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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Intergrated Transcription Factor Platform Resource Report Resource Website 10+ mentions |
Intergrated Transcription Factor Platform (RRID:SCR_008119) | data or information resource, database | ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page. | expression, gene, human, message, mouse, protein, rat, sequence, target, transcription factor | has parent organization: Fudan University; Shanghai; China | nif-0000-20862 | SCR_008119 | ITFP | 2026-02-14 02:06:41 | 25 | |||||||||
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Ingenuity Pathways Knowledge Base Resource Report Resource Website 1000+ mentions |
Ingenuity Pathways Knowledge Base (RRID:SCR_008117) | data or information resource, database | A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base . | gene, life science, molecule, protein, research, software, ontology, knowledge base, FASEB list |
is used by: Ingenuity Pathway Analysis is listed by: SoftCite has parent organization: QIAGEN |
Available to the research community, Commercial | nif-0000-20858 | SCR_008117 | Ingenuity Knowledge Base | 2026-02-14 02:06:33 | 4627 | ||||||||
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PrimerStudio Resource Report Resource Website 1+ mentions |
PrimerStudio (RRID:SCR_008232) | data or information resource, database | PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu. | eukaryotic, exon, gene, amplicon, amplifcation, analysis, dinucleotide, dna, genome, genomic, molecular probe and primer databases, mononucleotide, mutation, organism, pcr, primer, prokaryotic, region, repetitive, segment, sequence, snp, snp detection | nif-0000-21334 | SCR_008232 | PrimerStudio | 2026-02-14 02:06:13 | 1 | ||||||||||
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Microbial Genomics Program Resource Report Resource Website 1+ mentions |
Microbial Genomics Program (RRID:SCR_008140) | data or information resource, database | Through its Microbial Genome Program (MGP) and its Genomics:GTL (GTL) program, DOEs Office of Biological and Environmental Research (BER) has sequenced more than 485 microbial genomes and 30 microbial communities having specialized biological capabilities. Identifying these genes will help investigators discern how gene activities in whole living systems are orchestrated to solve myriad life challenges. The MGP was begun in 1994 as a spinoff from the Human Genome Program. The goal of the program was to sequence the genomes of a number of nonpathogenic microbes that would be useful in solving DOE''s mission challenges in environmental-waste cleanup, energy production, carbon cycling, and biotechnology. Past projects include microbial genome program, microbial cell project, and the Laboratory Science Program at the DOE Joint Genome Institute. The two ongoing projects are Genomics: GTL program and Community Sequencing Program at the DOE Joint Genome Institute. Sponsors: Site sponsored by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | energy, environmental, gene, biological, biotechnology, carbon, community, cylcling, genome, genomic, living, microbes, microbial, nonpathogenic, system | has parent organization: United States Department of Energy | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20962 | SCR_008140 | MGP | 2026-02-14 02:06:07 | 2 | ||||||||
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BoLA Nomenclature: International Society for Animal Genetics Resource Report Resource Website 10+ mentions |
BoLA Nomenclature: International Society for Animal Genetics (RRID:SCR_008142) | data or information resource, database | This website is intended to be the definitive source of information on the bovine major histocompatibility complex - its genes, proteins and polymorphism. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The BoLA nomenclature committee is a standing committee of the International Society for Animal Genetics. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The information gathered here is based on the BoLA workshop reports, which are published in Animal Genetics and the European Journal of Immunogenetics. The workshop report data are reproduced with the permission of the publishers Blackwell Science, and other text on the site is used with the permission of CRC Press. | gene, genetic, animal, antigen, bovine, complex, histocompatibility, immunogenetic, leucocyte, nomenclature, polymorphism, protein, journal article | has parent organization: University of Edinburgh; Scotland; United Kingdom | nif-0000-20967 | http://www.projects.roslin.ac.uk/bola/bolahome.html | SCR_008142 | International Society for Animal Genetics | 2026-02-14 02:06:34 | 16 | ||||||||
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Mammalian Protein Complex Data Base Resource Report Resource Website |
Mammalian Protein Complex Data Base (RRID:SCR_008209) | data or information resource, database | A database of manually annotated mammalian protein complexes. To obtain a high-quality dataset, information was extracted from individual experiments described in the scientific literature. Data from high-throughput experiments was not included. | gene, genome, mammalian, protein, proteomics, structure | The Munich Information Center for Protein Sequences ; MPCDB |
nif-0000-21273 | SCR_008209 | 2026-02-14 02:06:34 | 0 | ||||||||||
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AnoBase: An Anopheles database Resource Report Resource Website 1+ mentions |
