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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MPO Resource Report Resource Website 10+ mentions |
MPO (RRID:SCR_004855) | MPO, MP | data or information resource, ontology, controlled vocabulary | Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome. | mus, phenotype, obo |
is used by: NIF Data Federation is listed by: BioPortal is related to: Rat Genome Database (RGD) is related to: MouseBook is related to: Neurocarta is related to: phenomeNET has parent organization: OBO has parent organization: Mouse Genome Informatics (MGI) |
PMID:17989687 | The community can contribute to this resource | nlx_83784 | http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype http://purl.bioontology.org/ontology/MP |
SCR_004855 | Mammalian Phenotype Ontology | 2026-02-14 02:00:48 | 19 | |||||
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O'Brien Reagan York and Jacobsen Drug-induced Cardiotoxicity Biomarkers Resource Report Resource Website |
O'Brien Reagan York and Jacobsen Drug-induced Cardiotoxicity Biomarkers (RRID:SCR_003717) | O'Brien et al Cardiotoxicity Biomarkers | data or information resource, narrative resource, standard specification | Serum / plasma biomarkers, Cardiac troponins T (cTnT) and I (cTnI), in safety assessment studies for rats, dogs, and monkeys are qualified biomarkers for the following contexts of use: # When there is previous indication of cardiac structural damage with a particular drug, cardiac troponin testing can help estimate a lowest toxic dose or a highest non-toxic dose to help choose doses for human testing. In this case, cardiac troponins may serve as a clinical chemistry correlate to the histology. For example, in a safety assessment study, lower doses without increases in cardiac troponins may be used to support a no observed effect level (NOEL) identified by histology. # When there is known cardiac structural damage with a particular pharmacologic class of a drug and histopathologic analyses do not reveal structural damage, circulating cardiac troponins may be used to support or refute the inference of low cardiotoxic potential. # When unexpected cardiac structural toxicity is found in a nonclinical study, the retroactive (reflex) examination of serum or plasma from that study for cardiac troponins can be used to help determine a no observed adverse effect level (NOAEL) or lowest observed adverse effect level (LOAEL). The results of this testing may support inclusion of cardiac troponin testing in subsequent safety assessment studies. | serum, plasma, biomarker, cardiac troponins t, cardiac troponins i, heart, biomarker, drug development, drug, gold standard |
is recommended by: U.S. Food and Drug Administration has parent organization: Drug Development Tools Qualification Programs |
Cardiotoxicity, Drug-induced Cardiotoxicity | Public | nlx_157893 | SCR_003717 | O'Brien Reagan York and Jacobsen Drug-induced Cardiotoxicity Biomarkers | 2026-02-14 02:00:30 | 0 | ||||||
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ILSI HESI Drug-induced Nephrotoxicity Biomarkers Resource Report Resource Website |
ILSI HESI Drug-induced Nephrotoxicity Biomarkers (RRID:SCR_003716) | HESI Nephrotoxicity Biomarkers | data or information resource, narrative resource, standard specification | Urinary kidney biomarkers, Clusterin and Renal Papillary Antigen-1 (RPA-1), that sponsors may use to determine more conservative NOAELs for estimating starting doses in the initial human clinical trial of a drug that displays nonclinical nephrotoxicity as determined by histopathology. When tested with a limited number of nephrotoxic compounds, the Receiver Operating Characteristic (ROC) analyses showed that urinary clusterin and renal papillary antigen-1 (RPA-1) have better sensitivity and specificity than BUN and creatinine for the detection of specific kidney pathologies in male rats. Clusterin and RPA-1 provide additional and complementary information to BUN, serum creatinine (sCr), and histopathology for the detection of acute drug-induced nephrotoxicity in safety assessment studies. | biomarker, drug development, drug, urinary, urinary biomarker, gold standard, clusterin, renal papillary antigen, kidney, gold standard |
is recommended by: U.S. Food and Drug Administration is related to: Health and Environmental Sciences Institute (HESI) has parent organization: Drug Development Tools Qualification Programs |
Nephrotoxicity, Drug-induced nephrotoxicity | Public | nlx_157892 | SCR_003716 | HESI Drug-induced Nephrotoxicity Biomarkers, ILSI / HESI Nephrotoxicity Working Group Drug-induced Nephrotoxicity Biomarkers, International Life Sciences Institute / Health and Environmental Sciences Institute Nephrotoxicity Working Group Drug-induced Nephrotoxicity Biomarkers | 2026-02-14 02:00:52 | 0 | ||||||
