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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PlantsP Resource Report Resource Website 10+ mentions |
PlantsP (RRID:SCR_013256) | data or information resource, database | A database of plant protein kinases and phosphatases as well as genomic information for these enzymes. Because protein kinases and phosphatases control so many processes in plants, and occur in networks that unite different cellular processes, a genome wide approach is needed to make significant advances in discovering the roles of these enzymes in the regulation of plant function. | nif-0000-03310 | SCR_013256 | PlantsP | 2026-08-29 11:30:41 | 15 | |||||||||||
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U12DB: The U12 Intron Database Resource Report Resource Website 1+ mentions |
U12DB: The U12 Intron Database (RRID:SCR_013410) | data or information resource, database | This is a searchable database of U12-type introns. U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. Investigations into the evolution and mechanism of U12-depending splicing would be facilitated by access to a catalog of such introns. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.Two pathways for the removal of eukaryotic spliceosomal introns exist: a major pathway that is dependent on the main U2 snRNA-containing spliceosome and a minor pathway that is dependent on the low abundance U12 snRNA-containing spliceosome. The two spliceosomes share only one snRNA, U5, but have many of the same protein components in common. They are distinguished mainly by the splice signal sequences in the pre-mRNA to which they bind. U12 consensus sequences for the donor site, RTATCCTTT, and branch point, TTCCTTRAY, are highly conserved and distinct from the U2 consensi. The two spliceosomes also differ in the order of spliceosomal assembly. U11 and U12 form a dimer which then recognizes the donor site and branch point simultaneously, whereas U1 and U2 recognize these sites independently before associating.Computational scans for U12 introns have previously been performed for human (Levine and Durbin, 2001) and Arabidopsis (Zhu and Brendel, 2003). Both scans used similar methodology, essentially predicting introns and confirming them using alignment to expressed sequence. We extended this approach to 20 genomes using spliced alignment of sequence flanking known introns or transcript-confirmed intron predictions to the genomic sequence of orthologous genes. Details can be found in forthcoming article in the Nucleic Acids Research database issue. | nif-0000-03600 | SCR_013410 | U12DB | 2026-08-29 11:30:42 | 4 | |||||||||||
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Long-term Recordings of Gait Dynamics: Unconstrained and Metronomic Walking Resource Report Resource Website |
Long-term Recordings of Gait Dynamics: Unconstrained and Metronomic Walking (RRID:SCR_013258) | data or information resource, database | Stride interval fluctuations were studied in ten young, healthy men. Participants had no history of any neuromuscular, respiratory or cardiovascular disorders, and were taking no medications. Mean age was 21.7 years (range: 18-29 years). Height was 1.77 ���� 0.08 meters (mean ���� S.D.) and weight was 71.8 ���� 10.7 kg. All subjects provided informed written consent. Subjects walked continuously on level ground around an obstacle free, long (either 225 or 400 meters), approximately oval path and the stride interval was measured using ultra-thin, force sensitive switches taped inside one shoe. For more details, please see the accompanying publication. Each subject was given an arbitrary id (si01, si02, ... si10). For each subject, there are six data files: normal (.norm), slow (.slow) and fast (.fast) walking for 1 hour each as well as walking in time to a metronome at normal (.metnrm), slow (.metslw) and fast (.metfst) paces. | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | PMID:8727526 | nlx_35625 | SCR_013258 | Long-term Recordings of Gait Dynamics: Unconstrained and Metronomic Walking | 2026-08-29 11:30:28 | 0 | |||||||||
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Genetic Codes Resource Report Resource Website 10+ mentions |
Genetic Codes (RRID:SCR_013092) | data or information resource, database | Genetic Codes is a summary resource of the taxonomy of each record and assignment of the correct genetic code for every entry in the GenBank database. GenBank format by historical convention displays mRNA sequences using the DNA alphabet. Thus, for the convenience of people reading GenBank records, the genetic code tables shown here use T instead of U. The following genetic codes are described here: The Standard Code The Vertebrate Mitochondrial Code The Yeast Mitochondrial Code The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code The Invertebrate Mitochondrial Code The Ciliate, Dasycladacean and Hexamita Nuclear Code The Echinoderm and Flatworm Mitochondrial Code The Euplotid Nuclear Code The Bacterial, Archaeal and Plant Plastid Code The Alternative Yeast Nuclear Code The Ascidian Mitochondrial Code The Alternative Flatworm Mitochondrial Code Blepharisma Nuclear Code Chlorophycean Mitochondrial Code Trematode Mitochondrial Code Scenedesmus Obliquus Mitochondrial Code Thraustochytrium Mitochondrial Code | genbank, genetic code, mrna sequences | has parent organization: NCBI | nif-0000-02888 | SCR_013092 | Genetic Codes | 2026-08-29 11:30:40 | 46 | |||||||||
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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 | 2026-08-29 11:30:27 | 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 | Biological Interaction database for Protein-nucleic Acid | 2026-08-29 11:30:13 | 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 | 2026-08-29 11:30:41 | 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 | ColiSNP | 2026-08-29 11:30:27 | 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 | 2026-08-29 11:30:11 | 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 | Rice Pipeline | 2026-08-29 11:30:41 | 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 | BTKbase | 2026-08-29 11:30:11 | 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 | 2026-08-29 11:30:27 | 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 | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-08-29 11:30:28 | 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 | 2026-08-29 11:30:41 | 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 | OryGenesDB | 2026-08-29 11:30:27 | 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 | anatomic Gene Expression Mapping | 2026-08-29 11:30:28 | 12 | |||||
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Japanese Single Nucleotide Polymorphisms Resource Report Resource Website 10+ mentions |
Japanese Single Nucleotide Polymorphisms (RRID:SCR_013076) | data or information resource, database | JSNP is a database of Japanese Single Nucleotide Polymorphisms. It includes BLAST capability, keyword search, mapping information, and other tools that allow users to gather information on SNP's. SNPs are the most common form of DNA sequence variation. They are useful polymorphic markers to investigate genes susceptible to diseases or those related to drug responsiveness. Furthermore, a small subset of SNPs directly influences to the quality and/or quantity of the gene product, and increase a risk to certain diseases and to severe side effect by drugs. Through a discovery of a large number of SNPs, we would like to contribute to identification of disease-related genes and also to establish a diagnostic method to avoid drug side-effect. | FASEB list | has parent organization: University of Tokyo; Tokyo; Japan | nif-0000-03063 | SCR_013076 | JSNP | 2026-08-29 11:30:27 | 42 | |||||||||
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MIT-BIH polysomnographic Resource Report Resource Website 1+ mentions |
MIT-BIH polysomnographic (RRID:SCR_013078) | data or information resource, database | MIT-BIH Polysomnographic Database is a collection of recordings of multiple physiologic signals during sleep. Subjects were monitored in Boston''s Beth Israel Hospital Sleep Laboratory for evaluation of chronic obstructive sleep apnea syndrome, and to test the effects of constant positive airway pressure (CPAP), a standard therapeutic intervention that usually prevents or substantially reduces airway obstruction in these subjects. The database contains over 80 hours'' worth of four-, six-, and seven-channel polysomnographic recordings, each with an ECG signal annotated beat-by-beat, and EEG and respiration signals annotated with respect to sleep stages and apnea | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | nlx_45862 | SCR_013078 | MIT-BIH polysomnographic | 2026-08-29 11:30:40 | 1 | ||||||||||
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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 | DeathDomain.org/, DeathDomain Database, Death Domain database: A manually curated database of protein-protein interactions for Death Domain Superfamily | 2026-08-29 11:30:12 | 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 | 2026-08-29 11:30:41 | 8 |
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