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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cereal Plant Development Ontology Resource Report Resource Website |
Cereal Plant Development Ontology (RRID:SCR_005095) | GRO-CPD | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology. | obo |
is listed by: BioPortal is related to: Plant Ontology has parent organization: Gramene |
nlx_157358 | http://www.gramene.org/plant_ontology/ | SCR_005095 | 2026-09-05 06:25:29 | 0 | ||||||||
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Provisional Cell Ontology Resource Report Resource Website 1+ mentions |
Provisional Cell Ontology (RRID:SCR_018332) | PCL | controlled vocabulary, data or information resource, ontology, portal | Collection of ontology of provisional cells determined by experimental methods. | Ontology, provisional cell, experimental method, BioPortal |
is related to: BioPortal is related to: BioPortal Metadata Ontology |
Free, Freely available | SCR_018332 | Provisional Cell Ontology | 2026-09-05 06:28:34 | 4 | ||||||||
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Biositemaps Resource Report Resource Website 1+ mentions |
Biositemaps (RRID:SCR_001976) | Biositemaps | service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites. | broadcast, data federation, defined rdf schema, infrastructure, meta-data, rdf, retrieve, biomedical, biositemap, sitemap |
lists: Adaptively Sampled Particle Fluids lists: DicomWorks lists: MEDx lists: Medical Image Processing and Visualization lists: Surface-Based Atlases lists: RESNET lists: SurfRelax lists: FEATURE lists: Cardiovascular Model Repository lists: Simtk.org lists: ConTrack lists: Allopathfinder lists: Molecular Simulation Trajectories Archive of a Villin Variant lists: BioPortal lists: SumsDB lists: NeuronDB lists: BrainInfo lists: Protege lists: i2b2 Cross-Institutional Clinical Translational Research project lists: GeneChip Operating Software lists: Honig Lab lists: Proteomics Identifications (PRIDE) lists: ASAP: the Alternative Splicing Annotation Project lists: MiMI Plugin for Cytoscape lists: Substructure Index-based Approximate Graph Alignment lists: Proteome Commons Tranche repository lists: caTIES - Cancer Text Information Extraction System lists: REDCap lists: miniTUBA lists: Einstein-Montefiore ICTR Research Informatics Core lists: T-profiler lists: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse lists: GCG/SeqWeb lists: Solstice lists: California National Primate Research Center lists: BioGPS: The Gene Portal Hub lists: Blox lists: Subcellular Location Image Finder lists: PeptideAtlas lists: Clair library lists: Lyngby lists: SimTKCore lists: Velos lists: Ingenuity Pathway Analysis lists: Philips lists: Talktech lists: SUN Interface Engine lists: Quadramed - Medicus, Quantim lists: Wisconsin National Primate Research Center lists: i2b2 Research Data Warehouse lists: Merge Healthcare Incorporated lists: Clinical Trial Management Application lists: Cerner Millenium lists: Open Clinical Report Repository lists: Quovadx, Inc. lists: VectorValuedHistogramNormalizer lists: Morphometry BIRN lists: Talairach Daemon lists: LONI Visualization Tool lists: LONI Debabeler lists: LONI Pipeline Processing Environment lists: Brede Wiki lists: medInria lists: FreeSurfer lists: ITK-SNAP lists: VoxBo lists: Ensembl lists: MRIcron lists: Synchronized Histological Image Viewing Architecture lists: LONI ShapeViewer lists: LONI ShapeTools lists: FFT Library lists: NUTMEG lists: bioDBcore lists: Mutant Mouse Resource and Research Center lists: Brainscape lists: MindSeer lists: University of Southern California LONI Software lists: Statistics Online Computational Resource lists: NIH MRI Study of Normal Brain Development lists: Ontology Development and Information Extraction lists: Mindtouch DekiWiki lists: National Mesothelioma Virtual Bank lists: MGH-USC Human Connectome Project lists: Fusion ICA Toolbox lists: Biomedical Resource Ontology lists: Biomedical Informatics Research Network lists: 3D Slicer lists: Analysis of Functional NeuroImages lists: Automated Image Registration lists: TOADS-CRUISE Brain Segmentation Tools lists: BrainImage Software lists: Brede Toolbox lists: Whole Brain Catalog lists: Low Resolution Electromagnetic Tomography lists: Cambridge Brain Activation lists: ModelDB lists: fMRI Data Center lists: EEGLAB lists: 3DViewnix lists: MIPAV: Medical Image Processing and Visualization lists: NeuroLens lists: WFU PickAtlas lists: Protein Subcellular Location Image Database lists: STRIDE Virtual Biospecimen Bank lists: BrainVoyager is related to: Biomedical Resource Ontology is related to: Software Distribution Sets is related to: REX is related to: Rat Genome Database (RGD) has parent organization: National Centers for Biomedical Computing has parent organization: National Institutes of Health is parent organization of: Resource Discovery System |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10583 | SCR_001976 | 2026-09-05 06:32:25 | 1 | ||||||||
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RightField Resource Report Resource Website 1+ mentions |
RightField (RRID:SCR_002649) | RightField | software application, software resource | An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies. | annotation, semantic, ontology, term selection, excel, java, bio.tools |
is listed by: BioPortal is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: SEEK is related to: Workflow4Ever has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:21622664 | Free, Available for download, Freely available | biotools:rightfield, nlx_156077 | https://bio.tools/rightfield | SCR_002649 | 2026-09-05 06:32:28 | 3 | ||||||