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MONARCH Initiative Resource Report Resource Website 10+ mentions |
MONARCH Initiative (RRID:SCR_000824) | Monarch | data or information resource, database | Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN. | disease, animal model, phenotype, model organism, in vitro model, gene, pathway, gene expression, protein interaction, genetic interaction, orthology, disease, publication, author, genetic, genomic, model system, genotype, drug, in vivo model |
uses: Animal QTLdb uses: Ensembl Variation uses: Human Phenotype Ontology is used by: NIF Data Federation is related to: Mouse Genome Informatics (MGI) is related to: Rat Genome Database (RGD) is related to: Zebrafish Information Network (ZFIN) is related to: openSNP is related to: Ancora is related to: PhenoGen Informatics is related to: Lifespan Observations Database has parent organization: Oregon Health and Science University; Oregon; USA is parent organization of: monarch-ontologies |
NIH Office of the Director R24 OD011883 | PMID:26269093 | Free, Freely available | r3d100011594, nlx_152525, SCR_001373, nlx_152748 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources https://doi.org/10.17616/R31M09 |
SCR_000824 | MONARCH Integrated Disease Model, MONARCH Integrated Disease Models View, MONARCH Disease Models View, The MONARCH Initiative | 2026-02-14 01:59:54 | 12 | ||||
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EthoVision XT Resource Report Resource Website 100+ mentions |
EthoVision XT (RRID:SCR_000441) | EthoVision XT | software resource | Video tracking software that tracks and analyzes the behavior, movement, and activity of any animal. | behavior, tracking | has parent organization: Noldus | rid_000100 | SCR_000441 | 2026-02-14 01:59:45 | 345 | |||||||||
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Public Expression Profiling Resource Resource Report Resource Website 10+ mentions |
Public Expression Profiling Resource (RRID:SCR_007274) | PEPR | data or information resource, database | An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ). | microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysis |
is listed by: OMICtools is related to: Gene Expression Omnibus |
NINDS ; United States Department of Defense ; NHGRI ; NHLBI |
PMID:14681485 PMID:14596642 |
Public, Account required, (to download, For the analysis and visualization tools), The community can contribute to this resource | nif-0000-00014, OMICS_00776 | SCR_007274 | 2026-02-14 02:06:28 | 16 | ||||||
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ChimerDB Resource Report Resource Website 10+ mentions |
ChimerDB (RRID:SCR_007596) | data or information resource, database | Knowledgebase of fusion transcripts collected from various public resources such as the Sanger CGP, OMIM, PubMed, and Mitelman's database. It is an alignment viewer to facilitate examining reliability of fusion transcripts and inferring functional significance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | knowledge base, fusion transcript, transcript alignment, alignment viewer | has parent organization: Ewha Womans University; Seoul; South Korea | Tumor, Cancer | Korean Ministry of Education Science and Technology ; Gwangju Institute of Science and Technology ; Korean Ministry of Science and Technology R01-2008-000-20818-0; Korean Ministry of Science and Technology 2007-03983; National Core Research Center R15-2006-020; Korean Rural Development Administration 20070401034010 |
PMID:19906715 PMID:16381848 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02659 | http://genome.ewha.ac.kr/ChimerDB/ | SCR_007596 | 2026-02-14 02:06:29 | 29 | |||||
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ECgene: Gene Modeling with Alternative Splicing Resource Report Resource Website 10+ mentions |
ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) | ECgene | data or information resource, database | Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. | est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snp |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:17132829 PMID:15805497 PMID:15608289 |
nif-0000-02780, OMICS_01884 | http://genome.ewha.ac.kr/ECgene/ | SCR_007634 | ECgene - Genome Annotation for Alternative Splicing | 2026-02-14 02:06:00 | 12 | ||||||
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Mammalian Degradome Database Resource Report Resource Website 10+ mentions |
Mammalian Degradome Database (RRID:SCR_007624) | Degradome Database | data or information resource, database | A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647. | degradome, mammalian, protease inhibitor, protease, gene, protease gene, genetic disease, proteolysis, protease structure, ancillary domain, genomic, genome |
is related to: Ancillary Domains Associated With Human and Mouse Proteases has parent organization: University of Oviedo; Oviedo; Spain |
