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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Minimal Information about any Sequence Controlled Vocabularies Resource Report Resource Website |
Minimal Information about any Sequence Controlled Vocabularies (RRID:SCR_010363) | MIXSCV | controlled vocabulary, data or information resource, ontology | Controlled vocabularies for the MIxS (Minimal Information about any Sequence) family of metadata checklists. See http://gensc.org/gc_wiki/index.php/MIxS for details on the MIxS checklists. | obo | is listed by: BioPortal | nlx_157481 | SCR_010363 | Minimal Information about any Sequence (MIxS) Controlled Vocabularies, MIxS Controlled Vocabularies | 2026-09-05 06:26:40 | 0 | ||||||||
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Gene Regulation Ontology Resource Report Resource Website |
Gene Regulation Ontology (RRID:SCR_010590) | GRO, BOOTStrep | controlled vocabulary, data or information resource, ontology | Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). | owl, genomic, proteomic, biological process, gene regulation, gene expression, gene, transcription factor, process, molecule, biological_process |
is listed by: BioPortal is listed by: OBO has parent organization: European Bioinformatics Institute |
nlx_157415, nlx_46399 | http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html, http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest | SCR_010590 | Gene Regulation Ontology - Ontological resource from the BOOTStrep project for the representation of gene regulation events | 2026-09-05 06:26:43 | 0 | |||||||
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Spatial Ontology Resource Report Resource Website |
Spatial Ontology (RRID:SCR_007860) | BSPO | controlled vocabulary, data or information resource, ontology | A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth. | obo | is listed by: BioPortal | SCR_007860 | 2026-09-05 06:26:15 | 0 | ||||||||||
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Human Dermatological Disease Ontology Resource Report Resource Website 1+ mentions |
Human Dermatological Disease Ontology (RRID:SCR_007648) | DERMO | controlled vocabulary, data or information resource, ontology | Ontology of human dermatologic disease | obo | is listed by: BioPortal | Dermatologic disease | nlx_157428 | SCR_007648 | 2026-09-05 06:26:14 | 1 | ||||||||
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Host Pathogen Interactions Ontology Resource Report Resource Website |
Host Pathogen Interactions Ontology (RRID:SCR_007647) | HPIO | controlled vocabulary, data or information resource, ontology | Ontology for host pathogen interactions in farmed animals | owl | is listed by: BioPortal | nlx_157427 | SCR_007647 | 2026-09-05 06:26:14 | 0 | |||||||||
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Stanford University; Stanford; California Resource Report Resource Website 50+ mentions |
Stanford University; Stanford; California (RRID:SCR_011538) | university | Private, non profit university in Stanford, California, USA for research and undergraduate and graduate studies. Known for its academic strength, wealth, proximity to Silicon Valley, and ranking as one of the world's top universities. Particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups. | private, university, institution, undergraduate, program, resource, graduate |
uses: ShareLaTeX uses: ReadCube uses: Scizzle uses: Sparrho uses: GenomeCompiler uses: LabArchives is affiliated with: Integrative Human Microbiome Project is affiliated with: Diabetes Epigenome Atlas is related to: Stanford Research Institute International 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: ShareLaTeX is related to: LabArchives is related to: Diabetic Foot Consortium is related to: GENSCAN is related to: Center for Expanded Data Annotation and Retrieval is parent organization of: MAXCHELATOR is parent organization of: Sea Urchin Embryology is parent organization of: SNPiR is parent organization of: GERP is parent organization of: Wnt homepage is parent organization of: Biozon is parent organization of: VectorDB- Molecular Biology Vector Sequence Database is parent organization of: HighWire Press is parent organization of: BFCounter is parent organization of: Clarity resources is parent organization of: PoissonSeq is parent organization of: Flybrain at Stanford is parent organization of: Stanford Genomics Service Center Core Facility is parent organization of: STRUCTURE