cmungall/Biological process refactor.md

## Biological process refactor.md

      
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              Biological process refactor.md
            
          
    Bold Hypothesis: GO BPs can be cleanly separated into cellular
processes and larger processes formed from assemblages of these. Any
process should be diagrammable. If the diagram is expressed using cell
parts and molecules, it is cellular. If the diagram is expressed using
cells or tissues it is at a larger level of organization.
Additionally, we may have grouping classes which can abstract over
both branches, in terms of some objective or phenotype. Examples are:
growth (to increase the size of the organism or a part), immune system
process (to protect the organism from foreign threats)
CELLULAR PROCESS

A process that happens at the level of a cell. More likely to be conserved
Current CP hierarchy:

GO:0009987 ! cellular process

GO:0000075 ! cell cycle checkpoint
GO:0000920 ! cell separation after cytokinesis
GO:0006457 ! protein folding
GO:0006914 ! autophagy
GO:0007165 ! signal transduction
GO:0010496 ! intercellular transport
GO:0016043 ! cellular component organization
GO:0019835 ! cytolysis
GO:0022402 ! cell cycle process
GO:0036166 ! phenotypic switching
GO:0043335 ! protein unfolding
GO:0044237 ! cellular metabolic process MERGE UP (see below)
GO:0044763 ! single-organism cellular process
GO:0044764 ! multi-organism cellular process
GO:0051716 ! cellular response to stimulus SEE BELOW
GO:0071554 ! cell wall organization or biogenesis
GO:1990748 ! cellular detoxification SEE BELOW


TO BE MOVED TO CELLULAR PROCESS


GO:0008152 ! metabolic process ↖️

GO:0006807 ! nitrogen compound metabolic process
GO:0009056 ! catabolic process
GO:0009058 ! biosynthetic process
GO:0010166 ! wax metabolic process
GO:0032259 ! methylation
GO:0042445 ! hormone metabolic process
GO:0044033 ! multi-organism metabolic process
GO:0044237 ! cellular metabolic process
GO:0044238 ! primary metabolic process
GO:0044710 ! single-organism metabolic process 🗑️
GO:0071704 ! organic substance metabolic process
GO:1900872 ! pentadec-1-ene metabolic process
GO:1901049 ! atropine metabolic process
GO:1901902 ! tyrocidine metabolic process
GO:1902421 ! hydrogen metabolic process


GO:0001906 ! cell killing ↖️

GO:0001909 ! leukocyte mediated cytotoxicity
GO:0031640 ! killing of cells of other organism
GO:0097278 ! complement-dependent cytotoxicity


GO:0071840 ! cellular component organization or biogenesis ↖️

GO:0016043 ! cellular component organization
GO:0044085 ! cellular component biogenesis


GO:0099531 ! presynaptic process involved in chemical synaptic transmission ↖️

GO:0007269 ! neurotransmitter secretion
GO:0016079 ! synaptic vesicle exocytosis
GO:0016080 ! synaptic vesicle targeting
GO:0016081 ! synaptic vesicle docking
GO:0016082 ! synaptic vesicle priming
GO:0031629 ! synaptic vesicle fusion to presynaptic active zone membrane
GO:0051583 ! dopamine uptake involved in synaptic transmission
GO:0099069 ! synaptic vesicle tethering involved in synaptic vesicle exocytosis
GO:0099502 ! calcium-dependent activation of synaptic vesicle fusion
GO:0099703 ! induction of synaptic vesicle exocytosis by positive regulation of presynaptic cytosolic calcium ion concentration


GO:0098754 ! detoxification ↖️

GO:0010127 ! mycothiol-dependent detoxification
GO:0010312 ! detoxification of zinc ion
GO:0051410 ! detoxification of nitrogen compound
GO:0061687 ! detoxification of inorganic compound
GO:0071722 ! detoxification of arsenic-containing substance
GO:1990748 ! cellular detoxification MERGE


I would argue that GO only cares about detoxification at the cellular level.
NO ACTION

These are currently directly under BP, and should remain


GO:0051704 ! multi-organism process 👍

GO:0009405 ! pathogenesis
GO:0035636 ! multi-organism signaling
GO:0035821 ! modification of morphology or physiology of other organism
GO:0044033 ! multi-organism metabolic process
GO:0044110 ! growth involved in symbiotic interaction
GO:0044111 ! development involved in symbiotic interaction
GO:0044366 ! feeding on or from other organism
GO:0044406 ! adhesion of symbiont to host
GO:0044419 ! interspecies interaction between organisms
GO:0044703 ! multi-organism reproductive process
GO:0044706 ! multi-multicellular organism process
GO:0044764 ! multi-organism cellular process
GO:0051703 ! intraspecies interaction between organisms
GO:0051705 ! multi-organism behavior
GO:0051707 ! response to other organism
GO:0051816 ! acquisition of nutrients from other organism during symbiotic interaction
GO:0098630 ! aggregation of unicellular organisms
GO:0098740 ! multi organism cell adhesion
GO:1902579 ! multi-organism localization


