Taxon constraints inherited from uberon are too metazoan-specific

[cmungall]

See this ticket, starting from this comment yesterday: https://github.com/geneontology/go-ontology/issues/21217#issuecomment-1066102512

@balhoff summarizes:

The owltools taxon subset command is more aggressive than normal taxon constraint reasoning. In this case there is a pretty large reasoner explanation, but it includes the relation that anatomical structures start existing during or after zygote stage, zygote stage is part of embryo stage, and then embryo stage relates to all sorts of stuff that is not in yeast.

We could either do a lot of work in Uberon to make all these relationships more taxon-specific, or provide you with a different script that only removes terms over the standard taxon constraint propagation rules.

This summary is correct: Here is the source of the confusion: all classes in Uberon were originally intended for metazoa. CARO was originally intended as the true species-neutral form. However, CARO is not well maintained and it's confusing having latticey terms that are trivially differentiated only be species, so GO has been using Uberon terms as if they were species neutral

Action, from immediate to longer term:

1. [ ] @balhoff - what about as an immediate fix using robot to filter for a conservative set of ObjectProperties prior to the taxon operation?
2. [x] I made an issue to make the relationship metazoan specific in uberon, which will fix this: https://github.com/obophenotype/uberon/issues/2348
3. [ ] we need better checksums as part of the QC process more generally

Note the uberon fix may take some discussion, and then will need to be percolated to GO

The final item will take some time but broadly speaking we should be annotating terms we know for sure to be in a taxon with present-in taxon. It would also be good to see a diff with each release of which terms dropped out for main taxa. Some of this should be apparent from the snapshot releases - I assume yesterday we would have been an increase in taxon violations for pombe - but I don't think we have an alert mechanism for deltas here.

[ValWood]

thanks!

[kimrutherford]

Thanks Jim and Chris. We'll be happy with whatever solution you can come up with. We have no problem with moving away from OWLTools if that's the best plan.

[balhoff]

@ValWood @kimrutherford I've made a little replacement script which is kind of the opposite of what Chris suggested. Instead of filtering axioms based on certain properties out of the ontology, it lets you provide additional properties which you want to chain 'in taxon' over. This way you can take the standard taxon constraint reasoning and make it "stronger" as desired. I ran it and only specified regulates as an additional chain property. This results in a go-plus with an additional 927 terms that had been filtered using the owltools command. This brings back GO:0061246, but I'm sure also some terms you don't want. But those could be targets for improved taxon constraints. If you think this sounds like a good way to go, I can package the script for you.

Here are the terms that came back:

