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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RESNET Resource Report Resource Website 1000+ mentions |
RESNET (RRID:SCR_002121) | ResNet | data or information resource, database | Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | biological relationship, biomedical, literature, interaction, FASEB list |
is listed by: Biositemaps has parent organization: Indiana University School of Medicine; Indiana; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20909 | http://www.ariadnegenomics.com/products/databases/ariadne-resnet/ | SCR_002121 | Ariadne ResNet Databases, ResNet Databases | 2026-08-29 11:29:15 | 1384 | ||||||
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CORUM Resource Report Resource Website 100+ mentions |
CORUM (RRID:SCR_002254) | CORUM | data or information resource, database |
Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded. The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
mammalian protein, protein, protein complex, protein function, FASEB list |
is listed by: OMICtools is related to: Interaction Reference Index is related to: ConsensusPathDB has parent organization: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany |
BMBF 031U212C | PMID:19884131 PMID:17965090 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02688, OMICS_01904, r3d100011272 | http://mips.gsf.de/genre/proj/corum | SCR_002254 | CORUM the Comprehensive Resource of Mammalian protein complexes, CORUM - the Comprehensive Resource of Mammalian protein complexes | 2026-08-29 11:29:22 | 164 | ||||
|
GeneSeer Resource Report Resource Website |
GeneSeer (RRID:SCR_002626) | GeneSeer | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database to access gene information through common names and allows identification of homologs and paralogs for a given gene. This publicly available tool leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as humans. | gene, homolog, paralog, genome, search engine, ortholog | PMID:16176584 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156048 | http://katahdin.mssm.edu/geneseer/scripts/main.pl | http://geneseer.cshl.org/ | SCR_002626 | 2026-08-29 11:29:24 | 0 | ||||||
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Mammalian Mitochondrial Genomics Database Resource Report Resource Website |
Mammalian Mitochondrial Genomics Database (RRID:SCR_003084) | MamMiBase | data or information resource, database | Database developed to assist the phylogeneticist user in retrieving individual gene sequence alignments for genes in complete mammalian mitochondrial genomes. Data retrieval in MamMiBase requires three stages. At the first stage, the user must select the mammalian species or group that (s)he wishes to study. In the second stage, the user will select the outgroup from a list that included all species selected in the first stage plus Xenopus laevis and Gallus gallus. Finally, at the third stage, the user will select individual mitochondrial gene alignments or a phylogenetic tree that (s)he wishes to download. | phylogeny, mitochondrial, genome, gene, sequence | has parent organization: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil | Brazilian Ministry of Science Technology and Innovation ; National Research Council ; Rio de Janeiro Science Foundation ; FAPERJ |
PMID:15713730 | Free, Freely available | nif-0000-03099 | SCR_003084 | 2026-08-29 11:29:26 | 0 | ||||||
|
ARACNE Resource Report Resource Website 100+ mentions |
ARACNE (RRID:SCR_002180) | ARACNE | software application, software resource | An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis. | cellular network, cellular, network, microarray, expression profile, deconvolution, regulatory network |
is listed by: OMICtools is related to: B Cell Interactome has parent organization: Columbia University; New York; USA |
PMID:16723010 | Free, Freely available | OMICS_01851 | SCR_002180 | Algorithm for the Reconstruction of Accurate Cellular Networks | 2026-08-29 11:30:40 | 163 | ||||||
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ProtChemSI Resource Report Resource Website 1+ mentions |
ProtChemSI (RRID:SCR_006115) | ProtChemSI | data or information resource, database | The database of protein-chemical structural interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one considers the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The current version includes data from the Protein Data Bank as of August 2011. The database is updated monthly. | protein, chemical, 3d structure, biological network, interaction, ligand, prediction, fasta, fasta sequence, smiles string, complex, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
PMID:21573205 | Acknowledgement requested | nlx_151590, biotools:protchemsi | https://bio.tools/protchemsi | SCR_006115 | Protein-Chemical Structural Interactions, ProtChemSI: protein-chemical interaction database, ProtChemSI - the database of protein-chemical structural interactions | 2026-08-29 11:29:44 | 3 | |||||