is parent organization of: RVD is parent organization of: OpenSim is parent organization of: PharmGKB is parent organization of: JETTA is parent organization of: Phoenix is parent organization of: WEBMAXC STANDARD is parent organization of: Ontology Development and Information Extraction is parent organization of: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse is parent organization of: Phenotree is parent organization of: Quantitative Enrichment of Sequence Tags is parent organization of: WholeCellKB is parent organization of: Simbios is parent organization of: Neurogrid is parent organization of: T-lex is parent organization of: HighWire is parent organization of: Tissue Microarray Database is parent organization of: Stanford TMA Software is parent organization of: TMA-Combiner is parent organization of: Stanford Center for Biomedical Informatics Research is parent organization of: amide is parent organization of: Wnt Database is parent organization of: OligoGenome is parent organization of: HyBrow (Hypothesis Browser) is parent organization of: DataWrangler is parent organization of: BenchWise is parent organization of: Neurobiological Image Management System is parent organization of: Target genes of Wnt/beta-catenin signaling is parent organization of: HPMR - Human Plasma Membrane Receptome is parent organization of: LPFC: A Library of Protein Family Cores is parent organization of: YDPM - Yeast Deletion Project is parent organization of: SimTKCore is parent organization of: Postdoctoral Program for Veterinarians is parent organization of: Alizadehlab: MeeboChip and HeeboChip Open Source Project is parent organization of: Q-Value Software is parent organization of: LAGAN is parent organization of: xjView: A Viewing Program For SPM is parent organization of: Exon Array Browser is parent organization of: Coursera is parent organization of: iPOP is parent organization of: SSRL Structural Molecular Biology is parent organization of: SpliceMap is parent organization of: MAPP is parent organization of: SAM is parent organization of: Stanford University School of Medicine; California; USA is parent organization of: ProbCons is parent organization of: Genovo is parent organization of: American Parkinson's Disease Association Information and Referral Center is parent organization of: Sequencing of Candida Albicans is parent organization of: Jambalaya is parent organization of: Simbiome is parent organization of: SciTran is parent organization of: Brain RNA-Seq is parent organization of: CytoSPADE is parent organization of: BioPortal is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: STOP is parent organization of: NCBO Annotator is parent organization of: PubSearch is parent organization of: EM3D is parent organization of: Joint Center for Structural Genomics is parent organization of: ToRNADo is parent organization of: SGD is parent organization of: Stanford CNI is parent organization of: Stanford CoreNLP is parent organization of: GenomeSpace is parent organization of: Encode is parent organization of: OpenNeuro is parent organization of: Poldracklab Portal is parent organization of: Diabetes Epigenome Atlas is parent organization of: MrDiffusion is parent organization of: Stanford Center for Reproducible Neuroscience is parent organization of: Stanford Diabetes Research Center Diabetes Genomics Analysis Core is parent organization of: Biostrings is parent organization of: CIBERSORT is parent organization of: Shannon is parent organization of: VORTEX is parent organization of: Optogenetics Resource Center is parent organization of: Brain RNA-Seq is parent organization of: LeafCutter is parent organization of: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility is parent organization of: Stanford University Human Immune Monitoring Center Core Facility is parent organization of: Preseq is parent organization of: CRISPR-ERA is parent organization of: WEBMAXC EXTENDED is parent organization of: Stanford Graduate School of Business Data, Analytics, and Research Computing Core Facility is parent organization of: Stanford University Community of Shared Advanced Research Platforms is parent organization of: Stanford Sarafan Chemistry, Engineering and Medicine for Human Health Knowledge Centers Core Facility is parent organization of: Stanford Sarafan Protein Engineering Knowledge Center Core Facility is parent organization of: Stanford Sarafan Metabolomics Knowledge Center Core Facility is parent organization