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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Rice Metabolic Pathway Database Resource Report Resource Website 1+ mentions |
Rice Metabolic Pathway Database (RRID:SCR_002128) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP. | gene, biochemical pathway, rice | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20922 | http://www.gramene.org/pathway/ricecyc.html | SCR_002128 | Rice Metabolic Pathways, RiceCyc | 2026-08-04 09:40:34 | 9 | ||||||||
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EchoBASE Resource Report Resource Website 1+ mentions |
EchoBASE (RRID:SCR_002430) | EchoBASE | database, data or information resource | A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium. | gene, bio.tools |
is listed by: bio.tools is listed by: Debian |
GlaxoSmithKline ; BBSRC |
PMID:15608209 | nif-0000-02781, biotools:echobase, r3d100011646 | https://bio.tools/echobase, https://doi.org/10.17616/R38W6H | SCR_002430 | EchoBASE: an integrated post-genomic database for Escherichia coli | 2026-08-04 09:40:38 | 6 | |||||
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Phevor Resource Report Resource Website 1+ mentions |
Phevor (RRID:SCR_002273) | Phevor | data analysis service, production service resource, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles. | genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, allele | has parent organization: University of Utah School of Medicine; Utah; USA | PMID:24702956 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000139 | SCR_002273 | Phenotype Driven Variant Ontological Re-Ranking Tool | 2026-08-04 09:40:36 | 9 | ||||||
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AceView Resource Report Resource Website 100+ mentions |
AceView (RRID:SCR_002277) | AceView/WormGenes | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. | est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard | has parent organization: NCBI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21007, r3d100010651 | https://doi.org/10.17616/R3260G | http://www.ncbi.nih.gov/IEB/Research/Acembly/ | SCR_002277 | AceView genes, AceView/WormGenes, The AceView Genes | 2026-08-04 09:40:36 | 186 | |||||
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RegPrecise Resource Report Resource Website 50+ mentions |
RegPrecise (RRID:SCR_002149) | RegPrecise | database, data or information resource | Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | regulon, genome, transcription factor, gene, operon, transcription factor binding site, taxonomy, rna, effector, pathway, ortholog, function, FASEB list |
is listed by: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy ; NSF DBI-0850546 |
PMID:24175918 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01869 | SCR_002149 | 2026-08-04 09:40:34 | 80 | ||||||
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Familial Hypertrophic Cardiomyopathy DNA Mutation Database Resource Report Resource Website 1+ mentions |
Familial Hypertrophic Cardiomyopathy DNA Mutation Database (RRID:SCR_002346) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI. | familial, gene, gene-, genetic, cardiomyopathy, clinic, correlation, defect, disorder, genotype, hypertrophic, locus, mutation, or disease- specific databases, phenotype, research, sarcomere, system- | PMID:10502780 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21151 | SCR_002346 | FHC Mutation Database | 2026-08-04 09:40:37 | 2 | ||||||||
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DBTBS Resource Report Resource Website 10+ mentions |
DBTBS (RRID:SCR_002345) | DBTBS | database, data or information resource | Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins. | gene, gene regulatory network, transcription factor binding site, transcription factor, regulated operon, motif, promoter, motif conservation |
is listed by: OMICtools has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:17962296 PMID:14681362 PMID:11125112 |
Acknowledgement requested | nif-0000-02736, OMICS_01859 | SCR_002345 | DBTBS: a database of Bacillus subtilis promoters and transcription factors., DBTBS: a database of Bacillus subtilis promoters and transcription factors | 2026-08-04 09:40:37 | 30 | |||||
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eggNOG Resource Report Resource Website 1000+ mentions |
eggNOG (RRID:SCR_002456) | eggNOG | database, data or information resource | A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014) | orthologous gene, ortholog, gene, function, FASEB list |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 |
PMID:24297252 PMID:22096231 |
Free, Available for download, Freely available | nif-0000-02789, OMICS_01689 | SCR_002456 | eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups, eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups), evolutionary genealogy of genes: Non-supervised Orthologous Groups | 2026-08-04 09:40:40 | 3564 | |||||
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EDAS - EST-Derived Alternative Splicing Database Resource Report Resource Website 1+ mentions |
EDAS - EST-Derived Alternative Splicing Database (RRID:SCR_002449) | EDAS | database, data or information resource | Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test. | alternative splicing, gene, protein, mrna, est, exon, intron, rat, dog |
is listed by: OMICtools has parent organization: Moscow State University; Moscow; Russia |
PMID:16909834 | Free, Freely available | nif-0000-02786, OMICS_01885 | SCR_002449 | EDAS: EST Derived Alternative Splicing Database, EST Derived Alternative Splicing Database | 2026-08-04 09:40:38 | 1 | ||||||
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PubGene Resource Report Resource Website 10+ mentions |
PubGene (RRID:SCR_002119) | database, data or information resource | It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate. | gene, information, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is parent organization of: Coremine Medical |
