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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Alternative Splicing Annotation Project II Database Resource Report Resource Website 1+ mentions |
Alternative Splicing Annotation Project II Database (RRID:SCR_000322) | ASAP II | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated. They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also search human data for tissue- and cancer-specific splice forms at the bottom of the gene summary page. The p-values for tissue-specificity as log-odds (LOD) scores, and highlight the results for LOD >= 3 and at least 3 EST sequences are all also reported. | exon, gene structure, genome, alternative splicing, cancer genome alignment, intron, isoform, orthologous exon, orthologous gene, orthologous intron, protein sequence, splice site, tissue, genome alignment, cancer |
is related to: ASAP: the Alternative Splicing Annotation Project has parent organization: University of California at Los Angeles; California; USA |
NCRR U54 RR021813; NIDCR DE-FC02-02ER63421 |
PMID:17108355 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02572 | SCR_000322 | ASAP II Database, Alternative Splicing Annotation Project II | 2026-02-14 02:05:31 | 2 | |||||
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NHLBI Grand Opportunity Exome Sequencing Project Resource Report Resource Website 10+ mentions |
NHLBI Grand Opportunity Exome Sequencing Project (RRID:SCR_010798) | NHLBI GO ESP, GO ESP | knowledge environment | Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations. | next-generation sequencing, protein coding region, human, genome, phenotype, exome sequencing |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NHLBI RC2 HL-103010; NHLBI RC2 HL-102923; NHLBI RC2 HL-102924; NHLBI RC2 HL-102925; NHLBI RC2 HL-102926 |
OMICS_00277 | SCR_010798 | NHLBI Grand Opportunity Exome Sequencing Project (ESP), NHLBI GO Exome Sequencing Project (ESP) | 2026-02-14 02:02:03 | 31 | |||||||
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PhyloPhlAn Resource Report Resource Website 100+ mentions |
PhyloPhlAn (RRID:SCR_013082) | PhyloPhlAn | software resource | Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic tree, whole-genome sequence, genome, protein |
is listed by: OMICtools is listed by: Debian has parent organization: Harvard T.H. Chan School of Public Health |
PMID:23942190 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01525 | https://sources.debian.org/src/phylophlan/ | SCR_013082 | PhyloPhlAn: microbial Tree of Life using 400 universal proteins | 2026-02-14 02:02:27 | 339 | |||||
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Drosophila RNAi Screening Center Resource Report Resource Website 1+ mentions |
Drosophila RNAi Screening Center (RRID:SCR_000733) | DRSC | data or information resource, database | Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays. | genome, screening, drosophila, fly, insect, rnai | has parent organization: Harvard University; Cambridge; United States | NIH Office of the Director R24 OD011176 | PMID:16381918 | nif-0000-02846 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources http://flyRNAi.org/cgi-bin/RNAi_screens.pl |
SCR_000733 | Development of Validated Drosophila in vivo RNAi Models of Human Diseases | 2026-02-14 02:06:01 | 2 | |||||
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Microbial Genetics Resource at JGI Resource Report Resource Website |
Microbial Genetics Resource at JGI (RRID:SCR_000570) | JGI Microbial Genetics Program | data or information resource, database | Mission: Dynamically evolve sequencing, finishing, annotation and analysis processes, exploit new technologies, and develop expertise to deliver high quality and high throughput sequence-based microbial science by listening to and responding to DOE Users and scientific community needs. GOALS 1. Expand product catalog and increase sample throughput while maintaining highest quality The MGP has been expanding its product catalog beyond a finished microbial genome and has projected to significantly up ramp throughput for the majority of its current products namely Draft Genomes, Single Cell Genomes, Quick Draft Genomes, Resequencing projects and RNAseq Project. This projected increase in microbial genomes is going hand-in-hand with and has been stimulated by new high throughput technologies and capabilities (de novo microbial Illumina assemblies, single cell genomics, Genologic sample tracking). The increased throughput will support the user community as well as JGI scientists by enabling DOE-relevant science at a grander scale. As the Program aims to generate hundreds of microbial genomes per year, our goal is to scale our production efficiency and maintain our trademark quality to best support our science mission. 2. Expand sequence space One of the ongoing missions of the MGP is to expand the coverage of the phylogenomic sequence space by generating reference genome datasets from highly diverse braches in bacterial and archaeal tree of life. The value of such effort includes the generation of phylogenetic anchors for metagenomic datasets, the improvement of annotation, an increased insight into phylogenetic distribution of functions, the discovery of novel genes, protein families, pathways and a better understanding on evolutionary diversication. 