Default dictionaries¶
Below you can see a table with description of ODM default dictionaries:
| Dictionary | Description |
|---|---|
| Assay Type | A comprehensive list of molecular profiling approaches including sequencing types, epigenetic assays, and transcriptomics Domain: Methodology. Reference ontologies: EFO, OBI, OLS (assorted) ODM default dictionary, June 2025 |
| Cell Ontology - CL | A structured vocabulary for cell types in animals Domain: Cell Types / Development / Single-Cell, Version: 2025-04-10 The original data is available via the https://purl.obolibrary.org/obo/cl/releases/2025-04-10/cl.owl |
| Cell Ontology for Human Lung Maturation - LUNGMAP CELL | Cell Ontology for Human Lung Maturation from LungMAP project Domain: Single-Cell / Tissue Atlas / Development, Version: 3.2 The original data is available via the https://data.bioontology.org/ontologies/LUNGMAP_H_CELL/submissions/6/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb |
| Cellosaurus Controlled Vocabulary | A controlled vocabulary which describes cell lines used in biomedical research Domain: Cell Lines / Experimental Materials, Version: 2025-04-10 The original data is available via the https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo |
| Chemical Entities of Biological Interest - ChEBI Ontology | Ontology focuses on chemical nomenclature and structures, and provides a wide range of other chemical information such as formulae and links to other databases Domain: Chemistry / Metabolomics, Version: 2025-06-02 The original data is available via the https://purl.obolibrary.org/obo/chebi/241/chebi.owl |
| Disease Ontology - DOID | Classification of human diseases by etiology Domain: Diseases / Human Health, Version: 2025-05-30 The original data is available via the https://purl.obolibrary.org/obo/doid/releases/2025-05-30/doid.owl |
| Disease Ontology Extended | Classification of human diseases by etiology enriched by term "Healthy" and its synonyms Domain: Diseases / Human Health, Version: 2025-05-30, extended by term "Healthy" The original data is available via the https://purl.obolibrary.org/obo/doid/releases/2025-05-30/doid.owl |
| EMBRACE Data And Methods - EDAM | Ontology representing biomedical investigations, protocols, materials, and data analysis Domain: Experimental Design / Investigations, Version: 2025-05-01 The original data is available via the https://edamontology.org/EDAM_1.25.owl |
| Environment Ontology - ENVO | Ontology for environmental and habitat descriptors, processes, ecosystems, and exposures Domain: Environment / Exposure / Ecology, Version: 2025-02-05 The original data is available via the https://purl.obolibrary.org/obo/envo/releases/2025-02-05/envo.owl |
| Experimental Factor Ontology - EFO | Ontology of experimental variables and sample annotations integrating multiple domains Domain: Experimental Factors / Study Design / Traits, Version: 3.78.0 The original data is available via the https://www.ebi.ac.uk/efo/releases/v3.78.0/efo.owl |
| Experimental Scope | Indicates the objective of the experiment, such as discovery vs. targeted profiling Domain: Study Design. Reference ontology: Custom ODM default dictionary, June 2025 |
| Gene Ontology - GO | Describes gene functions: biological process, molecular function, cellular component Domain: Molecular Function / Biological Process, Version: 2024-11-03 The original data is available via the https://purl.obolibrary.org/obo/go/releases/2024-11-03/extensions/go-plus.owl |
| Genotype Ontology - GENO | OWL model of genotypes, variation, and phenotype-environment associations Domain: Genotypes / Alleles / Genomic Variation, Version: 2023-10-08 The original data is available via the https://purl.obolibrary.org/obo/geno/releases/2023-10-08/geno.owl |
| Hugo Gene Nomenclature - HGNC | Official human gene symbols and names approved by the HUGO Gene Nomenclature Committee Domain: Genes / Genomics, Version: dev, Released: 2025-05-02 The original data is available via the https://data.bioontology.org/ontologies/HGNC/submissions/4/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb |
| Human Biological Sex | Standardized terms for recording biological sex, including common chromosomal variations and intersex conditions. Intended for use in biomedical, clinical and omics datasets Domain: Demographics. Reference ontologies: NCIT, EFO ODM default dictionary, June 2025 |
| Human Phenotype Ontology - HPO | Standardized vocabulary of phenotypic abnormalities and clinical features in human disease Domain: Phenotypes / Clinical / Rare Diseases, Version: 2025-01-16 The original data is available via the https://purl.obolibrary.org/obo/hp/releases/2025-01-16/hp-international.owl |
| Library Preparation Methods | Methods for preparing nucleic acids or proteins for sequencing or profiling (e.g., Smart-Seq, ChIP) Domain: Methodology. Reference ontologies: EFO, OBI, custom curation ODM default dictionary, June 2025 |
| Mass Spectrometry Ontology - MS | Vocabulary for proteomics mass spectrometry experiments and instrumentation Domain: Proteomics / Mass Spectrometry / Instrumentation, Version: 4.1.194 The original data is available via the https://purl.obolibrary.org/obo/ms.owl |
| Microarray Platforms | Commercial and academic platforms used in microarray experiments, including scanners and array systems Domain: Technology. Reference ontologies: EFO, OBI ODM default dictionary, June 2025 |
