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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneNote Resource Report Resource Website 1+ mentions |
GeneNote (RRID:SCR_007679) | GeneNote | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented June 14, 2013. GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. It offers: An expression profile (tissue vector) for each gene in the human genome Gene and tissue clustering based on expression profiles A full genome ranking procedure according to the gene''s tendency for tissue specificity, from tissue-specific to housekeeping genes. | gene expression profile, human gene, human genome, tissue vector, data set | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02885 | SCR_007679 | 2026-09-05 06:31:42 | 1 | |||||||||
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Histone Database Resource Report Resource Website 1+ mentions |
Histone Database (RRID:SCR_007711) | data or information resource, database | Histone Database is a database of histones and their corresponding sequences. Sequence- and text-based searches were performed on NCBI's redundant and non-redundant (nr) peptide sequence databases. These databases are derived from GenBank, EMBL, and DDBJ translated DNA coding regions, plus protein sequences from the PDB (Protein Data Bank), SWISS-PROT, the PIR (Protein Information Resource), and the PRF (Protein Research Foundation). :Users can search by keyword, sequence fragment, category, organism, and redundancy of the set. | histone | has parent organization: National Human Genome Research Institute | nif-0000-02961 | SCR_007711 | Histone Database | 2026-09-05 06:31:43 | 5 | |||||||||
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Klotho: Biochemical Compounds Declarative Database Resource Report Resource Website |
Klotho: Biochemical Compounds Declarative Database (RRID:SCR_007714) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry. | has parent organization: University of Missouri; Missouri; USA | NIGMS R01-GM56529; NSF DBI-9117005 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03073 | SCR_007714 | Klotho | 2026-09-05 06:31:43 | 0 | ||||||||
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GeneFarm Resource Report Resource Website 1+ mentions |
GeneFarm (RRID:SCR_007674) | data or information resource, database | GeneFarm is a database of structural and functional annotation of plant gene and protein families. The goal of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for plant nuclear genes and gene products and to enter them into added-value database. The improved annotation will allow better data mining of the plant genomes (mainly Arabidopsis thaliana), and more secure planning and design of experiments. It is also a necessary step for building knowledge management tools for integrating plant genomic data, either for plant breeding or to get a broader interactive view of plant biological processes, like gene interaction networks. This re-annotation project, launched is mainly focused on gene families. A complete annotation pipeline using the most efficient prediction tools has been defined. The involved partners, each contributing with genes from his/her field of expertise, have exhaustively annotated families of homologous genes. A database named GeneFarm (Gene Families for Arabidopsis Management) gathers all these expert-curated annotations of plant gene families. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot. | plant gene, plant nuclear gene, plant protein | nif-0000-02881 | SCR_007674 | GeneFarm | 2026-09-05 06:31:42 | 2 | ||||||||||
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Genomic Distribution of structural Superfamilies Resource Report Resource Website 1+ mentions |
Genomic Distribution of structural Superfamilies (RRID:SCR_007670) | data or information resource, database | Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. GenDiS has been curated in direct correspondence with SCOP and represents 4001 highly resolved domains in 1194 structural superfamilies across protein sequence databases. Sequences showing reliable homology to entries in SCOP and PASS2 databases have been obtained from the non-redundant protein sequence database and aligned. Similar alignments of the superfamily members are provided in the genome level. GenDiS provides a platform for cross genome comparison at the superfamily level. GenDis relates proteins sequence information across all strata of taxonomy. One may navigate through the database to obtain structural homologues across different levels in taxonomic classification. The nomenclature of the various genomes and their hierarchy is in direct correspondence with the taxonomy database maintained at the NCBI. Sequence homologues for the various structural members are obtained from the non-redundant protein sequence database employing sensitive sequence search methods. Multiple approaches such as PSI-BLAST, HMMsearch of the HMMer suite and an interacting motif constrained PHI-BLAST have been employed to identify homologues in the sequence databases. | protein, protein superfamily | nif-0000-02874 | SCR_007670 | GenDiS | 2026-09-05 06:31:42 | 2 | ||||||||||
