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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, software resource, software toolkit, source code | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NCI R01 CA227388; NCI R37 CA222574; NCI U01 CA233100; NIGMS T32 GM008313; NSF |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | 2026-09-05 06:35:57 | 4 | |||||||||
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Conditional AutoRegressive Deconvolution Resource Report Resource Website 1+ mentions |
Conditional AutoRegressive Deconvolution (RRID:SCR_026310) | CARD | software resource, software toolkit, source code | Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations. | Deconvolution method, spatial transcriptomics, cell-type-specific expression, single-cell RNA sequencing, cell-type composition across tissue locations, | NHGRI R01HG011883; NIGMS R01GM126553; NIGMS R01GM144960 |
PMID:35501392 | Free, Available for download, Freely available | SCR_026310 | , CARD: Conditional AutoRegressive Deconvolution, Conditional autoregressive-based deconvolution | 2026-09-05 06:35:18 | 3 | |||||||
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AutoDockTools Resource Report Resource Website 1000+ mentions |
AutoDockTools (RRID:SCR_026401) | ADT | software application, software resource | Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. | automated docking, selective receptor flexibility, predict binding, bind to receptor of known 3D structure, ligand, analyze dockings | NIGMS RO1 GM069832 | PMID:19399780 | Free, Available for download, Freely available | https://autodock.scripps.edu/ | SCR_026401 | AutoDockTools: the Graphical User Interface for AutoDock | 2026-09-05 06:35:21 | 2063 | ||||||
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NucleAIzer Resource Report Resource Website 1+ mentions |
NucleAIzer (RRID:SCR_026500) | software resource, source code | Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool. | nucleus segmentation, image style transfer, | Academy of Finland ; European Regional Development Funds ; NIGMS R35 GM122547; Swedish Research Council |
DOI:10.1016/j.cels.2020.04.003 | Free, Available for download, Freely available | SCR_026500 | 2026-09-05 06:35:23 | 4 | |||||||||
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Mitochondrial Function and In Vivo Imaging Core Resource Report Resource Website |
Mitochondrial Function and In Vivo Imaging Core (RRID:SCR_028891) | MF-II Core | access service resource, core facility, service resource | The Mitochondrial Function and In Vivo Imaging (MF-II) Core provides specialized expertise, advanced instrumentation, and comprehensive services for assessing mitochondrial function, metabolism, cardiopulmonary physiology, and in vivo structure and function. The Core supports cardiovascular, pulmonary, and vascular research through high-resolution metabolic and mitochondrial analyses, noninvasive imaging, hemodynamic assessment, and established preclinical disease models. The MF-II Core works collaboratively with investigators to provide experimental design consultation, technical expertise, data acquisition, and analysis to generate high-quality, reproducible data. | Mitochondrial Function, Mitochondrial Bioenergetics, Cellular Metabolism, Oxygen Consumption, Glycolysis, High-Resolution Respirometry, Seahorse XFe96, Oroboros, Echocardiography, Cardiac Function, Hemodynamics, In Vivo Imaging, Micro-CT, PET Imaging, Laser Doppler, Cardiopulmonary Physiology, Preclinical Imaging, Animal Models, Pulmonary Hypertension, Cardiovascular Biology | NIGMS P30GM149398 | SCR_028891 | 2026-09-05 06:36:21 | 0 | ||||||||||
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Structure-function linkage database Resource Report Resource Website 10+ mentions |
Structure-function linkage database (RRID:SCR_001375) | SFLD | data or information resource, database | A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function. | software, enzyme, structure-function relationship, blast, reaction, superfamily, hidden markov model, sequence alignment, protein similarity network, sequence, structure, function |
uses: UCSF Chimera has parent organization: Resource for Biocomputing Visualization and Informatics |
NIGMS R01GM60595; NIGMS P01GM071790; NIGMS U54GM093342 |
PMID:18428763 PMID:16489747 |
Free, Freely available, | nlx_152532 | SCR_001375 | 2026-09-05 06:24:34 | 18 | ||||||
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Sherlock Resource Report Resource Website 50+ mentions |