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Mathematical Modelling Ontology Resource Report Resource Website |
Mathematical Modelling Ontology (RRID:SCR_000910) | MAMO | controlled vocabulary, data or information resource, ontology | Ontology that is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. | owl | is listed by: BioPortal | nlx_157467 | SCR_000910 | 2026-09-05 06:29:53 | 0 | |||||||||
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Hymenoptera Anatomy Ontology Resource Report Resource Website 1+ mentions |
Hymenoptera Anatomy Ontology (RRID:SCR_003340) | HAO | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants) | owl, anatomy, organismal |
is listed by: BioPortal is listed by: OBO |
NSF DBI 0850223 | Free, Freely available | nlx_157435 | http://purl.bioontology.org/ontology/HAO, http://purl.obolibrary.org/obo/hao.owl | SCR_003340 | 2026-09-05 06:29:56 | 3 | ||||||
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NIF Cell Ontology Resource Report Resource Website |
NIF Cell Ontology (RRID:SCR_003977) | NIFCELL | controlled vocabulary, data or information resource, ontology | Ontology for cell types from NIFSTD | owl |
is listed by: BioPortal has parent organization: NIFSTD |
nlx_157492 | SCR_003977 | Neuroscience Information Framework (NIF) Cell Ontology, Neuroscience Information Framework Cell Ontology | 2026-09-05 06:29:57 | 0 | ||||||||
|
Mass Spectrometry Ontology Resource Report Resource Website |
Mass Spectrometry Ontology (RRID:SCR_003579) | MS | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary for the annotation of mass spectrometry experiments. | obo |
is listed by: BioPortal has parent organization: HUPO Proteomics Standards Initiative |
nlx_157465 | SCR_003579 | 2026-09-05 06:29:56 | 0 | |||||||||
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Ontology for Parasite LifeCycle Resource Report Resource Website |
Ontology for Parasite LifeCycle (RRID:SCR_003427) | OPL | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:29:56 | 0 | |||||||
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Ontology for Genetic Interval Resource Report Resource Website |
Ontology for Genetic Interval (RRID:SCR_003423) | OGI | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:29:56 | 0 | |||||||
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Ontology of Physical Exercises Resource Report Resource Website |
Ontology of Physical Exercises (RRID:SCR_003836) | OPE | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:29:57 | 0 | |||||||||
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Biomedical Resource Ontology Resource Report Resource Website 1+ mentions |
Biomedical Resource Ontology (RRID:SCR_004443) | BRO | controlled vocabulary, data or information resource, ontology | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO). | sitemap, resource type, owl, resource |
is listed by: BioPortal is listed by: Biositemaps is related to: Biositemaps is related to: iBIOFind is related to: bioDBcore has parent organization: National Centers for Biomedical Computing |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143813 | http://bioportal.bioontology.org/ontologies/1104, https://bioportal.bioontology.org/ontologies/BRO | SCR_004443 | 2026-09-05 06:29:57 | 4 | ||||||
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Regulation of Gene Expression Ontolology Resource Report Resource Website |
Regulation of Gene Expression Ontolology (RRID:SCR_006124) | REXO | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:29:59 | 0 | |||||||||
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Reproductive Trait and Phenotype Ontology Resource Report Resource Website |
Reproductive Trait and Phenotype Ontology (RRID:SCR_006245) | REPO | controlled vocabulary, data or information resource, ontology | Ontology for livestock reproductive traits and phenotypes | owl | is listed by: BioPortal | nlx_157574 | SCR_006245 | 2026-09-05 06:29:59 | 0 | |||||||||
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SBO Resource Report Resource Website 1+ mentions |
SBO (RRID:SCR_006753) | SBO | controlled vocabulary, data or information resource, database, ontology | 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 | 2026-09-05 06:30:00 | 4 | |||||
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Student Health Record Ontology Resource Report Resource Website |
Student Health Record Ontology (RRID:SCR_005854) | SHR | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:29:59 | 0 | ||||||||
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Neurobehavior Ontology Resource Report Resource Website 1+ mentions |
Neurobehavior Ontology (RRID:SCR_006201) | NBO | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:30:00 | 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 | 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 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 | 2026-09-05 06:30:03 | 0 | |||||||||
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Human Physiology Simulation Ontology Resource Report Resource Website |
Human Physiology Simulation Ontology (RRID:SCR_010340) | HUPSON | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-05 06:30:03 | 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 | controlled vocabulary, data or information resource, ontology | Ontology of logical observation identifier names and codes (LOINC); Version 2.26; January 2, 2009 | umls | is listed by: BioPortal | nlx_157460 | SCR_010341 | 2026-09-05 06:30:03 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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