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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Pharma-Planta Consortium Resource Report Resource Website 1+ mentions |
Pharma-Planta Consortium (RRID:SCR_003880) | Pharma-Planta | consortium, data or information resource, organization portal, portal | Consortium to develop efficient and safe strategies for the production of clinical-grade protein pharmaceuticals in plants, and to define the procedures needed for the production of these proteins in compliance with the strict regulatory standards that govern the manufacture of all pharmaceuticals. Ultimately the consortium aimed to take a candidate product all the way through the development pipeline culminating in a phase I human clinical trial. The consortium has a wide range of expertise spanning the areas of molecular biology, plant biology, immunology, recombinant protein expression technology, vaccinology, and plant biotechnology. The objectives listed at the beginning of the Pharma-Planta project are as follows: # To produce a recombinant pharmaceutical molecule in transgenic plants, which will be developed through all regulatory requirements, GMP (good manufacturing practice) standards and pre-clinical toxicity testing. This will then be evaluated in Phase I human clinical trials. # To develop robust risk assessment practices for recombinant pharmaceutical molecules produced in plants, based on health and environmental impact, working with regulatory authorities within the EU as well as public groups to ensure that the production systems are as safe and as acceptable as possible, and that they comply with all biosafety regulations. # To define and carry out a coordinated program for securing and managing intellectual property that will facilitate the availability of high priority plant-derived recombinant pharmaceuticals to the poor in developing countries while simultaneously allowing the products to be developed commercially in Europe and North America. # To develop and refine new strategies for the expression of recombinant pharmaceuticals in plants, which can be used on a generic basis for molecules that are normally expressed poorly. # To develop and generate transgenic plants expressing a second generation of recombinant molecules that will be used in future clinical trials. In 2011 they reached their benchmark for success launching a phase I clinical study of an antibody that neutralizes HIV, produced in and isolated from tobacco plants. This antibody could one day become an inexpensive component of a microbicide used to prevent the spread of HIV/AIDS. The project has also spun off many additional technologies that are being adopted by researchers all over the world, and has resulted in more than 100 publications in peer-reviewed scientific journals. | drug, clinical trial, drug development, basic research, tool development, recombinant protein, pharmaceutical, protein, antibody, tobacco plant, hiv, aids, pharmaceutical protein, pre-clinical |
is listed by: Consortia-pedia is related to: Mainz Institute of Molecular Biology Bioinformatics Core Facility is related to: St Georges University of London; London; United Kingdom is related to: RWTH Aachen University; Aachen; Germany is related to: National University of Ireland; Galway; Ireland is related to: John Innes Centre; Norwich; United Kingdom is related to: CIRAD is related to: Oxford Brookes University; Oxford; United Kingdom is related to: University of Warwick; Coventry; United Kingdom is related to: BOKU University; Vienna; Austria is related to: POLYMUN Scientific is related to: University of Verona; Verona; Italy is related to: ENEA is related to: Diamyd Medical is related to: Blaise Pascal University; Clermont-Ferrand; France is related to: INRA - French National Institute for Agricultural Research; Paris; France is related to: University of Cambridge; Cambridge; United Kingdom is related to: University of Glasgow; Glasgow; United Kingdom is related to: Heidelberg University; Baden-Wurttemberg; Germany is related to: Catholic University of Louvain; Louvain-la-Neuve; Belgium is related to: University of Leeds; West Yorkshire; United Kingdom is related to: Italian National Research Council is related to: Council for Scientific and Industrial Research; Gauteng; South Africa is related to: Rothamsted Research; Harpenden; UK is related to: University of Neuchatel; Neuchatel; Switzerland is related to: Max Planck Institute of Molecular Plant Physiology; Golm; Germany is related to: Trinity College Dublin; Dublin; Ireland is related to: Leibniz Institute of Plant Genetics and Crop Plant Research; Saxony-Anhalt; Germany is related to: VIB; Flanders; Belgium is related to: Agricultural University of Athens; Athens; Greece is related to: Mosaic Systems is related to: University of Lleida; Lleida; Spain is related to: Sartorius is related to: University of Surrey; Surrey; United Kingdom has parent organization: Mainz Institute of Molecular Biology Bioinformatics Core Facility has parent organization: St Georges University of London; London; United Kingdom |