3. Make Single Cell Genomes a robust User product As the vast majority of microbes are uncultured to date, single cell genomics will be a crucial component of the MGP over the next several years to drive not only JGI science but also User community proposed single cell research. Going hand-in-hand are R&D efforts in selective single cell isolations, testing the effects of fixation of single cell sequencing, as well as single cell transcriptomics. 4. Sequence Pangenomes Combining similar genomes together creating pangenomes will allow more compact genome sequence storage and visualization and expedite analysis and annotation. Moreover, the pangenome as a representation of the whole group of organisms may be more representative of a given species within the environment. The MGP thus thrives to enable the sequencing and analysis of pangenomes. Current technology allows the sequencing of one organism strain at a time. Assuming that for most cases, several dozen strains may need to be sequenced in order to generate a more accurate pangenome for every microbial species, it becomes evident that the cost for doing so may be prohibitively high. Our goal here will be to explore new approaches and technologies for generating these pangenomes at a very low cost and analogous to what is the cost today for a single strain. 5. Expand and improve microbial annotation using transcriptomic data To improve annotation of gene structure, establish accurate transcription level and timing, provide information on gene regulation and generate information for expanding understanding of systems biology, the MGP thieves to generate transcriptomics data for larger sets of Bacteria and/or Archaea. This will enable the identification of novel regulator RNAs, as well as facilitate the understanding of uncharacterized protein families. 6. Maintain and evolve a top quality data management system To enable state of the art and world class comparative analysis of internal and external scientific projects, the JGI data integration and visualization management system for comparative analysis of microbial genomes, namely IMG, needs to be maintained and continuously evolved. The system needs to be able to support and integrate all data generated by JGI (WGS, reseq, RNAseq, -other omics data), as well as by the user community, enabling annotation and manual curation of the annotation, comparative analysis, gene-centric and pathway centric analyzes. The system should also facilitate the interation of associated metadata, enable data sharing and distribution, as well as automated data GenBank submissions. Lastly, the system needs to have the ability to scale enabling the annotation of thousands of genomes per year. 7. Drive Flagship projects To stay at the forefront of microbial genomic research, be recognized as such and enable the development new methods and tools, the MGP aims to drive DOE mission relevant flagship projects. Novel tools and methods developed will ultimately serve the user community if proven useful and implemented as part of a larger pipeline. MGP flagship projects are the GEBA and GEBA uncultured projects, as well as the GEBA-RNB, the proposed Microbial Earth and the Microbial Dark Matter Projects. | genomics, microbe, bacteria, archaea, sequencing, annotation, genome, microbial | has parent organization: DOE Joint Genome Institute | DOE | nlx_144369 | SCR_000570 | Microbial Genetics Program - Exploration of Microbial Diversity, Microbial Genetics Program at JGI | 2026-02-14 02:06:00 | 0 | |||||||
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tbvar Resource Report Resource Website |
tbvar (RRID:SCR_001178) | tbvar | data or information resource, database | Database of the variome of Mycobacterium tuberculosis (Mtb) comprising of over 29,000 single nucleotide variations created from re-analyzed data sets corresponding to over 400 isolates of Mtb. Using a systematic computational pipeline, potential functional variants and drug-resistance associated variants have been annotated. The database has an option to annotate variants from clinical re-sequencing of Mtb. | single nucleotide variation, genome, gene annotation, variome, genome variation, gene, variant location |
is listed by: OMICtools has parent organization: CSIR-Institute of Genomics and Integrative Biology; Delhi; India |
Tuberculosis | PMID:24408216 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02180 | SCR_001178 | 2026-02-14 02:05:44 | 0 | ||||||
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Ensembl Metazoa Resource Report Resource Website 10+ mentions |
Ensembl Metazoa (RRID:SCR_000800) | data or information resource, database | Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species. | database, genome, metazoan, software, specie, taxonomic, FASEB list |
has parent organization: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: European Bioinformatics Institute |
EMBL - EBI | PMID:21785142 | nif-0000-33714 | SCR_000800 | EnsemblMetazoa | 2026-02-14 02:05:33 | 37 | |||||||
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Archaeal and Bacterial ABC Transporter Database Resource Report Resource Website 1+ mentions |
