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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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EpoDB - Erythropoiesis Database Resource Report Resource Website 1+ mentions |
EpoDB - Erythropoiesis Database (RRID:SCR_007642) | data or information resource, database | Database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites. This database is no longer maintained or updated. | erythropoiesis, red blood cell, vertebrate red blood cell | PMID:9399855 PMID:9847180 |
nif-0000-02809 | SCR_007642 | EpoDB | 2026-08-29 11:29:57 | 2 | |||||||||
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ERGR- Ethanol-Related Genome Resource Resource Report Resource Website 1+ mentions |
ERGR- Ethanol-Related Genome Resource (RRID:SCR_007643) | data or information resource, database | The aim of the Ethanol-Related Gene Resource (ERGR) database is to provide a comprehensive and useful gene resource to the Ethanol/Alcohol research community. Currently, the ERGR database contains more than 30 large datasets from literature and 21 mouse QTLs from public database. These data are from 5 organisms (human, mouse, rat, fly and worm) and produced by multiple approaches (expression, association, linkage, QTL, literature search etc). Users can browse or search the database in different levels. Moreover, ERGR provides data integration (union and intersection) and candidate gene selection based on multiple datasets or organisms. | ethanol, ethanol research, alcohol, alcohol research | has parent organization: Virginia Commonwealth University; Virginia; USA | nif-0000-02812 | http://bioinfo.vipbg.vcu.edu/ERGR/ | SCR_007643 | ERGR | 2026-08-29 11:29:52 | 2 | ||||||||
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MitoDat - Mendelian Inheritance and the Mitochondrion Resource Report Resource Website |
MitoDat - Mendelian Inheritance and the Mitochondrion (RRID:SCR_007799) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins, although it also includes proteins from other animals in addition to those currently known only from yeast and other fungal mitochondria, as well as from plant mitochondria. he database consolidates information from various biological databases, eg., GenBank, SwissPro, Genome Data Base (GDB), Online Mendelian Inheritance in Man (OMIM), et al. Because the mitochondrion has a central role in cellular metabolism, it is involved in many human diseases. This database should help us in studying these diseases. We are also hyperlinked to the Report of the committee on human mitochondrial DNA, maintained by the Wallace group at Emory. It can be accessed here and also from the results when searching mitoDat for mitochondrially encoded genes. The Report of the committee on human mitochondrial DNA is currently the most comprehensive source of information on mitochondrial DNA mutations, other defects, and disorders in which the mitochondrial DNA deficiencies have been associated. | software |
is listed by: 3DVC has parent organization: Emory University; Georgia; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03142 | SCR_007799 | MitoDat | 2026-08-29 11:30:06 | 0 | ||||||||
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miRGen Resource Report Resource Website 50+ mentions |
miRGen (RRID:SCR_007796) | data or information resource, database | An integrated database of positional relationships between animal miRNAs and genomic annotation sets and animal miRNA targets according to combinations of widely used target prediction programs. miRGen has three connected interfaces which query this data. The Genomics interface allows the user to explore where whole-genome collections of miRNAs are located with respect to UCSC genome browser annotation sets such as Known Genes, Refseq Genes, Genscan predicted genes, CpG islands, and pseudogenes. The Targets interface provides access to unions and intersections of four widely used target prediction programs, and experimentally supported targets from TarBase. The Clusters interface provides predicted miRNA clusters at any given inter-miRNA distance, and provides specific functional information on the targets of miRNAs within each cluster. | FASEB list | has parent organization: University of Pennsylvania; Philadelphia; USA | nif-0000-03137 | http://www.diana.pcbi.upenn.edu/miRGen | SCR_007796 | miRGen | 2026-08-29 11:29:55 | 51 | ||||||||
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Mitochondriome Resource Report Resource Website |