European Union FP6 | nlx_158208 | SCR_003880 | 2026-09-12 12:56:04 | 2 | ||||||||
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Amorfix Resource Report Resource Website 1+ mentions |
Amorfix (RRID:SCR_003783) | AMF | commercial organization | Product development company focused on therapeutic products and diagnostic devices targeting misfolded protein diseases. On July, 2015 the company name was changed to ProMIS Neurosciences, Inc. | diagnostic, therapy, alzheimer, protein, misfolded protein disease | Alzheimer's disease, Amyotrophic Lateral Sclerosis, Cancer | Crossref funder ID: 100007611, nlx_158072, grid.422608.a | https://ror.org/045rtab03 | SCR_003783 | Amorfix Life Science, Amorfix Life Sciences Ltd., Amorfix Life Sciences, ProMIS Neurosciences | 2026-09-12 12:56:02 | 2 | |||||||
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Proteome Sciences Resource Report Resource Website 1+ mentions |
Proteome Sciences (RRID:SCR_004106) | PS | commercial organization | Commercial company delivering content for personalized medicine in the areas of Biomarker Services, Biomarker Assays, Isobaric and Isotopic Reagents and Proprietary Biomarkers. A global leader in applied proteomics, they use high sensitivity proprietary technologies to detect biomarkers (differentially expressed proteins in diseases) and to develop rapid assays for testing. The biomarkers discovered in body fluids or tissues are validated, developed and commercialized as diagnostic, prognostic or therapeutic products through strategic alliances and out-licensing. | protein, peptide, biomarker, pharmaceutical, diagnostic, electrophoretics ltd, electrophoretics, proteomics, assay, isobaric, isotopic, reagent, personalized medicine, mass spectrometry, tandem mass tag | is related to: EMIF | Neurodegenerative disorder, Cancer, Stroke, Alzheimer's disease, Traumatic brain injury | nlx_158582 | SCR_004106 | Proteome Science, Proteome Sciences plc | 2026-09-12 12:56:09 | 3 | |||||||
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WholeCellKB Resource Report Resource Website 1+ mentions |
WholeCellKB (RRID:SCR_004104) | WholeCellKB | data access protocol, data or information resource, database, model, software resource, source code, web service | A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: * Their subcellular organization, * Their chromosome sequences, * The essentiality, location, length, direction, and homologs of each gene, * The organization and promoter of each transcription unit, * The expression and degradation rate of each RNA gene product, * The specific folding and maturation pathway of each RNA and protein species including the localization, N-terminal cleavage, signal sequence, prosthetic groups, disulfide bonds, and chaperone interactions of each protein species, * The subunit composition of each macromolecular complex, * Their genetic code, * The binding sites and footprint of every DNA-binding protein, * The structure, charge, and hydrophobicity of every metabolite, * The stoichiometry, catalysis, coenzymes, energetics, and kinetics of every chemical reaction, * The regulatory strength of each transcription factor on each promoter, * Their chemical composition, and * The composition of its typical SP-4 laboratory growth medium. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. Users can download the WholeCellKB source code and content to create and customize - including the content, data model, and user interface - their own model organism database. | model organism, whole-cell model, gene, protein, reaction, pathway, phenotype, genotype, simulation, cell, organism | has parent organization: Stanford University; Stanford; California | PMID:23175606 PMID:22817898 |
Free, Open unspecified license, Acknowledgement requested, The community can contribute to this resource | nlx_158579 | http://wholecellkb.stanford.edu | SCR_004104 | Mycoplasma genitalium database, WholeCellKB-MG, Whole Cell KB | 2026-09-12 12:56:09 | 1 | |||||
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Binding Site Resource Report Resource Website 1+ mentions |
Binding Site (RRID:SCR_004051) | commercial organization | Company provides specialist diagnostic products to clinicians and laboratory professionals worldwide. Specialist protein company committed to research, development, manufacture and distribution of immunodiagnostic assays for global laboratory market. Specialized in antibody specificity technology, Binding Site gives clinicians and laboratory staff tools to significantly improve diagnosis and management of those patients with specific cancers and immune disorders. Binding Site manufactures wide range of products for plasma protein analysis including Freelite, Hevylite and SPAplus. | Diagnostic products, protein, diagnosis, monitoring, assay, immunodiagnostic assays | is related to: Kidney Health Initiative | Cancer, Immune disorder, Multiple Myeloma, Primary immunodeficiency disease | nlx_158482 | SCR_004051 | The Binding Site, The Binding Site Group Ltd, Binding Site Inc, The Specialist Protein Company, Binding Site Group Ltd | 2026-09-12 12:56:07 | 2 | ||||||||