GO:0000753 "cell morphogenesis involved in conjugation with cellular fusion"
GO:0000768 "syncytium formation by plasma membrane fusion"
GO:0000769 "syncytium formation by mitosis without cytokinesis"
GO:0000902 "cell morphogenesis"
GO:0000904 "cell morphogenesis involved in differentiation"
GO:0001066 "plastid single subunit type RNA polymerase activity"
GO:0001410 "chlamydospore formation"
GO:0001778 "plasma membrane repair"
GO:0001941 "postsynaptic membrane organization"
GO:0002160 "desmosome maintenance"
GO:0002175 "protein localization to paranode region of axon"
GO:0002576 "platelet degranulation"
GO:0002934 "desmosome organization"
GO:0003133 "endodermal-mesodermal cell signaling"
GO:0003399 "cytoneme morphogenesis"
GO:0003401 "axis elongation"
GO:0005518 "collagen binding"
GO:0005579 "membrane attack complex"
GO:0006622 "protein targeting to lysosome"
GO:0006949 "syncytium formation"
GO:0007027 "negative regulation of axonemal microtubule depolymerization"
GO:0007040 "lysosome organization"
GO:0007041 "lysosomal transport"
GO:0007042 "lysosomal lumen acidification"
GO:0007179 "transforming growth factor beta receptor signaling pathway"
GO:0007181 "transforming growth factor beta receptor complex assembly"
GO:0007338 "single fertilization"
GO:0007339 "binding of sperm to zona pellucida"
GO:0007343 "egg activation"
GO:0007344 "pronuclear fusion"
GO:0007528 "neuromuscular junction development"
GO:0007529 "establishment of synaptic specificity at neuromuscular junction"
GO:0008088 "axo-dendritic transport"
GO:0008089 "anterograde axonal transport"
GO:0008090 "retrograde axonal transport"
GO:0008307 "structural constituent of muscle"
GO:0008333 "endosome to lysosome transport"
GO:0008360 "regulation of cell shape"
GO:0008377 "light-induced release of internally sequestered calcium ion"
GO:0008543 "fibroblast growth factor receptor signaling pathway"
GO:0009566 "fertilization"
GO:0009653 "anatomical structure morphogenesis"
GO:0009663 "plasmodesma organization"
GO:0009826 "unidimensional cell growth"
GO:0009887 "animal organ morphogenesis"
GO:0009932 "cell tip growth"
GO:0010070 "zygote asymmetric cell division"
GO:0010171 "body morphogenesis"
GO:0010199 "organ boundary specification between lateral organs and the meristem"
GO:0010481 "epidermal cell division"
GO:0010482 "regulation of epidermal cell division"
GO:0010497 "plasmodesmata-mediated intercellular transport"
GO:0010623 "programmed cell death involved in cell development"
GO:0010635 "regulation of mitochondrial fusion"
GO:0010636 "positive regulation of mitochondrial fusion"
GO:0010637 "negative regulation of mitochondrial fusion"
GO:0010710 "regulation of collagen catabolic process"
GO:0010711 "negative regulation of collagen catabolic process"
GO:0010712 "regulation of collagen metabolic process"
GO:0010713 "negative regulation of collagen metabolic process"
GO:0010714 "positive regulation of collagen metabolic process"
GO:0010720 "positive regulation of cell development"
GO:0010721 "negative regulation of cell development"
GO:0010769 "regulation of cell morphogenesis involved in differentiation"
GO:0010770 "positive regulation of cell morphogenesis involved in differentiation"
GO:0010771 "negative regulation of cell morphogenesis involved in differentiation"
GO:0010880 "regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum"
GO:0010927 "cellular component assembly involved in morphogenesis"
GO:0014808 "release of sequestered calcium ion into cytosol by sarcoplasmic reticulum"
GO:0014872 "myoblast division"
GO:0015126 "canalicular bile acid transmembrane transporter activity"
GO:0015722 "canalicular bile acid transport"
GO:0015841 "chromaffin granule amine transport"
GO:0016056 "rhodopsin mediated signaling pathway"
GO:0016057 "regulation of membrane potential in photoreceptor cell"
GO:0016058 "maintenance of membrane potential in photoreceptor cell by rhodopsin mediated signaling"
GO:0016059 "deactivation of rhodopsin mediated signaling"
GO:0016060 "metarhodopsin inactivation"
GO:0016062 "adaptation of rhodopsin mediated signaling"
GO:0016063 "rhodopsin biosynthetic process"
GO:0016188 "synaptic vesicle maturation"
GO:0016189 "synaptic vesicle to endosome fusion"
GO:0016256 "N-glycan processing to lysosome"
GO:0017015 "regulation of transforming growth factor beta receptor signaling pathway"
GO:0017145 "stem cell division"
GO:0018985 "pronuclear envelope synthesis"
GO:0019896 "axonal transport of mitochondrion"
GO:0022400 "regulation of rhodopsin mediated signaling pathway"
GO:0022603 "regulation of anatomical structure morphogenesis"
