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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | atlas, data or information resource, database | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | SciCrunch Registry | 2026-10-17 01:33:32 | 1 | |||||
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Biological Interaction database for Protein-nucleic Acid Resource Report Resource Website |
Biological Interaction database for Protein-nucleic Acid (RRID:SCR_013371) | BIPA | data or information resource, database |
A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces. There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids. |
amino acid, interaction, nucleic acid, protein | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-20819 | http://www-cryst.bioc.cam.ac.uk/bipa | SCR_013371 | SciCrunch Registry | Biological Interaction database for Protein-nucleic Acid | 2026-10-17 01:33:35 | 0 | |||||||
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NGS Expert Blog Resource Report Resource Website |
NGS Expert Blog (RRID:SCR_013218) | NGS Expert Blog | blog, data or information resource, narrative resource | Blog including established profound know-how and proprietary protocols to cover a broad range of applications. | next generation sequencing | is listed by: OMICtools | OMICS_01718 | SCR_013218 | SciCrunch Registry | 2026-10-17 01:35:10 | 0 | |||||||||
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ColiSNP: Database of Single Nucleotide Polymorphism Resource Report Resource Website 1+ mentions |
ColiSNP: Database of Single Nucleotide Polymorphism (RRID:SCR_013100) | data or information resource, database | ColiSNP is a website made up of two databases focused on SNPS. The first database is a database of Single Nucleotide Polymorphism (SNP) located in the protein coding region, and the second is a database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region. The database of Single Nucleotide Polymorphism (SNP) located in the protein coding region is a database of Single Nucleotide Polymorphism (SNP) mapped on protein structure. Users can search the data of SNP on this web site and display the structure of protein with SNP by RasMol. The database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region is a database of Single Nucleotide Polymorphism (SNP) mapped on regulation region. Users can search genes mapped snp on regulation region. | single nucleotide polymorphism, snp, snp in gene regulation region, snp in protein coding region | nif-0000-02677 | SCR_013100 | SciCrunch Registry | ColiSNP | 2026-10-17 01:33:34 | 1 | ||||||||||
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Australian Prostate Cancer Tissue Bank Resource Report Resource Website 1+ mentions |
Australian Prostate Cancer Tissue Bank (RRID:SCR_013221) | biomaterial supply resource, material resource, tissue bank | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 31,2023. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_13972 | SCR_013221 | SciCrunch Registry | 2026-10-17 01:33:34 | 1 | |||||||||||
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Rice Pipeline Resource Report Resource Website 1+ mentions |
Rice Pipeline (RRID:SCR_013344) | data or information resource, database | A unification tool which dynamically collects and compiles data from scientific databases in National Institute of Agrobiological Sciences (NIAS), and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Oryza sativa into easy to navigate. The mission of Rice PIPELINE is to provide a unique scientific resource of rice that pools publicly available data commonly sought after for any clone sequence, clone name, GenBank accession number, or keyword. | nif-0000-03408 | SCR_013344 | SciCrunch Registry | Rice Pipeline | 2026-10-17 01:35:12 | 4 | |||||||||||
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BTKbase Resource Report Resource Website 10+ mentions |
BTKbase (RRID:SCR_013101) | data or information resource, database | A mutation registry for X-linked agammaglobulinemia (XLA). BTKbase lists mutation entries of 1,111 patients from 973 unrelated families showing 602 unique molecular events. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement. Two thirds of cases are familial, and one third of cases are believed to arise from new mutations. Mutations of the BTK gene are found in approximately 80% of patients with agammaglobulinemia. The localization of the mutations on the gene and protein for BTK can be analyzed by clicking sequences on the web pages. It includes a mutation browser, which gives users access to mutations in Bruton tyrosine kinase (BTK) protein sequences, and XLA fact file, and forms for users to submit mutation to the dataset. | bruton tyrosine kinase, xla, x-linked agammaglobulinemia |
is listed by: 3DVC has parent organization: University of Tampere; Tampere; Finland |
Agammaglobulinemia | nif-0000-02625 | SCR_013101 | SciCrunch Registry | BTKbase | 2026-10-17 01:34:14 | 14 | ||||||||