Archaeal and Bacterial ABC Transporter Database (RRID:SCR_001692) | ABCdb, | data or information resource, database | ABCdb is a public resource devoted to the ATP-binding Cassette (ABC) transporters encoded by completely sequenced prokaryotic genomes. In order to establish, in a complete genome, the repertory of ABC systems, we have to: i) identify the different partners, ii) assemble the partners in putative systems, and iii) classify the system into the correct functional subfamily (Quentin et al., 2002). The main pitfalls were the identification of loosely conserved domains and the assembly of partners encoded by genes dispersed over the chromosome. In order to face the avalanche of newly sequenced genomes, we decided to also feed into the database the raw prediction issued by this automatic procedure, before time consuming review by an expert occurs. Therefore, the database comprises two sections: CleanDb, for data checked by an expert and AutoDb for raw data. The ABC proteins are involved in a wide variety of physiological processes in Archaea, Bacteria and Eucaryota where they are encoded by large families of paralogous genes. The majority of ABC domains energize the transport of compounds across membranes. In bacteria, ABC transporters are involved in the uptake of a wide variety of molecules, as well as in mechanisms of virulence and antibiotic resistance. In eukaryotes, most of them are involved in drug resistance and in human cell, many are associated with diseases. Sequence analysis reveals that members of the ABC superfamily can be organized into sub-families, and suggests that they have diverged from common ancestral forms. A typical ABC transporter system is composed of an assembly of protein domains that serve different functions: i) two Nucleotide Binding Domains (NBD) that energize transport via ATP hydrolysis, ii) two Membrane Spanning Domains (MSD) that act as a membrane channel for the substrate, and iii) for the importer, a Solute Binding Protein (SBP) that confers substrates specificity on the transporter. The different partners of an ABC system are generally encoded by neighboring genes. The database includes information on: * ABC transporters * Protein partners * Protein domains (NBD, MSD and SBP) * Classification of ABC transporters and their protein partners * Taxonomy of the species Each model Protein includes a link to the Peptide sequence, general information extracted from EMBL files, and specific tags to store results of predictions. The results of the annotation procedure are reachable through the class Prediction. The origin of the proteins is modeled as a path through the classes Chromosome, Strain, Species, and Taxon. Assembly and protein compilation tables are also provided for each of the chromosomes ( Assembly and Protein ). | abc transporters, archaea, bacteria, prokaryotic genomes, genome, complete genome | has parent organization: Paul Sabatier University - Toulouse III; Toulouse; France | Centre National de la Recherche Scientifique ; ACI-IMPbio |
PMID:16499625 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02530 | SCR_001692 | Archaeal and Bacterial ABC Systems database | 2026-02-14 02:06:03 | 5 | |||||
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Published Association Database Resource Report Resource Website |
Published Association Database (RRID:SCR_001841) | PADB | data or information resource, database | It aims to help researchers to utilize information more efficiently from the published association data. This database is freely accessible only for academic users under the GNU GPL PADB indexes the sentences containing "associat*" or "case-control*" or "cohort*" or "meta-analysis" or "systematic review" or "odds ratio*" or "hazard ratio*" or "risk ratio*" or "relative risk*" from PubMed abstracts and automatically extracts the numeric values of odds ratios, hazard ratios, risk ratios and relative risks data when available. PADB automatically identifies HUGO official symbols of human genes using NCBI Entrez Gene data, and each gene is linked to the UCSC genome browser and International HapMap Project database. Furthermore, molecular pathways listed in BioCarta or KEGG databases can be accessed through the link using CGAP gene annotation data. Also, each record in PADB is linked to GAD or HPLD if it is available from those databases. Currently, (Last Update of Database Contents : Dec. 20, 2006) PADB indexes more than 1,500,000 abstracts including about 190,000 risk values ranging from 0.00001 to 4878.9 and 3,442 human genes related to 461 molecular pathways. Sponsors: This work was supported by the Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea and a faculty research grant of Yonsei University College of Medicine for 2006, Seoul, Korea. | gene, genome, hazard ratio, hugo, human, index, molecular pathway, ncbi, numeric value, ratio, risk ration, symbol | PMID:17877839 | Free, Freely available | nif-0000-10405 | http://medclue.com/padb/ | SCR_001841 | Published Association Database | 2026-02-14 02:05:36 | 0 | ||||||
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Genome Network Platform Resource Report Resource Website 10+ mentions |
Genome Network Platform (RRID:SCR_001737) | GNP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed. | gene, genome, chip, human, interaction, micro array, protein, protein-protein interaction, qrt-pcr, rat, rna, sequence, short rna, tiling array, transcription, transcription control, transcription factor, transcription starting position, yeast two hybrid, data set, cage, data analysis service |
is listed by: 3DVC has parent organization: National Institute of Genetics; Shizuoka; Japan |
PMID:24927841 | Free, Freely Available | nif-0000-10237 | http://genomenetwork.nig.ac.jp/index_e.html | SCR_001737 | 2026-02-14 02:05:45 | 20 | ||||||