Sherlock (RRID:SCR_001628) | Sherlock | data or information resource, service resource | Service to discover disease genes in GWAS using eQTL signature matching by simply submitting your list of GWAS associations (SNPs and p-values). It is important to upload all SNPs in your association study, not just the top hits. Sherlock may be able to group multiple lower-confidence SNPs to discover functionally-important genes. | genome-wide association study, expression quantitative trait locus, disease gene, snp, gene expression, gene, disease, association, p-value, cis, trans, genetic variation, mapping, phenotype, FASEB list | has parent organization: University of California at San Francisco; California; USA | NIGMS R01GM070808; NIGMS U19GM61390; NIGMS P50 GM081879 |
PMID:23643380 | Free, Freely available | nlx_153895 | SCR_001628 | 2026-09-05 06:24:36 | 90 | ||||||
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ALFRED Resource Report Resource Website 50+ mentions |
ALFRED (RRID:SCR_001730) | ALFRED | data or information resource, data repository, database, service resource, storage service resource | A public curated compilation of allele frequency data on anthropologically defined human population samples linked to the molecular genetics-human genome databases. Only data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. Researchers wishing to have their data entered into ALFRED should contact them. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED provides easy searching options including versatile "Keyword search" and also has numerous summary tables providing quick overviews of contents by chromosome, population, average heterozygosity, Fst and others, all available under various tabs from the ALFRED homepage. | allele frequency, dna polymorphism, haplotype, high throughput, genome, population, sample, education, polymorphism, allele, chromosome, heterozygosity, fst, loci, pathway, genetics, FASEB list | has parent organization: Yale School of Medicine; Connecticut; USA | NIGMS P01GM 57672 | PMID:19325849 PMID:11125124 PMID:12209575 |
Free, Freely Available | nif-0000-02541, r3d100012700 | https://doi.org/10.17616/R3GZ2J | SCR_001730 | The ALlele FREquency Database, ALlele FREquency Database | 2026-09-05 06:24:38 | 74 | ||||
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ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | data or information resource, data repository, database, service resource, storage service resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571, r3d100010666 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-09-05 06:24:40 | 53 | ||||
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PhosphoSitePlus: Protein Modification Site Resource Report Resource Website 1000+ mentions |
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) | PSP | data or information resource, knowledge environment resource, portal | A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. | portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Cytoscape is related to: ConsensusPathDB has parent organization: Cell Signaling Technology |
NCI ; NIAAA R44 AA014848; NIGMS R43 GM65768 |
PMID:22135298 | Free, Freely available | biotools:phosphositeplus, nif-0000-10399 | https://bio.tools/phosphositeplus | SCR_001837 | PhosphoSitePlus, PhosphoSite | 2026-09-05 06:24:40 | 1003 | ||||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | data analysis software, data processing software, software application, software resource | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-09-05 06:24:39 | 9 | ||||
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BioCyc Resource Report Resource Website 1000+ mentions |
BioCyc (RRID:SCR_002298) | data or information resource, database | A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site. | database, pathway/genome databases, PGDB, genome, metabolic pathway, microbiome, FASEB list |
uses: Pathway Tools is used by: PathCase Pathways Database System lists: Pathway Tools lists: EcoCyc lists: MetaCyc lists: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is listed by: LabWorm is listed by: Human Microbiome Project is related to: Pathway Tools is related to: PathCase Pathways Database System is related to: EcoCyc is related to: MetaCyc is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: EcoCyc is related to: Gramene is related to: NCBI BioSystems Database is related to: KOBAS is related to: Tuberculosis Database is related to: Pathway Tools has parent organization: Stanford Research Institute International |
NIGMS GM080746 | PMID:16246909 | Restricted | nif-0000-00369, r3d100011259 | https://doi.org/10.17616/R36G8H | SCR_002298 | BioCyc Database Collection | 2026-09-05 06:24:46 | 1063 | |||||