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Reflect Resource Report Resource Website 50+ mentions |
Reflect (RRID:SCR_002714) | Reflect | data access protocol, software application, software resource, web service | Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community. | text mining, semantic mark up, gene, protein, computational linguistics, small molecule, domain structure, sub-cellular localization, 3d structure, interaction, chemical structure |
is listed by: OMICtools is listed by: FORCE11 has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: European Bioinformatics Institute |
PMID:19513049 | nif-0000-23349, OMICS_01196 | http://reflect.ws/ | SCR_002714 | Reflect: Protein small molecules | 2026-09-12 12:55:45 | 88 | ||||||
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Ablynx Resource Report Resource Website 10+ mentions |
Ablynx (RRID:SCR_002940) | Ablynx | material service resource, production service resource, reagent manufacture, service resource | A biopharmaceutical company engaged in the discovery and development of Nanobodies, a novel class of antibody-derived therapeutic proteins based on single-domain antibody fragments, for a range of serious life-threatening human diseases including inflammation, hematology, oncology and pulmonary disease. | nanobody, protein, antibody fragment, human disease, oncology, hematology, tumor, blood, therapy, therapeutic, pharmaceutical, drug product, drug | Inflammation, Cancer, Pulmonary disease, Thrombosis, Alzheimer's disease, Rheumatoid arthritis, Osteoporosis, Thrombotic thrombocytopenic purpura, Respiratory syncytial virus | nif-0000-30052 | SCR_002940 | 2026-09-12 12:55:49 | 18 | |||||||||
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Protein Information Resource Resource Report Resource Website 50+ mentions |
Protein Information Resource (RRID:SCR_002837) | PIR | data or information resource, portal, topical portal | Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO. | annotation, genomic, mining, protein, protein bioinformatics, proteomic, research, sequence, structure, systems biology, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NCBI Protein Database has parent organization: University of Delaware; Delaware; USA has parent organization: Georgetown University; Washington D.C.; USA is parent organization of: PRO is parent organization of: PIRSF is parent organization of: PR is parent organization of: UniProt |
NLM P41 LM05798 | PMID:12520019 | Free, Freely available | biotools:pir, nif-0000-21327, nif-0000-00143, SCR_008229 | https://bio.tools/pir, http://pir.georgetown.edu/ | SCR_002837 | PIR - Protein Information Resource | 2026-09-12 12:55:47 | 85 | ||||
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Gramene Resource Report Resource Website 500+ mentions |
Gramene (RRID:SCR_002829) | GR | data or information resource, database | Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. | crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Gene Ontology is related to: Plant Ontology is related to: Trait Ontology is related to: EnvO is related to: BioCyc has parent organization: Cold Spring Harbor Laboratory has parent organization: Cornell University; New York; USA is parent organization of: Trait Ontology is parent organization of: Plant Environmental Conditions is parent organization of: Plant Trait Ontology is parent organization of: Cereal Plant Development Ontology is parent organization of: Cereal Plant Gross Anatomy Ontology |
USDA IFAFS 00-52100-9622; USDA 58-1907-0-041; USDA 1907-21000-030; NSF 0321685; NSF 0703908; NSF 0851652 |
PMID:21076153 PMID:17984077 PMID:16381966 |
Free, Freely available | r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene | https://bio.tools/gramene, https://doi.org/10.17616/R3GG7M | SCR_002829 | GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL | 2026-09-12 12:55:47 | 863 | ||||
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Clustal W2 Resource Report Resource Website 5000+ mentions |
Clustal W2 (RRID:SCR_002909) | alignment software, data processing software, image analysis software, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF. | multiple, sequence, alignment, cladogram, phylogram, evolution, phylogenetic, tree, protein, nucleic, acid, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Clustal Omega is related to: UniProt is related to: Clustal Omega is related to: VectorBase is related to: TopoSNP is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:17846036 PMID:20439314 DOI:10.1093/bioinformatics/btm404 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02562, nif-0000-30076 | http://www.ch.embnet.org/software/ClustalW.html, https://sources.debian.org/src/clustalx/ | http://www.ebi.ac.uk/tools/clustalw/ | SCR_002909 | European Bioinformatics Institute - ClustalW2 | 2026-09-12 12:55:48 | 7871 | ||||