AnoBase: An Anopheles database (RRID:SCR_008166) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance. | gene, genetic, anopheles gambiae, anopheline, biological, biology, community, genomic, in-situ hybridization, insecticide, invertebrate databases, malaria, mosquito, proteomic, specie, vector, image |
is related to: VectorBase has parent organization: Foundation for Research and Technology-Hellas; Heraklion; Greece is parent organization of: Malaria Ontology |
NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21031 | http://www.anobase.org/ | SCR_008166 | AnoBase | 2026-02-14 02:06:41 | 2 | ||||||
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Migratory Locust EST Database Resource Report Resource Website 1+ mentions |
Migratory Locust EST Database (RRID:SCR_008201) | data or information resource, database | The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies. | ecologically, entomology, est, fruitfly, functional, gene, agronomically, analysis, annotation, codon, comparative, data, domain, genomic, hemimetabolous, homologous, honeybee, insect, invertebrate, invertebrate databases, locust, locusta migratoria, medically, migratory, molecular, mosquito, nematode, orthologous, orthopteran, pathway, pest, protein, sequence, silkworm, specie, transcriptome, transcriptomic, unigene, ontology | has parent organization: BGI; Shenzhen; China | nif-0000-21244 | SCR_008201 | LocustDB | 2026-02-14 02:06:42 | 7 | |||||||||
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LitMiner Resource Report Resource Website 1+ mentions |
LitMiner (RRID:SCR_008200) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modeling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. It is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships. Key terms belonging to four different categories are used for the annotation process: -Genes: Names of genes and gene products. Gene name recognition is based on Ensembl . Synonyms and aliases are resolved. -Chemical Compounds: Names of chemical compounds and their respective aliases. -Diseases and Phenotypes: Names of diseases and phenotypes -Tissues and Organs: Names of tissues and organs LitMiner uses a database of disease and phenotype terms for literature annotation. Currently, there are 2225 diseases or phenotypes, 801 tissues and organs, and 10477 compounds in the database. | gene, biomedical, chemical, compound, disease, identification, literature, medline interfaces, mining, modeling, phenotype, promoter, regulation, regulatory, relationship, tissue, tool, bio.tools |
is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21241, biotools:litminer | https://bio.tools/litminer | SCR_008200 | LitMiner | 2026-02-14 02:06:12 | 2 | |||||||
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AltSplice Database of Alternative Spliced Events Resource Report Resource Website 1+ mentions |
AltSplice Database of Alternative Spliced Events (RRID:SCR_008162) | data or information resource, database | AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases | event, exon, gene, alternative, annotation, bioinformatic, biology, breast cancer, cdna, chip, diagnosis, disease, dna, human, infertility, intron, isoform, male, microarray, mis-splicing, model, nucleotide, pathological, pattern, property, protein, regulatory, splice, splicing, structure, transcript | has parent organization: European Molecular Biology Laboratory | nif-0000-21021 | SCR_008162 | AltSplice Database of Alternative Spliced Events | 2026-02-14 02:06:07 | 3 | |||||||||
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Alternative Exon Database Resource Report Resource Website |
Alternative Exon Database (RRID:SCR_008157) | AEdb | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs. | element, exon, expression, gene, alignment, alternative, brain, conservation, cross-specie, disease, isoform, mechanism, minigene, pattern, peptide, regulatory, sequence, signal, splice, splicing, structure intron, tissue, transcript, nucleotide sequence, gene structure, intron, splice site, alternative splicing, sequence, alternative exon, function, constitutive exon, alternative exon, regulatory sequence, transcript regulatory motif, minigene, disease | has parent organization: European Bioinformatics Institute | PMID:16381912 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21009 | SCR_008157 | 2026-02-14 02:06:34 | 0 | |||||||
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Plasmid Genome Database Resource Report Resource Website 10+ mentions |
Plasmid Genome Database (RRID:SCR_008228) | data or information resource, database | The Plasmid Genome Database aims to collate biological and genomic data for all bacterial plasmids in the hopes of enabling rapid, interrogation of both meta- and genomic data. Data maintained includes access to all plasmid genomes and information on core genomic features obtained from parsing the original EMBL/DDBJ/NCBI submission. In addition a suite of third party analyses has been performed for each genome to supplement the original annotation. This site also links to Genome Atlases provided by the Centre for Biological Sequence Analysis (CBS). The motivation behind the construction of this site derived from observations from genome sequencing projects: the abundance and inferred importance of the horizontal gene pool (HGP) in bacterial adaptation and evolution. In so far as plasmids are autonomously replicating, extrachromosomal elements they are a readily identifiable and accessible component of the HGP. Also plasmids have been identified in almost all bacterial divisions, ranging in size from less than 2 kbp to > 1.5 Mbp and as such represent a defined, yet diverse and complex sample of genes in the HGP. | element, evolution, extrachromosomal, gene, adaptation, atlas, autonomous, bacterial, biological, division, genome, genomic, hgp, plasmid, pool, prokaryote databases, replicate | nif-0000-21323 | http://www.genomics.ceh.ac.uk/plasmiddb/ | SCR_008228 | PGD | 2026-02-14 02:06:34 | 21 | |||||||||