GO:0098743 ! cell aggregation 👍

GO:0001502 ! cartilage condensation
GO:0098630 ! aggregation of unicellular organisms


GO:0007610 ! behavior 👍

GO:0002209 ! behavioral defense response
GO:0007622 ! rhythmic behavior
GO:0007626 ! locomotory behavior
GO:0007631 ! feeding behavior
GO:0019098 ! reproductive behavior
GO:0044708 ! single-organism behavior
GO:0051705 ! multi-organism behavior
GO:0051780 ! behavioral response to nutrient


GO:0032501 ! multicellular organismal process  👍 (consider 🗑️)

GO:0003008 ! system process
GO:0032504 ! multicellular organism reproduction
GO:0044266 ! multicellular organismal macromolecule catabolic process
GO:0044274 ! multicellular organism biosynthetic process
GO:0044706 ! multi-multicellular organism process
GO:0044707 ! single-multicellular organism process


GROUPINGS


GO:0032502 ! developmental process

GO:0003006 ! developmental process involved in reproduction
GO:0009653 ! anatomical structure morphogenesis
GO:0009838 ! abscission
GO:0009847 ! spore germination
GO:0022611 ! dormancy process
GO:0031128 ! developmental induction
GO:0044111 ! development involved in symbiotic interaction
GO:0044767 ! single-organism developmental process
GO:0048646 ! anatomical structure formation involved in morphogenesis
GO:0048856 ! anatomical structure development
GO:0097737 ! acquisition of mycelium reproductive competence
GO:0098727 ! maintenance of cell number


cell development needs to go to CP


GO:0000003 ! reproduction __

GO:0019953 ! sexual reproduction
GO:0019954 ! asexual reproduction
GO:0032504 ! multicellular organism reproduction
GO:0032505 ! reproduction of a single-celled organism


GO:0002376 ! immune system process GROUPING

GO:0001776 ! leukocyte homeostasis
GO:0002200 ! somatic diversification of immune receptors
GO:0002252 ! immune effector process
GO:0002253 ! activation of immune response
GO:0002262 ! myeloid cell homeostasis
GO:0002339 ! B cell selection
GO:0002404 ! antigen sampling in mucosal-associated lymphoid tissue
GO:0002440 ! production of molecular mediator of immune response
GO:0002507 ! tolerance induction
GO:0002520 ! immune system development
GO:0006955 ! immune response
GO:0019882 ! antigen processing and presentation
GO:0031294 ! lymphocyte costimulation
GO:0035172 ! hemocyte proliferation
GO:0042386 ! hemocyte differentiation
GO:0045058 ! T cell selection
GO:0045321 ! leukocyte activation
GO:0050900 ! leukocyte migration
GO:0090713 ! immunological memory process


GO:0022610 ! biological adhesion GROUPING

GO:0007155 ! cell adhesion ↖️
GO:0007302 ! nurse cell nucleus anchoring ↖️
GO:0022608 ! multicellular organism adhesion ↖️
GO:0044406 ! adhesion of symbiont to host ↖️
GO:0090675 ! intermicrovillar adhesion ↖️


GO:0023052 ! signaling GROUPING

GO:0035636 ! multi-organism signaling OBSOLETE
GO:0044700 ! single organism signaling GROUPING

GO:0007267 ! cell-cell signaling ↖️
GO:0021807 ! motogenic signaling initiating cell movement in cerebral cortex ↖️
GO:0021837 ! motogenic signaling involved in postnatal olfactory bulb interneuron migration ↖️
GO:0021838 ! motogenic signaling involved in interneuron migration from the subpallium to the cortex ↖️
GO:0035426 ! extracellular matrix-cell signaling ↖️
GO:0035637 ! multicellular organismal signaling ↖️


GO:0040007 ! growth GROUPING

GO:0001545 ! primary ovarian follicle growth
GO:0001546 ! preantral ovarian follicle growth
GO:0001550 ! ovarian cumulus expansion
GO:0007117 ! budding cell bud growth
GO:0016049 ! cell growth
GO:0030447 ! filamentous growth
GO:0042702 ! uterine wall growth
GO:0044110 ! growth involved in symbiotic interaction
GO:0048589 ! developmental growth
GO:0080189 ! primary growth
GO:0080190 ! lateral growth


