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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BioSample Database at EBI Resource Report Resource Website 10+ mentions |
BioSample Database at EBI (RRID:SCR_004856) | BioSD | data or information resource, database | Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI''''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples) | cell line, cell, nucleotide, sequencing, proteomics, peptide, protein, genomics, gene expression, biological sample, molecular, sequence, structure, cell line, topical portal, aggregator, gold standard, bio.tools |
uses: European Nucleotide Archive (ENA) uses: Proteomics Identifications (PRIDE) uses: ArrayExpress uses: ENCODE uses: Coriell Institute for Medical Research uses: 1000 Genomes: A Deep Catalog of Human Genetic Variation uses: International HapMap Project uses: International Mouse Strain Resource is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BioSample has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory; Heidelberg; Germany ; European Union FP7 HEALTH-F4-2010-241669; European Union FP7 HEALTH-F4-2007-201413 |
PMID:22096232 | The community can contribute to this resource, Acknowledgement requested | biotools:biosamples, r3d100012628, OMICS_01025, nlx_143930 | https://bio.tools/biosamples, https://doi.org/10.17616/R37R3P | SCR_004856 | BioSamples database, BioSamples, BioSamples Database at EBI, BioSample Database at the EBI, EBI BioSample Database, BioSample Database, BioSD at EBI, BioSD - BioSample Database | 2026-09-19 12:56:47 | 16 | ||||
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Sys-BodyFluid Resource Report Resource Website 1+ mentions |
Sys-BodyFluid (RRID:SCR_005335) | data or information resource, database | A database of bodily fluid proteome data. It contains information on proteins from humanplasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Our body fluid protein database, Sys-BodyFluid, contains 11 body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Over 10,000 proteins are included in the Sys-BodyFluid. These body fluid proteome data come from 50 peer-review publications of different laboratories all over the world. Protein annotation are provided including protein description, Gene ontology, Domain information, Protein sequence and involved pathway. User can access the proteome data by protein name, protein accession number, sequence similarity. In addition, user could perform query cross different body fluids to get more comprehensive understanding. The difference and similarity between these 11 body fluids are also analyzed. Thus , the Sys-BodyFluid database could serve as a reference database for body fluid research and disease proteomics. plasm, serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid, protein, proteomics | bronchoalveolar lavage fluid, cerebrospinal fluid, human milk, nipple aspirate fluid, plasm, protein, proteomics, saliva, seminal fluid, serum, synovial fluid, tear fluid, urine | has parent organization: Shandong University; Shandong; China | nif-0000-03526 | SCR_005335 | Sys-BodyFluid | 2026-09-19 12:56:50 | 3 | |||||||||
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PolySearch Resource Report Resource Website 10+ mentions |
PolySearch (RRID:SCR_005291) | PolySearch | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is Given X, find all Y''s where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences. | text mining, disease, gene, protein, drug, metabolite, snp, gene sequence, pathway, tissue, gene family, subcellular localization, organ |
is listed by: OMICtools has parent organization: University of Alberta; Alberta; Canada |
OMICS_01194 | SCR_005291 | 2026-09-19 12:56:50 | 20 | |||||||||
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Structure Superposition Database Resource Report Resource Website 1+ mentions |
Structure Superposition Database (RRID:SCR_005236) | data or information resource, database | The SSD has been developed to address the need for resources and tools for understanding large sets of superpositions in order to understand evolutionary relationships and to make predictions of function. We have therefore created the Structure Superposition Database (SSD) for accessing, viewing and understanding large sets of structure superposition data. It contains the results of pairwise, all-by-all superpositions of a representative set of 115 (beta/alpha) barrel structures (TIM barrels). The initial implementation of the SSD contains the results of pairwise, all-by-all superpositions of a representative set of 115 (/alpha)8 barrel structures (TIM barrels). Future plans call for extending the database to include representative structure superpositions for many additional folds. The SSD can be browsed with a user interface module developed as an extension to Chimera, an extensible molecular modeling program. Features of the user interface module facilitate viewing multiple superpositions together. | alpha barrel structure, barrel structure, beta barrel structure, protein, quaternary structure, structure superposition | nif-0000-03504 | SCR_005236 | SSD | 2026-09-19 12:56:50 | 2 | ||||||||||
