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