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GeneAnnot Resource Report Resource Website 10+ mentions |
GeneAnnot (RRID:SCR_007673) | data or information resource, database | GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match. Where such matches are not found, probe-sets are annotated by their relation to GenBank mRNA sequences and UniGene clusters. The results are integrated with the GeneCards, GeneLoc and GeneNote databases. HG-U95, HG-U133, HG-U133 | affymetrix, hg-u133, hg-u95, probe set | nif-0000-02878 | SCR_007673 | GeneAnnot | 2026-09-05 06:31:42 | 21 | ||||||||||
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Hepatitis Virus B Database Resource Report Resource Website 1+ mentions |
Hepatitis Virus B Database (RRID:SCR_007705) | data or information resource, database | HepSEQ is the International Repository for Hepatitis B Virus Strain Data. It is web-accessible, quality-based, molecular, clinical and epidemiological database for hepatitis B infection and provides a tool for the research community or for those involved in hepatitis B case management. This database currently has 1012 patient records and 1253 viral sequences. The quality of all submitted sequences is checked. The tools provided include: SeqMatch: search the database for matching sequences Genotyper: genotype HBV strains (based on HBV surface antigen genes) Gene Mutation: display the sequences that contain mutations in HBV coding regions Mutation Annotator: annotate sequences for mutation known to be associated with anti-viral resistance This web database development is funded by the UK Department of Health is curated and is hosted by the Health Protection Agency. | hepatitis b, viral genome, viral sequence | nif-0000-02952 | http://www.hpa-bioinfodatabases.org.uk/hepatitis_open/main.php | SCR_007705 | HepSEQ | 2026-09-05 06:31:43 | 3 | |||||||||
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Highly Expressed Genes Database (HEG-DB) Resource Report Resource Website 1+ mentions |
Highly Expressed Genes Database (HEG-DB) (RRID:SCR_007704) | data or information resource, database | Genomic database that includes prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. | gene expression prediction, prokaryote, prokaryotic genome | nif-0000-02948 | http://genomes.urv.cat/HEG-DB | SCR_007704 | HEG-DB | 2026-09-05 06:31:43 | 1 | |||||||||
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Kinomer Resource Report Resource Website 1+ mentions |
Kinomer (RRID:SCR_007707) | data or information resource, database | Kinomer is a multilevel HMM library that models these protein kinase groups. It allows accurate identification of protein kinases and classification to the appropriate kinase group. Profile hidden Markov models (HMMs) are statistical descriptions of sequence conservation from multiple sequence alignments, and have been shown to outperform standard pairwise sequence comparison methods, both in terms of sensitivity and specificity. HMMs form the basis of protein family and domain description libraries such as SUPERFAMILY and Pfam. | has parent organization: University of Dundee; Scotland; United Kingdom | nif-0000-03072 | SCR_007707 | Kinomer | 2026-09-05 06:31:43 | 7 | ||||||||||
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GenAtlas Resource Report Resource Website 10+ mentions |
GenAtlas (RRID:SCR_007669) | data or information resource, database | GENATLAS contains relevant information with respect to gene mapping and genetic diseases. GENATLAS compiles the information relevant to the mapping efforts of the Human Genome Project. This information is collected from more than 48,000 articles in the literature, collected in more than 870 reviews. The articles are daily analyzed by annotators to update the GENATLAS database. Only the objects with a known cytogenetic location are retained. GENATLAS repertories three kinds of objects Genes database ( more than 21.000 entries) Phenotypes database ( 4104 entries , 2000 cloned) References database linked to the two previous ( more than 48000 entries) | gene mapping, genetic disease, human genome project, FASEB list | nif-0000-02872 | SCR_007669 | GenAtlas | 2026-09-05 06:31:42 | 34 | ||||||||||
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functional RNAdb Resource Report Resource Website 50+ mentions |