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TranspoGene Resource Report Resource Website 1+ mentions |
TranspoGene (RRID:SCR_005634) | data or information resource, database | A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. | element, eukaryotic, evolutionary, exon, exonization, family, fruit fly, gene, genome, alternative, chicken, coding, disease, divergence, genomic, hosting, human, human genome databases, intron, location, map, maps, mouse, mrna, nematode, organism, pattern, promoter, protein, sea squirt, sequence, splicing, transcript, transcriptome, transposed, viewers, worm, zebrafish | has parent organization: Tel Aviv University; Ramat Aviv; Israel | nif-0000-03579 | SCR_005634 | TranspoGene | 2026-09-19 12:56:53 | 9 | |||||||||
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Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | data or information resource, database | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-09-19 12:57:30 | 2 | ||||||
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RARTF Resource Report Resource Website 1+ mentions |
RARTF (RRID:SCR_013457) | RARTF | data or information resource, database | Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. | transcription factor, protein, gene, microarray, expression profile |
is listed by: OMICtools is related to: InterProScan |
PMID:16769687 | Free | OMICS_00562 | SCR_013457 | RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database | 2026-09-19 12:57:31 | 2 | ||||||
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Embassy-domsearch Resource Report Resource Website |
Embassy-domsearch (RRID:SCR_016086) | software resource, software toolkit, source code | Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. | dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology |
is used by: RAVEN is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/embassy-domsearch/ | SCR_016086 | 2026-09-19 12:57:35 | 0 | |||||||||
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Mass Spectral Library Resource Report Resource Website 10+ mentions |
Mass Spectral Library (RRID:SCR_014668) | data or information resource, database | A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals. | library, database, spectra, mass spectrometry, metabolomics, metabolites, protein, lipid, contaminant | is listed by: Metabolomics Workbench | Available with the NIST MS Search Program for Windows | SCR_014668 | 2026-09-19 12:57:34 | 21 | ||||||||||
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Viral Integrated Structural Evolution Dynamic Database Resource Report Resource Website 1+ mentions |
Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) | VIStEDD | data or information resource, database | Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein. | Virus, SARS-CoV-2, COVID-19, proteins coded by virus, viral evolution, protein, data, amino acid, protein modeling, molecular dynamic simulation, evolutionary analysis, protein-protein interaction, protein- protein interaction mapping, protein data folder system, rotating protein video, protein function, molecular dynamic simulation | has parent organization: Michigan State University; Michigan; USA | COVID-19 | NIEHS K01 ES025435; NIGMS R01 GM108618 |
PMID:32511397 | Free, Freely available | SCR_018793 | Viral Integrated Structural Evolution Dynamic Database, SARS-CoV-2 dynamicome database | 2026-09-19 12:57:37 | 3 | |||||
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EPSD Eukaryotic Phosphorylation Site Database Resource Report Resource Website 1+ mentions |
EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) | EPSD | data or information resource, database | Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies. | protein, phosphorylation, site, eukaryotes, phosphoproteomic, data | has parent organization: Huazhong University of Science and Technology; Wuhan; China | Special Project on Precision Medicine under the National Key R&D Program 2017YFC0906600; the Fundamental Research Funds for the Central Universities 2017KFXKJC001; the Natural Science Foundation of China 31671360 |
Free, Freely available | SCR_016514 | Eukaryotic Phosphorylation Site Database, EPSD | 2026-09-19 12:57:36 | 1 | |||||||
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SRMAtlas Resource Report Resource Website 1+ mentions |
SRMAtlas (RRID:SCR_016996) | SRM Atlas, SRMatlas | atlas, data or information resource, database | Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome. | collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptide | American Recovery and Reinvestment Act ; European Research Council ; Luxembourg Centre for Systems Biomedicine University Luxembourg ; NCRR S10 RR027584; NHGRI RC2 HG005805; NIGMS P50 GM076547; NIGMS R01 GM087221; Swiss National Science Foundation |