Free, Freely Available | biotools:pubgene, nif-0000-20908 | https://bio.tools/pubgene | SCR_002119 | PubGene | 2026-08-04 09:40:33 | 39 | |||||||
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ConsensusPathDB Resource Report Resource Website 500+ mentions |
ConsensusPathDB (RRID:SCR_002231) | CPDB | database, data or information resource | An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered. | gene regulatory network, pathway, gene regulatory network, molecular interaction, interaction, gene regulation, protein interaction, genetic interaction, biochemical reaction, drug-target interaction, molecule, visualization, gene, protein, complex, metabolite, FASEB list |
is listed by: OMICtools is related to: BIND is related to: BioCarta Pathways is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: CORUM is related to: Database of Interacting Proteins (DIP) is related to: DrugBank is related to: HPRD - Human Protein Reference Database is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Integrating Network Objects with Hierarchies is related to: InnateDB is related to: IntAct is related to: KEGG is related to: MINT is related to: MIPS Mammalian Protein-Protein Interaction Database is related to: MatrixDB is related to: NetPath is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDZBase is related to: Pathway Interaction Database is related to: PIG - Pathogen Interaction Gateway is related to: PINdb is related to: PharmGKB is related to: PhosphoPOINT is related to: PhosphoSitePlus: Protein Modification Site is related to: Reactome is related to: Small Molecule Pathway Database is related to: SignaLink is related to: SPIKE is related to: Therapeutic Target Database is related to: WikiPathways has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
European Union HEALTH-F4-2007-200767 | PMID:23143270 PMID:21071422 PMID:20847220 PMID:18940869 |
Free, Freely available | nif-0000-02684, OMICS_01903, r3d100012822 | https://doi.org/10.17616/R3HF8Z | SCR_002231 | ConsensusPathDB, ConsensusPathDB-human | 2026-08-04 09:40:35 | 667 | ||||
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Full-Malaria: Malaria Full-Length cDNA Database Resource Report Resource Website 1+ mentions |
Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) | database, data or information resource | FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan. | drug, eukaryotic, expression, function, gene, alignment, amino acid, cdna, chromosome, clone, coding, comparative, genome, genomic, human, malaria, medical, nucleotide, oligo-capping, organism, parasite, pathogen, physical, plasmodium falciparum, promoter, protein, region, sequence, sequencing, unicellular eukaryote genome databases, vaccine | has parent organization: University of Tokyo; Tokyo; Japan | PMID:18987005 PMID:14681428 |
nif-0000-21157 | SCR_002348 | Full-Malaria | 2026-08-04 09:40:38 | 2 | ||||||||
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Human Gene Connectome Server Resource Report Resource Website 1+ mentions |
Human Gene Connectome Server (RRID:SCR_002627) | HGCS | data analysis service, analysis service resource, production service resource, service resource | An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. | gene, disease, phenotype, genome, connectome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Human Gene Connectome |
PMID:23509278 | Free | nlx_156049, biotools:hgcs | https://bio.tools/hgcs | SCR_002627 | 2026-08-04 09:40:42 | 5 | ||||||
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RIKEN Arabidopsis Transposon mutants Resource Report Resource Website |
RIKEN Arabidopsis Transposon mutants (RRID:SCR_003230) | RIKEN Arabidopsis Transposon mutants | database, data or information resource | RIKEN Arabidopsis Transposon mutants is a series of mutant lines which have a Ds transposon in the genome of Arabidopsis thaliana Nssen ecotype (background by Fedoroff and Smith). This web page provides information on the mutants produced in our laboratory. Each mutant line is assigned by stipulated line codes (ex. 13-4480-1). We determined the flanking sequences of Ds insertion for each independent line. Transposon insertion sites of mutants were estimated by a BLASTN homology against the genome sequence database of Arabidopsis thaliana Columbia ecotype. The closest genes (predicted by AGI) to the transposon insertion sites were picked up. The results of the BLASTP homology search against the nr database of NCBI for the closest genes have been collected for keyword searches. | gene, mutant, arabidopsis thaliana, transposon | has parent organization: RARGE - RIKEN Arabidopsis Genome Encyclopedia | PMID:15840642 | Free, Freely available | nif-0000-31394 | http://rarge-v2.psc.riken.jp/about/line | SCR_003230 | 2026-08-04 09:40:51 | 0 | ||||||
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GOToolBox Functional Investigation of Gene Datasets Resource Report Resource Website 10+ mentions |
GOToolBox Functional Investigation of Gene Datasets (RRID:SCR_003192) | GOToolBox | software resource, source code, service resource | The GOToolBox web server provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. The web version of the GOToolBox is free for non-commercial users only. Users from commercial companies are allowed to use the site during a reasonable testing period. For a regular use of the web version, a license fee should be paid. We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license. Platform: Online tool | gene, annotation, statistical analysis, slimmer-type tool, function, cluster, gene association, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Center for Genomic Regulation; Barcelona; Spain |
Action Bioinformatique inter-EPST ; French Ministere de l'Education de la Recherche et de la Technologie ; Fondation pour la Recherche Medicale |
