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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Provisional Cell Ontology Resource Report Resource Website 1+ mentions |
Provisional Cell Ontology (RRID:SCR_018332) | PCL | data or information resource, ontology, portal, controlled vocabulary | 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 | 2026-02-14 02:03:34 | 3 | ||||||||
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Mathematical Modelling Ontology Resource Report Resource Website |
Mathematical Modelling Ontology (RRID:SCR_000910) | MAMO | data or information resource, ontology, controlled vocabulary | 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 | 2026-02-14 02:04:50 | 0 | |||||||||
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Biositemaps Resource Report Resource Website 1+ mentions |
Biositemaps (RRID:SCR_001976) | Biositemaps | software resource, service 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 | 2026-02-14 02:06:54 | 1 | ||||||||
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RightField Resource Report Resource Website 1+ mentions |
RightField (RRID:SCR_002649) | RightField | software resource, software application | 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 | 2026-02-14 02:06:33 | 3 | ||||||
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Animal Natural History and Life History Ontology Resource Report Resource Website 1+ mentions |
Animal Natural History and Life History Ontology (RRID:SCR_010292) | ADW | data or information resource, ontology, controlled vocabulary | An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. | owl |
is listed by: BioPortal has parent organization: University of Michigan; Ann Arbor; USA |
nlx_157319 | SCR_010292 | 2026-02-14 02:05:01 | 1 | |||||||||
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Coding Symbols for a Thesaurus of Adverse Reaction Terms Resource Report Resource Website |
Coding Symbols for a Thesaurus of Adverse Reaction Terms (RRID:SCR_010294) | COSTART | data or information resource, ontology, controlled vocabulary | Ontology for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. It is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999. | umls | is listed by: BioPortal | nlx_157367 | SCR_010294 | 2026-02-14 02:04:51 | 0 | |||||||||
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NCBITaxon Resource Report Resource Website 1+ mentions |
NCBITaxon (RRID:SCR_000479) | NCBITAXON | data or information resource, ontology, controlled vocabulary | Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl. | owl |
is listed by: BioPortal has parent organization: NCBI Taxonomy |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157490 | SCR_000479 | National Center for Biotechnology Information Organismal Classification, National Center for Biotechnology Information (NCBI) Organismal Classification, NCBI Organismal Classification | 2026-02-14 02:05:01 | 4 | |||||||
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Habronattus Courtship Ontology Resource Report Resource Website |
Habronattus Courtship Ontology (RRID:SCR_010334) | HC | data or information resource, ontology, controlled vocabulary | An ontology for courtship behavior of the spider Habronattus californicus. A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. | protege | is listed by: BioPortal | nlx_157423 | http://www.mesquiteproject.org/ontology/Habronattus/index.html | SCR_010334 | 2026-02-14 02:04:44 | 0 | ||||||||
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Family Health History Ontology Resource Report Resource Website |
Family Health History Ontology (RRID:SCR_010068) | FHHO | data or information resource, ontology, controlled vocabulary | Ontology that facilitates representing the family health histories of persons related by biological and/or social family relationships (e.g. step, adoptive) who share genetic, behavioral, and/or environmental risk factors for disease. SWRL rules are included to compute 3 generations of biological relationships based on parentage and family history findings based on personal health findings. | owl | is listed by: BioPortal | nlx_157402 | SCR_010068 | 2026-02-14 02:04:50 | 0 | |||||||||
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Dispedia Core Ontology Resource Report Resource Website |
Dispedia Core Ontology (RRID:SCR_010309) | DCO | data or information resource, ontology, controlled vocabulary | Ontology that is a schema for information brokering and knowledge management in the complex field of rare diseases. On the one hand, the Dispedia schema uses semantic technologies to describe patients affected by rare diseases, and on the other hand, to record expertise concerning these particular diseases in machine-processable form. In addition to the differentiated attribution of facts to the individual need for information, Dispedia enables information brokering which adjusts to the type of recipient, its character as well as its personal attitude. The schema was initially geared to an exemplified disease, Amyotrophe Lateralsclerose (ALS). | owl | is listed by: BioPortal | Rare disease, Amyotrophic lateral sclerosis | nlx_157389 | SCR_010309 | 2026-02-14 02:05:06 | 0 | ||||||||