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Protochlamydia amoebophila UWE25 Resource Report Resource Website |
Protochlamydia amoebophila UWE25 (RRID:SCR_008222) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK. | ecology, endosymbiont, environmental, eukaryote, eukaryotic, evolutionary, functional, gene, genetic, acanthamoeba, amoebae, blindness, cell, chlamydia, classification, clinical, genome, human, intracellular, lateral, lineage, mechanism, microorganism, obligate, parachlamydia, pathogen, pathogenic, sequence, sexually, strain, survival, symbiont, transmitted disease, uwe25, virulence | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21310 | SCR_008222 | Protochlamydia amoebophila UWE25 | 2026-02-14 02:06:34 | 0 | |||||||||
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Comprehensive Systems-Biology Database Resource Report Resource Website 10+ mentions |
Comprehensive Systems-Biology Database (RRID:SCR_008185) | data or information resource, database | CSB.DB presents the results of bio-statistical analysis on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life''s complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The main focus of the CSB project is the generation of new easily accessible knowledge about the relationship and the hierarchy of cellular components. Thus new progress towards understanding lifes complexity pyramid is made. For this aim statistical and computational algorithms are applied to organism specific data derived from publicly available multi-parallel technologies, currently such as expression profiles. The underlying data are derived from various research activities. Thus CSB project provides an integrated and centralized public resource allowing universal access on the generated knowledge CSB.DB: A Comprehensive Systems-Biology Database. The derived knowledge should support the formulation of new hypotheses about the respective functional involvement of genes beyond their (inter-) relationships. Another major goal of the CSB project is to supply the researchers with necessary information to formulate these new hypotheses without demanding any a-priori statistical knowledge of the user. The CSB project mainly focuses on application of required statistical tests as well as to assist the user during exploration of results with information / help files to support hypothesis generation | expression, gene, generation, algorithm, arabidopsis thaliana databases, biochemical, biology, bio-statistical, cellular, compound, computational, hierarchy, metabolite, organism, physiological, plant, system, transcript |
is listed by: 3DVC has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany |
nif-0000-21102 | SCR_008185 | CSB.DB | 2026-02-14 02:06:41 | 11 | |||||||||
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CDKN2A Database Resource Report Resource Website |
CDKN2A Database (RRID:SCR_008179) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The CDKN2A Database presents the germline and somatic variants of the CDKN2A tumor suppressor gene recorded in human disease through June 2003, annotated with evolutionary, structural, and functional information, in a format that allows the user to either download it or manipulate it for their purposes online. The goal is to provide a database that can be used as a resource by researchers and geneticists and that aids in the interpretation of CDKN2A missense variants. Most online mutation databases present flat files that cannot be manipulated, are often incomplete, and have varying degrees of annotation that may or may not help to interpret the data. They hope to use CDKN2A as a prototype for integrating computational and laboratory data to help interpret variants in other cancer-related genes and other single nucleotide polymorphisms (SNPs) found throughout the genome. Another goal of the lab is to interpret the functional and disease significance of missense variants in cancer susceptibility genes. Eventually, these results will be relevant to the interpretation of single nucleotide polymorphisms (SNPs) in general. The CDKN2A locus is a valuable model for assessing relationships among variation, structure, function, and disease because: Variants of this gene are associated with hereditary cancer: Familial Melanoma (and related syndromes); somatic alterations play a role in carcinogenesis; allelic variants occur whose functional consequences are unknown; reliable functional assays exist; and crystal structure is known. All variants in the database are recorded according to the nomenclature guidelines as outlined by the Human Genome Variation Society. This database is currently designed for research purposes only and is not yet recommended as a clinical resource. Many of the mutations reported here have not been tested for disease association and may represent normal, non-disease causing polymorphisms. | evolutionary, familial, function, functional, gene, gene-, genetic, allele, allelic, alteration, cancer, carcinogenesis, cdkn2a, crystal, disease, genome, germline, hereditary, human, locus, melanoma, missense, model, mutation, nucleotide, or disease- specific databases, polymorphism, single, snp, somatic, structural, structure, suppressor, syndrome, system-, tumor, variant, variation | has parent organization: University of Vermont; Vermont; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21079 | SCR_008179 | CDKN2A Database | 2026-02-14 02:06:07 | 0 | ||||||||
