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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | data or information resource, data repository, database, service resource, storage service resource | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-09-12 12:55:33 | 8 | ||||
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Candida Genome Database Resource Report Resource Website 500+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | data or information resource, data repository, database, service resource, storage service resource | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | biotools:cgd, nif-0000-02634, r3d100010617 | https://bio.tools/cgd | SCR_002036 | 2026-09-12 12:55:36 | 506 | |||||
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InteroPorc Resource Report Resource Website 1+ mentions |
InteroPorc (RRID:SCR_002067) | InteroPorc | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code | Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8. | orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Integr8 : Access to complete genomes and proteomes is related to: IntAct is related to: MINT is related to: Database of Interacting Proteins (DIP) is related to: PSICQUIC Registry has parent organization: CEA; Gif sur Yvette; France |
European Union FELICS 021902 RII3; Marie Curie Fellowship ; French National Agency of Research ANR Biosys06_134823 SULFIRHOM; French Atomic Energy Commission |
PMID:18508856 | Open unspecified license, Acknowledgement requested | nif-0000-20816, biotools:interoporc | https://bio.tools/interoporc | SCR_002067 | InteroPorc: Automatic molecular interaction predictions, Automatic molecular interaction predictions | 2026-09-12 12:55:36 | 6 | ||||
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Protein Structure Initiative Resource Report Resource Website |
Protein Structure Initiative (RRID:SCR_002161) | data or information resource, portal, topical portal | The Structural Genomics Project aims at determination of the 3D structure of all proteins. It also aims to reduce the cost and time required to determine three-dimensional protein structures. It supports selection, registration, and tracking of protein families and representative targets. This aim can be achieved in four steps : -Organize known protein sequences into families. -Select family representatives as targets. -Solve the 3D structure of targets by X-ray crystallography or NMR spectroscopy. -Build models for other proteins by homology to solved 3D structures. PSI has established a high-throughput structure determination pipeline focused on eukaryotic proteins. NMR spectroscopy is an integral part of this pipeline, both as a method for structure determinations and as a means for screening proteins for stable structure. Because computational approaches have estimated that many eukaryotic proteins are highly disordered, about 1 year into the project, CESG began to use an algorithm. The project has been organized into two separate phases. The first phase was dedicated to demonstrating the feasibility of high-throughput structure determination, solving unique protein structures, and preparing for a subsequent production phase. The second phase, PSI-2, has focused on implementing the high-throughput structure determination methods developed in PSI-1, as well as homology modeling and addressing bottlenecks like modeling membrane proteins. The first phase of the Protein Structure Initiative (PSI-1) saw the establishment of nine pilot centers focusing on structural genomics studies of a range of organisms, including Arabidopsis thaliana, Caenorhabditis elegans and Mycobacterium tuberculosis. During this five-year period over 1,100 protein structures were determined, over 700 of which were classified as unique due to their < 30% sequence similarity with other known protein structures. The primary goal of PSI-1 was to develop methods to streamline the structure determination process, resulted in an array of technical advances. Several methods developed during PSI-1 enhanced expression of recombinant proteins in systems like Escherichia coli, Pichia pastoris and insect cell lines. New streamlined approaches to cell cloning, expression and protein purification were also introduced, in which robotics and software platforms were integrated into the protein production pipeline to minimize required manpower, increase speed, and lower costs. The goal of the second phase of the Protein Structure Initiative (PSI-2) is to use methods introduced in PSI-1 to determine a large number of proteins and continue development in streamlining the structural genomics pipeline. Currently, the third phase of the PSI is being developed and will be called PSI: Biology. The consortia will propose work on substantial biological problems that can benefit from the determination of many protein structures Sponsors: PSI is funded by the U.S. National Institute of General Medical Sciences (NIGMS), | elegans, escherichia, eukaryotic, expression, arabidopsis, biology, bottleneck, caenorhabditis, cell, clone, coli, crystallography, genomic, homology, insect, membrane, myobacterium, nmr, organism, pastoris, pichia, protein, purification, sequence, spectroscopy, structural, structure, thaliana, tuberculosis, x-ray | nif-0000-20950 | SCR_002161 | PSI | 2026-09-12 12:55:37 | 0 | ||||||||||
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PROVEAN Resource Report Resource Website 1000+ mentions |
