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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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QUDT Resource Report Resource Website 1+ mentions |
QUDT (RRID:SCR_010416) | QUDT | data or information resource, ontology, controlled vocabulary | Collection of ontologies that define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units. | owl | is listed by: BioPortal | nlx_157564 | SCR_010416 | Quantities Units Dimensions and Types Ontology, QUDT - Quantities Units Dimensions and Data Types Ontologies | 2026-02-14 02:01:46 | 1 | ||||||||
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Ontology for MicroRNA Target Prediction Resource Report Resource Website |
Ontology for MicroRNA Target Prediction (RRID:SCR_010387) | OMIT | data or information resource, ontology, controlled vocabulary | Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans'' various diseases and biological processes (usually through miRs'' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth. | obo | is listed by: BioPortal | nlx_157519 | SCR_010387 | 2026-02-14 02:01:58 | 0 | |||||||||
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Role Ontology Resource Report Resource Website |
Role Ontology (RRID:SCR_010420) | ROLEO | data or information resource, ontology, controlled vocabulary | Ontology in the domain of role classification that aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles. | owl | is listed by: BioPortal | nlx_157578 | SCR_010420 | 2026-02-14 02:01:46 | 0 | |||||||||
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Infectious Disease Ontology Resource Report Resource Website |
Infectious Disease Ontology (RRID:SCR_010345) | IDO | data or information resource, ontology, controlled vocabulary | Ontologies designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases. Please note: The ontology metrics displayed by BioPortal do not distinguish IDO-developed terms from terms imported from other ontologies. | owl | is listed by: BioPortal | Infectious disease | nlx_157439 | SCR_010345 | 2026-02-14 02:01:57 | 0 | ||||||||
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International Classification of External Causes of Injuries Resource Report Resource Website 1+ mentions |
International Classification of External Causes of Injuries (RRID:SCR_010348) | ICECI | data or information resource, ontology, controlled vocabulary | A system of classifications to enable systematic description of how injuries occur. It is designed especially to assist injury prevention. It was originally designed for use in settings in which information is recorded in a way that allows statistical reporting--for example, injury surveillance based on collection of information about cases attending a sample of hospital emergency departments. It has also been found useful for other purposes. For example, it has been used as a reference classification during revision of another classification, to record risk-factor exposure of children in a cohort study, as the basis for special-purpose classifications and in a growing number of other ways. | owl | is listed by: BioPortal | nlx_157447 | SCR_010348 | 2026-02-14 02:01:57 | 1 | |||||||||
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International Classification of Diseases Version 10 - Clinical Modification Resource Report Resource Website |
International Classification of Diseases Version 10 - Clinical Modification (RRID:SCR_010350) | ICD10CM | data or information resource, ontology, controlled vocabulary | Ontology of the International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01 | umls | is listed by: BioPortal | nlx_157449 | SCR_010350 | 2026-02-14 02:01:45 | 0 | |||||||||
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Maize Gross Anatomy Ontology Resource Report Resource Website |
Maize Gross Anatomy Ontology (RRID:SCR_010353) | ZEA | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157462 | http://www.maizemap.org/ | SCR_010353 | 2026-02-14 02:01:58 | 0 | |||||||
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Major Histocompatibility Complex Ontology Resource Report Resource Website |
Major Histocompatibility Complex Ontology (RRID:SCR_010354) | MHC | data or information resource, ontology, controlled vocabulary | Ontology that contains terms necessary for describing and categorizing concepts related to Major Histocompatibility Complex, in general, for a number of model species, and also for humans. | owl | is listed by: BioPortal | nlx_157463 | SCR_010354 | MaHCO, MaHCO - An MHC Ontology | 2026-02-14 02:01:45 | 0 | ||||||||
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Microbial Culture Collection Vocabulary Resource Report Resource Website |
Microbial Culture Collection Vocabulary (RRID:SCR_010361) | MCCV | data or information resource, ontology, controlled vocabulary | Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers | owl | is listed by: BioPortal | nlx_157478 | SCR_010361 | 2026-02-14 02:01:57 | 0 | |||||||||
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Minimal Information about any Sequence Ontology Resource Report Resource Website |
Minimal Information about any Sequence Ontology (RRID:SCR_010364) | MIXS | data or information resource, ontology, controlled vocabulary | Ontology providing an RDF representation of the MIxS (Minimal Information about any Sequence) family of checklists. | owl | is listed by: BioPortal | nlx_157482 | SCR_010364 | 2026-02-14 02:01:45 | 0 | |||||||||
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NIF Dysfunction Ontlogy Resource Report Resource Website |
NIF Dysfunction Ontlogy (RRID:SCR_010365) | NIFDYS | data or information resource, ontology, controlled vocabulary | Ontology that contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon provided entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It was built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It used an abstract biomedical layer on top of that - OBO-UBO which was constructed as a proposal to the OBO Foundry. This was meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex biomaterial entities have already been factored to separately maintained ontology - BIRNLexBiomaterialEntity.owl which this BIRNLex-Main.owl file imports. The Ontology of Biomedical Investigation (OBI) is also imported and forms the foundation for the formal description of all experiment-related artifacts. The BIRNLex will serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease. | owl |