functional RNAdb (RRID:SCR_007664) | data or information resource, database | fRNAdb is a database of comprehensive non-coding RNA (ncRNA) sequences including known (or previously reported) ncRNAs, which are acquired from other sequence databases, and ncRNA sequences reported by the joint research groups of the Functional RNA Project. It is funded by the New Energy and Industrial Technology Development Organization. | functional rna, ncrna, non-coding rna | has parent organization: National Institute of Advanced Industrial Science and Technology | nif-0000-02853 | SCR_007664 | fRNAdb | 2026-09-05 06:31:42 | 54 | |||||||||
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FLYSNP Resource Report Resource Website 1+ mentions |
FLYSNP (RRID:SCR_007663) | data or information resource, database | This project aims to provide the information and technical resources to support high-throughput positional cloning in Drosophila melanogaster. These resources include a high-density genome-wide map of single nucleotide polymorphisms (SNPs), and inexpensive, high-throughput assays for SNP genotyping. The specific aims were as follows: 1. To establish a map of >2200 SNP marker loci in the Drosophila genome. These SNP markers have been identified in several commonly used genetic strains. The FlySNP project identified SNP markers within the sequenced, euchromatic regions of the X, 2nd and 3rd chromosomes. The average distance between SNPs is about 50 kb. 2. To establish robust, high-throughput assays for SNP genotyping. Assays have been established using PCR, microarray and mass-spectrometry methods. The tag-array mini-sequencing (TAMS) approach has proven to be an especially fast and reliable method for SNP genotyping. | drosophila melanogaster, drosophila snp, drosophila, drosophila clone | has parent organization: European Union | nif-0000-02847 | SCR_007663 | FLYSNP | 2026-09-05 06:31:42 | 2 | |||||||||
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CREMOFAC: A web-database of Chromatin Remodeling Factors Resource Report Resource Website 1+ mentions |
CREMOFAC: A web-database of Chromatin Remodeling Factors (RRID:SCR_007613) | data or information resource, database | CREMOFAC is a database for chromatin remodeling factors has been developed. The database harbors 64 types of remodeling factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways, and phylogenetic relationships has also been covered. | chromatin, chromatin remodeling factor, human chromatin, mouse chromatin, rat chromatin | nif-0000-02697 | SCR_007613 | CREMOFAC | 2026-09-05 06:31:41 | 2 | ||||||||||
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CR-EST - Crop ESTs Resource Report Resource Website 1+ mentions |
CR-EST - Crop ESTs (RRID:SCR_007612) | data or information resource, database | The Crop EST Database (CR-EST) is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK. Summarized numbers about genomic data of species are listed in tables. The main database content is original sequence data and cDNA library information from different organisms as well as results from BlastX searches against major protein sequence databases contained in NRPEP. Additionally sequence alignments of stackPACK clustering projects are available. This web application allows to BLAST against CR-EST ESTs and to query and retrieve data from Gene Ontology and metabolic pathway annotations as well as sequence similarities from stored results of BLASTX searches against the NRPEP database. CR-EST also features interactive JAVA-based tools, such as open reading frame visualization and explorative analysis of Gene Ontology mappings to ESTs. | nif-0000-02695, r3d100010124 | https://doi.org/10.17616/R3ZP4W | SCR_007612 | Crop EST | 2026-09-05 06:31:41 | 5 | ||||||||||
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GRSDB: G-Rich Sequences DataBase Resource Report Resource Website 1+ mentions |
GRSDB: G-Rich Sequences DataBase (RRID:SCR_007697) | data or information resource, database | GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB2 is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. Computations were performed with the help of an indigenously developed and previously published software program QGRS Mapper. What is new in GRSDB2: The entire database has been built with a new and much improved version of QGRS Mapper program. It contains data from a large number of eukaryotic genes from several organisms in addition to human and mouse. The data model is different than the first version in that it is centered around Entrez Gene rather than solely GenBank/RefSeq nucleotide entries. The search module has been greatly enhanced. It is possible to search the database with Entrez Gene ID, Gene Name, Gene Symbols, Aliases, relevant Accession numbers and many other parameters like numbers of poly A signals and