PROVEAN (RRID:SCR_002182) | PROVEAN | analysis service resource, data analysis service, production service resource, service resource, software resource | A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. | amino acid substitution, indel, function, protein, amino acid, substitution, protein variant, genome variant, next-generation sequencing, insertion, deletion |
is listed by: OMICtools has parent organization: J. Craig Venter Institute |
NIH ; NHGRI 5R01HG004701-04 |
PMID:23056405 | Free, Available for download, Freely available | OMICS_01849 | SCR_002182 | Protein Variation Effect Analyzer | 2026-09-12 12:55:37 | 2380 | |||||
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Autosomal Recessive Polycystic Kidney Disease Mutation Database Resource Report Resource Website 10+ mentions |
Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) | data or information resource, data repository, database, service resource, storage service resource | Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges. | clinical, gene, genetic, mutation, protein, recessive, renal | has parent organization: RWTH Aachen University; Aachen; Germany | Autosomal recessive polycystic kidney disease, Polycystic kidney disease | PMID:16199545 PMID:11919560 |
Permission required, Terms of use | nif-0000-21038 | http://www.humgen.rwth-aachen.de/index.asp?subform=database.html&nav=database_nav.html | SCR_002290 | Mutation Database Autosomal Recessive Polycystic Kidney Disease (ARPKD/PKHD1) | 2026-09-12 12:55:39 | 14 | |||||
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Community Structure-Activity Resource Resource Report Resource Website 10+ mentions |
Community Structure-Activity Resource (RRID:SCR_002206) | CSAR | data or information resource, data repository, data set, service resource, storage service resource | Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data. | crystal structure, binding affinity, protein-ligand complex, protein, small molecule, ligand, compound |
is used by: NIF Data Federation is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Michigan; Ann Arbor; USA |
NIGMS | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154720 | SCR_002206 | 2026-09-12 12:55:38 | 16 | |||||||
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ConSurf Database Resource Report Resource Website 100+ mentions |
ConSurf Database (RRID:SCR_002320) | ConSurfDB | data or information resource, database, service resource | Provides pre-calculated evolutionary conservation profiles for proteins of known structure in the PDB. Enables flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation of conservation profiles. | PDB, Protein DataBase, evolution, conservation, protein, structure, pre-calculated, profile, FASEB list |
is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Tel Aviv University; Ramat Aviv; Israel | PMID:20478830 PMID:15980475 PMID:12499312 PMID:11243830 |
Free, Freely available | nif-0000-21098, SCR_007609, BioTools:consurf-db, nif-0000-02685 | http://bental.tau.ac.il/new_ConSurfDB/, https://bio.tools/consurf-db | http://consurf-hssp.tau.ac.il | SCR_002320 | , consurf-db, ConSurf-DataBase, ConSurf-DB, ConSurfDB, ConSurf Server Database, ConSurfDataBase, ConSurf- Data Base | 2026-09-12 12:55:39 | 318 | |||
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glycosciences.de Resource Report Resource Website 10+ mentions |
glycosciences.de (RRID:SCR_002324) | GLYCOSCIENCES.de | data or information resource, database, portal, topical portal | Portal of glycoinformatics resources including databases and bioinformatics tools for glycobiology and glycomics research. Databases include a bibliography, structure, nuclear magnetic resonance (NMR), mass spectroscopy (ms) and a PDB search. | glycoinformatics, glycobiology, glycomics, carbohydrate, 3d structure, data analysis service, modeling, structure, nuclear magnetic resonance, mass spectroscopy, protein, glycan |
lists: LiGraph lists: pdb-data lists: PDB2MultiGif is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Giessen; Hesse; Germany is parent organization of: GlyProt is parent organization of: Distance Mapping is parent organization of: pdb-care is parent organization of: pdb2linucs is parent organization of: GlyVicinity is parent organization of: GlyTorsion is parent organization of: GlySeq is parent organization of: LINUCS is parent organization of: sumo is parent organization of: GlycoFragment is parent organization of: Glyco-CD is parent organization of: GlycoMapsDB is parent organization of: SWEET-DB is parent organization of: CARP |
DFG | PMID:16239495 | Free, Public | nif-0000-21103 | SCR_002324 | Glycosciences | 2026-09-12 12:55:39 | 25 | |||||
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PlantLoc Resource Report Resource Website 1+ mentions |
PlantLoc (RRID:SCR_003138) | PlantLoc | analysis service resource, data analysis service, production service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif. | subcellular localization, protein |
is listed by: OMICtools has parent organization: Tongji University; Shanghai; China |
PMID:23729470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01632 | SCR_003138 | PlantLoc: Plant Proteins Subcellular Localization Prediction Server | 2026-09-12 12:55:52 | 4 | ||||||
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MetaLocGramN Resource Report Resource Website 1+ mentions |
MetaLocGramN (RRID:SCR_003154) | MetaLocGramN | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice. | subcellular localization, protein, prediction, sequence, analysis, gram-negative protein, gram-negative, gram-negative bacteria |
is listed by: OMICtools is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: International Institute of Molecular and Cell Biology; Warsaw; Poland |