GO:0022604 "regulation of cell morphogenesis"
GO:0030265 "phospholipase C-activating rhodopsin mediated signaling pathway"
GO:0030280 "structural constituent of skin epidermis"
GO:0030281 "structural constituent of cutaneous appendage"
GO:0030321 "transepithelial chloride transport"
GO:0030345 "structural constituent of tooth enamel"
GO:0030353 "fibroblast growth factor receptor antagonist activity"
GO:0030382 "sperm mitochondrion organization"
GO:0030435 "sporulation resulting in formation of a cellular spore"
GO:0030437 "ascospore formation"
GO:0030476 "ascospore wall assembly"
GO:0030509 "BMP signaling pathway"
GO:0030510 "regulation of BMP signaling pathway"
GO:0030511 "positive regulation of transforming growth factor beta receptor signaling pathway"
GO:0030512 "negative regulation of transforming growth factor beta receptor signaling pathway"
GO:0030513 "positive regulation of BMP signaling pathway"
GO:0030514 "negative regulation of BMP signaling pathway"
GO:0030574 "collagen catabolic process"
GO:0030721 "spectrosome organization"
GO:0030990 "intraciliary transport particle"
GO:0030991 "intraciliary transport particle A"
GO:0030992 "intraciliary transport particle B"
GO:0031099 "regeneration"
GO:0031100 "animal organ regeneration"
GO:0031266 "TRAIL death-inducing signaling complex"
GO:0031321 "ascospore-type prospore assembly"
GO:0031322 "ascospore-type prospore-specific spindle pole body remodeling"
GO:0031382 "mating projection formation"
GO:0031383 "regulation of mating projection assembly"
GO:0031384 "regulation of initiation of mating projection growth"
GO:0031385 "regulation of termination of mating projection growth"
GO:0031529 "ruffle organization"
GO:0032053 "ciliary basal body organization"
GO:0032120 "ascospore-type prospore membrane formation"
GO:0032122 "oral apparatus organization"
GO:0032124 "macronucleus organization"
GO:0032125 "micronucleus organization"
GO:0032186 "cellular bud neck septin ring organization"
GO:0032252 "secretory granule localization"
GO:0032253 "dense core granule localization"
GO:0032254 "establishment of secretory granule localization"
GO:0032255 "maintenance of secretory granule location"
GO:0032256 "establishment of dense core granule localization"
GO:0032257 "maintenance of dense core granule location"
GO:0032400 "melanosome localization"
GO:0032401 "establishment of melanosome localization"
GO:0032402 "melanosome transport"
GO:0032418 "lysosome localization"
GO:0032438 "melanosome organization"
GO:0032510 "endosome to lysosome transport via multivesicular body sorting pathway"
GO:0032528 "microvillus organization"
GO:0032529 "follicle cell microvillus organization"
GO:0032530 "regulation of microvillus organization"
GO:0032531 "regulation of follicle cell microvillus organization"
GO:0032532 "regulation of microvillus length"
GO:0032533 "regulation of follicle cell microvillus length"
GO:0032963 "collagen metabolic process"
GO:0032964 "collagen biosynthetic process"
GO:0032965 "regulation of collagen biosynthetic process"
GO:0032966 "negative regulation of collagen biosynthetic process"
GO:0032967 "positive regulation of collagen biosynthetic process"
GO:0032980 "keratinocyte activation"
GO:0032989 "cellular component morphogenesis"
GO:0032990 "cell part morphogenesis"
GO:0033341 "regulation of collagen binding"
GO:0033342 "negative regulation of collagen binding"
GO:0033343 "positive regulation of collagen binding"
GO:0033363 "secretory granule organization"
GO:0033364 "mast cell secretory granule organization"
GO:0033366 "protein localization to secretory granule"
GO:0033367 "protein localization to mast cell secretory granule"
GO:0033368 "protease localization to mast cell secretory granule"
GO:0033369 "establishment of protein localization to mast cell secretory granule"
GO:0033370 "maintenance of protein location in mast cell secretory granule"
GO:0033371 "T cell secretory granule organization"
GO:0033372 "establishment of protease localization to mast cell secretory granule"
GO:0033373 "maintenance of protease location in mast cell secretory granule"
GO:0033374 "protein localization to T cell secretory granule"
GO:0033375 "protease localization to T cell secretory granule"
GO:0033376 "establishment of protein localization to T cell secretory granule"
GO:0033377 "maintenance of protein location in T cell secretory granule"
GO:0033378 "establishment of protease localization to T cell secretory granule"
GO:0033379 "maintenance of protease location in T cell secretory granule"