PMID:27453469 | Publicly available, Registration required | SCR_016996 | 2026-09-19 12:57:36 | 3 | ||||||||
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ALZPEDIA Resource Report Resource Website 1+ mentions |
ALZPEDIA (RRID:SCR_017548) | AlzPedia | data or information resource, database | Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge. | Summary, gene, protein, pathophysiology, Alzheimer, neurodegenerative, disorder | is related to: Alzheimer's Research Forum | Free, Freely available | SCR_017548 | 2026-09-19 12:57:37 | 3 | |||||||||
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LINCS Data Portal Resource Report Resource Website 10+ mentions |
LINCS Data Portal (RRID:SCR_014939) | data or information resource, portal | Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies. | portal, assay, lincs, kinome, dataset, small molecule, cell, gene, protein, peptide, and antibodies. |
is related to: LINCS Data Portal 2.0 has parent organization: University of Miami; Florida; USA is parent organization of: CycIF.org |
NIH Common Fund ; NHLBI 1U01HL111561; NHLBI 3U01HL111561-01S1; NHLBI 3U01HL111561-02S1; NHGRI U54HG006097; NHGRI U54 HG006093 |
Freely available | SCR_014939 | 2026-09-19 12:56:04 | 14 | |||||||||
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software application, software resource, standalone software | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-09-19 12:56:08 | 1572 | |||||||
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PsychENCODE Knowledge Portal Resource Report Resource Website 10+ mentions |
PsychENCODE Knowledge Portal (RRID:SCR_017500) | data or information resource, database, portal, project portal | Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain. | Rare, genetic, variant, psychiatric, disorder, regulatory, element, epigenetic, modification, RNA, protein, brain | Restricted | SCR_017500 | 2026-09-19 12:56:07 | 15 | |||||||||||
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BUSM Mass Spectrometry Resource Resource Report Resource Website |
BUSM Mass Spectrometry Resource (RRID:SCR_000823) | Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that conducts high-sensitivity structural determinations and analyses of biological compounds via mass spectrometry. The emphasis is on glycoconjugates, oligosaccharides and proteins. | systems biology technology center, mass spectrometry, glycoconjugate, oligosaccharide, protein | has parent organization: Boston University School of Medicine; Massachusetts; USA | NCRR P41RR010888 | nlx_152679 | SCR_000823 | Mass Spectrometry Resource for Biology and Medicine, Boston University School of Medicine Mass Spectrometry Resource, Boston University Mass Spectrometry Resource for Biology and Medicine | 2026-09-19 12:58:31 | 0 | |||||||
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National Magnetic Resonance Facility at Madison Resource Report Resource Website 1+ mentions |
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) | NMRFAM | access service resource, service resource, training resource | Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols. | nmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology center | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIGMS P41136463; NIGMS R24GM141526 |
Free, Freely Available | nlx_152672 | SCR_001449 | 2026-09-19 12:58:32 | 4 | |||||||
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National Biomedical Center for Advanced ESR Technology Resource Report Resource Website 1+ mentions |
National Biomedical Center for Advanced ESR Technology (RRID:SCR_001444) | ACERT | biomedical technology research center, training resource | Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories. | electron spin resonance, spectrometer, electron spin resonance spectrometer, structure, dynamics, protein, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS P41GM103521; NCRR P41RR016292 |
Free, Freely Available | nlx_152669 | SCR_001444 | ACERT National ESR Center, National Biomedical Center for Advanced Electron Spin Resonance Technology | 2026-09-19 12:58:32 | 1 | ||||||
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PROW Resource Report Resource Website 1+ mentions |
PROW (RRID:SCR_002434) | PROW | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It offers short, structured reviews of proteins and protein families, especially leukocyte surface membrane molecules. Index of information available from PROW includes CD molecule, Alternate names, Current Guides, Past Guides, Entrez Gene and Assigning workshop. Current guides: expanded format including Summary Sentence and Abstract Past guides: older guides with excellent information, some data may be dated | leukocyte, membrane, molecule, protein, protein property, surface | has parent organization: National Cancer Institute | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21340 | SCR_002434 | Protein Reviews On the Web, PROW - Protein Reviews on the Web, Protein Reviews on the Web | 2026-09-19 12:58:34 | 8 |
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