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Semantic Web for Earth and Environment Technology Ontology Resource Report Resource Website |
Semantic Web for Earth and Environment Technology Ontology (RRID:SCR_010426) | SWEET | data or information resource, ontology, controlled vocabulary | A mature foundational ontology developed at the NASA Jet Propulsion Laboratory, currently containing over 6000 concepts organized in 200 ontologies represented in OWL, whose top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). SWEET is now officially under the governance of the ESIP foundation. | owl | is listed by: BioPortal | nlx_157585 | SCR_010426 | 2026-02-14 02:05:02 | 0 | |||||||||
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Systems Chemical Biology and Chemogenomics Ontology Resource Report Resource Website |
Systems Chemical Biology and Chemogenomics Ontology (RRID:SCR_003928) | CHEMBIO | data or information resource, ontology, controlled vocabulary | Ontology for Systems Chemical Biology and Chemogenomics | owl | is listed by: BioPortal | nlx_157605 | SCR_003928 | 2026-02-14 02:04:44 | 0 | |||||||||
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Drosophila Development Ontology Resource Report Resource Website |
Drosophila Development Ontology (RRID:SCR_010310) | FB-DV | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the development of Drosophila melanogaster. | obo |
is used by: Virtual Fly Brain is listed by: BioPortal has parent organization: FlyBase |
nlx_157390 | SCR_010310 | 2026-02-14 02:04:44 | 0 | |||||||||
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Drosophila Gross Anatomy Ontology Resource Report Resource Website |
Drosophila Gross Anatomy Ontology (RRID:SCR_010311) | FB-BT | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the anatomy of Drosophila melanogaster. | obo |
is used by: Virtual Fly Brain is listed by: BioPortal |
nlx_157391 | SCR_010311 | 2026-02-14 02:05:01 | 0 | |||||||||
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Physico-Chemical Methods and Properties Resource Report Resource Website |
Physico-Chemical Methods and Properties (RRID:SCR_010407) | FIX | data or information resource, ontology, controlled vocabulary | Two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties. | obo, method, property, biophysical chemistry, physico-chemical |
is listed by: BioPortal is listed by: OBO has parent organization: CHEBI |
nlx_157552 | ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo | SCR_010407 | 2026-02-14 02:04:51 | 0 | ||||||||
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Syndromic Surveillance Ontology Resource Report Resource Website |
Syndromic Surveillance Ontology (RRID:SCR_010409) | SSO | data or information resource, ontology, controlled vocabulary | Ontology that encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions). | owl | is listed by: BioPortal | nlx_157600 | SCR_010409 | 2026-02-14 02:05:07 | 0 | |||||||||
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Orphanet Rare Disease Ontology Resource Report Resource Website |
Orphanet Rare Disease Ontology (RRID:SCR_010402) | ORDO | data or information resource, ontology, controlled vocabulary | Ontology to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (http://www.orpha.net) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14). | owl |
is listed by: BioPortal has parent organization: Orphanet has parent organization: European Bioinformatics Institute |
Rare disease | nlx_157540 | SCR_010402 | 2026-02-14 02:04:51 | 0 | ||||||||
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Parasite Experiment Ontology Resource Report Resource Website |
Parasite Experiment Ontology (RRID:SCR_010403) | PEO | data or information resource, ontology, controlled vocabulary | Ontology that models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway. | owl | is listed by: BioPortal | nlx_157541 | SCR_010403 | 2026-02-14 02:05:06 | 0 | |||||||||
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Pharmacogenomic Relationships Ontology Resource Report Resource Website |
Pharmacogenomic Relationships Ontology (RRID:SCR_010406) | PHARE | data or information resource, ontology, controlled vocabulary | Ontology that proposes concepts and roles to represent relationships of pharmacogenomics interest. | owl | is listed by: BioPortal | nlx_157546 | SCR_010406 | 2026-02-14 02:05:02 | 0 | |||||||||
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Ontology for Drug Discovery Investigations Resource Report Resource Website |
Ontology for Drug Discovery Investigations (RRID:SCR_010383) | DDI | data or information resource, ontology, controlled vocabulary | Ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI). | owl | is listed by: BioPortal | nlx_157514 | SCR_010383 | 2026-02-14 02:05:06 | 0 |
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