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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DelPhi Resource Report Resource Website 1000+ mentions |
DelPhi (RRID:SCR_008669) | simulation software, software application, software resource | DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast, accurate, and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions. DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems. Features of DelPhi include solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; and estimation of the best relaxation parameter at run time. | Poisson-Boltzmann equation, electrostatics, simulation software, mixed salt soluton |
has parent organization: Columbia University; New York; USA has parent organization: Howard Hughes Medical Institute |
NSF DBI-9904841 | nif-0000-33392 | SCR_008669 | 2026-08-09 09:04:59 | 1448 | |||||||||
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Disease Phenotype Ontology Resource Report Resource Website 10+ mentions |
Disease Phenotype Ontology (RRID:SCR_008687) | data or information resource, controlled vocabulary, ontology | The Disease Ontology group has developed a set of standard representations of phenotypes associated with diseases useful in bioinformatics applications. These are formalized into an ontological structure and are encoded in OWL. Neurodegenerative diseases have a wide and complex range of biological and clinical symptoms. While neurodegenerative diseases share many pathological features in common, they also contain unique signatures. Animal models of these disorders are key to translational research. However, animal models typically replicate only a subset of disease features or display features that are only indirectly related to a given disorder, whose relationship to the human condition may be across several diseases. Matching animal models to human diseases is therefore a significant informatics challenge. We have been working to develop ontologies that capture essential features of neurodegenerative diseases and associated animal models in a way that allows more flexible matching of animal models to human disorders and in a way that makes explicit commonalities and differences among animal models and human neurodegenerative disease. Creating ontologies for diseases and disorders is a very challenging task (Gupta et al., 2003) because of the complexity of the disorders and because of the limitations of current ontology formalisms. In order to simplify the approach and make it practical for use in information systems, we have focused on formal descriptions of phenotypes associated with diseases and animal models rather than on a formal model of the disease process itself. We employ the modular ontologies developed as part of the Neuroscience Information Framework (NIF: http://nif.nih.gov) and the Phenotype and Trait Ontology (PATO), an ontology of qualities associated with biological phenotypes, to create a flexible template for creating phenotypic statements at the class and instance levels. We show how these phenotypes can be used to look for commonalities across multiple neurodegenerative conditions and animal models. | has parent organization: University of California at San Diego; California; USA | nif-0000-35922 | SCR_008687 | DPO | 2026-08-09 09:05:01 | 42 | ||||||||||
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Biodiversity Ontology Resource Report Resource Website |
Biodiversity Ontology (RRID:SCR_010204) | BOF | data or information resource, controlled vocabulary, ontology | An ontology of biodiversity of INPA | owl | is listed by: BioPortal | nlx_157331 | SCR_010204 | 2026-08-09 09:05:17 | 0 | |||||||||
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Gene Expression Ontology Resource Report Resource Website 1+ mentions |
Gene Expression Ontology (RRID:SCR_010326) | GEXO | data or information resource, controlled vocabulary, ontology | An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations. | obo | is listed by: BioPortal | nlx_157413 | SCR_010326 | 2026-08-09 09:05:19 | 6 | |||||||||
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General Formal Ontology Resource Report Resource Website |
General Formal Ontology (RRID:SCR_010328) | GFO | data or information resource, controlled vocabulary, ontology | A top-level ontology integrating objects and processes. | owl | is listed by: BioPortal | nlx_157416 | http://www.onto-med.de/ontologies/gfo/ | SCR_010328 | 2026-08-09 09:05:35 | 0 | ||||||||
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General Formal Ontology for Biology Resource Report Resource Website |
General Formal Ontology for Biology (RRID:SCR_010329) | GFO-BIO | data or information resource, controlled vocabulary, ontology | A biological core ontology built on the General Formal Ontology. | owl | is listed by: BioPortal | nlx_157417 | http://www.onto-med.de/ontologies/gfo-bio/ | SCR_010329 | 2026-08-09 09:05:19 | 0 | ||||||||
|
Cognitive Atlas Ontology Resource Report Resource Website |
Cognitive Atlas Ontology (RRID:SCR_010295) | COGAT | data or information resource, controlled vocabulary, ontology | Ontology that characterizes the state of current thought in cognitive science. It defines a set of mental concepts along with a set of mental tasks, and the measurement relations between those classes. | owl |
is listed by: BioPortal has parent organization: Cognitive Atlas |
nlx_157368 | SCR_010295 | 2026-08-09 09:05:35 | 0 | |||||||||
|
Common Terminology Criteria for Adverse Events Resource Report Resource Website 10+ mentions |
Common Terminology Criteria for Adverse Events (RRID:SCR_010296) | CTCAE | data or information resource, controlled vocabulary, ontology | A coding system for reporting adverse events that occur in the course of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0 and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National Cancer Institution (NCI). | owl |