GO:0033380 "granzyme B localization to T cell secretory granule"
GO:0033381 "establishment of granzyme B localization to T cell secretory granule"
GO:0033382 "maintenance of granzyme B location in T cell secretory granule"
GO:0034217 "ascospore wall chitin biosynthetic process"
GO:0034223 "regulation of ascospore wall chitin biosynthetic process"
GO:0034238 "macrophage fusion"
GO:0034239 "regulation of macrophage fusion"
GO:0034240 "negative regulation of macrophage fusion"
GO:0034241 "positive regulation of macrophage fusion"
GO:0034242 "negative regulation of syncytium formation by plasma membrane fusion"
GO:0034294 "sexual spore wall assembly"
GO:0034295 "basidiospore formation"
GO:0034296 "zygospore formation"
GO:0034300 "sporangiospore formation"
GO:0034301 "endospore formation"
GO:0034302 "akinete formation"
GO:0034303 "myxospore formation"
GO:0034304 "actinomycete-type spore formation"
GO:0034307 "regulation of ascospore formation"
GO:0034330 "cell junction organization"
GO:0034331 "cell junction maintenance"
GO:0034408 "ascospore wall beta-glucan metabolic process"
GO:0034409 "ascospore wall (1->3)-beta-D-glucan metabolic process"
GO:0034412 "ascospore wall beta-glucan biosynthetic process"
GO:0034413 "ascospore wall (1->3)-beta-D-glucan biosynthetic process"
GO:0034446 "substrate adhesion-dependent cell spreading"
GO:0034769 "basement membrane disassembly"
GO:0035036 "sperm-egg recognition"
GO:0035037 "sperm entry"
GO:0035044 "sperm aster formation"
GO:0035046 "pronuclear migration"
GO:0035047 "centrosomal and pronuclear rotation"
GO:0035231 "cytoneme assembly"
GO:0035234 "ectopic germ cell programmed cell death"
GO:0035377 "transepithelial water transport"
GO:0035418 "protein localization to synapse"
GO:0035582 "sequestering of BMP in extracellular matrix"
GO:0035583 "sequestering of TGFbeta in extracellular matrix"
GO:0035646 "endosome to melanosome transport"
GO:0035733 "hepatic stellate cell activation"
GO:0035750 "protein localization to myelin sheath abaxonal region"
GO:0035751 "regulation of lysosomal lumen pH"
GO:0035752 "lysosomal lumen pH elevation"
GO:0035759 "mesangial cell-matrix adhesion"
GO:0035921 "desmosome disassembly"
GO:0036309 "protein localization to M-band"
GO:0036333 "hepatocyte homeostasis"
GO:0036334 "epidermal stem cell homeostasis"
GO:0036344 "platelet morphogenesis"
GO:0036445 "neuronal stem cell division"
GO:0036520 "astrocyte-dopaminergic neuron signaling"
GO:0038056 "negative regulation of BMP signaling pathway by negative regulation of BMP secretion"
GO:0038098 "sequestering of BMP from receptor via BMP binding"
GO:0038179 "neurotrophin signaling pathway"
GO:0038180 "nerve growth factor signaling pathway"
GO:0040036 "regulation of fibroblast growth factor receptor signaling pathway"
GO:0040037 "negative regulation of fibroblast growth factor receptor signaling pathway"
GO:0042045 "epithelial fluid transport"
GO:0042060 "wound healing"
GO:0042118 "endothelial cell activation"
GO:0042173 "regulation of sporulation resulting in formation of a cellular spore"
GO:0042174 "negative regulation of sporulation resulting in formation of a cellular spore"
GO:0042243 "asexual spore wall assembly"
GO:0042244 "spore wall assembly"
GO:0042246 "tissue regeneration"
GO:0042793 "plastid transcription"
GO:0042794 "plastid rRNA transcription"
GO:0042814 "monopolar cell growth"
GO:0042815 "bipolar cell growth"
GO:0042824 "MHC class I peptide loading complex"
GO:0042825 "TAP complex"
GO:0043083 "synaptic cleft"
GO:0043163 "cell envelope organization"
GO:0043572 "plastid fission"
GO:0043573 "leucoplast fission"
GO:0043886 "structural constituent of carboxysome"
GO:0043935 "sexual sporulation resulting in formation of a cellular spore"
GO:0043936 "asexual sporulation resulting in formation of a cellular spore"
GO:0043940 "regulation of sexual sporulation resulting in formation of a cellular spore"
GO:0043941 "positive regulation of sexual sporulation resulting in formation of a cellular spore"
GO:0043942 "negative regulation of sexual sporulation resulting in formation of a cellular spore"
GO:0043943 "regulation of asexual sporulation resulting in formation of a cellular spore"
GO:0043944 "negative regulation of asexual sporulation resulting in formation of a cellular spore"
GO:0043945 "positive regulation of asexual sporulation resulting in formation of a cellular spore"
GO:0044181 "filamentous growth of a multicellular organism"
GO:0044258 "intestinal lipid catabolic process"
GO:0044546 "NLRP3 inflammasome complex assembly"
GO:0044566 "chondrocyte activation"
