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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Peptide Resource Page: Your Complete Guide to Peptide Research and Suppliers Resource Report Resource Website |
Peptide Resource Page: Your Complete Guide to Peptide Research and Suppliers (RRID:SCR_006676) | PRP | data or information resource, portal, registry, topical portal | A guide to peptide-related research and products including custom peptide suppliers, peptide synthesis reagent suppliers that provide resins, coupling reagents, and protected amino acids as well as biologically active peptides and substrates, peptide synthesizers for solution or solid phase peptide synthesis, peptide sequence analysis services, software to calculate the chemical or biochemical properties of peptides, including the prediction of antigenicity or difficult-to-synthesize sequences. There is an additional section on Proteomics Tools for the identification of proteins from peptide sequences determined by mass spectrometry. The site also contains a set of links to educational materials about peptide related research topics. | peptide, training material, modified peptide, library, array, peptide synthesis, protein, peptide sequencing, proteomics | nif-0000-37062 | SCR_006676 | Peptide Resource Page | 2026-09-12 12:56:43 | 0 | |||||||||
|
MBInfo Resource Report Resource Website 10+ mentions |
MBInfo (RRID:SCR_006768) | MBInfo, MCMF | data or information resource, image collection, portal, topical portal, training resource, video resource | 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. | cell, molecule, function, cellular function, molecular function, mechanics, cellular process, mechanobiology, biochemistry, mechanotransduction, review, protein, cellular structure, mechanosensing, cell motility, protein-protein interaction, cytoskeletal system, filopodia, lamellipodium, lamellum, stress fiber, dendritic spine, protein-protein interaction, nucleic acid-protein, small molecule-protein, protein, nucleic acid, small molecule, interaction |
is related to: PSICQUIC Registry is related to: IntAct has parent organization: National University of Singapore; Singapore; Singapore |
Ministry of Education - Singapore ; National Research Foundation - Republic of Singapore |
Acknowledgement requested, Use of images requires consent | nif-0000-06680 | SCR_006768 | MBInfo: A modular approach to cellular functions, Manual of Cellular and Molecular Function | 2026-09-12 12:56:45 | 10 | ||||||
|
BAR Resource Report Resource Website 10+ mentions |
BAR (RRID:SCR_006748) | BAR | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available. | gene expression, protein, molecular marker, mapping, tool, genomic, genomics, functional genomics, interaction, molecular interaction, protein-protein interaction, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada |
nlx_152191, biotools:bioanalres_bar | https://bio.tools/bioanalres_bar | SCR_006748 | Bio-Analytic Resource for Plant Biology, Bio-Analytic Resource, Bio-Analytic Resource - the BAR | 2026-09-12 12:56:44 | 48 | ||||||
|
ENCODE Resource Report Resource Website 1000+ mentions |
ENCODE (RRID:SCR_006793) | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome. | Encyclopedia, DNA, element, functional, human, genome, protein, RNA, level, regulatory, gene, active, disease, analysis |
uses: Segway - a way to segment the genome is used by: BioSample Database at EBI is used by: VizHub is used by: GEMINI is used by: Deep Blue Epigenomic Data Server is recommended by: National Library of Medicine is listed by: OMICtools is affiliated with: GENCODE is related to: Factorbook is related to: UCSC Genome Browser is related to: modENCODE is related to: UCSC Genome Browser is related to: Encode is related to: Broad Institute Genomics Platform has parent organization: University of California at Santa Cruz; California; USA |
NHGRI | PMID:21526222 | Free, Freely available | nif-0000-02797, r3d100013051, SCR_017493, OMICS_00532 | http://encodeproject.org/ENCODE/, https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements, https://www.encodeproject.org/, https://doi.org/10.17616/R31NJMKB | SCR_006793 | ENCODE - Encyclopedia of DNA Elements, ENCODE + Epigenomics Roadmap Combined Data Browser, Encyclopedia of DNA Elements, Encyclopedia of DNA Elements (ENCODE) | 2026-09-12 12:56:45 | 4206 | |||||
|
CD-HIT-OTU Resource Report Resource Website 50+ mentions |
CD-HIT-OTU (RRID:SCR_006983) | CD-HIT-OTU | software resource | Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12). | 454, read, illumina, rrna, fasta, metagenome, sequence, clustering, metagenomics, next-generation sequencing, protein |
is listed by: OMICtools has parent organization: CD-HIT |
PMID:22772836 PMID:21899761 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01441 | SCR_006983 | 2026-09-12 12:56:48 | 89 | |||||||
|
Array Information Library Universal Navigator Resource Report Resource Website 1+ mentions |
Array Information Library Universal Navigator (RRID:SCR_006967) | AILUN | analysis service resource, data analysis service, data or information resource, database, production service resource, resource, service resource | Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species. | gene expression, gene, array, clone, probe, protein, proteomic, annotation, analytical service, probe id, comparison, microarray, probe sequence, gene identifier, annotation file, web service |
is related to: Gene Expression Omnibus is related to: Entrez Gene has parent organization: Stanford University School of Medicine; California; USA |