of: Stanford Nanofabrication Core Facility is parent organization of: Stanford Sarafan Macromolecular Structure Knowledge Center Core Facility is parent organization of: Stanford Sarafan Medicinal Chemistry Knowledge Center Core Facility is parent organization of: Stanford Graduate School of Business Behavioral Lab Core Facility is parent organization of: Stanford Nano Shared Core Facility is parent organization of: Stanford System Prototyping Core Facility is parent organization of: Stanford Graduate School of Business Library is parent organization of: Stanford Vincent V.C. Woo Sandbox Laboratory Core Facility is parent organization of: Stanford Behavioral and Functional Neuroscience Laboratory Core Facility is parent organization of: Stanford Neuroscience Gene Vector and Virus Core Facility is parent organization of: Stanford Visualization Laboratory Core Facility is parent organization of: Stanford Geochronology Cluster Core Facility is parent organization of: Stanford Stable Isotope Biogeochemistry Laboratory Core Facility is parent organization of: Stanford Neuroscience Preclinical Imaging Laboratory Core Facility is parent organization of: Stanford Environmental Measurements Core Facility is parent organization of: Stanford Microchemical Analysis Core Facility is parent organization of: Stanford Neuroscience Microscopy Service Core Facility is parent organization of: Stanford Doerr School of Sustainability Sample Preparation Laboratory Core Facility is parent organization of: Stanford SIGMA Shared Facility is parent organization of: Stanford School of Medicine Translational Applications Service Center Core Facility is parent organization of: Stanford University School of Medicine Beckman Center for Molecular and Genetic Medicine Core Facility is parent organization of: Stanford University Chemistry Department NMR Facility is parent organization of: Stanford University School of Medicine Biobank Core Facility is parent organization of: Stanford University School of Medicine Center for Innovation in In vivo Imaging Core Facility is parent organization of: Stanford University School of Medicine Richard M. Lucas Center for Imaging Core Facility is parent organization of: Stanford University School of Medicine PET/MRI Metabolic Service Center Core Facility is parent organization of: Stanford University School of Medicine In Vitro Biosafety Level3 Service Center Core Facility is parent organization of: Stanford University School of Medicine Human Pathology Histology Services Laboratory Core Facility is parent organization of: Stanford University School of Medicine Genetics Bioinformatics Service Center Core Facility is parent organization of: Stanford Canary Center Preclinical Imaging Core Facility is parent organization of: Stanford University School of Medicine Transgenic, Knockout and Tumor model Center Core Facility is parent organization of: Stanford University School of Medicine Veterinary Service Center Core Facility is parent organization of: Stanford University School of Medicine Cancer Institute Tissue Procurement Shared Resource Core Facility is parent organization of: Stanford University School of Medicine Clinical and Translational Research Unit Core Facility is parent organization of: Stanford University School of Medicine Institute for Stem Cell Biology and Regenerative Medicine FACS Core Facility is parent organization of: Stanford University School of Medicine Animal Diagnostic Laboratory Core Facility is parent organization of: Stanford University Computer Science Department Computer Core Facility is parent organization of: Stanford University Instrumentation Shop Core Facility is parent organization of: Stanford University Cyclotron and Radiochemistry Core Facility is parent organization of: Stanford University Biomaterials and Advanced Drug Delivery Laboratory Core Facility is parent organization of: Stanford University Chemistry Department Optics Core Facility is parent organization of: Stanford University School of Medicine Computational Services and Bioinformatics Core Facility is parent organization of: Stanford University School of Medicine Laboratory for Cell and Gene Medicine Core Facility is parent organization of: Stanford University Research Computing is parent organization of: Stanford University Physics Machine Shop Core Facility is parent organization of: Stanford University High Performance Computing Center Core Facility is parent organization of: Stanford Center for High Throughput