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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Stanford Center for Biomedical Informatics Research Resource Report Resource Website |
Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) | BMIR | laboratory portal, data or information resource, organization portal, portal | Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences. | biomedicine, informatics |
has parent organization: Stanford University; Stanford; California is parent organization of: CLENCH is parent organization of: BioPortal is parent organization of: Center for Expanded Data Annotation and Retrieval is parent organization of: Protege is parent organization of: WebProtege |
nlx_149147 | SCR_005698 | Stanford Medical Informatics | 2026-02-14 02:01:09 | 0 | ||||||||
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Cell Line Ontology Resource Report Resource Website 1+ mentions |
Cell Line Ontology (RRID:SCR_005840) | CLO | data or information resource, ontology, controlled vocabulary | A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan. | cell line, owl, ontology, standardization, information integration |
is listed by: BioPortal is listed by: OBO is related to: Cell Line Knowledge Base has parent organization: University of Michigan Medical School; Michigan; USA |
The community can contribute to this resource | nlx_149363 | http://bioportal.bioontology.org/ontologies/1245 http://purl.obolibrary.org/obo/clo.owl |
SCR_005840 | 2026-02-14 02:01:01 | 2 | |||||||
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Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology Resource Report Resource Website |
Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology (RRID:SCR_006776) | RPO | data or information resource, ontology, controlled vocabulary | A controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users'' communities | owl | is listed by: BioPortal | Primary Immunodeficiency Disease | nlx_157576 | SCR_006776 | Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology, RAPID phenotype ontology | 2026-02-14 02:01:15 | 0 | |||||||
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C. elegans Development Vocabulary Resource Report Resource Website |
C. elegans Development Vocabulary (RRID:SCR_006811) | WB-LS | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the development of Caenorhabditis elegans. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157346 | SCR_006811 | 2026-02-14 02:01:23 | 0 | |||||||||
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C. elegans Gross Anatomy Vocabulary Resource Report Resource Website |
C. elegans Gross Anatomy Vocabulary (RRID:SCR_006835) | WB-BT | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157347 | SCR_006835 | 2026-02-14 02:01:23 | 0 | |||||||||
|
Brucellosis Ontology Resource Report Resource Website |
Brucellosis Ontology (RRID:SCR_006795) | IDOBRU | data or information resource, ontology, controlled vocabulary | A biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium. | owl | is listed by: BioPortal | Zoonotic disease brucellosis | nlx_157345 | http://www.phidias.us/bbp/idobru/index.php | SCR_006795 | 2026-02-14 02:01:23 | 0 | |||||||
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C. elegans Phenotype Vocabulary Resource Report Resource Website |
C. elegans Phenotype Vocabulary (RRID:SCR_006924) | WB-PHENOTYPE | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of Caenorhabditis elegans phenotypes. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157348 | SCR_006924 | 2026-02-14 02:01:18 | 0 | |||||||||
|
Cerrado concepts and plant community dynamics Resource Report Resource Website 1+ mentions |
Cerrado concepts and plant community dynamics (RRID:SCR_007174) | CCON | data or information resource, ontology, controlled vocabulary | Ontology of Cerrado wood plant dynamics to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate. | owl | is listed by: BioPortal | nlx_157361 | SCR_007174 | 2026-02-14 02:01:27 | 2 | |||||||||
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Cardiac Electrophysiology Ontology Resource Report Resource Website |
Cardiac Electrophysiology Ontology (RRID:SCR_007065) | EP | data or information resource, ontology, controlled vocabulary | Ontology that contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels. | owl |
is listed by: BioPortal has parent organization: CardioVascular Research Grid (CVRG) |
nlx_157352 | SCR_007065 | 2026-02-14 02:01:26 | 0 | |||||||||
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Cereal Plant Gross Anatomy Ontology Resource Report Resource Website |
Cereal Plant Gross Anatomy Ontology (RRID:SCR_007061) | GRO-CPGA | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology, http://bioportal.bioontology.org/ontologies/1587. | obo |
is listed by: BioPortal is related to: Plant Ontology has parent organization: Gramene |
nlx_157359 | http://www.gramene.org/plant_ontology/ | SCR_007061 | 2026-02-14 02:01:27 | 0 | ||||||||