Lucile Packard Foundation for Childrens Health ; Howard Hughes Medical Institute ; Pharmaceutical Research and Manufacturers of America Foundation ; NLM K22 LM008261; NIDDK R01GM079719 |
PMID:17971777 | nif-0000-33004 | SCR_006967 | 2026-09-12 12:56:48 | 5 | |||||||
|
GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-09-12 12:56:48 | 6 | |||||
|
IntAct Resource Report Resource Website 1000+ mentions |
IntAct (RRID:SCR_006944) | IntAct | data or information resource, data repository, database, service resource, storage service resource | 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. | protein domain, motif, protein interaction, molecular interaction, interaction, protein, binary interaction, complex, data set, protein-protein interaction, pathway, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid, protein binding, chromatin, cancer, apoptosis, molecular biology, virus, source code, isoform, gold standard |
is used by: ChannelPedia is used by: MINT is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition 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 listed by: OMICtools is related to: 3D-Interologs 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: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: VirHostNet: Virus-Host Network is related to: PSICQUIC Registry is related to: UniProt is related to: SIB Swiss Institute of Bioinformatics is related to: I2D is related to: InnateDB is related to: MatrixDB is related to: MBInfo is related to: AgBase is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PSI-MI is related to: Agile Protein Interactomes DataServer has parent organization: European Bioinformatics Institute works with: IMEx - The International Molecular Exchange Consortium |
European Union contract FP7-HEALTH-2007-223411; European Union contract FP7-HEALTH-2007-200767 |
PMID:24234451 PMID:22121220 PMID:19850723 PMID:17145710 PMID:14681455 |
Apache License, v2, (software), Creative Commons Attribution License, (data), The community can contribute to this resource | OMICS_01918, r3d100010671, nif-0000-03026 | https://doi.org/10.17616/R3QS4R | SCR_006944 | IntAct | 2026-09-12 12:56:48 | 1955 | ||||
|
PrimerBank Resource Report Resource Website 1000+ mentions |
PrimerBank (RRID:SCR_006898) | PrimerBank | data or information resource, data repository, database, service resource, storage service resource | Database of human and mouse primer pairs for gene expression analysis by polymerase chain reaction (PCR) and quantitative PCR (qPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. All primers in PrimerBank were carefully designed to ensure gene specificity. All experimental validation data for mouse primers are available from PrimerBank. You can submit your primers. They will be added to the database once they are properly QCd. | electrophoresis, gene expression, quantitative pcr, gel, gene, agarose, algorithm, amplification, human, molecular probe, primer database, mouse, pcr, primer, primer pair, protein, quantification, reaction, secondary structure, polymerase chain reaction, real-time pcr, pcr primer, detection, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U01 HL66678 | PMID:22086960 PMID:19906719 PMID:19108745 PMID:14654707 |
Public, Acknowledgement requested, The community can contribute to this resource | nif-0000-21333, OMICS_02323, biotools:primerbank | https://bio.tools/primerbank | SCR_006898 | PrimerBank: PCR Primers for Gene Expression Detection and Quantification | 2026-09-12 12:56:47 | 1709 | ||||
|
YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-09-12 12:56:47 | 34 | |||||
|
Gene Interaction Extraction from the Literature Resource Report Resource Website 1+ mentions |
Gene Interaction Extraction from the Literature (RRID:SCR_008660) | GIN-IE | software resource | GIN-IE is a high precision system for extracting protein/gene interactions, interaction cue words, and directionality from the literature. Syntax-aware inferences about the roles of the entities are made by using the syntactic and dependency parse tree structures of the sentences. Negation and speculation are frequently occurring language phenomena that modify the factuality of the information contained in text. GIN-IE detects and distinguishes interactions that are extracted from negated or speculative sentences. GIN-IE has been integrated with the NCIBI PubMed daily update and processing pipeline. The extracted interactions are accessible through MimiWeb. | extract, gene, interaction, protein, sentence, structure |
is related to: National Center for Integrative Biomedical Informatics has parent organization: University of Michigan; Ann Arbor; USA |
nif-0000-33151 | SCR_008660 | 2026-09-12 12:57:07 | 1 | |||||||||
|
Protein Subcellular Location Image Database Resource Report Resource Website |
Protein Subcellular Location Image Database (RRID:SCR_008663) | PSLID | data or information resource, data repository, data set, database, image analysis service, service resource, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. Annotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees. The annotations in PSLID provide a description of sample preparation and fluorescence microscope imaging. |
protein, structure, subcellular, organelle, image, fluorescence microscope, annotation, classify, rank, cluster, subcellular localization, 3d spatial image, 2d spatial image, micrograph, content-based retrieval, green fluorescent protein |