Disease of proteolysis | European Union ; CancerDegradome-FP6 and FP7 ; Spanish Ministry of Science and Innovation ; Fundacion M Botin ; Fundacion Lilly ; Obra Social Cajastur |
PMID:18776217 | nif-0000-02746 | SCR_007624 | Mammalian Degradome Database | 2026-02-14 02:06:37 | 10 | |||||
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Disease Genes Conserved Sequence Tags Database Resource Report Resource Website |
Disease Genes Conserved Sequence Tags Database (RRID:SCR_000760) | data or information resource, database | A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions. | database, conserved sequence element, genomic sequence, human gene, pathogenesis, genetic disorder, blastz, cst | Telethon Foundation ; the Associazione Italiana per la Ricerca sul Cancro (AIRC) ; the Federazione Italiana per la Ricerca sul Cancro (FIRC) ; the Italian Ministry for Research (MURST) ; the National Council for Research (CNR) ; Regione Campania ; BioGeM |
PMID:15608249 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21121 | SCR_000760 | DG CST Database | 2026-02-14 02:05:33 | 0 | |||||||
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MitoMiner Resource Report Resource Website 50+ mentions |
MitoMiner (RRID:SCR_001368) | data or information resource, database | A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. | mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list |
uses: HomoloGene uses: UniProt uses: KEGG uses: OMIM uses: The Human Protein Atlas uses: Gene Ontology |
MRC | PMID:22121219 PMID:19208617 |
Public, Acknowledgement requested, Code: | nlx_152504 | SCR_001368 | MitoMiner - A database of the mitochondrial proteome | 2026-02-14 02:06:04 | 76 | ||||||
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BodyMap-Xs Resource Report Resource Website 1+ mentions |
BodyMap-Xs (RRID:SCR_001147) | BodyMap-Xs | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008 | expressed sequence tag, comparative genomics, anatomy, taxonomy, brain, blood, connective, reproductive, muscular, alimentary, lung, liver, urinary, endocrine, exocrine, embryo, homology, gene expression, ortholog, paralog | has parent organization: DNA DataBank of Japan (DDBJ) | Neoplasm, Normal | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; New Energy and Industrial Technology Development Organization |
PMID:16381946 PMID:11125076 PMID:10592203 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02617 | http://bodymap.jp/, http://bodymap.ims.u-tokyo.ac.jp/ | SCR_001147 | BodyMap-Xs: anatomical and taxonomical breakdown of animal EST, BodyMap, BodyMap- human and mouse gene expression database, BodyMap: human and mouse gene expression database, BodyMap-cross species, BodyMap-Xs(cross species) | 2026-02-14 02:05:44 | 1 | |||
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Integrated Gene-Disease Interaction Resource Report Resource Website |
Integrated Gene-Disease Interaction (RRID:SCR_006173) | data or information resource, database | Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD). | gene, phenotype, disease, interaction, integrated, database |
is used by: NIF Data Federation is related to: OMIM is related to: Comparative Toxicogenomics Database (CTD) has parent organization: Integrated |
NIDA ; NIH Blueprint for Neuroscience Research |
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_151674 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 http://neuinfo.org/nif/nifgwt.html?query=nlx_151674, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_151674-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 | SCR_006173 | Gene-Disease Interaction, NIF Integrated Gene-Disease Interaction, Integrated GDI, NIF Integrated Gene-Disease Interaction View, NIF Gene-Disease Interaction, Integrated Gene-Disease Interaction View | 2026-02-14 02:06:25 | 0 | ||||||
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BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | data or information resource, database | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | r3d100012402, nif-0000-10168 | http://biogps.gnf.org/ https://doi.org/10.17616/R33J20 |
SCR_006433 | 2026-02-14 02:06:00 | 725 | |||||
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Rodrigo Quian Quiroga EEG ERP and single cell recordings database Resource Report Resource Website |