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HaploReg Resource Report Resource Website 1000+ mentions |
HaploReg (RRID:SCR_006796) | HaploReg | data or information resource, database | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. | chromatin state, conservation, regulatory motif, alteration, variant, chromatin, motif, annotation, genome, variation, genome-wide association study, refsnp, refseq gene, snp, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Broad Institute |
NHGRI R01-HG004037; NHGRI RC1-HG005334; NSF 0644282 |
PMID:22064851 | biotools:HaploReg, nlx_151407 | http://compbio.mit.edu/HaploReg, https://bio.tools/HaploReg | SCR_006796 | 2026-08-29 11:29:44 | 1048 | ||||||
|
RNAdb Resource Report Resource Website 10+ mentions |
RNAdb (RRID:SCR_003578) | RNAdb | data or information resource, database | A comprehensive mammalian noncoding RNA database containing sequences and annotations for tens of thousands of noncoding RNAs. These include a wide range of microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs. All raw data from the original RNAdb 2.0 database can be downloaded in XML or FASTA format. This website serves to archive the final snapshot of the RNAdb 2.0 datasets for legacy purposes. It will remain active indefinitely. | non-protein-coding rna, rna | has parent organization: University of Queensland; Brisbane; Australia | PMID:17145715 | nif-0000-03417 | SCR_003578 | RNAdb 2.0 - A database of mammalian noncoding RNAs | 2026-08-29 11:29:21 | 10 | |||||||
|
GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-08-29 11:22:58 | 6 | |||||
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UD Chick EST Project Resource Report Resource Website 10+ mentions |
UD Chick EST Project (RRID:SCR_002236) | biomaterial supply resource, cell repository, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created. | gene, avian, cdna, chicken, clone, cytokine, dna, homology, immunology, mammalian, molecular, nucleotide, poultry, receptor, sequence, splenocyte, t cell |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Delaware; Delaware; USA |
PMID:16554550 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20971 | SCR_002236 | U.D. Chick EST Database, University of Delaware Chick EST Project, University of Delaware Chick EST Database | 2026-08-29 11:28:39 | 18 | |||||||
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BioRep Resource Report Resource Website 100+ mentions |
BioRep (RRID:SCR_004907) | BioRep | biomaterial supply resource, cell repository, material resource | Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories. | chromosome analysis, dhplc analysis, methylation, genotyping, gender analysis, sequencing service, nucleic acid isolation, catalog, cell line, dna, cell, tissue, frozen, liquid nitrogen, vapor nitrogen, refrigerator, fixed, paraffin embedded, slide, cryogenic, paraffin block, cryopreserved, molecular biology, microbiology, cytogenetics, media preparation, tissue microarray, cell array, frozen array, cell biology, research, transplantation, custom, blood, tissue, ebv transformed lymphoblast culture, fibroblast cell culture, nucleic acid, sequence, mycoplasma, karyotype |
is listed by: One Mind Biospecimen Bank Listing is related to: Coriell Institute for Medical Research |
Public: offer biorepository services to public and private research institutes, To the highest standards of quality and safety. BioRep is one of the few ''''Global Biorepository'''' able to serve the pharmaceutical industries for world wide clinical trials. | nlx_87504 | http://www.biorep.it/eng/ | SCR_004907 | 2026-08-29 11:28:42 | 187 | |||||||
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UM Miller School of Medicine Division of Comparative Pathology Resource Report Resource Website |
UM Miller School of Medicine Division of Comparative Pathology (RRID:SCR_012492) | UM Miller School of Medicine Division of Comparative Pathology | access service resource, core facility, service resource | The Division of Comparative Pathology is a full service veterinary pathology laboratory with both clinical pathology and histology services. Routine hematology and serum biochemistry testing is available for multiple species; we work well with low volume samples. Specialized testing is available or can be implemented as needed. Routine histology services including processing, embedding, and sectioning are available with many routine and special staining options. |
is listed by: ScienceExchange has parent organization: University of Miami Miller School of Medicine; Florida; USA |
SciEx_262 | SCR_012492 | University of Miami Leonard M. Miller School of Medicine Division of Comparative Pathology, University of Miami Miller School of Medicine Division of Comparative Pathology | 2026-08-29 11:32:45 | 0 |
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