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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 | 2026-09-05 06:24:45 | 16 | |||||||
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Simtk.org Resource Report Resource Website 10+ mentions |
Simtk.org (RRID:SCR_002680) | SimTK | simulation software, software application, software repository, software resource | A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code. | model, modeling, rna folding, protein folding, myosin dynamics, neuromuscular biomechanics, cardiovascular dynamics, biomolecular simulation, biomedical computing, repository, cardiovascular, neuromuscular, myosin, rna, simulation, biocomputation |
is used by: NIF Data Federation lists: Adaptively Sampled Particle Fluids lists: OpenMM lists: CPODES numerical integrator is listed by: Biositemaps is listed by: Integrated Models is listed by: DataCite is listed by: re3data.org is related to: OpenSim is related to: Simbody(tm): SimTK Multibody Dynamics Toolset is related to: SimVascular is related to: SAFA Footprinting Software is related to: Ion Simulator Interface is related to: LAPACK linear algebra library is related to: Neuromuscular Models Library has parent organization: Simbios is parent organization of: FEATURE is parent organization of: Cardiovascular Model Repository is parent organization of: ConTrack is parent organization of: Allopathfinder is parent organization of: Molecular Simulation Trajectories Archive of a Villin Variant is parent organization of: LAPACK linear algebra library is parent organization of: SimTKCore |
NIH ; NIGMS U54 GM072970 |
Free, Available for download, Freely available | nif-0000-23302, DOI:10.17616/R3QJ4B, DOI:10.18735 | https://doi.org/10.17616/R3QJ4B, https://doi.org/10.17616/r3qj4b, https://doi.org/10.18735/, https://dx.doi.org/10.18735/ | SCR_002680 | Simulation Toolkit, SimTK - the Simulation Toolkit | 2026-09-05 06:24:51 | 20 | |||||
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BioPortal Resource Report Resource Website 100+ mentions |
BioPortal (RRID:SCR_002713) | BioPortal | controlled vocabulary, data or information resource, data repository, ontology, repository, service resource, storage service resource | Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services. | biomedical, thesaurus, ontology mapping, annotation, metadata standard, ontology repository, portal, web service, obo, owl, rdf, rrf protege frame, lexgrid xml |
lists: MeGO lists: Porifera Ontology lists: EnvO lists: Research Network and Patient Registry Inventory Ontology lists: Semantic DICOM Ontology lists: Time Event Ontology lists: Variation Ontology lists: Vertebrate Skeletal Anatomy Ontology lists: Epoch Clinical Trial Ontology lists: Gazetteer lists: Human Disease Ontology lists: Information Artifact Ontology lists: NCBITaxon lists: Amphibian Taxonomy Ontology lists: Anatomic Pathology Lexicon lists: HIV ontology lists: International Classification of Primary Care - 2 PLUS lists: Mathematical Modelling Ontology lists: Nursing Interventions Classification lists: Phylogenetic Ontology lists: Bleeding History Phenotype Ontology lists: Body System Terms from ICD11 lists: Synthetic Biology Open Language Visual Ontology lists: Teleost Anatomy Ontology lists: Teleost Taxonomy Ontology lists: ECO lists: Bioassay Ontology lists: RightField lists: Gene Ontology lists: HGNC lists: Interaction Ontology lists: International Classification for Nursing Practice lists: Spider Ontology lists: Vertebrate Trait Ontology lists: Mental Functioning Ontology lists: Ascomycete Phenotype Ontology lists: Beta Cell Genomics Ontology lists: Biological Collections Ontology lists: Chemical Methods Ontology lists: Chemical Information Ontology lists: Common Anatomy Reference Ontology lists: Experimental Conditions Ontology lists: Dictyostelium Discoideum Anatomy Ontology lists: Fission Yeast Phenotype Ontology lists: Fly Taxonomy lists: FlyBase Controlled Vocabulary lists: Hymenoptera Anatomy Ontology lists: Influenza Ontology lists: Lipid Ontology lists: Kinetic Simulation Algorithm Ontology lists: Malaria Ontology lists: FMA lists: Minimal Anatomical Terminology lists: NEMO Ontology lists: Ontology for Genetic Interval lists: Ontology for Parasite LifeCycle lists: Ontology of Adverse Events lists: Ontology of Medically Related Social Entities lists: Ontology of Vaccine Adverse Events lists: Rat Strain Ontology lists: Plant Environmental Conditions lists: Plant Trait Ontology lists: Population and Community Ontology lists: RNA Ontology lists: Rat Strain Ontology lists: Subcellular Anatomy Ontology lists: Software Ontology lists: Suggested Ontology for Pharmacogenomics lists: Vertebrate Taxonomy Ontology lists: PharmGKB Ontology lists: Physico-Chemical Process lists: International Classification for Patient Safety lists: Adverse Event Reporting Ontology lists: Experimental Factor Ontology lists: Mass Spectrometry Ontology lists: Master Drug Data Base Clinical Drugs lists: Medaka Fish Anatomy and Development Ontology lists: Medical Diagnostic Categories - Diagnosis Related Groups lists: Medical Dictionary for Regulatory Activities lists: Minimal Standard Terminology of Digestive Endoscopy lists: Minimal Standard Terminology of Digestive Endoscopy - French lists: Ontology of Physical Exercises lists: Mosquito Gross Anatomy Ontology lists: Systematized Nomenclature of Medicine - International Version lists: Mosquito Insecticide Resistance Ontology lists: Mouse Experimental Design Ontology lists: Mouse Gross Anatomy and Development Ontology lists: Systematized Nomenclature of Medicine - Clinical Terms lists: Systems Chemical Biology and Chemogenomics Ontology lists: Mouse Pathology Ontology lists: NIF Cell Ontology lists: NHS Quality Indicators lists: Neural-Immune Gene Ontology lists: Ontology of Physics for Biology lists: Cell Type Ontology lists: Xenopus Anatomy Ontology lists: SO lists: Ontology of Pneumology lists: Open Biological and Biomedical Ontologies Relationship Types lists: Biomedical Resource Ontology lists: MGED Ontology lists: Pharmacovigilance Ontology lists: PhenX Phenotypic Terms lists: Bioinformatics Web Service Ontology lists: SysMO JERM Ontology of Systems Biology for Micro-Organisms lists: MeSH lists: PATO lists: BFO lists: MPO lists: PR lists: Cereal Plant Development Ontology lists: PhenomeBLAST Ontology lists: VIVO lists: Computer Assisted Brain Injury Rehabilitation Ontology lists: Computer Retrieval of Information on Scientific Projects Thesaurus lists: NIFSTD lists: Cell Line Ontology lists: Student Health Record Ontology lists: Zebrafish Anatomical Ontology lists: Physical Medicine and Rehabilitation lists: Randomized Controlled Trials Ontology lists: Human Phenotype Ontology lists: Read Codes Clinical Terms Version 3 lists: Reference Sequence Annotation lists: Regulation of Gene Expression Ontolology lists: Neurobehavior Ontology lists: Regulation of Transcription Ontology lists: Reproductive Trait and Phenotype Ontology lists: Skin Physiology Ontology lists: Vaccine Ontology lists: OMIM lists: MedlinePlus lists: Adult Mouse Anatomy Ontology lists: Bone Dysplasia Ontology lists: Bone and Cartilage Tissue Engineering Ontology lists: Botryllus schlosseri anatomy and development ontology lists: EDAM Ontology lists: LexGrid lists: RxNorm lists: Breast Cancer Grading Ontology lists: Breast Tissue Cell Lines Ontology lists: SBO lists: Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology lists: Brucellosis Ontology lists: Sleep Domain Ontology lists: C. elegans Development Vocabulary lists: Physician Data Query lists: C. elegans Gross Anatomy Vocabulary lists: Plant Ontology lists: C. elegans Phenotype Vocabulary lists: CPTAC Proteomics Pipeline Infrastructure Ontology lists: Cancer Research and Management ACGT Master Ontology lists: Cancer Chemoprevention Ontology lists: Cell Behavior Ontology lists: Cereal Plant Gross Anatomy Ontology lists: Cardiac Electrophysiology Ontology lists: Cerebrotendinous Xanthomatosis Ontology lists: Cell Cycle Ontology lists: Cell Culture Ontology lists: Cerrado concepts and plant community dynamics lists: Clinical Signs and Symptoms Ontology lists: Clusters of Orthologous Groups Analysis Ontology lists: Computational Neuroscience Ontology lists: BIRNLex lists: Computer-Based Patient Record Ontology lists: Congenital Heart Defects Ontology lists: Drug Interaction Knowledge Base Ontology lists: Healthcare Common Procedure Coding System lists: Host Pathogen Interactions Ontology lists: Human Dermatological Disease Ontology lists: Solanaceae Phenotype Ontology lists: Soy Ontology lists: Spatial Ontology lists: Surgical Secondary Events lists: eagle-i research resource ontology lists: Biological Pathways Exchange lists: Autism Spectrum Disorder Phenotype Ontology lists: BRENDA Tissue and Enzyme Source Ontology lists: BioTop Ontology lists: Family Health History Ontology lists: International Classification of Diseases Version 9 - Clinical Modification lists: BioModels Ontology lists: Bilingual Ontology of Alzheimer lists: BioPortal Metadata Ontology lists: Biochemical Substructure Ontology lists: Biodiversity Ontology