; NCI U01 CA105417; NCRR U24 RR021760 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-02-12 09:43:21 | 473 | |||||
|
ConTrack Resource Report Resource Website 10+ mentions |
ConTrack (RRID:SCR_002681) | ConTrack | software application, image processing software, software resource, data processing software | An algorithm for identifying pathways that are known to exist between two regions within DTI data of anisotropic tissue, e.g., muscle, brain, spinal cord. The ConTrack algorithms use knowledge of DTI scanning physics and apriori information about tissue architecture to identify the location of connections between two regions within the DTI data. Assuming a course of connection or pathway between these two regions is known to exist within the measured tissue, ConTrack can be used to estimate properties of these connections in-vivo. | diffusion tensor imaging, tractography, brain connectivity, mri, software, source code, pathway, fiber tractography, tissue analysis |
is listed by: Biositemaps has parent organization: Simtk.org |
NIH Roadmap for Medical Research ; NIGMS U54 GM072970; NEI EY015000 |
PMID:18831651 | Free, Available for download, Freely available | nif-0000-23303 | SCR_002681 | Connectivity Tracking, Connectivity Tracking (ConTrack) | 2026-02-12 09:43:25 | 13 | |||||
|
Diseasome Resource Report Resource Website 1+ mentions |
Diseasome (RRID:SCR_002792) | Diseasome | book, service resource, narrative resource, map, data or information resource, image, data set | A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems. | disease, disorder, genotype, phenotype, poster, network |
is related to: Allen Institute Neurowiki has parent organization: Gephi |
Dana-Farber Cancer Institute ; W. M. Keck Foundation ; NHGRI ; NIGMS |
PMID:17502601 | Free, Freely Available | nif-0000-24580 | SCR_002792 | Diseaseome | 2026-02-12 09:43:27 | 1 | |||||
|
PharmGKB Resource Report Resource Website 1000+ mentions |
PharmGKB (RRID:SCR_002689) | PharmGKB | data access protocol, data repository, software resource, service resource, web service, storage service resource, database, data or information resource, data set | Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed. | pharmacogenomics, microarray, pathway, phenotype, snp array, genotype, clinical, genetic variation, drug, gene, genetic variation, disease, cardiovascular, pulmonary, cancer, metabolic, transporter, drug response, small molecule, research, drug response, FASEB list |
is used by: NIF Data Federation is listed by: OMICtools is related to: WikiPathways is related to: ConsensusPathDB is related to: Integrated Molecular Interaction Database is related to: MalaCards is related to: phenomeNET has parent organization: Stanford University; Stanford; California is parent organization of: PharmGKB Ontology |
NIGMS R24 GM61374 | PMID:11908751 | Free, Freely available | nif-0000-00414, OMICS_01586, r3d100012325 | https://doi.org/10.17616/R31H1N | SCR_002689 | Pharmacogenomics Knowledge Base | 2026-02-12 09:43:26 | 1152 | ||||
|
Patterns of Gene Expression in Drosophila Embryogenesis Resource Report Resource Website 50+ mentions |
Patterns of Gene Expression in Drosophila Embryogenesis (RRID:SCR_002868) | BDGP insitu | source code, software resource, database, data or information resource, image collection | Database of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs. | embryo, embryogenesis, gene, anatomy, microarray, pattern, protocol, rna, gene expression, expression pattern, embryonic drosophila, in situ hybridization, annotation, est, FASEB list |
is related to: Gene Ontology has parent organization: Berkeley Drosophila Genome Project |
Howard Hughes Medical Institute ; NIH ; NIGMS R01 GM076655; NHGRI HG00750; NHGRI P41 HG00739 |
PMID:17645804 PMID:12537577 |
Free, Freely available, Available for download | nif-0000-25550, r3d100011327 | https://doi.org/10.17616/R32H0K | http://www.fruitfly.org/cgi-bin/ex/insitu.pl | SCR_002868 | BDGP Embryonic Expression Patterns | 2026-02-12 09:43:28 | 64 | |||
|
I2D Resource Report Resource Website 10+ mentions |
I2D (RRID:SCR_002957) | I2D | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | 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. | interaction, prediction, protein-protein interaction, high-throughput, model organism, mammal, eukaryote, visualization, interolog, protein |
is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: University of Toronto; Ontario; Canada |
National Science and Engineering Research Council RGPIN 203833-02; NIGMS P50-GM62413 |
PMID:17535438 PMID:15657099 |
Free, Available for download, Freely available | nif-0000-03005, r3d100010675 | https://doi.org/10.17616/R3BG8R | SCR_002957 | Interologous Interaction Database, OPHID, I2D - Interologous Interaction Database | 2026-02-12 09:43:29 | 23 | ||||
|
GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool Resource Report Resource Website 1+ mentions |
GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool (RRID:SCR_003191) | GOLEM | analysis service resource, source code, software resource, service resource, production service resource, data analysis service | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Welcome to the home of GOLEM: An interactive, graphical gene-ontology visualization, navigation,and analysis tool on the web. GOLEM is a useful tool which allows the viewer to navigate and explore a local portion of the Gene Ontology (GO) hierarchy. Users can also load annotations for various organisms into the ontology in order to search for particular genes, or to limit the display to show only GO terms relevant to a particular organism, or to quickly search for GO terms enriched in a set of query genes. GOLEM is implemented in Java, and is available both for use on the web as an applet, and for download as a JAR package. A brief tutorial on how to use GOLEM is available both online and in the instructions included in the program. We also have a list of links to libraries used to make GOLEM, as well as the various organizations that curate organism annotations to the ontology. GOLEM is available as a .jar package and a macintosh .app for use on- or off- line as a stand-alone package. You will need to have Java (v.1.5 or greater) installed on your system to run GOLEM. Source code (including Eclipse project files) are also available. GOLEM (Gene Ontology Local Exploration Map)is a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet. | gene ontology, ontology visualization, ontology analysis |