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National Resource Center for Cephalopods Resource Report Resource Website 1+ mentions |
National Resource Center for Cephalopods (RRID:SCR_002864) | NRCC | biomaterial supply resource, material resource, organism supplier | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The center serves the biomedical research community's increased needs for alternative invertebrate models by maintaining a consistent year-round supply of live cephalopod mollusks. These animals are suitable for a wide range of physiological and molecular biological investigations. Investigations are being conducted in the area of life history related to improved animal husbandry. Further studies focus on improving culture system design through development of computer automation and innovative water filtration technology. Current biomedical research on cephalopods includes neurophysiology of the giant axon; anatomy and neurophysiology of the equilibrium receptor organ as a comparative model of the vestibular system of invertebrates; chemoreception, basic nutrition, and protein metabolism; cellular receptor function; and brain, behavior, and learning. Services Provided: The center has built a computer-automated, environmentally controlled, recirculating seawater laboratory for the purpose of culturing cephalopods. The tank systems can be used to conduct a variety of experiments never before possible with cephalopods. Visiting researchers have access to dedicated facilities, including wet and dry laboratory space, office space, computer support and accommodations, as well as priority access to all available live animal resources. Off-site investigators can have live animals, dissected animal tissues/body fluids from all life stages, and a variety of molecular reagents (gene libraries and clones) delivered year-round. Staff expertise and an extensive literature library are available. All life stages of the squid (Sepioteuthis lessoniana) and the common cuttlefish (Sepia officinalis) are available year-round from laboratory culture populations. The sepiolid squid (Euprymna scolopes) can also be cultured on request. The squid Lolliguncula brevis is available year-round from local waters; the squids Loligo opalescens, L. pealeii, and L. plei can be obtained seasonally on request. The chambered nautilus, Nautilus pompilius, and Octopus bimaculoides are available on request. Animal costs vary by species and size. Any tissue or body fluid from these animals can also be provided. Fees for special services are negotiated on a case-by-case basis. | euprymna scolopes, function, gene, anatomy, animal, axon, behavior, biological, biomedical, brain, cellular, cephalopod mollusk, chemoreception, clone, culture, cuttlefish, invertebrate, inverteprate, laboratory, learning, lolliguncula brevis, metabolism, model, molecular, nautilus pompilius, neurophysiology, nutrition, octopus bimaculoides, organ, physiological, protein, reagent, receptor, research, sepia officinalis, sepiolid squid, sepioteuthis lessoniana, squid | has parent organization: University of Texas System; Texas; USA | National Institutes of Health ; National Center for Research Resources ; Texas Institute of Oceanography |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25474 | SCR_002864 | National Resource Center for Cephalopods | 2026-09-12 12:55:47 | 3 | ||||||
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PRO Resource Report Resource Website 1+ mentions |
PRO (RRID:SCR_002902) | controlled vocabulary, data or information resource, ontology | An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). | protein |
is listed by: OMICtools has parent organization: Protein Information Resource |
NIGMS 5R01GM080646-09 | PMID:21929785 | OMICS_06200 | SCR_002902 | Protein Ontology | 2026-09-12 12:55:48 | 4 | |||||||
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3D-Interologs Resource Report Resource Website |
3D-Interologs (RRID:SCR_003101) | 3D-interologs | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins. | interolog, protein-protein interaction, blast, homolog, protein, interaction, function |
is related to: IntAct is related to: UniProt is related to: Gene Ontology has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:21143789 | Resource:OMICtools, Resource:UniProt | nif-0000-00554, OMICS_01896 | https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-S3-S7 | SCR_003101 | 2026-09-12 12:55:51 | 0 | ||||||
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Eukaryotic Linear Motif Resource Report Resource Website 100+ mentions |