GO:0040011 ! locomotion GROUPING

GO:0031987 ! locomotion involved in locomotory behavior
GO:0033058 ! directional locomotion
GO:0036268 ! swimming
GO:0042330 ! taxis
GO:0048870 ! cell motility
GO:0051821 ! dissemination or transmission of organism from other organism involved in symbiotic interaction
GO:0052192 ! movement in environment of other organism involved in symbiotic interaction
GO:0060361 ! flight
GO:0071965 ! multicellular organismal locomotion


GO:0044699 ! single-organism process GROUPING

GO:0001788 ! antibody-dependent cellular cytotoxicity
GO:0001913 ! T cell mediated cytotoxicity
GO:0006791 ! sulfur utilization
GO:0006794 ! phosphorus utilization
GO:0007624 ! ultradian rhythm
GO:0008283 ! cell proliferation
GO:0009758 ! carbohydrate utilization
GO:0015976 ! carbon utilization
GO:0019740 ! nitrogen utilization
GO:0030447 ! filamentous growth
GO:0042267 ! natural killer cell mediated cytotoxicity
GO:0043473 ! pigmentation
GO:0044700 ! single organism signaling
GO:0044702 ! single organism reproductive process
GO:0044707 ! single-multicellular organism process
GO:0044708 ! single-organism behavior
GO:0044710 ! single-organism metabolic process
GO:0044763 ! single-organism cellular process
GO:0044767 ! single-organism developmental process
GO:0080190 ! lateral growth
GO:0097278 ! complement-dependent cytotoxicity
GO:0098602 ! single organism cell adhesion
GO:1902578 ! single-organism localization


GO:0048511 ! rhythmic process GROUPING

GO:0007622 ! rhythmic behavior
GO:0007623 ! circadian rhythm
GO:0007624 ! ultradian rhythm
GO:0022602 ! ovulation cycle process
GO:0042698 ! ovulation cycle


GO:0050896 ! response to stimulus TODO

GO:0006950 ! response to stress
GO:0006955 ! immune response
GO:0009605 ! response to external stimulus
GO:0009607 ! response to biotic stimulus
GO:0009628 ! response to abiotic stimulus
GO:0009719 ! response to endogenous stimulus
GO:0014823 ! response to activity
GO:0014854 ! response to inactivity
GO:0014874 ! response to stimulus involved in regulation of muscle adaptation
GO:0042221 ! response to chemical
GO:0043500 ! muscle adaptation
GO:0043627 ! response to estrogen
GO:0051606 ! detection of stimulus
GO:0051716 ! cellular response to stimulus
GO:0051775 ! response to redox state
GO:0072376 ! protein activation cascade


GO:0051179 ! localization GROUPING

GO:0032187 ! actomyosin contractile ring localization
GO:0033036 ! macromolecule localization
GO:0035732 ! nitric oxide storage
GO:0051234 ! establishment of localization
GO:0051235 ! maintenance of location
GO:0051641 ! cellular localization
GO:0051674 ! localization of cell
GO:1902578 ! single-organism localization
GO:1902579 ! multi-organism localization


GROUPINGS WITH OWL DEFINITIONS

No action required here


GO:0065007 ! biological regulation GROUPING

GO:0050789 ! regulation of biological process
GO:0065008 ! regulation of biological quality
GO:0065009 ! regulation of molecular function
GO:1902727 ! negative regulation of growth factor dependent skeletal muscle satellite cell proliferation
GO:1902728 ! positive regulation of growth factor dependent skeletal muscle satellite cell proliferation