Mitochondriome (RRID:SCR_007798) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A web site dedicated to providing links to mitochondrial data and databases, as well as links to other mitochondrial sites and relevant information. It provides links to databases, complete mitochondrial genomes, genome maps, and publications. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03141 | SCR_007798 | Mitochondriome | 2026-08-29 11:30:13 | 0 | ||||||||||
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miR2Disease Resource Report Resource Website 100+ mentions |
miR2Disease (RRID:SCR_007792) | data or information resource, database | A manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. Each entry in the miR2Disease contains detailed information on a miRNA-disease relationship, including miRNA ID, disease name, a brief description of the miRNA-disease relationship, miRNA expression pattern in the disease state, detection method for miRNA expression, experimentally verified miRNA target gene(s), and literature reference . All entries can be retrieved by miRNA ID, disease name or target gene. miR2Disease will be updated bimonthly. miR2Disease sincerely looks forward to recently established relationship between miRNA and human diseases to be submitted. | FASEB list | has parent organization: Harbin Institute of Technology; Harbin; China | nif-0000-03133 | http://mlg.hit.edu.cn:8080/miR2Disease | SCR_007792 | miR2Disease | 2026-08-29 11:30:05 | 108 | ||||||||
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miRGator Resource Report Resource Website 50+ mentions |
miRGator (RRID:SCR_007793) | miRGator | data or information resource, database | Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets. | genome, functional annotation, microrna, expression profile, mir-seq, mirna-mrna target relation, expression correlation, FASEB list |
is listed by: OMICtools has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
Korean Rural Development Administration 20070401034010; Korean Ministry of Science and Technology ; Ministry of Education and Human Resources Development |
PMID:23193297 PMID:21062822 PMID:17942429 |
nif-0000-03136, OMICS_00363 | http://203.255.191.19/MEXWebApp/, http://genome.ewha.ac.kr/miRGator/miRGator.html | SCR_007793 | miRGator: an integrated system for functional annotation of microRNAs | 2026-08-29 11:30:12 | 55 | |||||
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NPInter Resource Report Resource Website 100+ mentions |
NPInter (RRID:SCR_007825) | data or information resource, database | A database covering eight category functional interactions between noncoding RNAs (except tRNAs and rRNAs) and proteins related biomacromolecules (proteins, mRNAs and genomic DNAs) in six model organisms. Functional interactions imply both physical interactions between the ncRNA and protein, and other forms of interaction where the combination of an ncRNA and an mRNA or a genomic DNA sequence elicits a cellular reaction. This database is distinguished from other biomolecular interaction database by: 1. The data of NPInter is novel, in the sense that no earlier database has especially cataloged this type of data (ncRNA-protein interactions). The database now contains more than 700 published functional interactions from the six organisms E. coli, yeast, worm, fly, mouse and human in which functional interactions experiments have been concentrated. The amount of data is not large, but the NPInter covers almost all experimentally verified ncRNA functional interaction data which had been published before the end of last year. 2. The ncRNA functional interaction data are entered into NPInter only following publication in books or peer-reviewed journals. Entry is done manually by a curator, and thereafter double-checked by a second curator. 3. We introduce a classification of the functional interaction data, which is based on the functional interaction process the ncRNA takes part in. 4. NPInter also provides an efficient search option, allowing recovery of interactions, related publications and other information., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03199 | http://bioinfo.ibp.ac.cn/NPInter/index.php | SCR_007825 | NPInter | 2026-08-29 11:30:07 | 102 | |||||||||
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OGD - Oomycete Genomics Database Resource Report Resource Website 1+ mentions |
