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Definitions and examples of class-level relations |
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| Relations and relata |
Definitions |
Examples |
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| 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 |
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| mitochondrion is_a membranous cytoplasmic organelle |
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| protein kinase is_a kinase |
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| DNA is_a nucleic acid |
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| 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 |
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| photosynthesis is_a physiological process |
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| gonad development is_a organogenesis |
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| intracellular signaling cascade is_a signal transduction |
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| 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 |
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| nuclear pore complex part_of nuclear membrane |
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| nucleoplasm part_of nucleus |
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| promotor part_of gene |
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| 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 |
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| cytokinesis part_of cell proliferation |
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| transcription part_of gene expression |
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| neurotransmitter release part_of synaptic transmission |
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| 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 |
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| nucleolus located_in nucleus |
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| membrane receptor located_in cell membrane |
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| chlorophyll located_in thylakoid |
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| 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 |
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| thylakoid contained_in chloroplast membrane |
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| synaptic vesicle contained_in neuron |
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| 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 |
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| cell wall adjacent_to cytoplasm |
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| periplasm adjacent_to plasma membrane |
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| presynaptic membrane adjacent_to synaptic cleft |
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| 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 |
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| hemosiderin transformation_of hemoglobin |
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| red blood cell transformation_of reticulocyte |
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| fetus transformation_of embryo |
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| 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 |
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| triple oxygen molecule derives_from oxygen molecule |
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| Barr body derives_from X-chromosome |
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| mammal derives_from gamete |
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| 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 |
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| cytokinesis preceded_by DNA replication |
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| apoptotic cell death preceded_by nuclear chromatin degradation |
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| digestion preceded_by ingestion |
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| 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 |
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| photosynthesis has_participant chlorophyll |
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| apoptosis has_participant cell |
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| cell division has_participant chromosome |
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| 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 |
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| pathogenesis has_agent pathogen |
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| transcription has_agent RNA polymerase |
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| translation has_agent ribosome |
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Smith et al. Genome Biology 2005 6:R46 doi:10.1186/gb-2005-6-5-r46 |
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