GO:0022414 ! reproductive process GROUPING

GO:0000728 ! gene conversion at mating-type locus, DNA double-strand break formation
GO:0000734 ! gene conversion at mating-type locus, DNA repair synthesis
GO:0000742 ! karyogamy involved in conjugation with cellular fusion
GO:0000749 ! response to pheromone involved in conjugation with cellular fusion
GO:0000751 ! mitotic cell cycle G1 arrest in response to pheromone
GO:0000754 ! adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion
GO:0002077 ! acrosome matrix dispersal
GO:0003006 ! developmental process involved in reproduction
GO:0007117 ! budding cell bud growth
GO:0007289 ! spermatid nucleus differentiation
GO:0007290 ! spermatid nucleus elongation
GO:0007302 ! nurse cell nucleus anchoring
GO:0007303 ! cytoplasmic transport, nurse cell to oocyte
GO:0007316 ! pole plasm RNA localization
GO:0007318 ! pole plasm protein localization
GO:0007340 ! acrosome reaction
GO:0007344 ! pronuclear fusion
GO:0007534 ! gene conversion at mating-type locus
GO:0008302 ! female germline ring canal formation, actin assembly
GO:0010183 ! pollen tube guidance
GO:0010344 ! seed oilbody biogenesis
GO:0010708 ! heteroduplex formation involved in gene conversion at mating-type locus
GO:0022413 ! reproductive process in single-celled organism
GO:0030709 ! border follicle cell delamination
GO:0030717 ! karyosome formation
GO:0030719 ! P granule organization
GO:0030720 ! oocyte localization involved in germarium-derived egg chamber formation
GO:0030722 ! establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification
GO:0031292 ! gene conversion at mating-type locus, DNA double-strand break processing
GO:0032005 ! signal transduction involved in conjugation with cellular fusion
GO:0032219 ! cell wall macromolecule catabolic process involved in cytogamy
GO:0034624 ! DNA recombinase assembly involved in gene conversion at mating-type locus
GO:0034636 ! strand invasion involved in gene conversion at mating-type locus
GO:0035038 ! female pronucleus assembly
GO:0035039 ! male pronucleus assembly
GO:0035041 ! sperm chromatin decondensation
GO:0035042 ! fertilization, exchange of chromosomal proteins
GO:0035046 ! pronuclear migration
GO:0035092 ! sperm chromatin condensation
GO:0035093 ! spermatogenesis, exchange of chromosomal proteins
GO:0035471 ! luteinizing hormone signaling pathway involved in ovarian follicle development
GO:0043046 ! DNA methylation involved in gamete generation
GO:0043093 ! FtsZ-dependent cytokinesis
GO:0044702 ! single organism reproductive process
GO:0044703 ! multi-organism reproductive process
GO:0045450 ! bicoid mRNA localization
GO:0045478 ! fusome organization
GO:0048359 ! mucilage metabolic process involved in seed coat development
GO:0048497 ! maintenance of floral organ identity
GO:0048573 ! photoperiodism, flowering
GO:0048609 ! multicellular organismal reproductive process
GO:0051037 ! regulation of transcription involved in meiotic cell cycle
GO:0051663 ! oocyte nucleus localization involved in oocyte dorsal/ventral axis specification
GO:0055047 ! generative cell mitosis
GO:0060466 ! activation of meiosis involved in egg activation
GO:0060468 ! prevention of polyspermy
GO:0060469 ! positive regulation of transcription involved in egg activation
GO:0060474 ! positive regulation of flagellated sperm motility involved in capacitation
GO:0060477 ! peptidyl-serine phosphorylation involved in acrosome reaction
GO:0060519 ! cell adhesion involved in prostatic bud elongation
GO:0060783 ! mesenchymal smoothened signaling pathway involved in prostate gland development
GO:0060833 ! Wnt signaling pathway involved in animal/vegetal axis specification
GO:0060869 ! transmembrane receptor protein serine/threonine kinase signaling pathway involved in floral organ abscission
GO:0061363 ! negative regulation of progesterone biosynthesis involved in luteolysis
GO:0061500 ! gene conversion at mating-type locus, termination of copy-synthesis
GO:0070871 ! cell wall organization involved in conjugation with cellular fusion
GO:0071432 ! peptide mating pheromone maturation involved in conjugation with cellular fusion
GO:0072409 ! detection of stimulus involved in meiotic cell cycle checkpoint
GO:0090220 ! chromosome localization to nuclear envelope involved in homologous chromosome segregation
GO:0090379 ! secondary cell wall biogenesis involved in seed trichome differentiation
GO:1902064 ! regulation of transcription from RNA polymerase II promoter involved in spermatogenesis
GO:1902397 ! detection of stimulus involved in meiotic spindle checkpoint
GO:1902441 ! protein localization to meiotic spindle pole body
GO:1903046 ! meiotic cell cycle process
GO:1905198 ! manchette assembly


OTHER

phase is not even really a process but we keep under BP for convenience

GO:0044848 ! biological phase

GO:0022403 ! cell cycle phase
GO:0022601 ! menstrual cycle phase
GO:0044851 ! hair cycle phase
GO:0060206 ! estrous cycle phase
GO:0072690 ! single-celled organism vegetative growth phase