Subset that is relevant for a typical Model Organism Database (MOD)
- AnatomicalEntity - A subcellular location, cell type or gross anatomical part
- Article - a piece of writing on a particular topic presented as a stand-alone section of a larger publication
- Book - This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.
- Disease - A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
- Gene - A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.
- GeneFamily - any grouping of multiple genes or gene products related by common descent
- Genome - A genome is the sum of genetic material within a cell or virion.
- Genotype - An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background
- InformationContentEntityToNamedThingAssociation - association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate ‘mentions’ could be used. Conversely, for more specific associations (like ‘gene to disease association’, the publication should be captured as an edge property).
- LifeStage - A stage of development or growth of an organism, including post-natal adult stages
- MacromolecularComplex - A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
- NucleicAcidEntity - A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.
- OrganismTaxon - A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.
- PhenotypicFeature - A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.
- Polypeptide - A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.
- PopulationOfIndividualOrganisms - A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.
- Publication - Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).
- ReagentTargetedGene - A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.
- SequenceVariant - A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
- Serial - This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.
- SiRNA - A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.
- SmallMolecule - A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).
- Transcript - An RNA synthesized on a DNA or RNA template by an RNA polymerase.
- ExposureEvent - A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes