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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | data analysis service, analysis service resource, software resource, production service resource, service resource, database, data or information resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-08-04 09:41:25 | 3358 | |||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-08-04 09:41:27 | 8 | |||||||
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MolGen Resource Report Resource Website 10+ mentions |
MolGen (RRID:SCR_005700) | MolGen | topical portal, portal, data or information resource | The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches. | molecular biology, gram-positive bacteria, pathogen, transcript, protein, profile, high-throughput, dna microarray, proteomics, dna, microarray, functional genomics, bioinformatics, genetics, gene |
has parent organization: University of Groningen; Groningen; Netherlands is parent organization of: FIVA - Functional Information Viewer and Analyzer |
nlx_149166 | http://molgen.biol.rug.nl/molgen/index.php | SCR_005700 | Molecular Genetics | 2026-08-04 09:41:25 | 27 | |||||||
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Pandora - Protein ANnotation Diagram ORiented Analysis Resource Report Resource Website 1+ mentions |
Pandora - Protein ANnotation Diagram ORiented Analysis (RRID:SCR_005686) | Pandora | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA supports GO annotations as well as additional keywords (from UniProt Knowledgebase, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group. Platform: Online tool | protein, annotation, mass spectrometry, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
Israeli Ministry of Defense ; Hebrew University of Jerusalem; Jerusalem; Israel |
PMID:14500825 | Free for academic use | nlx_149131 | SCR_005686 | Protein ANnotation Diagram ORiented Analysis | 2026-08-04 09:41:24 | 2 | |||||
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GOfetcher Resource Report Resource Website |
GOfetcher (RRID:SCR_005681) | GOfetcher | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: Quick Search, Advanced Search, and Upload Files for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. Platform: Online tool | gene, nucleotide, protein, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Southern Mississippi; Mississippi; USA |
NSF EPS-0556308; U.S. Army ; Environmental Quality Program contract #W912HZ-05-P-0145 |
PMID:18728045 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149124 | http://mcbc.usm.edu/gofetcher/ | SCR_005681 | GOfetcher: a database with complex searching facility for gene ontology | 2026-08-04 09:41:24 | 0 | ||||
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ccPDB - Compilation and Creation of datasets from PDB Resource Report Resource Website 1+ mentions |
ccPDB - Compilation and Creation of datasets from PDB (RRID:SCR_005870) | ccPDB | web service, software resource, data access protocol, database, data or information resource | ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links. * Compilation of Datasets: Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. We are in process of collecting PDB datasetsfrom literature and maintaining at ccPDB. We are also requesting community to suggest datasets. In addition, we generate datasets from PDB, these datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution. * Creation of datasets: This module developed for creating customized datasets where user can create a dataset using his/her conditions from PDB. This module will be useful for those users who wish to create a new dataset as per ones requirement. This module have six steps, which are described in help page. * Web Services: We integrated following web services in ccPDB; i) Analyze of PDB ID service allows user to submit their PDB on around 40 servers from single point, ii) BLAST search allows user to perform BLAST search of their protein against PDB, iii) Structural information service is designed for annotating a protein structure from PDB ID, iv) Search in PDB facilitate user in searching structures in PDB, v)Generate patterns service facility to generate different types of patterns required for machine learning techniques and vi) Download useful information allows user to download various types of information for a given set of proteins (PDB IDs). * Important Links: One of major objectives of this web site is to provide links to web servers related to functional annotation of proteins. In first phase we have collected and compiled these links in different categories. In future attempt will be made to collect as many links as possible. | secondary structure, nucleic acid interaction, ligand interaction, structure, nucleic acid, interaction, ligand, data set, function, protein, annotate, tight-turn, nucleotide interacting residue, metals interacting residue, dna/rna binding residue, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Institute of Microbial Technology; Chandigarh; India |
OSDD ; DBT ; Council of Scientific and Industrial Research; New Delhi; India |
PMID:22139939 | biotools:ccpdb, nlx_149416 | https://bio.tools/ccpdb | SCR_005870 | Compilation and Creation of datasets from PDB, ccPDB - Compilation Creation of datasets from PDB | 2026-08-04 09:41:28 | 2 | |||||
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Labome Resource Report Resource Website 1+ mentions |
Labome (RRID:SCR_007384) | material resource, reagent supplier | Database of hundreds of thousands of products submitted by reagent provider partners, and millions of webpages selected from reagent suppliers. All are organized according to genes, species, and reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones, biochemicals, and others). | antibody, reagent, protein, peptide, elisa, cdna clone, microrna, biochemical, database | is used by: NIF Data Federation | nif-0000-00384 | SCR_007384 | Labome.com, ExactAntigen / Labome, ExactAntigen, ExactAntigen.com | 2026-08-04 09:41:50 | 2 | |||||||||
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A statistical framework for genomic data fusion Resource Report Resource Website 100+ mentions |
A statistical framework for genomic data fusion (RRID:SCR_007219) | data set, software resource, source code, data or information resource | A statistical framework for genomic data fusion is a computational framework for integrating and drawing inferences from a collection of genome-wide measurements. Each dataset is represented via a kernel function, which defines generalized similarity relationships between pairs of entities, such as genes or proteins. The kernel representation is both flexible and efficient, and can be applied to many different types of data. Furthermore, kernel functions derived from different types of data can be combined in a straightforward fashion. Recent advances in the theory of kernel methods have provided efficient algorithms to perform such combinations in a way that minimizes a statistical loss function. These methods exploit semidefinite programming techniques to reduce the problem of finding optimizing kernel combinations to a convex optimization problem. Computational experiments performed using yeast genome-wide datasets, including amino acid sequences, hydropathy profiles, gene expression data and known protein-protein interactions, demonstrate the utility of this approach. A statistical learning algorithm trained from all of these data to recognize particular classes of proteins--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data. Matlab code to center a kernel matrix and Matlab code for normalization are available. | kernel matrix, random, gene expression, blast, smith-waterman, pfam hmm, hydrophobicity fft, linear interaction, diffusion kernel, protein, membrane, ribosomal | has parent organization: University of Washington; Seattle; USA | PMID:15130933 | nlx_149420 | SCR_007219 | 2026-08-04 09:41:48 | 155 | |||||||||
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COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | data processing software, software application, software resource | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-08-04 09:42:09 | 164 | ||||||
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NCBI Resource List Resource Report Resource Website |
NCBI Resource List (RRID:SCR_005628) | NCBI Resources | portal, organization portal, data or information resource | The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation. | database, download, submission, tool, chemical, bioassay, data, software, dna, rna, domain, structure, gene, expression, genetics, medicine, genomes, map, homology, literature, protein, sequence analysis, taxonomy, training, tutorial, variation, gold standard | has parent organization: NCBI | NLM | nlx_146242 | SCR_005628 | NCBI Resource Guide, NCBI Resource List (A-Z) | 2026-08-04 09:41:24 | 0 | |||||||
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B Cell Interactome Resource Report Resource Website 1+ mentions |
B Cell Interactome (RRID:SCR_008655) | BCI | database, data or information resource, model | A network of protein-protein, protein-DNA and modulatory interactions in human B cells. The network contains known interactions (reported in public databases) and predicted interactions by a Bayesian evidence integration framework which integrates a variety of generic and context specific experimental clues about protein-protein and protein-DNA interactions with inferences from different reverse engineering algorithms, such as GeneWays and ARACNE. Modulatory interactions are predicted by the MINDY, an algorithm for the prediction of modulators of transcriptional interactions (please refer to the publication section for more information). The BCI can be downloaded as one tab delimited file containing the complete network (BCI.txt) with each type of interaction explicitly defined. | expression, generic, bayesian, b cell, dna, human, interaction, interactome, modulatory, protein, transcriptional |
is related to: ARACNE has parent organization: Columbia University; New York; USA |
PMID:18277385 | Available for download | nif-0000-33034 | SCR_008655 | 2026-08-04 09:42:11 | 1 | |||||||
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LINCS Data Portal Resource Report Resource Website 10+ mentions |
LINCS Data Portal (RRID:SCR_014939) | portal, data or information resource | 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 | 2026-08-04 09:43:34 | 13 | |||||||||
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software application, standalone software, software resource | 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 | 2026-08-04 09:44:15 | 1309 | |||||||
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PsychENCODE Knowledge Portal Resource Report Resource Website 10+ mentions |
PsychENCODE Knowledge Portal (RRID:SCR_017500) | database, portal, project portal, data or information resource | 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 | 2026-08-04 09:44:09 | 12 | |||||||||||