Eukaryotic Linear Motif (RRID:SCR_003085) | ELM | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive. | linear motif, regulatory protein, motif, protein sequence, functional site, prediction, disease, virus, cell compartment, phylogeny, globular domain clash, structure, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: SMART is related to: Pfam has parent organization: European Molecular Biology Laboratory |
EMBL international PhD program ; EMBL Interdisciplinary PostDoc fellowship ; Federal Government Department of Education and Science FKZ01GS0862; European Community Seventh Framework Programme FP7/2009 241955; European Community Seventh Framework Programme FP7/2009 242129; Polish Ministry of Science and Higher Education IP2010-0483-70; Biotechnology and Biological Sciences Research Council BB/F010486/1; Region Alsace and College Doctoral Europeen ; Science Foundation Ireland 08/IN.1/B1864; BBSRC BB/I006230/1; German Research Foundation SFB796; Swiss National Science Foundation |
PMID:22110040 | Free, Available for download, Freely available | biotools:elm, nif-0000-30486 | https://bio.tools/elm | SCR_003085 | Eukarotic Linear Motif resource for Functional Sites in Proteins | 2026-09-12 12:55:51 | 325 | ||||
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DGAP Resource Report Resource Website 1+ mentions |
DGAP (RRID:SCR_003036) | DGAP | data or information resource, database, experimental protocol, narrative resource, resource | Produce resources to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes including an annotated public database, standardized protocols for gene expression and proteomic analysis, and ultimately diabetes-specific and insulin action-specific DNA chips for investigators in the field. The project aims to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. There are five major and one pilot project involving human and rodent tissues that are designed to: * Create a database of the genes expressed in insulin-responsive tissues, as well as accessible tissues, that are regulated by insulin, insulin resistance and diabetes. * Assess levels and patterns of gene expression in each tissue before and after insulin stimulation in normal and genetically-modified rodents; normal, insulin resistant and diabetic humans, and in cultured and freshly isolated cell models. * Correlate the level and patterns of expression at the mRNA and/or protein level with the genetic and metabolic phenotype of the animal or cell. * Generate genomic sequence from a panel of humans with type 2 diabetes focusing on the genes most highly regulated by insulin and diabetes to determine the range of sequence and expression variation in these genes and the proteins they encode, which might affect the risk of diabetes or insulin resistance. The DGAP project will define: * the normal anatomy of gene expression, i.e. basal levels of expression and response to insulin. * the morbid anatomy of gene expression, i.e., the impact of diabetes on expression patterns and the insulin response. * the extent to which genetic variability might contribute to the alterations in expression or to diabetes itself. | gene, insulin action, predisposition, gene expression, metabolic abnormality, diabetes, insulin resistance, genetics, insulin, genetic variation, proteomics, genomics, affymetrix oligonucleotide array, microarray, protein, genomic sequence, data set |
is related to: NIDDK Information Network (dkNET) has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: Broad Institute has parent organization: Dana-Farber Cancer Institute has parent organization: University of Massachusetts Medical School; Massachusetts; USA has parent organization: University of Southern Denmark; Odense; Denmark |
Type 2 diabetes, Normal, Insulin resistance | NIDDK | PMID:19786482 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30414 | SCR_003036 | The Diabetes Genome Anatomy Project, Diabetes Genome Anatomy Project | 2026-09-12 12:55:50 | 9 | ||||
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DaliLite Pairwise comparison of protein structures Resource Report Resource Website 50+ mentions |
DaliLite Pairwise comparison of protein structures (RRID:SCR_003047) | DaliLite | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Tool that computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol. The Dali method optimizes a weighted sum of similarities of intramolecular distances. Suboptimal alignments do not overlap the optimal alignment or each other. Suboptimal alignments detected by the program are reported if the Z-score is above 2; they may be of interest if there are internal repeats in either structure. SOAP Web services are also available. | pairwise alignment, protein structure, alignment, protein, structure | has parent organization: European Bioinformatics Institute | PMID:10980157 | Free, Freely available | nif-0000-30431 | SCR_003047 | DaliLite - Pairwise alignment of protein structures | 2026-09-12 12:55:50 | 59 | ||||||
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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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