Quantitative Biology Core Facility is parent organization of: Stanford University Quantitative Sciences Unit Core Facility is parent organization of: Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility is parent organization of: Stanford Spectrum Biostatistics Epidemiology and Research Design Core Facility is parent organization of: STRUCTURE is parent organization of: Stanford University Additive Manufacturing and Printing Core Facility is parent organization of: Stanford University Koret Human Neurosciences Community Laboratory Core Facility is parent organization of: Stanford University Microfluidics Foundry Core Facility is parent organization of: Stanford University School of Medicine Protein and Nucleic Acid Core Facility is parent organization of: WebProtege is parent organization of: Stanford Cryo-Electron Microscopy Center Core Facility is parent organization of: Stanford Geomicrobiology Shared Laboratories Core Facility is parent organization of: Stanford University Cosmogenic Isotope Lab Core Facility is parent organization of: Stanford Research Computing Core Facility is parent organization of: Stanford University Mineralogy and Petrology Lab Core Facility is parent organization of: Stanford University MicroCT Core Facility is parent organization of: Stanford Ecosystems Shared Laboratory Core Facility is parent organization of: DADA2 is parent organization of: OpenMM is parent organization of: Stanford CVI Biobank has organization facet: MARIA |
nlx_44253, grid.168010.e, Wikidata:Q41506, Crossref funder ID:100005492, ISNI:419368956 | https://ror.org/00f54p054 | SCR_011538 | 2026-09-05 06:27:07 | 70 | |||||||||
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RNA Ontology Resource Report Resource Website 1+ mentions |
RNA Ontology (RRID:SCR_003470) | RNAO | controlled vocabulary, data or information resource, ontology | An ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs. | owl, obo, molecular structure, molecular, rna, sequence, alignment, structure, base pairing, base stacking, motif |
is listed by: BioPortal is listed by: OBO is listed by: Google Code |
Free, Available for download, Freely available | nlx_157566 | http://purl.bioontology.org/ontology/RNAO, http://rnao.googlecode.com/svn/trunk/rnao.obo | SCR_003470 | 2026-09-05 06:29:56 | 1 | |||||||
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Influenza Ontology Resource Report Resource Website |
Influenza Ontology (RRID:SCR_003346) | FLU | controlled vocabulary, data or information resource, ontology | An application ontology established by a collaborative group of influenza researchers that includes consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS) | owl, health, pathological, organismal, cellular, sequence, surveillance |
is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology has parent organization: University of Maryland; Maryland; USA |
Influenza | Free, Freely available | nlx_157440 | http://purl.obolibrary.org/obo/flu.owl, http://influenzaontologywiki.igs.umaryland.edu/ | http://purl.bioontology.org/ontology/FLU | SCR_003346 | 2026-09-05 06:29:56 | 0 | |||||
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Mouse Experimental Design Ontology Resource Report Resource Website |
Mouse Experimental Design Ontology (RRID:SCR_003879) | MEDO | controlled vocabulary, data or information resource, ontology | Ontology of experimental design for high-throughput mouse analysis pipelines. | owl | is listed by: BioPortal | nlx_157487 | SCR_003879 | 2026-09-05 06:29:57 | 0 | |||||||||
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Cell Type Ontology Resource Report Resource Website 10+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | controlled vocabulary, data or information resource, ontology | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | cellontology.org, Obo-cell-type, Cell Ontology | 2026-09-05 06:29:57 | 10 | |||
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Skin Physiology Ontology Resource Report Resource Website |
Skin Physiology Ontology (RRID:SCR_006253) | SPO | controlled vocabulary, data or information resource, ontology | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | owl | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157589 | SCR_006253 | 2026-09-05 06:29:59 | 0 | ||||||||
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Physician Data Query Resource Report Resource Website 1+ mentions |