GO:0044782 "cilium organization"
GO:0045036 "protein targeting to chloroplast"
GO:0045037 "protein import into chloroplast stroma"
GO:0045038 "protein import into chloroplast thylakoid membrane"
GO:0045216 "cell-cell junction organization"
GO:0045217 "cell-cell junction maintenance"
GO:0045729 "respiratory burst at fertilization"
GO:0045743 "positive regulation of fibroblast growth factor receptor signaling pathway"
GO:0045881 "positive regulation of sporulation resulting in formation of a cellular spore"
GO:0046819 "protein secretion by the type V secretion system"
GO:0048011 "neurotrophin TRK receptor signaling pathway"
GO:0048103 "somatic stem cell division"
GO:0048468 "cell development"
GO:0048469 "cell maturation"
GO:0048489 "synaptic vesicle transport"
GO:0048490 "anterograde synaptic vesicle transport"
GO:0048491 "retrograde synaptic vesicle transport"
GO:0048496 "maintenance of animal organ identity"
GO:0048499 "synaptic vesicle membrane organization"
GO:0048513 "animal organ development"
GO:0048532 "anatomical structure arrangement"
GO:0048569 "post-embryonic animal organ development"
GO:0048588 "developmental cell growth"
GO:0048646 "anatomical structure formation involved in morphogenesis"
GO:0048790 "maintenance of presynaptic active zone structure"
GO:0048799 "animal organ maturation"
GO:0048856 "anatomical structure development"
GO:0048858 "cell projection morphogenesis"
GO:0048859 "formation of anatomical boundary"
GO:0048860 "glioblast division"
GO:0050254 "rhodopsin kinase activity"
GO:0050807 "regulation of synapse organization"
GO:0050808 "synapse organization"
GO:0051386 "regulation of neurotrophin TRK receptor signaling pathway"
GO:0051387 "negative regulation of neurotrophin TRK receptor signaling pathway"
GO:0051388 "positive regulation of neurotrophin TRK receptor signaling pathway"
GO:0051510 "regulation of unidimensional cell growth"
GO:0051511 "negative regulation of unidimensional cell growth"
GO:0051512 "positive regulation of unidimensional cell growth"
GO:0051513 "regulation of monopolar cell growth"
GO:0051514 "negative regulation of monopolar cell growth"
GO:0051515 "positive regulation of monopolar cell growth"
GO:0051516 "regulation of bipolar cell growth"
GO:0051517 "negative regulation of bipolar cell growth"
GO:0051518 "positive regulation of bipolar cell growth"
GO:0051519 "activation of bipolar cell growth"
GO:0051520 "termination of bipolar cell growth"
GO:0051521 "termination of monopolar cell growth"
GO:0051522 "activation of monopolar cell growth"
GO:0051523 "cell growth mode switching, monopolar to bipolar"
GO:0051524 "cell growth mode switching, bipolar to monopolar"
GO:0051642 "centrosome localization"
GO:0051660 "establishment of centrosome localization"
GO:0051661 "maintenance of centrosome location"
GO:0051823 "regulation of synapse structural plasticity"
GO:0051826 "negative regulation of synapse structural plasticity"
GO:0051835 "positive regulation of synapse structural plasticity"
GO:0055107 "Golgi to secretory granule transport"
GO:0060033 "anatomical structure regression"
GO:0060052 "neurofilament cytoskeleton organization"
GO:0060142 "regulation of syncytium formation by plasma membrane fusion"
GO:0060143 "positive regulation of syncytium formation by plasma membrane fusion"
GO:0060155 "platelet dense granule organization"
GO:0060233 "oenocyte delamination"
GO:0060234 "neuroblast delamination"
GO:0060284 "regulation of cell development"
GO:0060404 "axonemal microtubule depolymerization"
GO:0060466 "activation of meiosis involved in egg activation"
GO:0060467 "negative regulation of fertilization"
GO:0060468 "prevention of polyspermy"
GO:0060470 "positive regulation of cytosolic calcium ion concentration involved in egg activation"
GO:0060471 "cortical granule exocytosis"
GO:0060472 "positive regulation of cortical granule exocytosis by positive regulation of cytosolic calcium ion concentration"
GO:0060560 "developmental growth involved in morphogenesis"
GO:0060622 "regulation of ascospore wall beta-glucan biosynthetic process"
GO:0060624 "regulation of ascospore wall (1->3)-beta-D-glucan biosynthetic process"
GO:0060830 "ciliary receptor clustering involved in smoothened signaling pathway"
GO:0061026 "cardiac muscle tissue regeneration"
GO:0061041 "regulation of wound healing"
GO:0061045 "negative regulation of wound healing"
GO:0061109 "dense core granule organization"
GO:0061159 "establishment of bipolar cell polarity involved in cell morphogenesis"
GO:0061160 "regulation of establishment of bipolar cell polarity regulating cell shape"