lists: Biological Imaging Methods Ontology lists: International Classification of Functioning Disability and Health lists: Biologie Hors Nomenclature lists: International Classification of Primary Care lists: Biomedical Research Integrated Domain Group Model lists: KB Bio 101 lists: Bionutrition Ontology lists: Artificial Intelligence Rheumatology Consultant System Ontology lists: Leukocyte Surface Marker Ontology lists: Cell Line Ontology by Mahadevan lists: Cellular microscopy phenotype ontology lists: ABA Adult Mouse Brain Ontology lists: AEO lists: African Traditional Medicine Ontology lists: Alzheimer's disease ontology lists: Amino Acid Ontology lists: Amphibian Gross Anatomy Ontology lists: Animal Natural History and Life History Ontology lists: Coding Symbols for a Thesaurus of Adverse Reaction Terms lists: Cognitive Atlas Ontology lists: Common Terminology Criteria for Adverse Events lists: Comparative Data Analysis Ontology lists: Content Archive Resource Exchange Lexicon lists: Crop Ontology lists: Current Procedural Terminalogy Hierarchy lists: Current Procedural Terminology lists: DICOM Controlled Terminology lists: Dataset processing lists: Dengue Fever Ontology lists: Dermatology Lexicon lists: Diagnosis Ontology of Clinical Care Classification lists: Diagnostic Ontology lists: Disease core ontology applied to Rare Diseases lists: Dispedia Core Ontology lists: Drosophila Development Ontology lists: Drosophila Gross Anatomy Ontology lists: EDDA Study Design Terminology lists: Electrocardiography Ontology lists: Eligibility Feature Hierarchy lists: Enzyme Mechanism Ontology lists: Enzyme Reaction Ontology for partial chemical perspectives lists: Epilepsy Ontology lists: Loggerhead Nesting Ontology lists: Fanconi Anemia Ontology lists: Fire Ontology lists: Flora Phenotype Ontology lists: Fungal Gross Anatomy Ontology lists: Human Developmental Anatomy Ontology abstract version 1 lists: G Protein-Coupled Receptor BioAssays Ontology lists: Galen Ontology lists: Gene Expression Ontology lists: Gene Ontology Extension lists: General Formal Ontology lists: General Formal Ontology for Biology lists: Genome Component Ontology lists: Genomic Clinical Decision Support Ontology lists: GeoSpecies Ontology lists: Glycomics Ontology lists: Habronattus Courtship Ontology lists: Health Indicator Ontology lists: Health Level Seven Reference Implementation Model Version 3 lists: Human Developmental Anatomy Ontology abstract version 2 lists: Human Developmental Anatomy Ontology timed version lists: Human Interaction Network Ontology lists: Human Physiology Simulation Ontology lists: Logical Observation Identifier Names and Codes lists: IMGT-ONTOLOGY lists: Image and Data Quality Assessment Ontology lists: Immune Disorder Ontology lists: Infectious Disease Ontology lists: InterNano Nanomanufacturing Taxonomy lists: Interaction Network Ontology lists: International Classification of External Causes of Injuries lists: International Classification of Diseases Version 10 lists: International Classification of Diseases Version 10 - Clinical Modification lists: International Classification of Diseases Version 10 - Procedure Coding System lists: MR dataset acquisition lists: Maize Gross Anatomy Ontology lists: Major Histocompatibility Complex Ontology lists: Medical image simulation lists: Menelas Project Top-Level Ontology lists: Mental State Assessment lists: Metagenome Sample Vocabulary lists: Metagenome and Microbes Environmental Ontology lists: MicroRNA Ontology lists: Microbial Culture Collection Vocabulary lists: Microbial Typing Ontology lists: Minimal Information about any Sequence Controlled Vocabularies lists: Minimal Information about any Sequence Ontology lists: NIF Dysfunction Ontlogy lists: NIF Subcellular Ontology lists: NMR-Instrument Component of Metabolomics Investigations Ontology lists: Name Reaction Ontology lists: NanoParticle Ontology lists: National Cancer Institute Thesaurus lists: National Drug Data File lists: National Drug File - Reference Terminology lists: Natural Products Ontology lists: Neglected Tropical Disease Ontology lists: Neomark Oral Cancer Ontology version 3 lists: Neomark Oral Cancer Ontology version 4 lists: Neural Motor Recovery Ontology lists: NeuroMorpho.Org species ontology lists: NeuroMorpho.Org species ontology old lists: Non-Randomized Controlled Trials Ontology lists: Nursing Care Coordination Ontology lists: Ontological Knowledge Base Model for Cystic Fibrosis lists: Ontology for Drug Discovery Investigations lists: Ontology for General Medical Science lists: Ontology for Genetic Disease Investigations lists: Ontology for Genetic Susceptibility Factor lists: Ontology for MicroRNA Target Prediction lists: Symptom Ontology lists: Ontology for Newborn Screening Follow-up and Translational Research lists: Ontology of Alternative Medicine French lists: Ontology of Biological and Clinical Statistics lists: Ontology of Clinical Research lists: Ontology of Core Data Mining Entities lists: Ontology of Data Mining Investigations lists: Pediatric Terminology lists: Ontology of Experimental Variables and Values lists: Ontology of General Purpose Datatypes lists: Ontology of Geographical Region lists: Ontology of Glucose Metabolism Disorder lists: Ontology of Homology and Related Concepts in Biology lists: Ontology of Language Disorder in Autism lists: Orphanet Rare Disease Ontology lists: Parasite Experiment Ontology lists: Pathogen Transmission Ontology lists: Pathogenic Disease Ontology lists: Pharmacogenomic Relationships Ontology lists: Physico-Chemical Methods and Properties lists: Plant Anatomy lists: Syndromic Surveillance Ontology lists: Plant Structure Development Stage lists: Portfolio Management Application lists: Protein Modification Ontology lists: Protein-Protein Interaction Ontology lists: Proteomics Data and Process Provenance Ontology lists: Provenance Ontology lists: QUDT lists: Quantitative Imaging Biomarker Ontology lists: Radiology Lexicon lists: Robert Hoehndorf Version of MeSH lists: Role Ontology lists: STATistics Ontology lists: Sage Bionetworks Synapse Ontology lists: Sample Processing and Separation Techniques Ontology lists: Santa Barbara Coastal Observation Ontology lists: Semantic Types Ontology lists: Semantic Web for Earth and Environment Technology Ontology lists: Semanticscience Integrated Ontology lists: Single-Nucleotide Polymorphism Ontology lists: Situation-Based Access Control Ontology lists: Taxonomic Rank Vocabulary lists: Taxonomy for Rehabilitation of Knee Conditions lists: Terminological and Ontological Knowledge Resources Ontology lists: Tick Gross Anatomy Ontology lists: Tissue Microarray Ontology lists: Traditional Medicine Constitution Value Set lists: Traditional Medicine Meridian Value Sets lists: Traditional Medicine Other Factors Value Set lists: Traditional Medicine Signs and Symptoms Value Set lists: Translational Medicine Ontology lists: Tribolium Ontology lists: Units Ontology lists: Units of Measurement Ontology lists: Upper-Level Cancer Ontology lists: Vertebrate Homologous Organ Group Ontology lists: Veterans Health Administration National Drug File lists: Vital Sign Ontology lists: WHO Adverse Reaction Terminology lists: Web-Service Interaction Ontology lists: Wheat Trait Ontology lists: XEML Environment Ontology lists: suicideo lists: suicideonto lists: Pseudogene lists: Terminology for the Description of Dynamics lists: Gene Regulation Ontology lists: UBERON lists: CHEBI lists: Cognitive Paradigm Ontology lists: Emotion Ontology lists: Clinical Measurement Ontology lists: Measurement Method Ontology lists: NCI Thesaurus lists: Ontology for Biomedical Investigations lists: Biological Pathways Exchange is listed by: Biositemaps is listed by: FORCE11 is related to: Provisional Cell Ontology has parent organization: National Center for Biomedical Ontology has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Biomedical Informatics Research is parent organization of: NCBO Annotator |
NIGMS U24 GM143402 | PMID:19483092 PMID:21672956 PMID:18999306 |
Free, Available for download, Freely available | nif-0000-23346, r3d100012344 | https://www.force11.org/node/4646, https://doi.org/10.17616/R3J362 | SCR_002713 | BioPortal Knowledgebase | 2026-09-05 06:24:52 | 363 | ||||
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Molecular Simulation Trajectories Archive of a Villin Variant Resource Report Resource Website |
Molecular Simulation Trajectories Archive of a Villin Variant (RRID:SCR_002704) | Molecular Simulation Trajectories Archive of a Villin Variant | d spatial image, data or information resource, data set | An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations. | dynamic, atom, headpiece, molecular, simulation, solvent, protein folding, villin, molecule, trajectory, simulation, molecular dynamics trajectory |
is listed by: Biositemaps has parent organization: Simtk.org |
Stanford University; California; USA ; Graduate Fellowship ; NIH ; NIGMS R01-GM062868; NSF MCB-0317072 |
PMID:17950314 | Acknowledgement requested, Available in Gromacs and PDB formats. | nif-0000-23331 | SCR_002704 | 2026-09-05 06:24:52 | 0 | ||||||