is listed by: BioPortal has parent organization: Neuroscience Information Framework |
nlx_157493 | SCR_010365 | Neuroscience Information Framework (NIF) Dysfunction Ontlogy, Neuroscience Information Framework Dysfunction Ontlogy | 2026-02-14 02:01:57 | 0 | ||||||||
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University of California at San Francisco; California; USA Resource Report Resource Website 1+ mentions |
University of California at San Francisco; California; USA (RRID:SCR_010605) | UCSF | university | Public research university in San Francisco, California. Part of University of California system. Dedicated entirely to health sciences. Major center of medical and biological research and teaching. Ranked as one of top universities in biomedical field in USA and around world. | institution, university, health science, medical, biological, teaching, center, biomedical |
is affiliated with: Diabetes Research Centers is related to: NCIRE is related to: ONE Study is related to: Alzheimers Disease Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: Diabetic Foot Consortium has parent organization: University of California; California; USA is parent organization of: DOCK is parent organization of: MochiView is parent organization of: Kravitz Dataset 2 is parent organization of: uManager is parent organization of: UCSF Brain Tumor Tissue Bank is parent organization of: CryptoBase is parent organization of: Resource for Biocomputing Visualization and Informatics is parent organization of: Hyperpolarized MRI Technology Resource Center is parent organization of: Sherlock is parent organization of: Center for Imaging of Neurodegenerative Diseases is parent organization of: WikiPathways is parent organization of: International Gene Trap Consortium is parent organization of: Microstructural correlation toolbox is parent organization of: NUTMEG is parent organization of: AltAnalyze - Alternative Splicing Analysis Tool is parent organization of: Integrative Modeling Platform is parent organization of: UCSF Spot is parent organization of: Allelic Variations of The XP Genes is parent organization of: Edinburgh Postnatal Depression Scale is parent organization of: AIDS and Cancer Specimen Resource is parent organization of: UCSF DNA Bank is parent organization of: Babel is parent organization of: UCSF DataShare is parent organization of: Scientific Data Sharing Project is parent organization of: ModBase is parent organization of: UCSF Laboratory for Visual Neuroscience is parent organization of: UCSF AIDS Specimen Bank is parent organization of: Gene Map Annotator and Pathway Profiler is parent organization of: ExPANdS is parent organization of: UCSF Center for AIDS Prevention Studies (CAPS) is parent organization of: HOLLOW is parent organization of: MAPPFinder is parent organization of: iBioSeminars is parent organization of: Bioelectromagnetism Matlab Toolbox is parent organization of: UCSF Brain Tumor Tissue Bank is parent organization of: Krogan Lab Interactome Database is parent organization of: BayGenomics is parent organization of: CanPredict is parent organization of: MODELLER is parent organization of: DeRisi Lab is parent organization of: CTSpedia is parent organization of: Kravitz Dataset1 is parent organization of: UCSF Helen Diller Family Comprehensive Cancer Center is parent organization of: Clinical Research Resource HUB is parent organization of: National Bio-Organic Biomedical Mass Spectrometry Resource Center is parent organization of: Program to Reduce Incontinence by Diet and Exercise is parent organization of: Brain Health Registry is parent organization of: The Li Lab at UCSF is parent organization of: UCSF Nikon Imaging Center is parent organization of: UCSF School of Medicine; California; USA is parent organization of: Microarrays.org is parent organization of: University of California, San Francisco School of Pharmacy is parent organization of: PRICE is parent organization of: HMMSplicer is parent organization of: ArrayOligoSelector is parent organization of: stepNorm is parent organization of: National Center for X-ray Tomography is parent organization of: SURPI is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging is parent organization of: PSCBS is parent organization of: Sparky is parent organization of: Cytokine Registry is parent organization of: Protein Prospector is parent organization of: University of California San Francisco Diabetes Research Center Mouse Genetics Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Islet Production Core Facility is parent organization of: University of California San Francisco Parnassus Flow Cytometry Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Lentiviral RNAi Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Microscopy Core Facility is parent organization of: University of California San Francisco Diabetes Research Center is parent organization of: University of California San Francisco Diabetes Research Center Mouse Metabolism Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Mouse Metabolism and Imaging Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Human Metabolism Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Genetics and Genomics Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center is parent organization of: Cystic Fibrosis Center - University of California San Francisco is parent organization of: UCSF ChimeraX is parent organization of: MotionCor2 is parent organization of: Clonotator is parent organization of: FoXS is parent organization of: covidcounties.org is parent organization of: DoubletFinder is parent organization of: syndRomics is parent organization of: PhotometryBox is parent organization of: University of California at San Francisco Immunology Lab Core Facility is parent organization of: Similarity Ensemble Approach is parent organization of: University of California at San Francisco Advanced Microscopy Core Facility is parent organization of: University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility is parent organization of: UCSF Helen Diller Family Comprehensive Cancer Center Flow and Cell Sorting Core Facility |