is listed by: 3DVC is listed by: Biositemaps has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Merck Company Foundation ; NIGMS GM075205; NCI R33 CA83219; NSF MCB-8920118 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33313 | SCR_008663 | PSLID - Protein Subcellular Location Image Database, Protein Subcellular Location Image Database | 2026-09-12 12:57:07 | 0 | ||||||
|
Ingenuity Pathway Analysis Resource Report Resource Website 5000+ mentions Rating or validation data |
Ingenuity Pathway Analysis (RRID:SCR_008653) | IPA | pathway analysis tool | A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest. | software, drug, gene, analysis, chemical, metabolic, model, pathway, protein, signal, molecular signaling, genomic, pathway analysis tool |
uses: Ingenuity Pathways Knowledge Base is listed by: Biositemaps is listed by: OMICtools is listed by: SoftCite |
Commercial license | nif-0000-33144, OMICS_00399 | http://www.ingenuity.com/products/ipa, http://www.ingenuity.com/products/ipa/microrna-research | SCR_008653 | QIAGEN Ingenuity Pathway Analysis | 2026-09-12 12:57:07 | 6828 | ||||||
|
Quertle: Relationship-Driven Biomedical Search Resource Report Resource Website |
Quertle: Relationship-Driven Biomedical Search (RRID:SCR_008676) | data or information resource, database, disease-related portal, portal, research forum portal, topical portal | Quertle is a biomedical search engine focused on delivering informative results to biomedical researchers using advanced linguistic technologies, along with an in-depth understanding of the biomedical field. Quertle''s friendly interface makes it simple to search and refine results. Using advanced semantics, Quertle finds quality results, not just long lists. And it hods: all of PubMed, a growing number of full-text documents, news, and more. Features: :- Find Relationships, not Just :- Focus on Core Concepts: Since Quertle searches for Relationships, all the terms in your query must be found together in a meaningful way. Thus, Quertle immediately gives you results with more relevance. :- Unleash the Strength of Power Terms: Use Power Terms to search for categories of objects. For instance, you can use Protein to search for any protein, rather than the occurrence of the term, protein. View all Power Terms. :- Search Full-text Documents: The Quertle search engine has been optimized to search full-text documents, including the Material and Methods section (but not the Bibliography). :- Use Real Biology & Chemistry Terms: Quertle recognizes capital TWIST as the transcription factor (not the verb), and capital NO as nitrous oxide(not a negative). So, use proper capitalization in your query, and you won''t be lost in a sea of irrelevant results. :- Look for the Quertle Difference on the Results Page : More relevant results : Easy filtering and breadcrumb tracking : Automatic identification of key concepts : Single-click access to PDFs of full-text documents :Keyword: Biomedical, Search engine, Database, Researcher, Linguistic, Technology, Semantic, Relationship, Protein, Biology, Chemistry, : | all the terms in your query must be found together in a meaningful way. thus, biology, chemistry, chemistry terms: quertle recognizes capital twist as the transcription factor (not the verb), database, if you search for two or more terms, including the material and methods section (but not the bibliography). - use real biology &, linguistic, not just the terms scattered within the same document. - focus on core concepts: since quertle searches for relationships, protein, quertle immediately gives you results with more relevance. - unleash the strength of power terms: use power terms to search for categories of objects. for instance, rather than the occurrence of the term, relationship, researcher, search engine, semantic, technology, use proper capitalization in your query, you can use protein to search for any protein, you will find occurrences of a conceptual relationship | nif-0000-33690 | SCR_008676 | Quertle | 2026-09-12 12:57:07 | 0 | ||||||||||
|
Molecular Libraries Program Resource Report Resource Website 10+ mentions |
Molecular Libraries Program (RRID:SCR_008847) | MLP | analysis service resource, data or information resource, material analysis service, organization portal, portal, production service resource, service resource, topical portal | High throughput screening services to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways, along with medicinal chemistry and informatics. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. The NIH Molecular Libraries Initiative NIH is designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. As these HTS Technologies were not previously available to the public sector, many investigators may not be familiar with the components and requirements of high throughput screening. A key challenge is to identify small molecules effective at modulating a given biological process or disease state. The Molecular Libraries Roadmap, through one of its components, the Molecular Libraries Probe Production Centers Network (MLPCN), offers biomedical researchers access to the large-scale screening capacity, along with medicinal chemistry and informatics necessary to identify chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. There are two kinds of data that are available to the scientific community through a dedicated database: Chemical Compounds and Bioassay Results (NCBI). Various types of data, including informative records on substances, compound structures, and biologically active properties of small molecules are housed respectively within PubChem''''s three primary databases: PCSubstance, PCCompound, and PCBioAssay. To date, PubChem contains over 11 million substance records, details