| MicroRNA Ontology - MIRNAO | Ontology representing microRNA-related biological concepts and their relationships, including molecular components, roles, and regulation processes Domain: microRNA / Gene Regulation, Version: 1.7 The original data is available via the https://bioportal.bioontology.org/ontologies/MIRNAO |
| Mouse Genomic Informatics - MGI | A curated subset of genetic markers and genomic features from Mus musculus, based on the Mouse Genome Informatics (MGI) resource. Includes marker IDs, synonyms, chromosomal and genetic positions, marker types, and feature types Domain: Genes / Genomics, Version: 2025-06-11 The original data is available via the https://www.informatics.jax.org/downloads/reports/MRK_List2.rpt.gz |
| National Cancer Institute Thesaurus - NCIT | NCI thesaurus used in clinical, translational, and basic research Domain: Clinical / Translational / Research, Version: 2025-06-04 The original data is available via the https://purl.obolibrary.org/obo/ncit/releases/2024-05-07/ncit.owl |
| NCBI Taxonomy | A standard hierarchical nomenclature and classification dictionary for organisms from NCBI Domain: Taxonomy / Species, Version: 2025-03-13 The original data is available via the https://purl.obolibrary.org/obo/ncbitaxon/2025-03-13/ncbitaxon.owl |
| Ontology for Biomedical Investigations - OBI | Ontology representing biomedical investigations, protocols, materials, and data analysis Domain: Experimental Design / Investigations, Version: 2025-05-01 The original data is available via the https://purl.obolibrary.org/obo/obi/2025-05-01/obi.owl |
| Ontology of Biological Attributes - OBA | Biological attributes and traits across all life kingdoms; interoperable with VT/TO Domain: Traits / Measurements / Phenotypic Data, Version: 2025-03-28 The original data is available via the https://purl.obolibrary.org/obo/oba.owl |
| Phenotypic Quality Ontology - PATO | Phenotypic qualities such as shape, color, size, and other observable characteristics Domain: Phenotypic Qualities / Single-Cell / Imaging, Version: 2025-05-14 The original data is available via the https://purl.obolibrary.org/obo/pato.owl |
| Protein modification - PSI-MOD | Ontology of protein chemical modifications forming a DAG structure Domain: Proteomics / Protein Modifications, Version: 1.031.6 The original data is available via the https://purl.obolibrary.org/obo/mod.owl |
| Protein Ontology - PRO | Protein isoforms and modifications ontology, includes taxon-specific and neutral entities Domain: Protein Classes / Modifications / Families, Version: 71 The original data is available via the https://data.bioontology.org/ontologies/PR/submissions/90/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb |
| Rat Genome Database - RGD | A selected dictionary of Rattus norvegicus gene symbols, synonyms, and related attributes, derived from the Rat Genome Database (RGD) Domain: Genes / Genomics, Version: 2025-06-06 The original data is available via the https://download.rgd.mcw.edu/data_release/RAT/ |
| Rat Strain Ontology - RS | Ontology describing rat strains. Domain: Taxonomy / Species, Version: 2025-05-31 The original data is available via the https://purl.obolibrary.org/obo/rs/6.249/rs.owl |
| Sequence Ontology - SO | Controlled vocabulary for sequence annotation and genomic feature descriptions Domain: Genomics / Genomic Features / Variants, Version: 2024-11-18 The original data is available via the https://purl.obolibrary.org/obo/so.owl |
| Sequencing Platforms | Commercial and legacy sequencing hardware platforms, e.g., Illumina, PacBio Domain: Technology. Reference ontologies: EFO, OBI ODM default dictionary, June 2025 |
| The BRENDA Tissue Ontology - BTO | Vocabulary for enzyme source tissues, cell lines, types and cultures Domain: Tissues / Biological Samples, Version: 2021-10-26 The original data is available via the https://purl.obolibrary.org/obo/bto.owl |
| Therapeutic Area | Medical or therapeutic focus of the study, covering main therapeutic areas Domain: Study Design. Reference ontologies: Custom ODM default dictionary, June 2025 |
| Uberon Anatomical Entities | A cross-species anatomy ontology organizing structures by anatomy, function, and development Domain: Anatomy / Cross-species, Version: 2025-05-28 The original data is available via the https://purl.obolibrary.org/obo/uberon/releases/2025-05-28/uberon.owl |
| Units – Biological Counts | Covers units used for reporting biological counts, such as cell counts and molecule counts Domain: Units / Quantitative. Reference ontologies: UO, NCIT, QUDT ODM default dictionary, June 2025 |
| Units – Dimensionless | Units with no physical dimension, such as percent, pH, and optical density. Commonly used in ratios Domain: Units / Ratios. Reference ontologies: UO, NCIT ODM default dictionary, June 2025 |
| Units – Dose, Mass, and Volume | Covers measurement units for dose, mass, volume, and derived quantities (e.g., ng/mL, mg/kg) Domain: Units / Quantitative. Reference ontologies: UO, NCIT, NIST*, QUDT ODM default dictionary, June 2025 |
| Units – Length | Standard length units from nanometers to kilometers, including imperial alternatives Domain: Units / Quantitative. Reference ontologies: UO, NCIT, QUDT ODM default dictionary, June 2025 |
| Units – Temperature and Energy | Units used to measure temperature and energy release in scientific experiments (e.g., °C, joule) Domain: Units / Quantitative. Reference ontologies: UO, NCIT, NIST ODM default dictionary, June 2025 |
| Units – Time and Frequency | Measurement units for time (e.g., seconds, days) and frequency (e.g., Hz, rates) Domain: Units / Quantitative. Reference ontologies: UO, NCIT, QUDT ODM default dictionary, June 2025 |