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AREX Resource Report Resource Website 10+ mentions |
AREX (RRID:SCR_002170) | AREX | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Arabidopsis gene Expression Database collects Arabidopsis gene expression data from genome-wide and gene-specific sources and integrative search tools are provided. Currently the database contains only root gene expression data, but has the capability to contain data from any part of the plant. The aim of Arabidopsis gene Expression Database is to: (1) Integrate genome-wide and gene-specific ("traditional") types of expression pattern data, using ontologies to describe data whenever possible, in particular to describe expression patterns. (2) Provide user-friendly search tools, for example to search for genes expressed with a certain pattern, or to search for the expression pattern of specific genes (from gene-specific experiments and from microarray data). Expression pattern predicted from the microarray data is called digital in situ. | expression, gene, arabidopsis, genome, microarray, pattern | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20955 | SCR_002170 | The Arabidopsis Gene Expression Database, Arabidopsis Gene Expression Database | 2026-02-14 02:05:38 | 14 | ||||||||
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HEXEvent Resource Report Resource Website 1+ mentions |
HEXEvent (RRID:SCR_002106) | HEXEvent | data or information resource, database | A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser. This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites). In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons. | exon, splicing, est, splice event, gene, chromosome, genome, splice |
is listed by: OMICtools is related to: UCSC Genome Browser has parent organization: University of California at Irvine; California; USA |
PMID:23118488 | THIS RESOURCE IS NO LONGER IS SERVICE. | OMICS_01888 | SCR_002106 | HEXEvent - a database of Human EXon splicing Events | 2026-02-14 02:05:46 | 3 | ||||||
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Bacteriome.org Resource Report Resource Website 1+ mentions |
Bacteriome.org (RRID:SCR_001934) | Bacteriome.org | data or information resource, database | Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong. | functional interaction, genetics, genome, protein, protein-protein interaction, protein interaction, function, evolution, structure, gene, phylogenetic profile, chromosome, blast, phylogenetic, complex, network |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
Canadian Institutes of Health Research | PMID:219798435 PMID:17942431 |
nif-0000-02592, OMICS_01899 | http://128.100.134.188/bacteriome/ | SCR_001934 | Bacteriome.org - Bacterial Protein Interaction Database | 2026-02-14 02:05:36 | 4 | |||||
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NHGRI Dog Genome Project Resource Report Resource Website 1+ mentions |
NHGRI Dog Genome Project (RRID:SCR_002256) | NHGRI Dog Genome Project | data or information resource, database | The Dog Genome Project at the National Human Genome Research Institute is working to develop resources necessary to map and clone canine genes in an effort to utilize dogs as a model system for genetics and cancer research. The US National Human Genome Research Institute (NHGRI) agreed to fund a project to sequence the entire genome of a boxer dog named Tasha, because it recognized the value of the dog as an unrivaled model for the study of human disease. The National Human Genome Research Institute (NHGRI) led the National Institutes of Health's (NIH) contribution to the International Human Genome Project, which had as its primary goal the sequencing of the human genome. This project was successfully completed in April 2003. Now, the NHGRI's mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease. To that end NHGRI supports the development of resources and technology that will accelerate genome research and its application to human health. A critical part of the NHGRI mission continues to be the study of the ethical, legal and social implications (ELSI) of genome research. NHGRI also supports the training of investigators and the dissemination of genome information to the public and to health professionals. | gene, genetic, cancer, canine, clone, disease, dog, genome, health, human, map, model, system | PMID:16102268 | nif-0000-20975 | SCR_002256 | National Human Genome Research Institute Dog Genome Project | 2026-02-14 02:05:38 | 1 | ||||||||
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GeneCards Resource Report Resource Website 5000+ mentions |
GeneCards (RRID:SCR_002773) | GeneCards | data or information resource, database | Database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs and compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents. | genome, human gene, genome, gene, genomic, proteomic, transcriptomic, genetic, function, ortholog, disease, mutation, single nucleotide polymorphism, gene expression, gene function, pathway, protein-protein interaction, drug, compound, reagent, antibody, recombinant protein, clone, expression assay, rnai reagent, FASEB list |
is listed by: OMICtools is related to: MOPED - Model Organism Protein Expression Database |
PMID:20689021 | Free, Freely available | nif-0000-02879, OMICS_01652, r3d100012015 | http://bioinfo.weizmann.ac.il/genecards/ https://doi.org/10.17616/R3D643 |
SCR_002773 | GeneCards - The Human Gene Compendium | 2026-02-14 02:05:41 | 6546 | |||||