alternatively spliced products. Complex queries can also be performed. In addition, it is now possible to search the database with Gene Ontology terms. The list of genes matching the query can be sorted. The website also allows to manipulate the list to form sets of genes and perform further computations on these sets through a ''Workbench''. The Gene View, Data View and Graphic View for individual database entries have been significantly enhanced with several additional computational capabilities and links. The data can now be exported into Excel for further analysis. In addition, we have added a Sequence View which displays mapped G-quadruplexes in the context of pre-mRNA sequence. GRSDB2 replaces GRSDB at, http://bioinformatics.ramapo.edu/grsdb/index.php | quadruplex-forming g-rich sequences | has parent organization: Ramapo College; New Jersey; USA | PMID:18045785 | nif-0000-02930 | SCR_007697 | GRSDB, GRSDB2 | 2026-09-05 06:31:43 | 1 | ||||||||
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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 | 2026-09-05 06:31:44 | 0 | ||||||
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GrainGenes Resource Report Resource Website 100+ mentions |
GrainGenes (RRID:SCR_007696) | data or information resource, database | Grain Genes is a genome database for Triticeae and Avena. It contains tools that allow users to browse graingenes, search the MySQL database, and view maps, genetic markers, gene expression and sequences. | agriculture, avena, plant genome, triticeae, FASEB list | nif-0000-02925, r3d100012363 | https://doi.org/10.17616/R3D08J, https://doi.org/10.17616/R3D08J | SCR_007696 | GrainGenes | 2026-09-05 06:31:43 | 322 | |||||||||
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Gene Ontology Partition Database Resource Report Resource Website |
Gene Ontology Partition Database (RRID:SCR_007693) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The GO Partition Database was designed to feature ontology partitions with GO terms of similar specificity. The GO partitions comprise varying numbers of nodes and present relevant information theoretic statistics, so researchers can choose to analyze datasets at arbitrary levels of specificity. The GO Partition Database, featuring GO partition sets for functional analysis of genes from human and ten other commonly-studied organisms with a total of 131,972 genes. | gene ontology | has parent organization: Harvard University; Cambridge; United States | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02920 | http://bcl.med.harvard.edu/proj/gopart | http://bcl.med.harvard.edu/proteomics/proj/gopart/menu.php | SCR_007693 | GOPaD | 2026-09-05 06:31:43 | 0 | ||||||
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GPX-Macrophage Resource Report Resource Website |
GPX-Macrophage (RRID:SCR_007694) | data or information resource, database | A database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. The objectives of the database are: Provide access to quality assessed gene expression datasets Rapid access to gene expression profile macrophage treated with a variety of conditions Provide datasets for Systems biology | immunology, macrophage |
is listed by: 3DVC has parent organization: University of Edinburgh; Scotland; United Kingdom |
nif-0000-02924 | http://ebola.gti.ed.ac.uk:8090/GPX/htdocs/index.html | SCR_007694 | GPXdb | 2026-09-05 06:31:43 | 0 | ||||||||
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GOA Resource Report Resource Website 500+ mentions |
GOA (RRID:SCR_007691) | GOA, GOA REF | data or information resource, database | An annotation program which aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). It is a central dataset for other major multi-species databases, such as Ensembl and NCBI. Because of the multi-species nature of the UniProtKB, UniProtKB-GOA assists in the curation of 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. Gene Association Files can be accessed from the Downloads section of the website. | gene ontology, chicken proteome, cow proteome, human proteome, xref, gene, gene association, gold standard |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is related to: FlyMine is related to: UniProt DAS is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures has parent organization: European Bioinformatics Institute |
Public, Available to the research community, All UniProtKB-GOA Gene Association Files are released approximately every four weeks | nif-0000-02916 | SCR_007691 | UniProtKB-GOA, Gene Ontology Annotation (UniProtKB-GOA) Database, GOA - Gene Ontology Annotation, Gene Ontology Annotation, GO Annotation at EBI | 2026-09-05 06:31:43 | 678 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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