PMID:22705560 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01626 | SCR_003154 | 2026-09-12 12:55:52 | 3 | |||||||
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HUPO Proteomics Standards Initiative Resource Report Resource Website 10+ mentions |
HUPO Proteomics Standards Initiative (RRID:SCR_003158) | HUPO PSI | controlled vocabulary, data or information resource, knowledge environment, meeting resource, narrative resource, ontology, standard specification, training resource | Initiative to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The main organizational unit is the work group, with a Gel Electrophoresis (GEL) work group, a Mass Spectrometry (MS) work group, a Molecular Interactions (MI) work group, a Protein Modifications (MOD) work group, a Proteomics Informatics (PI) work group, and a Sample Processing (SP) work group. The Gel Electrophoresis (GEL) work group aims to develop reporting requirements that supplement the Minimum Information About a Proteomics Experiment (MIAPE) parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images. The Mass Spectrometry Standards Working Group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the field of proteomics mass spectrometry. A past achievement is the mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released but is now deprecated in favor of mzML. The Molecular Interactions workgroup is concentrating on improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases; and improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms. The Proteomics Informatics Standards Group (PSI-PI) goals are to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products. The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be "classical" one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, "tagging" proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics. * Minimum reporting requirements: The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME). * XML formats for data exchange: Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a "parent" FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals. * Controlled vocabularies (CVs) and ontology: Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO). | proteomics, work group, gel electrophoresis, mass spectrometry, molecular interaction, protein modification, proteomics informatics, sample processing, controlled vocabulary, miape, transcriptome, metabolome, proteome, metadata, mass spectrometry informatics, community standards, annotation system, protein-protein interaction, protein, data format, annotation, minimal reporting requirement, nomenclature, reporting guideline, data exchange format, ontology development, rdf development, FASEB list |
is listed by: OMICtools is related to: Proteomics Identifications (PRIDE) has parent organization: HUPO - Human Proteome Organisation is parent organization of: Mass Spectrometry Ontology is parent organization of: mzML is parent organization of: PSICQUIC Registry is parent organization of: Protein-Protein Interaction Ontology is parent organization of: Sample Processing and Separation Techniques Ontology |
Free, Freely available | nif-0000-00568, OMICS_01781 | SCR_003158 | The HUPO Proteomics Standards Initiative | 2026-09-12 12:55:52 | 46 | |||||||
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Rockland Immunochemicals Resource Report Resource Website 50+ mentions |
Rockland Immunochemicals (RRID:SCR_003278) | Rockland | commercial organization | A global biotechnology company manufacturing research tools, antibodies, and cGMP grade protein. | cancer, cardiovascular, cell biology, chromatin, nuclear signaling, developmental biology, epigenetics, immunology, protein, peptide, blood, blood product, cell lysate, stem cell, assay | Free, Freely available | nlx_152452, nif-0000-31467 | SCR_003278 | Rockland Immunochemicals Inc., Rockland antibodies & assays, Rockland antibodies and assays | 2026-09-12 12:55:55 | 54 | ||||||||
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ORFprimer Resource Report Resource Website 1+ mentions |
ORFprimer (RRID:SCR_003269) | ORFprimer | software resource | An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. | java, java swing, open reading frame, protein, high throughput sequencing, primer, primer design, pcr, pcr primer design |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02331 | SCR_003269 | ORFprimer - primer design for ORFs | 2026-09-12 12:55:54 | 1 | |||||||
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NESbase Resource Report Resource Website 1+ mentions |
NESbase (RRID:SCR_003268) | NESbase | data or information resource, data repository, database, service resource, storage service resource | Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature. Each NESbase entry contains information of whether NES was shown to be necessary and/or sufficient for export, and whether the export was shown to be mediated by the export receptor CRM1. The compiled information was used to make a sequence logo of the Leucine-rich NESs, displaying the conservation of amino acids within a window of 25 residues. Error reports and submissions of new data are most welcome! | nuclear export signal, protein, leucine | has parent organization: DTU Center for Biological Sequence Analysis | Danish National Research Foundation ; John and Birthe Meyer Foundation |
PMID:12520031 | Free, Available for download, Freely available | nif-0000-03188 | https://services.healthtech.dtu.dk/datasets/NESbase-1.0/ | SCR_003268 | 2026-09-12 12:55:54 | 7 | |||||
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BrainTrap: Fly Brain Protein Trap Database Resource Report Resource Website 1+ mentions |