GO:0061161 "positive regulation of establishment of bipolar cell polarity regulating cell shape"
GO:0061246 "establishment or maintenance of bipolar cell polarity regulating cell shape"
GO:0061305 "maintenance of bipolar cell polarity regulating cell shape"
GO:0061340 "establishment or maintenance of monopolar cell polarity regulating cell shape"
GO:0061361 "positive regulation of maintenance of bipolar cell polarity regulating cell shape"
GO:0061362 "negative regulation of maintenance of bipolar cell polarity regulating cell shape"
GO:0061389 "regulation of direction of cell growth"
GO:0061390 "positive regulation of direction of cell growth"
GO:0061391 "negative regulation of direction of cell growth"
GO:0061462 "protein localization to lysosome"
GO:0061484 "hematopoietic stem cell homeostasis"
GO:0061523 "cilium disassembly"
GO:0061684 "chaperone-mediated autophagy"
GO:0061702 "inflammasome complex"
GO:0061740 "protein targeting to lysosome involved in chaperone-mediated autophagy"
GO:0061763 "multivesicular body-lysosome fusion"
GO:0061764 "late endosome to lysosome transport via multivesicular body sorting pathway"
GO:0061773 "eNoSc complex"
GO:0061779 "Tapasin-ERp57 complex"
GO:0061789 "dense core granule priming"
GO:0061790 "dense core granule docking"
GO:0061833 "protein localization to tricellular tight junction"
GO:0061880 "regulation of anterograde axonal transport of mitochondrion"
GO:0061881 "positive regulation of anterograde axonal transport of mitochondrion"
GO:0061882 "negative regulation of anterograde axonal transport of mitochondrion"
GO:0061938 "protein localization to somatodendritic compartment"
GO:0062061 "TAP complex binding"
GO:0062063 "BBSome binding"
GO:0062066 "PSII associated light-harvesting complex II binding"
GO:0062067 "chloroplast photosystem I binding"
GO:0062068 "chloroplast photosystem II binding"
GO:0062091 "Ycf2/FtsHi complex"
GO:0062093 "lysophagy"
GO:0062237 "protein localization to postsynapse"
GO:0070050 "neuron cellular homeostasis"
GO:0070052 "collagen V binding"
GO:0070142 "synaptic vesicle budding"
GO:0070285 "pigment cell development"
GO:0070296 "sarcoplasmic reticulum calcium ion transport"
GO:0070369 "beta-catenin-TCF7L2 complex"
GO:0070560 "protein secretion by platelet"
GO:0070583 "spore membrane bending pathway"
GO:0070584 "mitochondrion morphogenesis"
GO:0070590 "spore wall biogenesis"
GO:0070591 "ascospore wall biogenesis"
GO:0070633 "transepithelial transport"
GO:0070634 "transepithelial ammonium transport"
GO:0070864 "sperm individualization complex"
GO:0070865 "investment cone"
GO:0070889 "platelet alpha granule organization"
GO:0070997 "neuron death"
GO:0071205 "protein localization to juxtaparanode region of axon"
GO:0071206 "establishment of protein localization to juxtaparanode region of axon"
GO:0071340 "skeletal muscle acetylcholine-gated channel clustering"
GO:0071539 "protein localization to centrosome"
GO:0071695 "anatomical structure maturation"
GO:0071711 "basement membrane organization"
GO:0071896 "protein localization to adherens junction"
GO:0071963 "establishment or maintenance of cell polarity regulating cell shape"
GO:0071964 "establishment of cell polarity regulating cell shape"
GO:0071998 "ascospore release from ascus"
GO:0072000 "extracellular polysaccharide catabolic process involved in ascospore release from ascus"
GO:0072316 "alpha-glucan catabolic process involved in ascospore release from ascus"
GO:0072537 "fibroblast activation"
GO:0072553 "terminal button organization"
GO:0072557 "IPAF inflammasome complex"
GO:0072558 "NLRP1 inflammasome complex"
GO:0072559 "NLRP3 inflammasome complex"
GO:0072578 "neurotransmitter-gated ion channel clustering"
GO:0072579 "glycine receptor clustering"
GO:0072596 "establishment of protein localization to chloroplast"
GO:0072598 "protein localization to chloroplast"
GO:0072673 "lamellipodium morphogenesis"
GO:0075009 "germ tube formation"
GO:0075010 "regulation of germ tube formation"
GO:0075011 "positive regulation of germ tube formation"
GO:0075012 "negative regulation of germ tube formation"
GO:0075214 "spore encystment"
GO:0075215 "modulation of spore encystment on host"
GO:0075216 "positive regulation of spore encystment on host"
GO:0075217 "negative regulation of spore encystment on host"
GO:0075218 "zoospore encystment on host"
GO:0075219 "modulation of zoospore encystment on host"
GO:0075220 "positive regulation of zoospore encystment on host"
GO:0075221 "negative regulation of zoospore encystment on host"
GO:0075239 "zoospore formation"
