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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | database, data or information resource | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | r3d100012402, nif-0000-10168 | http://biogps.gnf.org/, https://doi.org/10.17616/R33J20 | SCR_006433 | 2026-08-06 09:26:35 | 725 | |||||
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Scripps Research Institute Resource Report Resource Website 1+ mentions |
Scripps Research Institute (RRID:SCR_001907) | TSRI | institution | Nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California with a sister facility in Jupiter, Florida, the institute has laboratories employing scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world. | institution, American, medical, research, education, biomedical, private, organization |
uses: DIRECT2experts is related to: Clinical and Translational Science Awards Consortium is related to: The Pancreatic Beta-Cell Consortium is parent organization of: piCALL is parent organization of: GeneChip Operating Software is parent organization of: TSRI-Yates Lab is parent organization of: BioGPS: The Gene Portal Hub is parent organization of: METLIN is parent organization of: AutoDock Vina is parent organization of: ViReMa is parent organization of: Autopack is parent organization of: Integrative Neuroscience Initiative on Alcoholism is parent organization of: Joint Center for Structural Genomics is parent organization of: Functional Glycomics Research is parent organization of: VIPERdb is parent organization of: GOEx - Gene Ontology Explorer is parent organization of: VIPERdb is parent organization of: Zinc Finger Tools is parent organization of: XCMS is parent organization of: Chemoproteomic identification and therapeutic validation of proteins of metabolic significance is parent organization of: Leginon is parent organization of: outbreak.info is parent organization of: Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | grid.214007.0, ISNI: 122199231, Wikidata: Q793867, nif-0000-10475 | https://ror.org/02dxx6824 | SCR_001907 | The Scripps Research Institute, Scripps Research | 2026-08-01 12:01:54 | 1 | |||||
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Biositemaps Resource Report Resource Website 1+ mentions |
Biositemaps (RRID:SCR_001976) | Biositemaps | service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites. | broadcast, data federation, defined rdf schema, infrastructure, meta-data, rdf, retrieve, biomedical, biositemap, sitemap |
lists: Adaptively Sampled Particle Fluids lists: DicomWorks lists: MEDx lists: Medical Image Processing and Visualization lists: Surface-Based Atlases lists: RESNET lists: SurfRelax lists: FEATURE lists: Cardiovascular Model Repository lists: Simtk.org lists: ConTrack lists: Allopathfinder lists: Molecular Simulation Trajectories Archive of a Villin Variant lists: BioPortal lists: SumsDB lists: NeuronDB lists: BrainInfo lists: Protege lists: i2b2 Cross-Institutional Clinical Translational Research project lists: GeneChip Operating Software lists: Honig Lab lists: Proteomics Identifications (PRIDE) lists: ASAP: the Alternative Splicing Annotation Project lists: MiMI Plugin for Cytoscape lists: Substructure Index-based Approximate Graph Alignment lists: Proteome Commons Tranche repository lists: caTIES - Cancer Text Information Extraction System lists: REDCap lists: miniTUBA lists: Einstein-Montefiore ICTR Research Informatics Core lists: T-profiler lists: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse lists: GCG/SeqWeb lists: Solstice lists: California National Primate Research Center lists: BioGPS: The Gene Portal Hub lists: Blox lists: Subcellular Location Image Finder lists: PeptideAtlas lists: Clair library lists: Lyngby lists: SimTKCore lists: Velos lists: Ingenuity Pathway Analysis lists: Philips lists: Talktech lists: SUN Interface Engine lists: Quadramed - Medicus, Quantim lists: Wisconsin National Primate Research Center lists: i2b2 Research Data Warehouse lists: Merge Healthcare Incorporated lists: Clinical Trial Management Application lists: Cerner Millenium lists: Open Clinical Report Repository lists: Quovadx, Inc. lists: VectorValuedHistogramNormalizer lists: Morphometry BIRN lists: Talairach Daemon lists: LONI Visualization Tool lists: LONI Debabeler lists: LONI Pipeline Processing Environment lists: Brede Wiki lists: medInria lists: FreeSurfer lists: ITK-SNAP lists: VoxBo lists: Ensembl lists: MRIcron lists: Synchronized