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H-Invitational Database: Protein-Protein Interaction Viewer Resource Report Resource Website |
H-Invitational Database: Protein-Protein Interaction Viewer (RRID:SCR_008054) | data or information resource, database | The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project. The PPI view is now providing 32,198 human PPIs comprised of 9,268 H-InvDB proteins. H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. Sponsors: This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program. | evolutionary, expression, function, gene, genetic, 3-dimensional, alternative splicing, disease, domain, human, interaction, isoform, localization, metabolic, microsatellite, molecular, non-coding, pathway, polymorphism, protein, rna, snps, structure, sub-cellular, transcript | has parent organization: National Institute of Advanced Industrial Science and Technology | nif-0000-10401 | SCR_008054 | H0InvDB PPI View | 2026-02-14 02:06:33 | 0 | |||||||||
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Homologous Sequences in Ensembl Animal Genomes Resource Report Resource Website 1+ mentions |
Homologous Sequences in Ensembl Animal Genomes (RRID:SCR_008356) | HOMOLENS | data or information resource, database | Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations. | ensembl, evolution, gene, alignment, comparative, homologous, molecular, nucleotide, organism, phylogenetic, phylogeny, protein, sequence, specie, structure, taxon, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Claude Bernard University Lyon 1; Lyon; France |
biotools:homolens, nif-0000-25424 | https://bio.tools/homolens | SCR_008356 | 2026-02-14 02:06:42 | 3 | ||||||||
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PolygenicBlog Resource Report Resource Website |
PolygenicBlog (RRID:SCR_008789) | data or information resource, narrative resource, blog | A blog concerning the relationships between genes, risk factors and immunity in Alzheimer's disease, autism, Bipolar disorder, multiple sclerosis, Parkinson's disease, schizophrenia and chronic fatigue. | gene, risk factor, immunity, alzheimer's disease, autism, bipolar disorder, multiple sclerosis, parkinson's disease, schizophrenia, chronic fatigue |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: Polygenic Pathways |
Alzheimer's disease, Autism, Bipolar disorder, Multiple sclerosis, Parkinson's disease, Schizophrenia, Chronic fatigue | Public | nlx_144238 | SCR_008789 | Polygenic Blog | 2026-02-14 02:06:36 | 0 | |||||||
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Molecular Brain: Transcription Profiles of Mouse and Human Brains Resource Report Resource Website 1+ mentions |
Molecular Brain: Transcription Profiles of Mouse and Human Brains (RRID:SCR_008689) | data or information resource, database | MolecularBrain is an attempt to collect, collates, analyze and present the microarray derived gene expression data from various brain regions side by side. Transcription Profile of any gene in Mouse (online) and Human Brain (not yet) can be accessed as a histogram along with links to access various aspects of that gene. The expression levels were calculated from microarray data deposited at GEO (Gene expression omnibus). The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Gene information along with their expression values can be also accessed from the alphabetical list of gene symbols on the footer. The protocol and GEO sample information is available. | molecular, molecule, brain, transcription, mouse, human, gene, microarray, data, expression, database, tool, expression, molecular neuroanatomy resource | has parent organization: National Institutes of Health | nif-0000-37035 | SCR_008689 | Molecular Brain | 2026-02-14 02:06:43 | 3 | |||||||||
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Alzheimer Disease and Frontotemporal Dementia Mutation Database Resource Report Resource Website 1+ mentions |
Alzheimer Disease and Frontotemporal Dementia Mutation Database (RRID:SCR_008286) | data or information resource, database | A locus-specific database aimed at collecting known mutations and non-pathogenic coding variations in the genes related to Alzheimer disease (AD) and frontotemporal dementia (FTD), following the guidelines of the Human Genome Variation Society. Mutations can be retrieved based on the gene, phenotype and publication. The database contains mutations reported in the literature and at scientific meetings, and unpublished mutations directly submitted to the database. To date, AD&FTDMDB contains mutations in the genes encoding the Amyloid Beta Precursor Protein (APP), Presenilin 1 (PSEN1), Presenilin 2 (PSEN2), Chromatin Modifying Protein 2B (CHMP2B), fusion (involved in t(12;16) in malignant liposarcoma) (FUS), Granulin (GRN), Microtubule Associated Protein Tau (MAPT), TAR DNA binding protein (TARDBP) and Valosin-containing Protein (VCP) and holds 415 different mutations observed in 1027 patients or families. As of March 2013, the latest publications referenced were from 2008, indicating that this resource may not be up to date. | frontotemporal dementia, gene, alzheimers disease, genome, mrna, mutation, phenotype, single nucleotide polymorphism | has parent organization: University of Antwerp; Antwerp; Belgium | Alzheimer's disease, Frontotemporal dementia | PMID:17392794 | r3d100012441, nif-0000-23934 | https://doi.org/10.17616/R3277G https://doi.org/10.17616/R3277G |
SCR_008286 | ADandFTDMDB, AD and FTD Mutation Database | 2026-02-14 02:06:08 | 7 |
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Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