GO:0075240 "regulation of zoospore formation"
GO:0075241 "positive regulation of zoospore formation"
GO:0075242 "negative regulation of zoospore formation"
GO:0075243 "oospore formation"
GO:0075244 "regulation of oospore formation"
GO:0075245 "positive regulation of oospore formation"
GO:0075246 "negative regulation of oospore formation"
GO:0075247 "aeciospore formation"
GO:0075248 "regulation of aeciospore formation"
GO:0075249 "positive regulation of aeciospore formation"
GO:0075250 "negative regulation of aeciospore formation"
GO:0075251 "uredospore formation"
GO:0075252 "regulation of uredospore formation"
GO:0075253 "positive regulation of uredospore formation"
GO:0075254 "negative regulation of uredospore formation"
GO:0075255 "teliospore formation"
GO:0075256 "regulation of teliospore formation"
GO:0075257 "positive regulation of teliospore formation"
GO:0075258 "negative regulation of teliospore formation"
GO:0075286 "regulation of sporangiospore formation"
GO:0075287 "positive regulation of sporangiospore formation"
GO:0075288 "negative regulation of sporangiospore formation"
GO:0075289 "aplanospore formation"
GO:0075290 "regulation of aplanospore formation"
GO:0075291 "positive regulation of aplanospore formation"
GO:0075292 "negative regulation of aplanospore formation"
GO:0075296 "positive regulation of ascospore formation"
GO:0075297 "negative regulation of ascospore formation"
GO:0075298 "regulation of zygospore formation"
GO:0075299 "positive regulation of zygospore formation"
GO:0075300 "negative regulation of zygospore formation"
GO:0075302 "regulation of basidiospore formation"
GO:0075303 "positive regulation of basidiospore formation"
GO:0075304 "negative regulation of basidiospore formation"
GO:0080154 "regulation of fertilization"
GO:0089705 "protein localization to outer membrane"
GO:0090080 "positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway"
GO:0090117 "endosome to lysosome transport of low-density lipoprotein particle"
GO:0090120 "lysosome to ER cholesterol transport"
GO:0090140 "regulation of mitochondrial fission"
GO:0090141 "positive regulation of mitochondrial fission"
GO:0090160 "Golgi to lysosome transport"
GO:0090162 "establishment of epithelial cell polarity"
GO:0090163 "establishment of epithelial cell planar polarity"
GO:0090164 "asymmetric Golgi ribbon formation"
GO:0090165 "regulation of secretion by asymmetric Golgi ribbon formation"
GO:0090222 "centrosome-templated microtubule nucleation"
GO:0090258 "negative regulation of mitochondrial fission"
GO:0090287 "regulation of cellular response to growth factor stimulus"
GO:0090288 "negative regulation of cellular response to growth factor stimulus"
GO:0090303 "positive regulation of wound healing"
GO:0090451 "cotyledon boundary formation"
GO:0090470 "shoot organ boundary specification"
GO:0090673 "endothelial cell-matrix adhesion"
GO:0090674 "endothelial cell-matrix adhesion via fibronectin"
GO:0090691 "formation of plant organ boundary"
GO:0097061 "dendritic spine organization"
GO:0097062 "dendritic spine maintenance"
GO:0097090 "presynaptic membrane organization"
GO:0097106 "postsynaptic density organization"
GO:0097112 "gamma-aminobutyric acid receptor clustering"
GO:0097113 "AMPA glutamate receptor clustering"
GO:0097114 "NMDA glutamate receptor clustering"
GO:0097117 "guanylate kinase-associated protein clustering"
GO:0097119 "postsynaptic density protein 95 clustering"
GO:0097120 "receptor localization to synapse"
GO:0097169 "AIM2 inflammasome complex"
GO:0097212 "lysosomal membrane organization"
GO:0097213 "regulation of lysosomal membrane permeability"
GO:0097214 "positive regulation of lysosomal membrane permeability"
GO:0097215 "negative regulation of lysosomal membrane permeability"
GO:0097271 "protein localization to bud neck"
GO:0097479 "synaptic vesicle localization"
GO:0097480 "establishment of synaptic vesicle localization"
GO:0097688 "glutamate receptor clustering"
GO:0097736 "aerial mycelium formation"
GO:0097738 "substrate mycelium formation"
GO:0098633 "collagen fibril binding"
GO:0098639 "collagen binding involved in cell-matrix adhesion"
GO:0098695 "inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels"
GO:0098696 "regulation of neurotransmitter receptor localization to postsynaptic specialization membrane"
GO:0098697 "ryanodine-sensitive calcium-release channel activity involved in regulation of postsynaptic cytosolic calcium levels"
GO:0098699 "structural constituent of presynaptic actin cytoskeleton"
GO:0098722 "asymmetric stem cell division"