OGD - Oomycete Genomics Database (RRID:SCR_007828) | data or information resource, database | The Oomycete Genomics Database is a publicly accessible resource that includes functional assays and expression data, combined with transcript and genomic analysis and annotation. OGD builds upon data available from the Phytophthora Genome Consortium, Syngenta Phytophthora Consortium and the Phytophthora Functional Genomics Database. Data are analyzed and annotated using NCGR''s XGI System. The knowledge gained from these studies provide significant insight into key molecular processes regulating an economically important pathosystem and will provide novel tools for improvement of disease resistance in crop plants. | has parent organization: Ohio State University; Ohio; USA | nif-0000-03211 | http://www.oomycete.org/ | SCR_007828 | OGD | 2026-08-29 11:30:14 | 2 | |||||||||
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NONCODE Resource Report Resource Website 500+ mentions |
NONCODE (RRID:SCR_007822) | data or information resource, database | Collection of non-coding RNAs (excluding tRNAs and rRNAs) as an integrated knowledge database. Used to get text information such as class,name,location,related publication,mechanism through which it exerts its function, view figures which show their location in the genome or in a specific DNA fragment, and the regulation elements flanking the ncRNA gene sequences. | collection, long, non, coding, RNA, integrated, database, FASEB list |
has parent organization: Chinese Academy of Sciences; Beijing; China works with: Genotate |
Chinese Academy of Science Strategic Project of Leading Science and Technology ; National High Technology Research and Development Program of China ; National Natural Science Foundation of China ; Training Program of the Major Research Plan of the National Natural Science Foundation of China |
PMID:26586799 | nif-0000-03195, r3d100012169 | http://www.bioinfo.org/noncode/, https://doi.org/10.17616/R3194Q, https://doi.org/10.17616/R3194Q | http://bioinfo.ibp.ac.cn/NONCODE/index.htm, http://www.noncode.org/NONCODERv3/ | SCR_007822 | NONCODE 2016 | 2026-08-29 11:30:07 | 514 | |||||
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MHCBN: A comprehensive database of MHC binding and non-binding peptides Resource Report Resource Website 10+ mentions |
MHCBN: A comprehensive database of MHC binding and non-binding peptides (RRID:SCR_007785) | data or information resource, database | The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes. The version 4.0 of database provides information about peptides interacting with TAP and MHC linked autoimmune diseases. | has parent organization: Institute of Microbial Technology; Chandigarh; India | nif-0000-03123 | SCR_007785 | MHCBN | 2026-08-29 11:30:12 | 16 | ||||||||||
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metaTIGER Resource Report Resource Website 1+ mentions |
metaTIGER (RRID:SCR_007781) | data or information resource, database | metaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes. Phylogenomic information is provided by 2,257 large phylogenetic trees which can be interactively explored. High-throughput tree analysis can also be carried out to identify trees of interest, e.g. trees containing horizontal gene transfers. metaTIGER also provides novel facilities for viewing and comparing the metabolic profiles. | has parent organization: University of Leeds; West Yorkshire; United Kingdom | nif-0000-03118 | SCR_007781 | metaTIGER | 2026-08-29 11:30:05 | 2 | ||||||||||
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Metalloprotein Site Database Resource Report Resource Website 1+ mentions |
Metalloprotein Site Database (RRID:SCR_007780) | MDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. Database and Browser containing quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?, and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms). This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins. | software, web service |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NIGMS P01-GM48495 | PMID:11752342 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03116 | SCR_007780 | Metalloprotein Database and Browser | 2026-08-29 11:30:12 | 1 | |||||
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MfunGD - MIPS Mouse Functional Genome Database Resource Report Resource Website 50+ mentions |
MfunGD - MIPS Mouse Functional Genome Database (RRID:SCR_007783) | MfunGD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.Database for annotated mouse proteins and their occurrence in protein networks. It contains cDNA and protein sequences, annotation, gene models and mapping, FunCat, UCSC Genome Viewer, SIMAP, pseudogenes (Genome Viewer Track), InterPro, and splice variants. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system. To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database. The gene models are based on the RefSeq mouse cDNAs. The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database and the Comprehensive Resource of Mammalian Protein Complexes are linked to the MfunGD dataset. Links to external resources are also provided. MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture. | bio.tools |