Physician Data Query (RRID:SCR_006833) | PDQ | clinical trial, controlled vocabulary, data or information resource, database, ontology, people resource, registry | NCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in Spanish. | adult, pediatric, child, alternative, breast, clinical trial, colorectal, hypercalcemia, legal, lung, medicine, medullary, nausea, ovarian, pain, pathophysiology, pediatric, pharmaceutical, physician, prevention, prognosis, prostate, psychosocial, query, risk factor, screening, social, syndrome, thyroid, treatment, umls, genetics, medical, drug, peer review |
is listed by: BioPortal has parent organization: National Cancer Institute |
Cancer, Cancer-related condition | NCI | nif-0000-21318 | SCR_006833 | PDQ - NCI''s Comprehensive Cancer Database | 2026-09-05 06:30:00 | 2 | ||||||
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suicideonto Resource Report Resource Website |
suicideonto (RRID:SCR_010452) | suicideo | controlled vocabulary, data or information resource, ontology | Ontology of suicidology. | owl | is listed by: BioPortal | nlx_157633 | SCR_010452 | 2026-09-05 06:30:03 | 0 | |||||||||
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Human Developmental Anatomy Ontology abstract version 2 Resource Report Resource Website |
Human Developmental Anatomy Ontology abstract version 2 (RRID:SCR_010337) | EHDAA2 | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just ''heart'' really means ''heart (CS 9-20)''. Timing details will be added to the abstract version of the ontology in a future release. | obo | is listed by: BioPortal | nlx_157430 | SCR_010337 | 2026-09-05 06:30:03 | 0 | |||||||||
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Ontology of Data Mining Investigations Resource Report Resource Website |
Ontology of Data Mining Investigations (RRID:SCR_010394) | ONTODM-KDD | controlled vocabulary, data or information resource, ontology | Ontology for representing data mining investigations. Its goal is to allow the representation of knowledge discovery processes and be general enough to represent the data mining investigations. The ontology is based on the CRISP-DM process methodology. | owl | is listed by: BioPortal | nlx_157527 | SCR_010394 | 2026-09-05 06:30:03 | 0 | |||||||||
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Traditional Medicine Meridian Value Sets Resource Report Resource Website |
Traditional Medicine Meridian Value Sets (RRID:SCR_010436) | TM-MER | controlled vocabulary, data or information resource, ontology | Ontology of the meridian value set used in the International Classification of Traditional Medicine. | owl | is listed by: BioPortal | nlx_157613 | SCR_010436 | 2026-09-05 06:30:03 | 0 | |||||||||
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Cell Line Ontology by Mahadevan Resource Report Resource Website |
Cell Line Ontology by Mahadevan (RRID:SCR_010281) | MCCL | controlled vocabulary, data or information resource, ontology | A comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format. | owl, cell line | is listed by: BioPortal | Normal, Pathologic | nlx_157356 | SCR_010281 | Cell Line Ontology (by Mahadevan) | 2026-09-05 06:30:03 | 0 | |||||||
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National Drug File - Reference Terminology Resource Report Resource Website |
National Drug File - Reference Terminology (RRID:SCR_010372) | NDFRT | controlled vocabulary, data or information resource, ontology | Ontology of National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11 | umls | is listed by: BioPortal | nlx_157500 | SCR_010372 | 2026-09-05 06:30:03 | 0 | |||||||||
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Clinical Signs and Symptoms Ontology Resource Report Resource Website |
Clinical Signs and Symptoms Ontology (RRID:SCR_007226) | CSSO | controlled vocabulary, data or information resource, ontology | An ontology for describing clinical signs and symptoms. | owl | is listed by: BioPortal | nlx_157365 | http://mdb.bio.titech.ac.jp/csso | SCR_007226 | 2026-09-05 06:30:01 | 0 | ||||||||
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Cell Cycle Ontology Resource Report Resource Website |
Cell Cycle Ontology (RRID:SCR_007085) | CCO | controlled vocabulary, data or information resource, ontology | An application ontology integrating knowledge about the eukaryotic cell cycle. | obo | is listed by: BioPortal | nlx_157355 | http://www.semantic-systems-biology.org/cco/ | SCR_007085 | 2026-09-05 06:30:01 | 0 |
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