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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Randomized Controlled Trials Ontology Resource Report Resource Website |
Randomized Controlled Trials Ontology (RRID:SCR_005992) | RCTONT | data or information resource, controlled vocabulary, ontology | Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis. | owl | is listed by: BioPortal | nlx_157568 | SCR_005992 | 2026-08-09 09:04:20 | 0 | |||||||||
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DataCite Ontology Resource Report Resource Website |
DataCite Ontology (RRID:SCR_006215) | DataCite Ontology | data or information resource, controlled vocabulary, ontology | An ontology written in OWL 2 DL to enable the metadata properties of the DataCite Metadata Kernel Specification version 2.2 (http://test.datacite.org/schema/meta/kernel-2.2/index.html) to be described in RDF. This version of the DataCite Ontology has been completely revised and significantly expanded to permit accurate mapping of this new version of the DataCite Metadata Kernel Specification to RDF. | annotation, alternate resource identifier, description type, funder identifier, funder identifier scheme, identifier, identifier scheme, personal identifier, personal identifier scheme, primary resource identifier, resource identifier, resource identifier scheme, owl, rdf, metadata |
is listed by: FORCE11 has parent organization: DataCite |
Creative Commons Attribution License | nlx_151759 | https://www.force11.org/node/4673 | SCR_006215 | 2026-08-09 09:04:24 | 0 | |||||||
|
Read Codes Clinical Terms Version 3 Resource Report Resource Website 1+ mentions |
Read Codes Clinical Terms Version 3 (RRID:SCR_006055) | RCD | data or information resource, controlled vocabulary, ontology | Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre | umls | is listed by: BioPortal | nlx_157570 | SCR_006055 | Read Codes CTV3, Read Codes Clinical Terms Version 3 (CTV3) | 2026-08-09 09:04:20 | 1 | ||||||||
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Regulation of Transcription Ontology Resource Report Resource Website |
Regulation of Transcription Ontology (RRID:SCR_006238) | RETO | data or information resource, controlled vocabulary, ontology | An application ontology for the domain of gene transcription regulation. 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_157573 | SCR_006238 | 2026-08-09 09:04:24 | 0 | |||||||||
|
Ontology for Biomedical Investigations Resource Report Resource Website 10+ mentions |
Ontology for Biomedical Investigations (RRID:SCR_006266) | OBI | data or information resource, controlled vocabulary, ontology | An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project. | life-science, clinical, investigation, biomedical, protocol, instrumentation, experiment, biology, owl, molecular, cellular, organismal, multi-organismal |
is used by: Information Artifact Ontology is used by: Beta Cell Genomics Ontology is listed by: FORCE11 is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology is related to: Chemical Methods Ontology is related to: Genomic Standards Consortium |
PMID:20626927 | Creative Commons Attribution License v3 | nif-0000-06698 | http://purl.obofoundry.org/obo/obi.owl, http://purl.obofoundry.org/obo/obi, https://www.force11.org/node/4700 | SCR_006266 | OBI Ontology | 2026-08-09 09:04:25 | 21 | |||||
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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, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:44 | 2 | |||||||||
|
neuroConstruct Resource Report Resource Website 10+ mentions |
neuroConstruct (RRID:SCR_007197) | neuroConstruct | simulation software, software application, software resource | Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface. | cell, cellular, channel, conductance, data, dendrite, java, mechanism, membrane, model, morphology, network, neuron, neuronal network, pharmacology, physiology, simulation, software, synapse, visualization |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NEURON is related to: Open Source Brain is related to: NeuroML has parent organization: University College London; London; United Kingdom |
Wellcome Trust ; MRC |
nif-0000-00105 | http://www.nitrc.org/projects/neuroconstruct | SCR_007197 | neuroConstruct: Biophysical Neural Network Modeling Software | 2026-08-09 09:04:45 | 11 | ||||||
|
Cardiac Electrophysiology Ontology Resource Report Resource Website |
Cardiac Electrophysiology Ontology (RRID:SCR_007065) | EP | data or information resource, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:36 | 0 | |||||||||
|
Cereal Plant Gross Anatomy Ontology Resource Report Resource Website |
Cereal Plant Gross Anatomy Ontology (RRID:SCR_007061) | GRO-CPGA | data or information resource, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:36 | 0 | ||||||||
|
Cell Culture Ontology Resource Report Resource Website 1+ mentions |
Cell Culture Ontology (RRID:SCR_007096) | CCONT | data or information resource, controlled vocabulary, ontology | ontology for the formal representation of cell lines and their correspnding culture conditions. | owl | is listed by: BioPortal | nlx_157354 | SCR_007096 | 2026-08-09 09:04:34 | 1 | |||||||||
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Ikaros Project Resource Report Resource Website 50+ mentions |
Ikaros Project (RRID:SCR_007391) | simulation software, software application, software resource | Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models. | model, computational neuroscience, brain, robot, simulation, FASEB list |
is listed by: 3DVC has parent organization: Lund University; Lund; Sweden |
nif-0000-00426 | SCR_007391 | Ikaros | 2026-08-09 09:04:50 | 89 | |||||||||
|
MCell Resource Report Resource Website 50+ mentions |
MCell (RRID:SCR_007307) | simulation software, software application, software resource | Software modeling tool for realistic simulation of cellular signaling in complex 3-D subcellular microenvironment in and around living cells. Program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate movements and reactions of molecules within and between cells. | Monte Carlo, simulator, cellular, microphysiology, living, cell, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: CellOrganizer |
NIGMS P41 GM103712 | Free, Available for download, Freely available | nif-0000-00160 | https://github.com/mcellteam/mcell | SCR_007307 | Monte Carlo simulator of cellular microphysiology | 2026-08-09 09:04:48 | 62 | ||||||
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BIRNLex Resource Report Resource Website |
BIRNLex (RRID:SCR_007326) | data or information resource, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:40 | 0 | |||||||
|
Computational Neuroscience Ontology Resource Report Resource Website |
Computational Neuroscience Ontology (RRID:SCR_007289) | CNO | data or information resource, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:39 | 0 | ||||||||
|
Solanaceae Phenotype Ontology Resource Report Resource Website |
Solanaceae Phenotype Ontology (RRID:SCR_007832) | SPTO | data or information resource, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:47 | 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, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:45 | 0 | ||||||||
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Soy Ontology Resource Report Resource Website |
Soy Ontology (RRID:SCR_007847) | SOY | data or information resource, controlled vocabulary, ontology | Growth, trait and development ontology for soybean | obo |
is listed by: BioPortal has parent organization: SoyBase |
nlx_157593 | SCR_007847 | 2026-08-09 09:04:47 | 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, controlled vocabulary, ontology | Ontology for the healthcare common procedure coding system. | umls | is listed by: BioPortal | nlx_157426 | SCR_007598 | 2026-08-09 09:04:47 | 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, controlled vocabulary, ontology | 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 | 2026-08-09 09:04:55 | 0 | ||||||||
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R/TDTHAP Resource Report Resource Website 1+ mentions |
R/TDTHAP (RRID:SCR_007625) | software application, software resource | Software package for TDT with extended haplotypes in the R language. R is the public domain dialect of S. It should be possible to port this library to the commercial Splus product. The main problem would be translation of the help files. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/splus | is listed by: Genetic Analysis Software | nlx_154676, nlx_154602, SCR_000851 | http://www-gene.cimr.cam.ac.uk/clayton/software/ | SCR_007625 | TDTHAP | 2026-08-09 09:04:46 | 1 |
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