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Salk Institute Peptide Synthesis Core Facility Resource Report Resource Website |
Salk Institute Peptide Synthesis Core Facility (RRID:SCR_014848) | access service resource, core facility, service resource | Core facility that provides services such as peptide synthesis, incorporation of non-conventional and/or modified amino acids, HPCL characterization and purification, and Mass spec analysis. | core facility, la jolla, peptide synthesis, protein, amino acid, hpcl, mass spec | Salk Institute Peptide Synthesis Core Facility ; NCI CCSG P30 014195 |
Commercially available | SCR_014848 | 2026-08-04 09:43:32 | 0 | ||||||||||
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Rhode Island INBRE Molecular Informatics Core Facility Resource Report Resource Website 10+ mentions |
Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) | access service resource, core facility, service resource | Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research. | Analysis, interpretation, nucleotide, amino acid, sequence, protein, domain, structure, service, 3D visualization, modeling, USEDit |
has parent organization: University of Rhode Island; Rhode Island; USA has parent organization: USEDit |
NIGMS P20 GM103430 | Open | ABRF_3 | SCR_017685 | Rhode Island INBRE Molecular Informatics, RI-INBRE Bioinformatics Core; RI Genomics and Sequencing Center | 2026-08-04 09:44:15 | 12 | |||||||
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Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility Resource Report Resource Website |
Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility (RRID:SCR_017695) | REPR | access service resource, core facility, service resource | Resource offers range of mass spectrometry instrumentation, expertise in analysis of RNA, RNA modifications, and proteins involved in RNA metabolism/regulation, supports projects involving analysis of biomolecules, metabolites, and small synthetic molecules, provides consulting on experimental design, sample preparation and data interpretation, whole project development and grant writing contributions. | Mass, spectrometry, instrument, analysis, RNA, protein, biomolecule, data, grant, project, service, core | Open | ABRF_113, SCR_017715 | SCR_017695 | RNA Epitranscriptomics and Proteomics Resources | 2026-08-04 09:44:11 | 0 | ||||||||
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University of Nevada at Reno Nevada Proteomics Center Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada at Reno Nevada Proteomics Center Core Facility (RRID:SCR_017761) | access service resource, core facility, service resource | Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling. | Mass, spectral, proteomic, analysis, qualitative, quantitative, protein, plasma, serum, tissue, cell, line, physiological, pathway, interaction, signaling, stury, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20 GM103440 | Open | SCR_011043, SciEx_9701, ABRF_281 | https://coremarketplace.org/?FacilityID=281&citation=1 | SCR_017761 | Mick Hitchcock, Ph.D. Nevada Proteomics Center | 2026-08-04 09:44:13 | 6 | ||||||
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Virginia Commonwealth University Chemical and Proteomic Mass Spectrometry Core Facility Resource Report Resource Website |
Virginia Commonwealth University Chemical and Proteomic Mass Spectrometry Core Facility (RRID:SCR_017806) | CPMSC | access service resource, core facility, service resource | Core provides mass spectrometric services, from basic mass measurement to complex proteome analyses.Services include basic mass measurement, ESI-MS/MS,LC-MS,Exact mass measurement,Protein identification. | Mass, spectrometry, measurement, proteome, analysis, protein, identification, service, core | Open | ABRF_515 | SCR_017806 | Chemical and Proteomic Mass Spectrometry Core Facility | 2026-08-04 09:44:12 | 0 | ||||||||
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Texas University Health Science Center at San Antonio Biomolecular NMR Core Facility Resource Report Resource Website |
Texas University Health Science Center at San Antonio Biomolecular NMR Core Facility (RRID:SCR_017775) | access service resource, core facility, service resource | Core offers high field NMR instrumentation for structural studies of biological macromolecules. Instrumentation includes four-channel Bruker Avance 500, 600, and 700 MHz NMR spectrometers, ultra high sensitivity 5mm 1H-13C-15N triple-resonance cold probe for 600 MHz spectrometers. Service include acquisition and analysis of required spectra for elucidation of small molecule structures (includes synthetic molecules, natural products, cofactors, lipids, and short peptides (30 amino acids or less)). Types of projects conducted collaboratively include determination of three-dimensional structures of biological macromolecules, including proteins and nucleic acids, both alone and as complexes with various ligands. | Biomolecular, NMR, structural, study, macromolecule, spectrometry, acquisition, analysis, spectra, small, molecule, structure, lipid, peptide, cofactor, protein, nucleic acid, ligand, service, core | NIH National Center for Research Resources ; Houston Endowment ; UT Health San Antonio Children Cancer Research Center ; U. Texas Permanant University Fund ; UT Health San Antonio MD Anderson Cancer Center ; UT Health San Antonio Core Facilities Committee ; User Fees |
ABRF_353 | SCR_017775 | Biomolecular NMR Core | 2026-08-04 09:44:16 | 0 |
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