BrainTrap: Fly Brain Protein Trap Database (RRID:SCR_003398) | BrainTrap | d spatial image, data or information resource, database | This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download. | brain, exon, expression, 3d confocal, affinity, antibody, dataset, immunohistochemical, microscopy, image, protein, protein-trap, gene | has parent organization: University of Edinburgh; Scotland; United Kingdom | EPSRC ; British society for Developmental Biology ; Society for Experimental Biology ; Virtual Fly Brain e-Science Institute Theme ; BBSRC ; MRC |
PMID:20624714 | Free, Freely available | nif-0000-32989 | http://fruitfly.inf.ed.ac.uk/braintrap/ | SCR_003398 | Fly Brain Protein Trap Database, Brain Trap | 2026-09-12 12:55:57 | 1 | ||||
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Glioma Molecular Dignostic Initiatives Resource Report Resource Website 10+ mentions |
Glioma Molecular Dignostic Initiatives (RRID:SCR_003329) | GMDI | controlled vocabulary, data or information resource, data repository, narrative resource, service resource, standard specification, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. An initiative to develop a molecular classification schema that is both clinically and biologically meaningful, based on gene expression and genomic data from tumors (Gliomas) of patients who will be prospectively followed through natural history and treatment phase of their illness. The study will also explore gene expression profiles to determine the responsiveness of the patients and correlate with discrete chromosomal abnormalities. The initiative was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. The sample collection is accompanied by careful and prospective clinical data acquisition, allowing a variety of matched molecular and clinical data permitting a wide variety of analyses. GMDI has accrued fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and fresh frozen tumors in the prospective phase (from a variety of institutions). In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory. | molecular neuroanatomy resource, molecular data, clinical data, genomic analyses, genomics, gene, expression array, snp array, gene expression, microarray, glioma initiating cell, glioma stem cell, protein, glioma, molecular, diagnostic, dna, rna, tumor, tissue, blood, plasma, data repository |
is listed by: One Mind Biospecimen Bank Listing is related to: Repository of molecular brain neoplasia data has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31950 | http://search.engrant.com/project/NxvG9G/the_glioma_molecular_diagnostic_initiative_characterizing_brain_tumor_data | SCR_003329 | Glioma Molecular Diagnostic Initiative: Characterizing Brain Tumor Data | 2026-09-12 12:55:56 | 20 | ||||
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Nuclear Receptor Resource Resource Report Resource Website 1+ mentions |
Nuclear Receptor Resource (RRID:SCR_003285) | NRR | data or information resource, database, resource | Collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily. NRR Components: Androgen receptor, Estrogen receptor, Glucocorticoid receptor, Peroxisome proliferator, Steroid receptor protein, Thyroid receptor, Vitamin D receptor. | nuclear receptor, androgen receptor, estrogen receptor, glucocorticoid receptor, peroxisome proliferator, steroid receptor protein, thyroid receptor, vitamin d receptor, androgen, estrogen, glucocorticoid, peroxisome, steroid, thyroid hormone, vitamin d, mineralocorticoid receptor, mineralocorticoid, protein, structure, function |
is related to: NIDDK Information Network (dkNET) has parent organization: Georgetown University; Washington D.C.; USA |
NIDDK R01DK43382; NIDDK K04 DK02105 |
PMID:9471621 PMID:9016529 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03205 | http://nrr.georgetown.edu/NRR/nrrhome.htm | SCR_003285 | Nuclear Receptor Resource Project, NRR Project, Nuclear Receptor Resource (NRR) Project | 2026-09-12 12:55:55 | 1 | ||||
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ProbeMatchDB 2.0 Resource Report Resource Website |
ProbeMatchDB 2.0 (RRID:SCR_003433) | ProbeMatchDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. | experiment, human, microarray, mouse, oligo, operon, platform, probe, protein, proteomic, rate, sequence, study, gene, est, cdna, sts marker, orthologous gene, ortholog, microarray probe, nucleotide sequence |
is related to: UniGene is related to: HomoloGene has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan Microarray Network ; Nancy Pritzker Depression Research Network ; Department of Psychiatry pilot study ; NIMH L99 MH60398; NIDA R21 DA13754-01 |
PMID:11934751 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33156 | SCR_003433 | 2026-09-12 12:55:58 | 0 | ||||||
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PROSITE Resource Report Resource Website 1000+ mentions |
PROSITE (RRID:SCR_003457) | PROSITE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP. | protein domain, protein family, functional site, protein, structure, function, pattern, profile |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Federal government through the Federal Office of Education and Science ; European Union contract FELICS 021902RII3; European Union contract IMPACT 213037; FNS 315200-116864 |
PMID:23161676 PMID:19858104 PMID:12230035 |
Free, Freely available | OMICS_01699, nif-0000-03351 | http://www.expasy.org/prosite, http://www.expasy.ch/prosite/ | SCR_003457 | PROSITE - Database of protein domains families and functional sites | 2026-09-12 12:55:58 | 2341 |
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