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Table 2 Definitions and examples of class-level relations

From: Relations in biomedical ontologies

Relations and relata Definitions Examples
C is_a C1; Cs and C1s are continuants Every C at any time is at the same time a C1 myelin is_a lipoprotein
   serotonin is_a biogenic amine
   mitochondrion is_a membranous cytoplasmic organelle
   protein kinase is_a kinase
   DNA is_a nucleic acid
P is_a P1; Ps and P1s are processes Every P is a P1 endomitosos is_a DNA replication
   catabolic process is_a metabolic process
   photosynthesis is_a physiological process
   gonad development is_a organogenesis
   intracellular signaling cascade is_a signal transduction
C part_of C1; Cs and C1s are continuants Every C at any time is part of some C1 at the same time mitochondrial matrix part_of mitochondrion
   microtubule part_of cytoskeleton
   nuclear pore complex part_of nuclear membrane
   nucleoplasm part_of nucleus
   promotor part_of gene
P part_of P1; Ps and P1s are processes Every P is part of some P1 gastrulation part_of embryonic development
   cystoblast cell division part_of germ cell development
   cytokinesis part_of cell proliferation
   transcription part_of gene expression
   neurotransmitter release part_of synaptic transmission
C located_in C1; Cs and C1s are continuants Every C at any given time occupies a spatial region which is part of the region occupied by some C1 at the same time 66s pre-ribosome located_in nucleolus
   intron located_in gene
   nucleolus located_in nucleus
   membrane receptor located_in cell membrane
   chlorophyll located_in thylakoid
C contained_in C1; Cs are material continuants, C1s are immaterial continuants (holes, cavities) Every C at any given time is located in but shares no parts in common with some C1 at the same time thoracic aorta contained_in posterior mediastinal cavity
   cytosol contained_in cell compartment space
   thylakoid contained_in chloroplast membrane
   synaptic vesicle contained_in neuron
C adjacent_to C1; Cs and C1s are continuants Every C at any time is proximate to some C1 at the same time Golgi apparatus adjacent_to endoplasmic reticulum
   intron adjacent_to exon
   cell wall adjacent_to cytoplasm
   periplasm adjacent_to plasma membrane
   presynaptic membrane adjacent_to synaptic cleft
C transformation_of C1; Cs and C1s are material continuants Every C at any time is identical with some C1 at some earlier time facultative heterochromatin transformation_of euchromatin
   mature mRNA transformation_of pre-mRNA
   hemosiderin transformation_of hemoglobin
   red blood cell transformation_of reticulocyte
   fetus transformation_of embryo
C derives_from C1; Cs and C1s are material continuants Every C is such that in the first moment of its existence it occupies a spatial region which overlaps the spatial region occupied by some C1 in the last moment of its existence plasma cell derives_from B lymphocyte
   fatty acid derives_from triglyceride
   triple oxygen molecule derives_from oxygen molecule
   Barr body derives_from X-chromosome
   mammal derives_from gamete
P preceded_by P1; Ps and P1s are processes Every P is such that there is some earlier P1 translation preceded_by transcription
   meiosis preceded_by chromosome duplication
   cytokinesis preceded_by DNA replication
   apoptotic cell death preceded_by nuclear chromatin degradation
   digestion preceded_by ingestion
P has_participant C; Ps are processes, Cs are continuants Every P involves some C as participant mitochondrial acetylCoA formation has_participant pyruvate dehydrogenase complex
   translation has_participant amino acid
   photosynthesis has_participant chlorophyll
   apoptosis has_participant cell
   cell division has_participant chromosome
P has_agent C; Ps are processes, Cs are material continuants Every P involves some C as agent (the C is involved in and is causally responsible for the P) gene expression has_agent RNA polymerase
   signal transduction has_agent receptor
   pathogenesis has_agent pathogen
   transcription has_agent RNA polymerase
   translation has_agent ribosome