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HIV Molecular Immunology Database Resource Report Resource Website 1+ mentions |
HIV Molecular Immunology Database (RRID:SCR_002893) | HIV Molecular Immunology Database | data or information resource, database | An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database. | cytotoxic t cell, cytotoxic t lymphocyte, helper t-cell, antibody, binding site, epitope, t cell epitope, human immunodeficiency virus, immunology, molecule, genome, protein, alignment, b-cell, t-cell, annotation, ctl, t helper, coding region, cross-reactivity, escape mutation, antibody sequence, tcr usage, functional domain, immune response, progression, therapy | has parent organization: HIV Databases | Human immunodeficiency virus | NIAID | nif-0000-02965 | http://hiv-web.lanl.gov/immunology/ | SCR_002893 | Human Immunodeficiency Virus Molecular Immunology Database | 2026-02-14 02:05:41 | 2 | |||||
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GermOnline Resource Report Resource Website 10+ mentions |
GermOnline (RRID:SCR_002807) | GermOnline | data or information resource, database | Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repository, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: OMA Browser has parent organization: National Institute of Health and Medical Research; Rennes; France |
Swiss Institute of Bioinformatics ; bioinformatics platform of Biogenouest ; National Institute of Health and Medical Research; Rennes; France ; University of Rennes 1; Rennes; France |
PMID:21149299 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:germonline, nif-0000-02906, r3d100010248 | https://bio.tools/germonline https://doi.org/10.17616/R37K5Q |
SCR_002807 | 2026-02-14 02:05:41 | 17 | |||||
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Zebrafish Information Network (ZFIN) Resource Report Resource Website 500+ mentions |
Zebrafish Information Network (ZFIN) (RRID:SCR_002560) | ZFIN | data or information resource, database | Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases. | expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standard, bio.tools, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: Morpholino Database is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: InterMOD is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Phenoscape Knowledgebase is related to: MONARCH Initiative is related to: Bgee: dataBase for Gene Expression Evolution is related to: NIH Data Sharing Repositories is related to: HomoloGene is related to: Zebrafish International Resource Center is related to: Integrated Manually Extracted Annotation is related to: Zebrafish Genome Project has parent organization: University of Oregon; Oregon; USA is parent organization of: ZFIN Antibody Database is parent organization of: Zebrafish Anatomical Ontology is parent organization of: ZFIN Protocol Wiki is parent organization of: ZFIN Antibody Wiki |
NHGRI P41 HG002659; NHGRI R01 HG004834 |
PMID:23074187 PMID:21036866 PMID:16381936 |
Free, Available for download, Freely available | OMICS_01666, nif-0000-21427, biotools:zfin, r3d100010421, SCR_017504 | http://zfin.org/ZFIN/misc_html/tips.html#newrecord https://wiki.zfin.org/display/general/ZFIN+Data+Submissions https://bio.tools/zfin https://doi.org/10.17616/R3CK5Z |
SCR_002560 | Zebrafish Database, The Zebrafish Model Organism Database, Zebra Model Organism Database, ZebraFish Information Network, ZFIN | 2026-02-14 02:05:47 | 898 | ||||
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object-oriented Transcription Factors Database Resource Report Resource Website 1+ mentions |
object-oriented Transcription Factors Database (RRID:SCR_002435) | data or information resource, database | ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers. | eukaryotic, expression, factor, gene, basal, binding site, biochemical, biology, cellular, complex, genome, genomic, information, interaction, molecule, monomer, multisubunit, nucleotide sequences, transcriptional regulator sites, transcription factors, object, polypeptide, process, prokaryotic, property, protein, protein-protein interaction, regulatory, sequence, transcription | has parent organization: IFTI-Mirage | PMID:10592257 PMID:9847215 PMID:9399874 |
Free, Freely available | nif-0000-21303 | SCR_002435 | ooTFD | 2026-02-14 02:06:07 | 2 | |||||||
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ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters Resource Report Resource Website 1+ mentions |
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters (RRID:SCR_002276) | ABS | data or information resource, database | Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available. | gene, alignment, annotation, binding, computational, genome, nucleotide, ortholog, prediction, promoter, sequence, target, transcription, transcriptional factor, binding site, promoter sequence, protein motif, benchmark, transcription factor binding site, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IntegromeDB has parent organization: Center for Genomic Regulation; Barcelona; Spain |
European Union FP6 contract LSHG-CT-2003-503265 | PMID:16381947 | Acknowledgement requested, GNU General Public License, v2 | biotools:alggen, nif-0000-21006 | https://bio.tools/alggen | SCR_002276 | A database of Annotated regulatory Binding Sites from orthologous promoters | 2026-02-14 02:06:09 | 1 |
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