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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Odor Molecules DataBase Resource Report Resource Website 1+ mentions |
Odor Molecules DataBase (RRID:SCR_007286) | OdorDB | data or information resource, database | OdorDb is a database of odorant molecules, which can be searched in a few different ways. One can see odorant molecules in the OdorDB, and the olfactory receptors in ORDB that they experimentally shown to bind. You can search for odorant molecules based on their attributes or identities: Molecular Formula, Chemical Abstracts Service (CAS) Number and Chemical Class. Functional studies of olfactory receptors involve their interactions with odor molecules. OdorDB contains a list of odors that have been identified as binding to olfactory receptors. | genetics, cellular, molecular, olfactory, receptor, training material |
is related to: Olfactory Receptor DataBase has parent organization: Yale University; Connecticut; USA works with: ORModelDB |
Aging | Human Brain Project ; NIMH ; NIA ; NICD ; NINDS ; Multidisciplinary University Research Initiative ; NIDCD RO1 DC 009977 |
nif-0000-00056 | SCR_007286 | 2026-08-10 09:33:06 | 1 | |||||||
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MIPS Ustilago maydis Database Resource Report Resource Website 1+ mentions |
MIPS Ustilago maydis Database (RRID:SCR_007563) | data or information resource, database | The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite. | drug, environment, filamentous, functional, fungal, fungal genome databases, fungus, gene, genetic, basidiomycete, cell, codon, culture, dikaryotic, diploid, genome, genomic, germinate, haploid, host, human, infection, maize, mating, meiotic, model, molecular, morphogenesis, network, orf, pathogen, pathologist, phytopathogen, phytopathogenesis, plant, protein, recombination, sequence, signal, spore, strain, structure, teliospore, teosinte, tissue, tumor, ustilago maydis, virulence, yeast | nif-0000-21276 | SCR_007563 | MUMDB | 2026-08-10 09:33:11 | 9 | ||||||||||
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ChromDB- the chromatin database Resource Report Resource Website 50+ mentions |
ChromDB- the chromatin database (RRID:SCR_007597) | data or information resource, database | ChromDB is a chromatin database. Three types of sequences are included in the database: genomic-based (predominantly plant sequences); transcript-based (EST contigs or cDNAs for plants lacking a sequenced genome); and NCBI RefSeq sequences for a variety of model animal organisms. The Gene Record Page for any sequence indicates the type of sequence. The broad mission of ChromDB is display, annotate, and curate sequences of two broad functional classes of biologically important proteins: chromatin-associated proteins (CAPs) and RNA interference-associated proteins. Plant proteins are the major focus of the work support by The Plant Genome Research Program (PGRP) of the National Science Foundation. Our intent is to produce intensively curated sequence information and make it available to the research and teaching community in support of comparative analyses toward understanding the chromatin proteome in plants, especially in important crop species. In order to do a comparative analysis, it is necessary to include non-plant proteins in the database. Non-plant genes are not curated to the degree carried out for plants and to automate the process of data import, our non-plant genes are from the RefSeq database of NCBI. We reason that the inclusion of non-plant, model organisms will broaden the relevance and usefulness of ChromDB to the entire chromatin community and will provide a more complete data set for phylogenetic analyses in support of the evolution of the plant chromatin proteome. ChromDB is funded by a grant from the National Science Foundation Plant Genome Research Project(#DBI-0421679). | chromatin, chromatin-associated protein, crop species chromatin, plant chromatin proteome, plant protein, rna interference-associated proteins, FASEB list | has parent organization: University of Arizona; Arizona; USA | nif-0000-02661 | SCR_007597 | ChromDB | 2026-08-10 09:33:16 | 62 | |||||||||
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Ciliate IES-MDS database Resource Report Resource Website 1+ mentions |
Ciliate IES-MDS database (RRID:SCR_007599) | data or information resource, database | IES-MDS DB is a database of macronuclear and micronuclear genes in spirotrichous ciliates. The database contains information on 440 MDS pairs (each pair composed of the MIC and the MAC version of a given MDS), 392 IES and 361 pointer triples (each pointer has two active copies in the MIC and one copy in the MAC) (7). Out of the 440 MDSs, 235 are scrambled, and 65 are in the opposite strand in the MIC. A total of 320 IESs and 202 pointers are scrambled. For each pair of genes in the database the user can see the micronuclear and macronuclear organization and has the option to see all the MDS, IES and pointer sequences. Another option is to download the MIC sequence with the MDSs and pointers in uppercase and the IESs in lowercase. It is also possible to graphically compare the organization of several genes. | macronuclear gene, micronuclear gene, spirotrichous ciliate | has parent organization: Princeton University; New Jersey; USA | nif-0000-02663 | SCR_007599 | IES-MDS DB | 2026-08-10 09:33:12 | 1 | |||||||||
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ChemDB: The UC Irvine ChemDB Resource Report Resource Website 10+ mentions |