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Cell Culture Ontology Resource Report Resource Website 1+ mentions |
Cell Culture Ontology (RRID:SCR_007096) | CCONT | data or information resource, ontology, controlled vocabulary | ontology for the formal representation of cell lines and their correspnding culture conditions. | owl | is listed by: BioPortal | nlx_157354 | SCR_007096 | 2026-02-14 02:01:26 | 1 | |||||||||
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BIRNLex Resource Report Resource Website |
BIRNLex (RRID:SCR_007326) | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Lexicon that provides entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. These sources may include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer''s disease or schizophrenia. The BIRNLex is a specialized vocabulary utilized by BIRN scientists in the context of their research, including common terms for neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance required for large-scale data integration across disparate experimental studies.The BIRNLex offers well defined terms from several domains of importance to neuroimaging across scales. | controlled vocabulary, owl |
is listed by: BioPortal has parent organization: Drexel University College of Medicine; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00199 | http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/ | SCR_007326 | BIRNLex | 2026-02-14 02:01:24 | 0 | |||||||
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Computational Neuroscience Ontology Resource Report Resource Website |
Computational Neuroscience Ontology (RRID:SCR_007289) | CNO | data or information resource, ontology, controlled vocabulary | A controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations. | owl | is listed by: BioPortal | Creative Commons Attribution License, v3 Unported | nlx_157372 | SCR_007289 | 2026-02-14 02:01:23 | 0 | ||||||||
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Solanaceae Phenotype Ontology Resource Report Resource Website |
Solanaceae Phenotype Ontology (RRID:SCR_007832) | SPTO | data or information resource, ontology, controlled vocabulary | Ontology for Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance. | obo | is listed by: BioPortal | nlx_157592 | SCR_007832 | 2026-02-14 02:01:34 | 0 | |||||||||
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Computer-Based Patient Record Ontology Resource Report Resource Website |
Computer-Based Patient Record Ontology (RRID:SCR_007540) | CPRO | data or information resource, ontology, controlled vocabulary | A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR) | owl | is listed by: BioPortal | nlx_157375 | https://code.google.com/p/cpr-ontology/ | SCR_007540 | 2026-02-14 02:01:29 | 0 | ||||||||
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Soy Ontology Resource Report Resource Website |
Soy Ontology (RRID:SCR_007847) | SOY | data or information resource, ontology, controlled vocabulary | Growth, trait and development ontology for soybean | obo |
is listed by: BioPortal has parent organization: SoyBase |
nlx_157593 | SCR_007847 | 2026-02-14 02:01:34 | 0 | |||||||||
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Healthcare Common Procedure Coding System Resource Report Resource Website |
Healthcare Common Procedure Coding System (RRID:SCR_007598) | HCPCS | data or information resource, ontology, controlled vocabulary | Ontology for the healthcare common procedure coding system. | umls | is listed by: BioPortal | nlx_157426 | SCR_007598 | 2026-02-14 02:01:35 | 0 | |||||||||
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Drug Interaction Knowledge Base Ontology Resource Report Resource Website |
Drug Interaction Knowledge Base Ontology (RRID:SCR_007591) | DIKB | data or information resource, ontology, controlled vocabulary | An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence. | owl | is listed by: BioPortal | PMID:19435613 | nlx_157392 | SCR_007591 | 2026-02-14 02:01:29 | 0 | ||||||||
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Congenital Heart Defects Ontology Resource Report Resource Website 50+ mentions |
Congenital Heart Defects Ontology (RRID:SCR_007584) | CHD | data or information resource, ontology, controlled vocabulary | An ontology that describes the Congenital Heart Defects data. | owl | is listed by: BioPortal | Congenital Heart Defect | nlx_157376 | SCR_007584 | 2026-02-14 02:01:33 | 61 | ||||||||
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Surgical Secondary Events Resource Report Resource Website |
Surgical Secondary Events (RRID:SCR_007894) | SSE | data or information resource, ontology, controlled vocabulary | Memorial Sloan-Kettering Cancer Center''s ontology of surgical secondary events (adverse events). | owl | is listed by: BioPortal | SCR_007894 | 2026-02-14 02:01:34 | 0 |
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