about approximately 5.5 million unique compound structures with links to bioassay descriptions, relevant literature, references, and assay data points and over 250 bioassays, a good percentage of which were contributed by the pilot phase of the MLP. The deposition will continue during the current MLPCN phase. NIH anticipates that these projects will also facilitate the development of new drugs, by providing early stage chemical compounds that will enable researchers in the public and private sectors to validate new drug targets, which could then move into the drug-development pipeline. This is particularly true for rare diseases, which may not be attractive for development by the private sector. Funding opportunities are available through the site. | molecule, compound, probe, small molecule, high throughput screening, gene, cell, biochemical pathway, drug development, protein, pathway |
is used by: LINCS Information Framework is related to: BARD is related to: NIH Clinical Collection is related to: PubChem has parent organization: National Institutes of Health |
NIH | nlx_146246 | SCR_008847 | Molecular Libraries, Molecular Libraries Initiative | 2026-09-12 12:57:09 | 15 | |||||||
|
mtocDB Resource Report Resource Website |
mtocDB (RRID:SCR_008933) | mtocDB | data or information resource, database, image collection | A database of over 300 Electron Microscopy (EM) images of centrioles and centriole related structures from almost 60 species, described by a controlled vocabulary allowing detailed description of the observed structures. This knowledge is supplemented by a manually curated list of proteins known to be involved in centriole assembly, their (putative) orthologs, and localization information. mtocDB aims to characterize the naturally occurring morphological variation observed in centrioles and centriole associated structure alongside molecular information on the proteins involved in their assembly. Examining these in an evolutionary context will allow the cell biology community to infer meaningful relationships between cellular assembly mechanisms and the structures they form. This community resource for cell biologists interested in the the evolution of centrioles and centriole related structures aims to bridge the gap between structural morphology and molecular function by examining naturally occurring structural variation in a phylogenomic context. Centrioles are cylindrical microtubule arrays required for stability and duplication of the centrosome in animal cells, and for the assembly of cilia and flagella in many eukaryotes. The presence of centrioles throughout most eukaryotic branches suggests that this structure was present in the last eukaryotic common ancestor. Although centrioles show a typically well conserved structure, they can perform several functions and display a diversity of accessory structures. However, this diversity is not properly classified beyond model organisms, and the information contained in decades of electronic microscopy of other organisms remains untapped. | centriole, morphological variation, morphology, cell biology, cellular assembly, mechanism, structure, evolution, proteomics, genome, ortholog, electron microscopy, protein, centriole assembly, localization, microtubule, image, electron micrograph, micrograph | has parent organization: Instituto Gulbenkian de Ciencia; Oeiras; Portugal | Developed as a community resource, But as of 6/1/13, Requires an account pending resolution of copyright issues | nlx_151804 | SCR_008933 | Microtubule Organizing Center Database | 2026-09-12 12:57:10 | 0 | |||||||
|
NetOGlyc Resource Report Resource Website 500+ mentions |
NetOGlyc (RRID:SCR_009026) | NetOGlyc | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. | neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CBS Prediction Servers |
PMID:23584533 | Acknowledgement requested | nlx_153864, biotools:netoglyc | https://bio.tools/netoglyc | SCR_009026 | NetOGlyc Server | 2026-09-12 12:57:11 | 643 | |||||
|
PeptideMapper Resource Report Resource Website 1+ mentions |
PeptideMapper (RRID:SCR_005763) | PeptideMapper | data access protocol, software resource, web service | The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter. | peptide, sequence, protein, alignment, expressed sequence tag, mrna, est, htc, genbank, refseq, uniprot, ipi, vega, embl, hinvdb | has parent organization: Edwards Lab | NCI CA126189 | PMID:17437027 | nlx_149229 | SCR_005763 | PeptideMapper Web-Service, Peptide Mapper | 2026-09-12 12:56:31 | 4 | ||||||
|
TOPSAN Resource Report Resource Website 10+ mentions |
TOPSAN (RRID:SCR_005758) | TOPSAN | data or information resource, data repository, database, image collection, service resource, storage service resource | Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation. | protein, structure, 3d, protein structure, protein function, annotate, crowd sourcing, image, annotation, genomics, collaboration |
has parent organization: Sanford Burnham Prebys Medical Discovery Institute has parent organization: University of California at San Diego; California; USA |
NIGMS U54 GM074898; NIGMS P20 GM076221 |
PMID:20961957 PMID:20716366 PMID:20944203 PMID:20961957 |
Creative Commons Attribution v3 License, The community can contribute to this resource | nlx_149221 | SCR_005758 | he Open Protein Structure Annotation Network, TOPSAN Project, TOPSAN - The Open Protein Structure Annotation Network | 2026-09-12 12:56:31 | 10 | |||||
|
CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-09-12 12:56:31 | 20 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