ChemDB: The UC Irvine ChemDB (RRID:SCR_007594) | data or information resource, database | A database of general chemical information. The datasets are comprised of various available chemical datasets annotated with interesting properties to train and test machine-learning prediction and searching methods. Tools provided include ChemicalSearch, Virtual Chemical Space, Reaction Explorer, Datasets, and supplemental material. ChemicalSearch is a tool that allows users to find a chemical by basic criteria like molecular weight and predicted logP, or by the more abstract notion of structural similarity. Virtual Chemical Space is a tool which lets users interactively deconstruct target compounds into component precursors and reconstruct similar building-blocks into combinatorial libraries representing the virtual chemical space near the target compound. Reaction Explorer is a synthesis explorer and mechanism explorer. It provides an interactive system for learning and practicing reactions, syntheses and mechanisms in organic chemistry, with advanced support for the automatic generation of random problems, curved-arrow mechanism diagrams, and inquiry-based learning. | chemical, chemical property, chemical reaction, chemistry, compound, organic chemistry, synthesis, software |
is listed by: 3DVC has parent organization: University of California at Irvine; California; USA |
nif-0000-02657 | SCR_007594 | ChemDB | 2026-08-10 09:33:16 | 14 | |||||||||
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Chicken Variation Database Resource Report Resource Website 1+ mentions |
Chicken Variation Database (RRID:SCR_007595) | data or information resource, database | ChickVD hosts high-quality sequence variation data, variation analysis in the context of chicken genes, cDNAs, chicken orthologs of human disease genes, genetic markers, quantitative trait loci (QTLs) etc . All data are uniquely mapped onto the RJF draft genome and graphically represented in MapView, an efficient visualization tool that allows users to browse sequence variations in the genomic and functional context. The sub-viewer TraceView assists users to view the vivid graphics of the original traces around the detected SNP. Users may query the data by the online search tool and define concrete limitations to extract records that are best suited to their research needs. For the convenience of data presentation in ChickVD, different types of sequence variations (substitutions, insertions or deletions) are all referred as ???SNPs''. ChickVD is updated constantly as more data generated and is under the continued improvement for its content and functionality | chicken, chicken cdna, chicken gene, chicken genetics, chicken genome, chicken ortholog of human gene, chicken quantitative trait loci, genome visualization, mapview, traceview | has parent organization: BGI; Shenzhen; China | nif-0000-02658 | SCR_007595 | ChickVD | 2026-08-10 09:33:12 | 4 | |||||||||
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Defensins Knowledgebase Resource Report Resource Website 1+ mentions |
Defensins Knowledgebase (RRID:SCR_007623) | data or information resource, database | The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of 363 defensin records each containing sequence, structure and activity information. A web-based interface provides access to the information and allows for text-based searching on the data fields. With the rapidly increasing interest in defensins, we hope that the knowledgebase will prove to be a valuable resource in the field of antimicrobial peptide research. | antimicrobial peptide, defensin | has parent organization: Agency for Science Technology and Research | nif-0000-02744 | SCR_007623 | Defensins Knowledgebase | 2026-08-10 09:33:17 | 4 | |||||||||
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Cleansed EST Database Resource Report Resource Website 1+ mentions |
Cleansed EST Database (RRID:SCR_007587) | data or information resource, database | A database to provide cleansed EST sequences of classified dbEST libraries. All dbEST libraries were classified according to organism, sequencing center, and eVOC ontologies (for human libraries). For each dbEST library, we provide three different EST sequences: raw, pre-cleansed, and user-cleansed. pre-cleansed ESTs are obtained from major contamination databases and cleaned of contaminated sequences. User-cleansed ESTs, however, involve the use of an automatic user-cleansing pipeline, in which sequences in a user-selected library are cleansed on-the-fly according to user-input options. CleanEST contains 62,008,259 EST sequences (24,000 libraries) with contamination information. | est, cleansed est sequence, contamination database, dbest | nif-0000-02666 | SCR_007587 | CleanEST | 2026-08-10 09:33:16 | 1 | ||||||||||
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DataBase of Tunicate Gene Regulation Resource Report Resource Website 1+ mentions |
DataBase of Tunicate Gene Regulation (RRID:SCR_007620) | data or information resource, database | DBTGR provides information on tunicate gene regulation, such as the location of expression, or the identified regulatory elements present in promoter sequences. The database also contains the promoters of homologous genes in multiple species to allow identification of conserved cis elements. | promoter sequence, regulatory element, regulatory system, tunicate, tunicate gene expression reporter vector | has parent organization: University of Tokyo; Tokyo; Japan | nif-0000-02737 | SCR_007620 | DBTGR | 2026-08-10 09:33:17 | 1 | |||||||||
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Dragon Database for Exploration of Ovarian Cancer Genes Resource Report Resource Website 1+ mentions |