nlx_57854, GRID grid.266102.1; ISNI 0000 0001 2297 6811; Crossref Funder ID 100008069; Wikidata Q1061104 | https://ror.org/043mz5j54 | SCR_010605 | UC San Francisco, The University of California, San Francisco, University of California San Francisco, University of California at San Francisco | 2026-02-14 02:02:01 | 9 | |||||||
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vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2026-02-14 02:02:02 | 58 | ||||||||||
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IFOMIS Resource Report Resource Website |
IFOMIS (RRID:SCR_010604) | IFOMIS | knowledge environment, data or information resource, narrative resource, standard specification | The Institute for Formal Ontology and Medical Information Science (IFOMIS) comprehends an interdisciplinary research group, with members from Philosophy, Computer and Information Science, Logic, Medicine, and Medical Informatics, focusing on theoretically grounded research in both formal and applied ontology. Its goal is to develop a formal ontology that will be applied and tested in the domain of medical and biomedical information science. |
has parent organization: Saarland University; Saarbrucken; Germany is parent organization of: BFO |
Alexander von Humboldt-Stiftung | nlx_51151 | SCR_010604 | Institute for Formal Ontology and Medical Information Science | 2026-02-14 02:02:02 | 0 | ||||||||
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MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-02-14 02:02:02 | 463 | |||||||
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Life Extension Foundation Resource Report Resource Website |
Life Extension Foundation (RRID:SCR_010574) | institution | Established in 1980, the Life Extension Foundation is a nonprofit organization, whose long-range goal is to radically extend the healthy human lifespan by discovering scientific methods to control aging and eradicate disease. The largest organization of its kind in the world, the Life Extension Foundation has always been at the forefront of discovering new scientific breakthroughs for use in developing novel disease prevention and treatment protocols to improve the quality and length of human life. Through its private funding of research programs aimed at identifying and developing new therapies to slow and even reverse the aging process, the Life Extension Foundation seeks to reduce, and ultimately eliminate, such age-related killers as heart disease, stroke, cancer and Alzheimer''s disease. Long-time members are keenly aware of the scientific research that Life Extension Foundation funds to develop validated methods to slow and reverse the aging process. Less known is Life Extension''s multi-prong program to develop safer and more effective cancer therapies. One reason we focus so heavily on cancer research is that this dreaded disease represents a roadblock in our ability to develop effective means to combat aging. | is parent organization of: Life Extension | Aging | ISNI: 0000 0001 0300 2958, nlx_41735, grid.490868.b | https://ror.org/02vzd2x77 | SCR_010574 | 2026-02-14 02:02:01 | 0 | |||||||||
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Gossamer Resource Report Resource Website 1+ mentions |
Gossamer (RRID:SCR_010612) | Gossamer | software resource | A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability. | is listed by: OMICtools | OMICS_00017 | SCR_010612 | Gossamer: A Space-Efficient Genome Assembler | 2026-02-14 02:02:02 | 1 | |||||||||
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NeuroLOG Resource Report Resource Website 500+ mentions |
NeuroLOG (RRID:SCR_010582) | knowledge environment, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The NeuroLOG consortium is addressing: *Management and access of partly structured data, heterogeneous and distributed in an open environment. *Access control and protection of private medical data. *Control of workflows implied in complex computing process on grid infrastructures. *Extraction and quantification of relevant parameters for different pathologies: Multiple sclerosis, Brain Vascular Stroke, Brain tumors Four application pipelines have been proposed in the context of the project. The pipelines are formalized using the Scufl data flow language. *Multiple Sclerosis image analysis pipelines *Brain Stroke application pipeline (from GIN) *Stroke / tumours Anacom application pipeline (from IFR49) Different softwares developed and/or used in this project are presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is related to: OntoNeuroLOG has parent organization: University of Nice Sophia Antipolis; Nice; France |
French National Research Agency contract ANR-06-TLOG-024 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44086 | SCR_010582 | NeuroLOG Project, NeuroLOG | 2026-02-14 02:02:00 | 546 | ||||||||
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Meraculous Resource Report Resource Website 10+ mentions |
Meraculous (RRID:SCR_010700) | Meraculous | software resource | An algorithm for de novo genome assembly with short paired-end reads. | is listed by: OMICtools | OMICS_00021 | SCR_010700 | Meraculous: De Novo Genome Assembly with Short Paired-End Reads | 2026-02-14 02:02:03 | 39 | |||||||||
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UBERON Resource Report Resource Website 50+ mentions |
UBERON (RRID:SCR_010668) | UBERON | data or information resource, ontology, controlled vocabulary | An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human. | anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, obo |
is used by: Neuroscience Information Framework is listed by: BioPortal is related to: Gene Ontology has parent organization: OBO |
ARRA ; NSF ; NHGRI 5R01HG004838; NHGRI P41HG002273; DOE DE-AC02-05CH11231; NCRR 1U24RR029825-01; NHGRI P41HG002273-09S1 |
PMID:22293552 | nlx_74404 | SCR_010668 | Uber anatomy ontology, Uber-anatomy ontology | 2026-02-14 02:02:02 | 59 |
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