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UCSF Chimera Resource Report Resource Website 1000+ mentions |
UCSF Chimera (RRID:SCR_004097) | Chimera | d visualization software, data processing software, software application, software resource | Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials. | molecular modeling, electron microscopy, interactive visualization and analysis, molecular structures |
is used by: Structure-function linkage database is listed by: 3DVC is listed by: SoftCite is related to: Integrative Modeling Platform is related to: UCSF ChimeraX is related to: UCSF ChimeraX has parent organization: Resource for Biocomputing Visualization and Informatics |
NCRR P41 RR001081; NIGMS P41 GM103311 |
PMID:15264254 | Restricted | nlx_143560 | http://plato.cgl.ucsf.edu/chimera/ | SCR_004097 | Chimera - an Extensible Molecular Modeling System, UCSF Chimera - an Extensible Molecular Modeling System | 2026-09-05 06:25:14 | 2257 | ||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Burroughs-Wellcome Fund ; Japan Society for the Promotion of Science ; NHGRI HG002096; NHGRI HG006039; NIGMS R01GM126567; NIGMS R35GM139504; NSF ABI 1661218 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-09-05 06:24:23 | 2774 | ||||
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Transporter Classification Database Resource Report Resource Website 100+ mentions |
Transporter Classification Database (RRID:SCR_004490) | TCDB, TC | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, data repository, database, production service resource, service resource, software application, software resource, source code, storage service resource | Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run. | membrane transport, protein sequence, transporter, bio.tools, FASEB list |
is recommended by: National Library of Medicine is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Diego; California; USA |
NIGMS GM1077402 | PMID:19022853 PMID:16381841 |
Free, Freely available | nlx_47724, biotools:tcdb | https://bio.tools/tcdb | SCR_004490 | Transporter Classification Database | 2026-09-05 06:25:20 | 343 | ||||
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U-Compare Resource Report Resource Website 1+ mentions |
U-Compare (RRID:SCR_004911) | U-Compare | data processing software, service resource, software application, software resource, text-mining software, workflow software | An integrated text mining / natural language processing system based on the Unstructured Information Management Architecture (UIMA) Framework. It allows interoperability of text mining tools and allows the creation of text mining workflows, comparison and visualization of tools. U-Compare can be launched straight from the web or downloaded. As the name implies comparison of components and workflows is a central feature of the system. U-Compare allows sets of components to be run in parallel on the same inputs and then automatically generates statistics for all possible combinations of these components. Once a workflow has been created in U-Compare it can be exported and shared with other users or used with other UIMA compatible tools and so in addition to comparison, U-Compare also functions as a general purpose workflow creation tool. It contains a repository of 50+ biomedical text mining components. These components are included in the U-Compare single-click-to-launch package, ready to use by just drag-and-drop. You can also use this repository independent from the U-Compare system. Link with Taverna It has a link with Taverna for scientific workflows, http://bioinformatics.oxfordjournals.org/content/26/19/2486.abstract, where you can use U-Compare and its workflow from within the Taverna workflow. There are two ways, the U-Compare Taverna plugin and the U-Compare command line mode as a Taverna activity. We have recently integrated it with Peter Murray-Rust''''s OSCAR for Chemistry (see http://www.nactem.ac.uk/cheta/) Web Demo: http://www.nactem.ac.uk/software/cheta/ | statistics, text mining, natural language processing, interoperability, comparison, workflow, computational linguistics |
is listed by: FORCE11 is related to: Taverna is related to: Chemistry Using Text Annotations is related to: Oscar3 has parent organization: University of Tokyo; Tokyo; Japan has parent organization: National Centre for Text Mining has parent organization: University of Colorado Denver; Colorado; USA |
NIGMS R01 GM083649-04; NLM R01 LM008111-07; NIGMS R01GM083649; NLM R01LM008111; NLM R01LM009254 |
PMID:19414535 | nlx_87780 | SCR_004911 | 2026-09-05 06:25:26 | 5 |
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