is related to: Gene Ontology has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NSF IIS-0513552; NIGMS P50 GM071508 |
PMID:17032457 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30620 | https://lsi.princeton.edu/golem-interactive-graph-based-gene-ontology-navigation-and-analysis-tool | SCR_003191 | GOLEM An interactive graphical gene-ontology visualization navigation and analysis tool, GOLEM An interactive graphical gene-ontology visualization navigation analysis tool | 2026-02-12 09:43:32 | 3 | ||||
|
NLSdb: a database of nuclear localization signals Resource Report Resource Website 1+ mentions |
NLSdb: a database of nuclear localization signals (RRID:SCR_003273) | NLSdb | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree | nuclear localization signal, nuclear protein, nucleus, motif, predict, protein | has parent organization: Columbia University; New York; USA | NIGMS 1-P50-GM62413-01; NSF DBI-0131168 |
PMID:12520032 | Free for academic use, Acknowledgement requested, All others should inquire about a commercial license | nif-0000-03191 | http://cubic.bioc.columbia.edu/db/NLSdb/ | SCR_003273 | NLSdb - a database of nuclear localization signals | 2026-02-12 09:43:34 | 4 | ||||
|
EMDataResource.org Resource Report Resource Website 100+ mentions |
EMDataResource.org (RRID:SCR_003207) | EMDB, EMDataResource | project portal, data repository, service resource, storage service resource, data or information resource, portal | 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. | deposition, retrival, cryo, electron, microscopy, 3DEM, density, maps, atomic, model, metadata, structure |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is affiliated with: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI) is related to: PDBe - Protein Data Bank in Europe is related to: National Center for Macromolecular Imaging has parent organization: Rutgers University; New Jersey; USA has parent organization: European Bioinformatics Institute has parent organization: Baylor University; Texas; USA |
NIGMS R01 GM079429; BBSRC BBG022577 |
PMID:20935055 PMID:20888470 |
Free, Freely available | r3d100010552, nif-0000-30776 | https://doi.org/10.17616/R3T61P | EMDataBank.org | SCR_003207 | EMDataResource, EMDResource, EMDB, EMDataBank.org, EMDataBank - Unified Data Resource for 3DEM, EMDataBank | 2026-02-12 09:43:32 | 168 | |||
|
Database of Interacting Proteins (DIP) Resource Report Resource Website 100+ mentions |
Database of Interacting Proteins (DIP) (RRID:SCR_003167) | DIP | analysis service resource, data repository, service resource, production service resource, storage service resource, database, data analysis service, data or information resource | Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. | blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: NIH Data Sharing Repositories is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of California at Los Angeles; California; USA |
NIGMS | PMID:14681454 | Free, Available for download, Freely available | OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip | https://dip.doe-mbi.ucla.edu/dip/Main.cgi https://bio.tools/dip https://doi.org/10.17616/R3431F |
SCR_003167 | , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) | 2026-02-12 09:43:32 | 153 | ||||
|
GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | software resource, software application, data analysis software, data processing software | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-02-12 09:43:33 | 1078 | |||||
|
MouseNET Resource Report Resource Website 1+ mentions |
MouseNET (RRID:SCR_003357) | mouseNet | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. | gene, network, mouse, protein function, visualization, open reading frame, graph |
is listed by: OMICtools is related to: Gene Ontology is related to: mouseMAP has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NSF IIS-0513552; NIGMS P50 GM071508 |
PMID:18818725 | Free, Freely available | OMICS_01550, nif-0000-32003 | SCR_003357 | MouseNET | 2026-02-12 09:43:35 | 3 | |||||
|
Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | data repository, service resource, image repository, storage service resource, database, data or information resource | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639, r3d100011601 | http://www.cellimagelibrary.org/pages/about https://bio.tools/cellimagelibrary https://doi.org/10.17616/R3N92J |
SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-02-12 09:43:37 | 19 | ||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | 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. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome https://doi.org/10.17616/R3V59P |
SCR_003485 | Reactome Functional Interaction Network | 2026-02-12 09:43:37 | 4282 | |||||
|
National Institute of General Medical Sciences Image Gallery Resource Report Resource Website |
National Institute of General Medical Sciences Image Gallery (RRID:SCR_003480) | NIGMS Image Gallery | data or information resource, image collection, video resource | Database of scientific photos, illustrations, and videos made available by the National Institute of General Medical Sciences. | training material, database, illustration, media, news, photo, research | has parent organization: National Institute of General Medical Sciences | NIGMS | Permission is granted to use these images for educational, News media or research purposes, Provided the source for each image is credited. The material in this database may not be used to promote or endorse commercial products or services. | nif-0000-33708 | SCR_003480 | 2026-02-12 09:43:37 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
Email: info_at_ dknet.org