Histological Image Viewing Architecture lists: LONI ShapeViewer lists: LONI ShapeTools lists: FFT Library lists: NUTMEG lists: bioDBcore lists: Mutant Mouse Resource and Research Center lists: Brainscape lists: MindSeer lists: University of Southern California LONI Software lists: Statistics Online Computational Resource lists: NIH MRI Study of Normal Brain Development lists: Ontology Development and Information Extraction lists: Mindtouch DekiWiki lists: National Mesothelioma Virtual Bank lists: MGH-USC Human Connectome Project lists: Fusion ICA Toolbox lists: Biomedical Resource Ontology lists: Biomedical Informatics Research Network lists: 3D Slicer lists: Analysis of Functional NeuroImages lists: Automated Image Registration lists: TOADS-CRUISE Brain Segmentation Tools lists: BrainImage Software lists: Brede Toolbox lists: Whole Brain Catalog lists: Low Resolution Electromagnetic Tomography lists: Cambridge Brain Activation lists: ModelDB lists: fMRI Data Center lists: EEGLAB lists: 3DViewnix lists: MIPAV: Medical Image Processing and Visualization lists: NeuroLens lists: WFU PickAtlas lists: Protein Subcellular Location Image Database lists: STRIDE Virtual Biospecimen Bank lists: BrainVoyager is related to: Biomedical Resource Ontology is related to: Software Distribution Sets is related to: REX is related to: Rat Genome Database (RGD) has parent organization: National Centers for Biomedical Computing has parent organization: National Institutes of Health is parent organization of: Resource Discovery System |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10583 | SCR_001976 | 2026-08-05 10:43:30 | 1 | ||||||||
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bioDBcore Resource Report Resource Website 1+ mentions |
bioDBcore (RRID:SCR_002781) | BioDBCore | narrative resource, standard specification, database, data or information resource | A community-defined, uniform, generic description of the core attributes of biological databases. The BioDBCore checklist is overseen by the International Society for Biocuration (ISB), in collaboration with the BioSharing forum. A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them have been partly compiled with the support of Oxford University Press and Re3Data.org. Database providers are encouraged to either create or claim their BioDBCore entry and update it as appropriate., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | resource representation, resource ontology, database, interoperability, semantic standard, syntactic standard, biological database, model |
is used by: NIF Data Federation is listed by: 3DVC is listed by: Biositemaps is related to: FAIRsharing is related to: Biocatalogue - The Life Science Web Services Registry is related to: BioGPS: The Gene Portal Hub is related to: Bioinformatics Links Directory is related to: Biomedical Resource Ontology is related to: EDAM Ontology is related to: MIRIAM: Minimal Information Required In the Annotation of Models is related to: SciCrunch Registry is related to: PathGuide: the pathway resource list is related to: Integrated Manually Extracted Annotation has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:21205783 PMID:21097465 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24395 | SCR_002781 | 2026-08-06 09:25:43 | 2 | |||||||
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aGEM Resource Report Resource Website 10+ mentions |
aGEM (RRID:SCR_013349) | aGEM | database, data or information resource | Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, anatomy, gene expression, anatomical structure, developmental stage, functional genomics, genomics |
is related to: EMAGE Gene Expression Database is related to: Gene Expression Database is related to: Gene Expression Nervous System Atlas is related to: BioGPS: The Gene Portal Hub is related to: Allen Mouse Brain Reference Atlas is related to: Eurexpress is related to: HUDSEN is related to: The Human Protein Atlas is related to: OMIM is related to: KEGG has parent organization: Autonomous University of Madrid; Madrid; Spain |
National Institute for Bioinformatics ; AMIT Programme CDTI CEN-20101014; RESOLVE UE CE:FP7-202047; Ministerio de Ciencia e Innovacion BIO2010-16566; Biostruct-X FP7-Infrastructures-2011-1; Centrosoma 3D CSD2006-00023 |
PMID:22106336 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152022 | SCR_013349 | anatomic Gene Expression Mapping | 2026-08-06 09:28:07 | 12 |
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