PMID:15575967 | Free, Freely available | nif-0000-30623 | http://burgundy.cmmt.ubc.ca/GOToolBox/ | SCR_003192 | GOToolBox - Functional Investigation of Gene Datasets, GOToolBox : Functional Investigation of Gene Datasets | 2026-08-04 09:40:50 | 35 | ||||
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Human Gene and Protein Database (HGPD) Resource Report Resource Website 1+ mentions |
Human Gene and Protein Database (HGPD) (RRID:SCR_002889) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The Human Gene and Protein Database presents SDS-PAGE patterns and other informations of human genes and proteins. The HGPD was constructed from full-length cDNAs. For conversion to Gateway entry clones, we first determined an open reading frame (ORF) region in each cDNA meeting the criteria. Those ORF regions were PCR-amplified utilizing selected resource cDNAs as templates. All the details of the construction and utilization of entry clones will be published elsewhere. Amino acid and nucleotide sequences of an ORF for each cDNA and sequence differences of Gateway entry clones from source cDNAs are presented in the GW: Gateway Summary window. Utilizing those clones with a very efficient cell-free protein synthesis system featuring wheat germ, we have produced a large number of human proteins in vitro. Expressed proteins were detected in almost all cases. Proteins in both total and supernatant fractions are shown in the PE: Protein Expression window. In addition, we have also successfully expressed proteins in HeLa cells and determined subcellular localizations of human proteins. These biological data are presented on the frame of cDNA clusters in the Human Gene and Protein Database. To build the basic frame of HGPD, sequences of FLJ full-length cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto the genome sequences (NCBI Build 35 (UCSC hg17)). The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (http://flj.hinv.jp/) constructed as a human cDNA sequence analysis database focusing on mRNA varieties caused by variations in transcription start site (TSS) and splicing. | gene, cdna clusters, cdnas, cdna sequences, human, in vitro, mrna varieties, protein, sds-page | has parent organization: National Institute of Advanced Industrial Science and Technology | PMID:22140100 PMID:19073703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02956 | SCR_002889 | HGPD | 2026-08-04 09:40:46 | 6 | |||||||
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Greengenes Resource Report Resource Website 1000+ mentions |
Greengenes (RRID:SCR_002830) | database, data or information resource | Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, rrna, 16s rrna, gene, dna, rna, chimera, alignment, taxonomic classification, taxonomy, FASEB list |
is listed by: OMICtools is listed by: re3data.org is listed by: Human Microbiome Project has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy contract DE-AC02-05CH11231 | PMID:16820507 | Free, Freely available | OMICS_01512, r3d100010549, nif-0000-02927 | http://greengenes.lbl.gov, https://doi.org/10.17616/R36C8G | SCR_002830 | 2026-08-04 09:40:45 | 3125 | ||||||
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Interrupted CoDing Sequence Database Resource Report Resource Website |
Interrupted CoDing Sequence Database (RRID:SCR_002949) | ICDS Database | database, data or information resource | Database of interrupted coding sequences detected by a similarity-based approach in complete prokaryotic genomes. The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. To facilitate the experimental characterization of ICDS, optimized primers are proposed for re-sequencing purposes. The database is accessible by BLAST search or by genome. 118 Genomes are available in the database. | genome, blast, interrupted coding sequence, gene | has parent organization: University of Strasbourg; Strasbourg; France | PMID:16381882 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03036 | SCR_002949 | 2026-08-04 09:40:46 | 0 | |||||||
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Phenoscape Knowledgebase Resource Report Resource Website 10+ mentions |
Phenoscape Knowledgebase (RRID:SCR_002821) | Phenoscape Knowledgebase | database, data or information resource | Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26. | fish, gene, anatomy, model organism, ostariophysan, phenotype, taxis, ontology, anatomy, variation, taxon, genetic, evolution, development, web service, source code |
uses: Teleost Anatomy Ontology is related to: Zebrafish Information Network (ZFIN) is related to: Catalog of Fishes is related to: FishBase is related to: AmphibiaWeb is related to: NCBI Taxonomy is related to: Catalogue of Life has parent organization: NESCent - National Evolutionary Synthesis Center has parent organization: Phenoscape is parent organization of: Teleost Taxonomy Ontology |
NSF DBI-1062404; NSF DBI-1062542; NSF EF-0905606; NSF BDI-0641025; NSF EF-0423641 |
PMID:22736877 PMID:20505755 |
Free, Freely available | nif-0000-24925 | SCR_002821 | 2026-08-04 09:40:44 | 14 | ||||||
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IFTI-Mirage Resource Report Resource Website 1+ mentions |
IFTI-Mirage (RRID:SCR_000505) | portal, database, data or information resource | A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation. | bioinformatics, gene, expression, database, technology, method, tool, sequence, regulation |
is parent organization of: object-oriented Transcription Factors Database is parent organization of: TfSiteScan |
Public, Available to the research community | nlx_19877 | SCR_000505 | Institute for Transcriptional Informatics-Molecular Informatics Resource for the Analysis of Gene Expression, MIRAGE | 2026-08-04 09:40:09 | 5 |
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If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
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If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
