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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | ontology, data or information resource, controlled vocabulary | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/, http://bioportal.bioontology.org/ontologies/ECO | SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-08-04 09:40:39 | 19 | |||||
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Medical image simulation Resource Report Resource Website 1+ mentions |
Medical image simulation (RRID:SCR_010355) | OntoVIP | ontology, data or information resource, controlled vocabulary | Ontology that describes the content of the models used in medical image simulation developed in the context of the Virtual Imaging Platform project (VIP), a french project aiming at sharing medical image simulation resources. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI. | owl | is listed by: BioPortal | French National Research Agency ANR-09-COSI-03 | nlx_157472 | SCR_010355 | 2026-08-04 09:42:43 | 3 | ||||||||
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Mental State Assessment Resource Report Resource Website 1+ mentions |
Mental State Assessment (RRID:SCR_010357) | ONL-MSA | ontology, data or information resource, controlled vocabulary | Ontology that is a module of the OntoNeuroLOG ontology that covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores, developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeous resources in neuroimaging. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Grober-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT). | owl neuroimaging, mri, mental state assessment | is listed by: BioPortal | French National Research Agency ANR-06-TLOG-024 | nlx_157474 | SCR_010357 | MSA ontology | 2026-08-04 09:42:39 | 1 | |||||||
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Metagenome Sample Vocabulary Resource Report Resource Website |
Metagenome Sample Vocabulary (RRID:SCR_010358) | MSV | ontology, data or information resource, controlled vocabulary | An ontology for metagenome sample metadata that mainly defines predicates. | owl | is listed by: BioPortal | nlx_157475 | SCR_010358 | 2026-08-04 09:42:43 | 0 | |||||||||
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Mosquito Gross Anatomy Ontology Resource Report Resource Website |
Mosquito Gross Anatomy Ontology (RRID:SCR_003839) | TGMA | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of mosquitoes. | obo | is listed by: BioPortal | nlx_157485 | SCR_003839 | 2026-08-04 09:41:00 | 0 | |||||||||
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CPTAC Proteomics Pipeline Infrastructure Ontology Resource Report Resource Website |
CPTAC Proteomics Pipeline Infrastructure Ontology (RRID:SCR_006945) | CPTAC | ontology, data or information resource, controlled vocabulary | A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project | owl | is listed by: BioPortal | nlx_157349 | SCR_006945 | 2026-08-04 09:41:44 | 0 | |||||||||
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Ontology for Parasite LifeCycle Resource Report Resource Website |
Ontology for Parasite LifeCycle (RRID:SCR_003427) | OPL | ontology, data or information resource, controlled vocabulary | A reference ontology that models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. | owl, parasite, life cycle, host, vector, anatomical location |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157521 | https://github.com/OPL-ontology/OPL | SCR_003427 | 2026-08-04 09:40:54 | 0 | |||||||
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Ontology for Genetic Interval Resource Report Resource Website |
Ontology for Genetic Interval (RRID:SCR_003423) | OGI | ontology, data or information resource, controlled vocabulary | An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. | owl, genomic, genetic, dna, rna, allele, marker, chromosome, rna molecule |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157517 | https://bioportal.bioontology.org/ontologies/OGI | SCR_003423 | 2026-08-04 09:40:54 | 0 | |||||||
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Ontology of Physical Exercises Resource Report Resource Website |
Ontology of Physical Exercises (RRID:SCR_003836) | OPE | ontology, data or information resource, controlled vocabulary | Ontology that provides a reference for describing an exercise in terms of functional movements, engaged musculoskeletal system parts, related equipment or monitoring devices, intended health outcomes, as well as target ailments for which the exercise might be employed as a treatment or preventative measure. | owl | is listed by: BioPortal | nlx_157535 | SCR_003836 | 2026-08-04 09:41:00 | 0 | |||||||||
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Regulation of Gene Expression Ontolology Resource Report Resource Website |
Regulation of Gene Expression Ontolology (RRID:SCR_006124) | REXO | ontology, data or information resource, controlled vocabulary | An application ontology for the domain of gene expression 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_157572 | SCR_006124 | 2026-08-04 09:41:31 | 0 | |||||||||
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Reproductive Trait and Phenotype Ontology Resource Report Resource Website |