is listed by: Debian is listed by: bio.tools |
GSF National Research Center for Environment and Health ; German Federal Ministry of Research and Education |
PMID:16381934 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03121, biotools:mfungd | https://bio.tools/mfungd | SCR_007783 | Mouse Functional Genome Database | 2026-08-29 11:30:05 | 90 | ||||
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NucleaRDB Resource Report Resource Website 10+ mentions |
NucleaRDB (RRID:SCR_007782) | data or information resource, database | A database of information on nuclear receptors. Included in the database are sequence information, structural information, and mutation data. Users can BLAST sequences, view 2D structural data, see the chromosomal location of nuclear receptors genes, and utilize other tools found on the website. | has parent organization: Radboud University; Nijmegen; The Netherlands | nif-0000-03206 | SCR_007782 | NucleaRDB | 2026-08-29 11:30:12 | 10 | ||||||||||
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NetworKIN Resource Report Resource Website 100+ mentions |
NetworKIN (RRID:SCR_007818) | data or information resource, database | A method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins. This website allows a user to browse/search and investigate predictions made using the NetworKIN algorithm. The site is powered by the latest phosphoproteome in Phospho.ELM. Alternatively users can submit their own protein sequences and phosphorylation sites and obtain new NetworKIN predictions. | FASEB list | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | nif-0000-03190 | SCR_007818 | NetworKIN | 2026-08-29 11:30:14 | 112 | |||||||||
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IMGT/3Dstructure-DB Resource Report Resource Website 1+ mentions |
IMGT/3Dstructure-DB (RRID:SCR_007734) | data or information resource, database | A database of three-dimensional protein structures. It contains molecules, complexes, sequences, ligand/receptor pairings, and other useful tools. Currently, 1655 entries are managed , with 1602 IMGT/3Dstructure-DB cards (PDB) and 53 IMGT/2Dstructure-DB cards (INN). | nif-0000-03013, r3d100012539 | https://doi.org/10.17616/R39V06 | SCR_007734 | IMGT/3Dstructure-DB | 2026-08-29 11:29:53 | 1 | ||||||||||
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Database of Spatially Interacting Motifs in Proteins Resource Report Resource Website |
Database of Spatially Interacting Motifs in Proteins (RRID:SCR_007735) | iMOTdb | data or information resource, database | Comprehensive collection of spatially interacting motifs in proteins. Interacting motif database lists interacting motifs that are identified for all structural entries in PDB. Conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting common motifs shared among all superfamily members. | Conserved patterns, spatially interacting motifs, finger prints, structural entries, protein | has parent organization: Tata Institute of Fundamental Research; Mumbai; India | Wellcome Trust | PMID:16381866 | Free, Freely available | nif-0000-03018, SCR_008194, nif-0000-21218 | SCR_007735 | 2026-08-29 11:30:02 | 0 | ||||||
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Hyper Cell Line Database Resource Report Resource Website |
Hyper Cell Line Database (RRID:SCR_007730) | HyperCLDB | biomaterial supply resource, material resource, tissue bank | Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE. | cell, cell line, tumor, tissue, organ, blood, bodily fluid, ascitic fluid, brain, bone marrow, cancer, transforming agent, software, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: ATCC is related to: Cell Line Knowledge Base has parent organization: IST National Institute for Cancer Research; Genoa; Italy |
Cancer, Etc. | PMID:18927105 | nif-0000-03004, biotools:hypercldb | https://bio.tools/hypercldb | SCR_007730 | 2026-08-29 11:30:09 | 0 | ||||||
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X-linked SCID mutation database Resource Report Resource Website 1+ mentions |
X-linked SCID mutation database (RRID:SCR_007732) | data or information resource, database | IL2Rgbase is a database of mutations in the X-linked gene IL2RG, leading to the autoimmune disease XSCID. Data on mutations in any of the eight exons may be retrieved and examined, as well as intervening sequences. | has parent organization: National Institutes of Health | nif-0000-03008 | SCR_007732 | IL2Rgbase | 2026-08-29 11:30:09 | 3 |
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