is listed by: BioPortal has parent organization: National Cancer Institute |
Cancer | nlx_157370 | SCR_010296 | 2026-08-09 09:05:18 | 14 | ||||||||
|
Comparative Data Analysis Ontology Resource Report Resource Website |
Comparative Data Analysis Ontology (RRID:SCR_010297) | CDAO | data or information resource, controlled vocabulary, ontology | A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science | owl, biology, evolution, computer science, comparative analysis, phylogenetic tree, operational taxonomic unit, compared character, molecular |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge |
Public domain | nlx_157371 | http://purl.bioontology.org/ontology/CDAO, http://purl.obolibrary.org/obo/cdao.owl | SCR_010297 | 2026-08-09 09:05:28 | 0 | |||||||
|
Genome Component Ontology Resource Report Resource Website 1+ mentions |
Genome Component Ontology (RRID:SCR_010330) | GCO | data or information resource, controlled vocabulary, ontology | Ontology to define the abstract division of the total genetic information of an organism by its physical separation into different components, thereby providing a high level reference point to which more specific descriptions of the characteristics of these components can be linked. | owl | is listed by: BioPortal | nlx_157418 | SCR_010330 | 2026-08-09 09:05:29 | 1 | |||||||||
|
Content Archive Resource Exchange Lexicon Resource Report Resource Website |
Content Archive Resource Exchange Lexicon (RRID:SCR_010298) | CARELEX | data or information resource, controlled vocabulary, ontology | Categories and terms used to classify content (documents, images, etc) in electronic content repositories for life science / BioPharma. Initial version contains content model for use with clinical trial electronic Trial Master Files or eTMF archives. A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. Recent changes include: addition of electronic signature support, medical imaging classifications. | owl | is listed by: BioPortal | nlx_157377 | http://www.carelex.org | SCR_010298 | 2026-08-09 09:05:35 | 0 | ||||||||
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Amphibian Gross Anatomy Ontology Resource Report Resource Website 1+ mentions |
Amphibian Gross Anatomy Ontology (RRID:SCR_010291) | AAO | data or information resource, controlled vocabulary, ontology | A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. | obo | is listed by: BioPortal | nlx_157316 | SCR_010291 | 2026-08-09 09:05:28 | 1 | |||||||||
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Disease core ontology applied to Rare Diseases Resource Report Resource Website |
Disease core ontology applied to Rare Diseases (RRID:SCR_010308) | HRDO | data or information resource, controlled vocabulary, ontology | A core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. | owl |
is listed by: BioPortal is related to: Orphanet |
INSERM | nlx_157388 | SCR_010308 | 2026-08-09 09:05:19 | 0 | ||||||||
|
Current Procedural Terminalogy Hierarchy Resource Report Resource Website |
Current Procedural Terminalogy Hierarchy (RRID:SCR_010300) | CPTH | data or information resource, controlled vocabulary, ontology | Metathesaurus of current procedural terminalogy (CPT). | umls | is listed by: BioPortal | nlx_157379 | SCR_010300 | 2026-08-09 09:05:28 | 0 | |||||||||
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Dengue Fever Ontology Resource Report Resource Website |
Dengue Fever Ontology (RRID:SCR_010304) | IDODEN | data or information resource, controlled vocabulary, ontology | An ontology for dengue fever. | owl | is listed by: BioPortal | Dengue fever | nlx_157383 | http://code.google.com/p/dengue-fever-ontology/ | SCR_010304 | 2026-08-09 09:05:35 | 0 | |||||||
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Dermatology Lexicon Resource Report Resource Website |
Dermatology Lexicon (RRID:SCR_010305) | DERMLEX | data or information resource, controlled vocabulary, ontology | A standardized terminology of dermatologic diagnoses, therapies, procedures, and laboratory tests. | owl | is listed by: BioPortal | nlx_157384 | SCR_010305 | 2026-08-09 09:05:19 | 0 | |||||||||
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Diagnosis Ontology of Clinical Care Classification Resource Report Resource Website |
Diagnosis Ontology of Clinical Care Classification (RRID:SCR_010306) | DOCCC | data or information resource, controlled vocabulary, ontology | Diagnosis ontology of clinical care classification. | owl | is listed by: BioPortal | nlx_157385 | SCR_010306 | 2026-08-09 09:05:28 | 0 | |||||||||
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Bionutrition Ontology Resource Report Resource Website 1+ mentions |
Bionutrition Ontology (RRID:SCR_010272) | BNO | data or information resource, controlled vocabulary, ontology | Ontology that relates concepts and terminologies used for human nutrition in a clinical and biomedical setting. | owl | is listed by: BioPortal | nlx_157337 | SCR_010272 | 2026-08-09 09:05:34 | 1 | |||||||||
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BioTop Ontology Resource Report Resource Website 1+ mentions |
BioTop Ontology (RRID:SCR_010039) | BT | data or information resource, controlled vocabulary, ontology | A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. It can furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones. | owl | is listed by: BioPortal | nlx_157329 | http://purl.org/biotop | SCR_010039 | 2026-08-09 09:05:32 | 1 | ||||||||
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Eligibility Feature Hierarchy Resource Report Resource Website |
Eligibility Feature Hierarchy (RRID:SCR_010314) | ELIG | data or information resource, controlled vocabulary, ontology | A set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials. | owl | is listed by: BioPortal | Breast cancer | nlx_157395 | SCR_010314 | 2026-08-09 09:05:19 | 0 |
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