Dragon Database for Exploration of Ovarian Cancer Genes (RRID:SCR_007621) | data or information resource, database | :DDOC provides a comprehensive compilation of the published research related to the genes associated with ovarian cancer. DDOC provides details of the cell line, tissue or cell type, expression status, disease stage, tumor grade, OC type and laboratory method provided in the literature. The links to the relevant sources of data used to extract information related to genes are also included. Many aspects of the information provided in the DDOC were curated by biologists, which increases its accuracy. DDOC is freely accessible for academic and non-profit users. | ovarian cancer, ovarian cancer cell line, ovarian cancer gene, ovarian cancer stages, ovarian tissue | nif-0000-02742 | SCR_007621 | DDOC | 2026-08-10 09:33:13 | 5 | ||||||||||
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CATH: Protein Structure Classification Resource Report Resource Website 100+ mentions |
CATH: Protein Structure Classification (RRID:SCR_007583) | data or information resource, database | CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis Users can search CATH by ID/Sequence/text. They can also browse CATH from the top of the hierarchy, or download CATH data. | architecture, class, homologous superfamily, protein cluster, protein domain structure, topology, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: FunTree has parent organization: University College London; London; United Kingdom |
nif-0000-02640, r3d100012629, biotools:cath | https://bio.tools/cath, https://doi.org/10.17616/R32Z1F | SCR_007583 | CATH | 2026-08-10 09:33:16 | 306 | ||||||||
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Combinatorial Extension (CE) Resource Report Resource Website 1+ mentions |
Combinatorial Extension (CE) (RRID:SCR_007585) | CE | data or information resource, database | CE is a databases of alignments for all polypeptide chains. A representative set of proteins is available and kept current with the PDB, a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment. Complete details are described in the paper (PDF format). Databases of alignments for all polypeptide chains and a representative set of proteins is available and kept current with the PDB | polypeptide, polypeptide chain, protein, protein alignment, protein structure |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of California at San Diego; California; USA |
nif-0000-02648 | http://cl.sdsc.edu/ce.html | SCR_007585 | Combinatorial extension | 2026-08-10 09:33:12 | 5 | |||||||
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CASRDB- Calcium Sensing Receptor Database Resource Report Resource Website 10+ mentions |
CASRDB- Calcium Sensing Receptor Database (RRID:SCR_007581) | data or information resource, database | CASRdb is a calcium-sensing receptor locus-specific database for mutations causing familial (benign) hypocalciuric hypercalcemia, neonatal severe hyperparathyroidism, and autosomal dominant hypocalcemia. The information can be searched by mutation, genotype-phenotype, clinical data, in vitro analyses, and authors of publications describing the mutations. CASRdb is regularly updated for new mutations and it also provides a mutation submission form to ensure up-to-date information. The home page of this database provides links to different web pages that are relevant to the CASR, as well as disease clinical pages, sequence of the CASR gene exons, and position of mutations in the CASR. The CASRdb will help researchers to better understand and analyze the mutations, and aid in structure-function analyses. | familial hypocalciuric hypercalcemia, benign hypocalciuric hypercalcemia, calcium-sensing, hypocalciuric hypercalcemia, mutation causing hypocalciuric hypercalcemia | has parent organization: McGill University; Montreal; Canada | r3d100012040, nif-0000-02638 | https://doi.org/10.17616/R3X07T | SCR_007581 | CASRDB | 2026-08-10 09:33:12 | 21 | ||||||||
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dbPTM: An informational repository of proteins and post-translational modifications Resource Report Resource Website 100+ mentions |
dbPTM: An informational repository of proteins and post-translational modifications (RRID:SCR_007619) | data or information resource, database | dbPTM is a database that compiles information on protein post-translational modifications (PTM) such as the modified sites, solvent accessibility of surrounding amino acids, protein secondary and tertiary structures, protein domains, and protein variations. The version 2.0 of dbPTM integrates the experimentally validated PTM sites with referable literatures from Swiss-Prot, Phospho.ELM, O-GLYCBASE, and UbiProt. In all of the collected PTM information, about 25 types of PTM with enough experimentally validated sites are trained the profile hidden Markov models (HMMs) to detect the potential PTM sites with 100% specificity against Swiss-Prot proteins. To help users investigating more detail in each type of PTM, the substrate peptide specificity such as positional amino acid frequency, solvent accessibility and secondary structure surrounding the modified sites are also provided. Moreover, the information of orthologous protein clusters is provided to users for analyzing whether the PTM sites located in the evolutionary conserved regions or not., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein, protein post-translational modification, ptm | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02730 | SCR_007619 | dbPTM | 2026-08-10 09:33:12 | 114 | |||||||||
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Next-Gen Sequencing Resource Report Resource Website |
Next-Gen Sequencing (RRID:SCR_007245) | Next-Gen Sequencing | data or information resource, blog, narrative resource | A working guide to the rapidly developing world of Next-Generation DNA sequencing, with an emphasis on bioinformatics. | is listed by: OMICtools | OMICS_01717 | SCR_007245 | 2026-08-10 09:33:13 | 0 | ||||||||||
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GeneNote Resource Report Resource Website 1+ mentions |
GeneNote (RRID:SCR_007679) | GeneNote | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented June 14, 2013. GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. It offers: An expression profile (tissue vector) for each gene in the human genome Gene and tissue clustering based on expression profiles A full genome ranking procedure according to the gene''s tendency for tissue specificity, from tissue-specific to housekeeping genes. | gene expression profile, human gene, human genome, tissue vector, data set | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02885 | SCR_007679 | 2026-08-10 09:33:17 | 1 | |||||||||
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Histone Database Resource Report Resource Website 1+ mentions |
Histone Database (RRID:SCR_007711) | data or information resource, database | Histone Database is a database of histones and their corresponding sequences. Sequence- and text-based searches were performed on NCBI's redundant and non-redundant (nr) peptide sequence databases. These databases are derived from GenBank, EMBL, and DDBJ translated DNA coding regions, plus protein sequences from the PDB (Protein Data Bank), SWISS-PROT, the PIR (Protein Information Resource), and the PRF (Protein Research Foundation). :Users can search by keyword, sequence fragment, category, organism, and redundancy of the set. | histone | has parent organization: National Human Genome Research Institute | nif-0000-02961 | SCR_007711 | Histone Database | 2026-08-10 09:33:18 | 5 | |||||||||
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Klotho: Biochemical Compounds Declarative Database Resource Report Resource Website |
Klotho: Biochemical Compounds Declarative Database (RRID:SCR_007714) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry. | has parent organization: University of Missouri; Missouri; USA | NIGMS R01-GM56529; NSF DBI-9117005 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03073 | SCR_007714 | Klotho | 2026-08-10 09:33:18 | 0 | ||||||||
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GeneFarm Resource Report Resource Website 1+ mentions |
GeneFarm (RRID:SCR_007674) | data or information resource, database | GeneFarm is a database of structural and functional annotation of plant gene and protein families. The goal of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for plant nuclear genes and gene products and to enter them into added-value database. The improved annotation will allow better data mining of the plant genomes (mainly Arabidopsis thaliana), and more secure planning and design of experiments. It is also a necessary step for building knowledge management tools for integrating plant genomic data, either for plant breeding or to get a broader interactive view of plant biological processes, like gene interaction networks. This re-annotation project, launched is mainly focused on gene families. A complete annotation pipeline using the most efficient prediction tools has been defined. The involved partners, each contributing with genes from his/her field of expertise, have exhaustively annotated families of homologous genes. A database named GeneFarm (Gene Families for Arabidopsis Management) gathers all these expert-curated annotations of plant gene families. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot. | plant gene, plant nuclear gene, plant protein | nif-0000-02881 | SCR_007674 | GeneFarm | 2026-08-10 09:33:14 | 2 | ||||||||||
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Genomic Distribution of structural Superfamilies Resource Report Resource Website 1+ mentions |
Genomic Distribution of structural Superfamilies (RRID:SCR_007670) | data or information resource, database | Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. GenDiS has been curated in direct correspondence with SCOP and represents 4001 highly resolved domains in 1194 structural superfamilies across protein sequence databases. Sequences showing reliable homology to entries in SCOP and PASS2 databases have been obtained from the non-redundant protein sequence database and aligned. Similar alignments of the superfamily members are provided in the genome level. GenDiS provides a platform for cross genome comparison at the superfamily level. GenDis relates proteins sequence information across all strata of taxonomy. One may navigate through the database to obtain structural homologues across different levels in taxonomic classification. The nomenclature of the various genomes and their hierarchy is in direct correspondence with the taxonomy database maintained at the NCBI. Sequence homologues for the various structural members are obtained from the non-redundant protein sequence database employing sensitive sequence search methods. Multiple approaches such as PSI-BLAST, HMMsearch of the HMMer suite and an interacting motif constrained PHI-BLAST have been employed to identify homologues in the sequence databases. | protein, protein superfamily | nif-0000-02874 | SCR_007670 | GenDiS | 2026-08-10 09:33:17 | 2 |
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