Rodrigo Quian Quiroga EEG ERP and single cell recordings database (RRID:SCR_001580) | EEG ERP and single cell recordings | data or information resource, data set | 5 EEG, ERP and single cell recordings data sets where each file corresponds to the recording on a different subject in the left occipital electrode (O1), with linked earlobes reference. Each file contains several artifact-free trials, each of them containing 512 data points (256 pre- and 256 post-stimulation) stored with a sampling frequency of 250 Hz. Trials are stored consecutively in a 1 column file. Data was pre-filtered in the range 0.1-70Hz. All trials correspond to target stimulation with an oddball paradigm. STAR R based Data Sets Used * Dataset # 1: Human single-cell recording * Dataset # 2: Simulated extracellular recordings * Dataset # 3: EEG signals from rats * Dataset # 4: Pattern visual evoked potentials. * Dataset # 5: Tonic-clonic (Grand Mal) seizures. | eeg, erp, single cell, recording, grand mal seizure, extracellular recording, single cell, recording, adult rat, male | is related to: Neural Cipher | Epilepsy | PMID:12005869 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153817 | SCR_001580 | Rodrigo Quian Quiroga - EEG ERP and single cell recordings database | 2026-02-14 02:07:28 | 0 | |||||
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ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-02-14 02:07:19 | 35 | ||||||
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UniProt Chordata protein annotation program Resource Report Resource Website |
UniProt Chordata protein annotation program (RRID:SCR_007071) | Chordata protein annotation program | data or information resource, data set | Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms. | chordata, protein, protein annotation, functional annotation, human, non-human vertebrate, xenopus laevis, xenopus tropicalis, zebrafish, protein sequence, protein sequencing, nucleotide sequence, sequence, annotation, sequence variant, disease, proteome, gold standard |
is related to: Human Proteomics Initiative is related to: UniProtKB has parent organization: UniProt |
nlx_143879 | SCR_007071 | 2026-02-14 02:07:57 | 0 | |||||||||
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Integrated Nervous System Connectivity Resource Report Resource Website |
Integrated Nervous System Connectivity (RRID:SCR_006391) | NSC | data or information resource, data set | A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references. | connectivity, nervous system, macaque, brain, bird, data set |
uses: Avian Brain Circuitry Database uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Connectome Wiki uses: BrainMaps.org uses: CoCoMac uses: Brain Architecture Management System uses: BlueBrain Bluima Connectivity is used by: NIF Data Federation has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the terms of use by the original resource | nif-0000-07732 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8 https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8, http://neuinfo.org/nif/nifgwt.html?query=nif-0000-07732, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-07732-1 | SCR_006391 | NIF Integrated Nervous System Connectivity View, Neuroscience Information Framework Integrated Nervous System Connectivity, Integrated NSC View, Integrated NSC, NIF NSC, NIF Integrated NSC, Integrated Nervous System Connectivity View, Nervous System Connectivity | 2026-02-14 02:07:52 | 0 | ||||||
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Resource Identification Portal Resource Report Resource Website 10+ mentions |
Resource Identification Portal (RRID:SCR_004098) | RII Portal | data or information resource, portal | Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource. | antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG |
uses: Antibody Registry uses: SciCrunch Registry uses: Mouse Genome Informatics (MGI) uses: Zebrafish Information Network (ZFIN) uses: Rat Genome Database (RGD) uses: WormBase uses: FlyBase recommends: SciCrunch Registry recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: Rat Genome Database (RGD) is recommended by: Neuroscience Information Framework is recommended by: SciCrunch Registry is related to: NIF Data Federation has parent organization: SciCrunch |
NIGMS R24 GM144308 | The community can contribute to this resource | nlx_158572 | SCR_004098 | Resource Identification Initiative Portal | 2026-02-14 02:06:35 | 19 | ||||||
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cisRED: cis-regulatory element Resource Report Resource Website 10+ mentions |
cisRED: cis-regulatory element (RRID:SCR_002098) | cisRED | data or information resource, database | Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species. | atomic motif, conserved sequence motif, motif pattern, regulatory element, motif, atomic, promoter, chip-seq, transcription factor binding site, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: BC Cancer Agency |
Genome Canada ; BC Cancer Foundation ; Michael Smith Foundation for Health Research |
PMID:16381958 | Free, Freely available | nif-0000-02665, biotools:cisred, OMICS_01857, r3d100010619 | https://bio.tools/cisred https://doi.org/10.17616/R3XK69 |
SCR_002098 | cisRED - Databases of genome-wide regulatory module and element predictions | 2026-02-14 02:05:46 | 14 |
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