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doRiNA Resource Report Resource Website 10+ mentions |
doRiNA (RRID:SCR_013222) | doRiNA | data or information resource, database | In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions. | binding site, rna binding protein, microrna, post-transcription, rna, gene, genome, mammal, population variation, gene expression, transcript, regulator, protein, binding |
is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
MDC Systems Biology Network ; BMBF ; Senate of Berlin; Berlin; Germany ; DFG |
PMID:22086949 | nlx_151321, r3d100011087 | SCR_013222 | SciCrunch Registry | 2026-10-17 01:34:14 | 15 | |||||||
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PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | data or information resource, database, service resource | A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. | text mining, bio-entity relation extraction, literature, information extraction, cell cycle, regulation, protein interaction, cellular location, flowering, leave, root, seed, gene, normalization, interaction, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:19520768 | OMICS_01192, biotools:plan2l | https://bio.tools/plan2l | SCR_013346 | SciCrunch Registry | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-10-17 01:33:35 | 0 | ||||||
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Monoclonal Antibody Index Resource Report Resource Website |
Monoclonal Antibody Index (RRID:SCR_013227) | MAI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included. | antibody, monoclonal antibody, cancer, aids, sars, heart disease, vascular disease, coagulation disease, transplantation, inflammation, alzheimer's disease, autoimmunity, biomarker, proteomics, resource, research, database | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01773 | SCR_013227 | SciCrunch Registry | 2026-10-17 01:33:34 | 0 | ||||||||
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OryGenesDB Resource Report Resource Website 10+ mentions |
OryGenesDB (RRID:SCR_013226) | data or information resource, database | The Oryza sativa database displays sequence information resulting from the research of the Centre de cooperation internationale en recherche agronomique pour le developpement. It also includes related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data, etc.). Genome Browser (Gbrowse), a Web-based application for displaying genomic annotations and other features, is the core of our database. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 2007). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. We developed a set of tools around GBrowse to retrieve as exhaustively as possible information related to queries with several starting points. These tools allow a molecular geneticist to readily find insertion lines (T-DNA, Tos17, Ds) in genes of interest and to retrieve all the associated annotations related to these sequences. | nif-0000-03231 | SCR_013226 | SciCrunch Registry | OryGenesDB | 2026-10-17 01:35:10 | 28 | |||||||||||
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aGEM Resource Report Resource Website 10+ mentions |
aGEM (RRID:SCR_013349) | aGEM | data or information resource, database | Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, anatomy, gene expression, anatomical structure, developmental stage, functional genomics, genomics |
is related to: EMAGE Gene Expression Database is related to: Gene Expression Database is related to: Gene Expression Nervous System Atlas is related to: BioGPS: The Gene Portal Hub is related to: Allen Mouse Brain Reference Atlas is related to: Eurexpress is related to: HUDSEN is related to: The Human Protein Atlas is related to: OMIM is related to: KEGG has parent organization: Autonomous University of Madrid; Madrid; Spain |
National Institute for Bioinformatics ; AMIT Programme CDTI CEN-20101014; RESOLVE UE CE:FP7-202047; Ministerio de Ciencia e Innovacion BIO2010-16566; Biostruct-X FP7-Infrastructures-2011-1; Centrosoma 3D CSD2006-00023 |
PMID:22106336 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152022 | SCR_013349 | SciCrunch Registry | anatomic Gene Expression Mapping | 2026-10-17 01:33:33 | 12 | |||||
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Death Domain database Resource Report Resource Website 1+ mentions |
Death Domain database (RRID:SCR_013231) | DD database | data or information resource, database | A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily | protein interaction, death domain superfamily, death domain, protein-protein interaction, apoptosis, inflammation, immune cell signaling pathway, cellular signaling pathway, interaction, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Yeungnam University; North Gyeongsang; South Korea has parent organization: Seoul National University College of Medicine; Seoul; South Korea has parent organization: Myongji University; Gyeonggi-do; South Korea |
