Table 2

Definitions and examples of class-level relations

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

Smith et al. Genome Biology 2005 6:R46   doi:10.1186/gb-2005-6-5-r46