Reproductive Trait and Phenotype Ontology (RRID:SCR_006245) | REPO | ontology, data or information resource, controlled vocabulary | Ontology for livestock reproductive traits and phenotypes | owl | is listed by: BioPortal | nlx_157574 | SCR_006245 | 2026-08-04 09:41:33 | 0 | |||||||||
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SBO Resource Report Resource Website 1+ mentions |
SBO (RRID:SCR_006753) | SBO | ontology, database, data or information resource, controlled vocabulary | A set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web Services. | systems biology, computational modeling, web service, obo, gold standard |
is listed by: BioPortal is related to: BioModels.net is related to: OBO has parent organization: European Bioinformatics Institute |
NIGMS | PMID:17118155 | Free, The community can contribute to this resource | nlx_66206 | SCR_006753 | Systems Biology Ontology | 2026-08-04 09:41:40 | 4 | |||||
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Student Health Record Ontology Resource Report Resource Website |
Student Health Record Ontology (RRID:SCR_005854) | SHR | ontology, data or information resource, controlled vocabulary | Ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... . | owl | is listed by: BioPortal | nlx_157596 | SCR_005854 | SHR-Ontology | 2026-08-04 09:41:27 | 0 | ||||||||
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Neurobehavior Ontology Resource Report Resource Website 1+ mentions |
Neurobehavior Ontology (RRID:SCR_006201) | NBO | ontology, data or information resource, controlled vocabulary | An ontology consisting of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending the GO process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms. The prime application of NBO is to provide the vocabulary that is required to integrate behavior observations within and across species. It is currently being applied by several model organism communities as well as in the description of human behavior-related disease phenotypes. The main ontology is available in both the OBO Flatfile Format and the Web Ontology Language (OWL). | obo, neurobehavior, behavior, phenotype, behavioral process, biology, animal, normal, abnormal, owl, genetics |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Gene Ontology |
New BSD License, (Code) | nlx_151745 | http://purl.bioontology.org/ontology/NBO, http://behavior-ontology.googlecode.com/svn/trunk/behavior.owl, http://bioportal.bioontology.org/ontologies/1621 | SCR_006201 | Neurobehavior Ontology (NBO), Neuro Behavior Ontology, behavior-ontology, Behavioral Ontology | 2026-08-04 09:41:32 | 2 | ||||||
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Human Developmental Anatomy Ontology timed version Resource Report Resource Website |
Human Developmental Anatomy Ontology timed version (RRID:SCR_010338) | EHDA | ontology, data or information resource, controlled vocabulary | 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 timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. | obo | is listed by: BioPortal | nlx_157431 | SCR_010338 | 2026-08-04 09:42:39 | 0 | |||||||||
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Human Physiology Simulation Ontology Resource Report Resource Website |
Human Physiology Simulation Ontology (RRID:SCR_010340) | HUPSON | ontology, data or information resource, controlled vocabulary | Ontology as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles. | owl | is listed by: BioPortal | nlx_157434 | SCR_010340 | 2026-08-04 09:42:43 | 0 | |||||||||
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Logical Observation Identifier Names and Codes Resource Report Resource Website 1+ mentions |
Logical Observation Identifier Names and Codes (RRID:SCR_010341) | LOINC | ontology, data or information resource, controlled vocabulary | Ontology of logical observation identifier names and codes (LOINC); Version 2.26; January 2, 2009 | umls | is listed by: BioPortal | nlx_157460 | SCR_010341 | 2026-08-04 09:42:39 | 1 | |||||||||
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DICOM Controlled Terminology Resource Report Resource Website |
DICOM Controlled Terminology (RRID:SCR_010302) | DCM | ontology, data or information resource, controlled vocabulary | DICOM Controlled Terminology (PS3.16 2013 Annex D) | owl | is listed by: BioPortal | nlx_157381 | SCR_010302 | 2026-08-04 09:42:38 | 0 | |||||||||
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Diagnostic Ontology Resource Report Resource Website |
Diagnostic Ontology (RRID:SCR_010307) | DIAGONT | ontology, data or information resource, controlled vocabulary | A computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. They also report high percentage of agreement among five observers as a result of the inter-observer agreement that they conducted among them to tag 13 articles using the diagnostic ontology. Moreover, they extend their existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies. | owl | is listed by: BioPortal | nlx_157386 | SCR_010307 | 2026-08-04 09:42:42 | 0 | |||||||||
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Translational Medicine Ontology Resource Report Resource Website |
Translational Medicine Ontology (RRID:SCR_010439) | TMO | ontology, data or information resource, controlled vocabulary | A high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies. | owl | is listed by: BioPortal | nlx_157616 | SCR_010439 | 2026-08-04 09:42:45 | 0 |
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