Korean Ministry of Education Science and Technology 2011-0003406; Korean Ministry of Education Science and Technology 2011-0025697; Korean Ministry of Education Science and Technology 2008-05943; Korean Ministry of Education Science and Technology 2011-0022437 |
PMID:22135292 | nlx_149482, biotools:deathdomain | https://bio.tools/deathdomain | SCR_013231 | SciCrunch Registry | DeathDomain.org/, DeathDomain Database, Death Domain database: A manually curated database of protein-protein interactions for Death Domain Superfamily | 2026-10-17 01:34:14 | 2 | |||||
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DSAP Resource Report Resource Website 1+ mentions |
DSAP (RRID:SCR_013352) | DSAP | analysis service resource, data analysis service, production service resource, service resource | A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20478825 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dsap, OMICS_00357 | https://bio.tools/dsap | SCR_013352 | SciCrunch Registry | 2026-10-17 01:33:35 | 8 | ||||||
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FlyTrap- GFP Protein Trap Database Resource Report Resource Website 10+ mentions |
FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) | data or information resource, database | The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion. | gfp-tagged protein, protein, protein trapping screen | has parent organization: Yale University; Connecticut; USA | nif-0000-02849 | SCR_013354 | SciCrunch Registry | FlyTrap | 2026-10-17 01:33:33 | 26 | |||||||||
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CollecTF Resource Report Resource Website 10+ mentions |
CollecTF (RRID:SCR_014405) | data or information resource, database | A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements. | database, transcription factor binding site, bacteria | is related to: xFITOM | NSF MCB-1158056 | PMID:24234444 | The community can contribute to this resource | SCR_014405 | SciCrunch Registry | 2026-10-17 01:33:37 | 33 | ||||||||
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Neurofly Resource Report Resource Website 1+ mentions |
Neurofly (RRID:SCR_013833) | atlas, data or information resource | An on-going atlas project of the Virtual Insect Brain Project with the goal of reconstructing and standardizing Gal4 expression patterns in Drosophila brains. Neurofly will be a web-based tool that will enable the online comparison of mutations and Gal4 expression patterns in the Drosophila brain. To this end, a database of reconstructed and standardized Gal4 expression patterns - on the basis of the existing Drosophila StandardBrain - was developed along with tools for 3D image data set processing. Users will be able to evaluate the expression patterns intersections of various Gal4 driver lines and/or mutations. | atlas, database, Drosophila, Gal4, tool, Virtual Insect Brain Project |
is listed by: Educational Resources in Neuroscience is related to: Educational Resources in Neuroscience has parent organization: University of Wurzburg; Bavaria; Germany |
Free, Public | SCR_013833 | SciCrunch Registry | Virtual Insect Brain Lab | 2026-10-17 01:33:35 | 1 | |||||||||
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GlycoEpitope Resource Report Resource Website 1+ mentions |
GlycoEpitope (RRID:SCR_014404) | data or information resource, database | A database of carbohydrate antigens and matching antibodies. Epitopes and antibodies are listed within the database. Users may also search for epitopes and antibodies by keyword, epitope ID, tissue, receptor, enzyme, and other fields. | database, carbohydrate, antigen, antibody | has parent organization: Ritsumeikan University; Kyoto; Japan | DOI:10.4172/jpb.10000e24 | Public, Free | http://www.ebi.ac.uk/miriam/main/collections/MIR:00000478 | SCR_014404 | SciCrunch Registry | GlycoEpitope: Index, GlycoEpitope Index | 2026-10-17 01:35:20 | 5 | |||||||
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UniCarb-DB Resource Report Resource Website 1+ mentions |
UniCarb-DB (RRID:SCR_014407) | data or information resource, database | An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS. | database, carbohydrate, glycomic ms, spectral library, structural ms, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Gothenburg; Gothenburg; Sweden has parent organization: UniCarbKB |
Nectar ; Australian National Data Service ; Swedish Foundation for International Cooperation in Research and Higher Education ; Swiss Institute of Bioinformatics ExPASy |
DOI:10.1093/bioinformatics/btr137 | Available to the research community | biotools:unicarb-db | https://bio.tools/unicarb-db | SCR_014407 | SciCrunch Registry | UniCarb-DB structural- MS spectral library database | 2026-10-17 01:34:17 | 8 | |||||
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Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | data or information resource, database | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | SciCrunch Registry | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-10-17 01:34:15 | 2 |
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