GO:0098724 "symmetric stem cell division"
GO:0098726 "symmetric division of skeletal muscle satellite stem cell"
GO:0098776 "protein transport across the cell outer membrane"
GO:0098777 "protein secretion by the type VIII secretion system"
GO:0098821 "BMP receptor activity"
GO:0098879 "structural constituent of postsynaptic specialization"
GO:0098880 "maintenance of postsynaptic specialization structure"
GO:0098882 "structural constituent of presynaptic active zone"
GO:0098883 "synapse pruning"
GO:0098885 "modification of postsynaptic actin cytoskeleton"
GO:0098886 "modification of dendritic spine"
GO:0098887 "neurotransmitter receptor transport, endosome to postsynaptic membrane"
GO:0098918 "structural constituent of synapse"
GO:0098919 "structural constituent of postsynaptic density"
GO:0098928 "presynaptic signal transduction"
GO:0098930 "axonal transport"
GO:0098934 "retrograde dendritic transport"
GO:0098935 "dendritic transport"
GO:0098937 "anterograde dendritic transport"
GO:0098939 "dendritic transport of mitochondrion"
GO:0098943 "neurotransmitter receptor transport, postsynaptic endosome to lysosome"
GO:0098957 "anterograde axonal transport of mitochondrion"
GO:0098958 "retrograde axonal transport of mitochondrion"
GO:0098959 "retrograde dendritic transport of mitochondrion"
GO:0098961 "dendritic transport of ribonucleoprotein complex"
GO:0098963 "dendritic transport of messenger ribonucleoprotein complex"
GO:0098964 "anterograde dendritic transport of messenger ribonucleoprotein complex"
GO:0098967 "exocytic insertion of neurotransmitter receptor to postsynaptic membrane"
GO:0098968 "neurotransmitter receptor transport postsynaptic membrane to endosome"
GO:0098969 "neurotransmitter receptor transport to postsynaptic membrane"
GO:0098970 "postsynaptic neurotransmitter receptor diffusion trapping"
GO:0098971 "anterograde dendritic transport of neurotransmitter receptor complex"
GO:0098972 "anterograde dendritic transport of mitochondrion"
GO:0098973 "structural constituent of postsynaptic actin cytoskeleton"
GO:0098974 "postsynaptic actin cytoskeleton organization"
GO:0099010 "modification of postsynaptic structure"
GO:0099011 "neuronal dense core vesicle exocytosis"
GO:0099014 "neuronal dense core vesicle organization"
GO:0099074 "mitochondrion to lysosome transport"
GO:0099078 "BORC complex"
GO:0099084 "postsynaptic specialization organization"
GO:0099087 "anterograde axonal transport of messenger ribonucleoprotein complex"
GO:0099088 "axonal transport of messenger ribonucleoprotein complex"
GO:0099089 "establishment of endoplasmic reticulum localization to postsynapse"
GO:0099113 "negative regulation of presynaptic cytosolic calcium concentration"
GO:0099120 "socially cooperative development"
GO:0099123 "somato-dendritic dopamine secretion"
GO:0099124 "axonal dopamine secretion"
GO:0099129 "cochlear outer hair cell electromotile response"
GO:0099135 "chimeric colonial development"
GO:0099136 "chimeric non-reproductive fruiting body development"
GO:0099137 "altruistic, chimeric, non-reproductive fruiting body development"
GO:0099140 "presynaptic actin cytoskeleton organization"
GO:0099145 "regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane"
GO:0099152 "regulation of neurotransmitter receptor transport, endosome to postsynaptic membrane"
GO:0099159 "regulation of modification of postsynaptic structure"
GO:0099172 "presynapse organization"
GO:0099173 "postsynapse organization"
GO:0099174 "regulation of presynapse organization"
GO:0099175 "regulation of postsynapse organization"
GO:0099179 "regulation of synaptic membrane adhesion"
GO:0099180 "zinc ion import into synaptic vesicle"
GO:0099181 "structural constituent of presynapse"
GO:0099184 "structural constituent of postsynaptic intermediate filament cytoskeleton"
GO:0099185 "postsynaptic intermediate filament cytoskeleton organization"
GO:0099186 "structural constituent of postsynapse"
GO:0099187 "presynaptic cytoskeleton organization"
GO:0099188 "postsynaptic cytoskeleton organization"
GO:0099190 "postsynaptic spectrin-associated cytoskeleton organization"
GO:0099506 "synaptic vesicle transport along actin filament"
GO:0099507 "ligand-gated ion channel activity involved in regulation of presynaptic membrane potential"
GO:0099508 "voltage-gated ion channel activity involved in regulation of presynaptic membrane potential"
GO:0099509 "regulation of presynaptic cytosolic calcium ion concentration"
GO:0099514 "synaptic vesicle cytoskeletal transport"
GO:0099517 "synaptic vesicle transport along microtubule"
GO:0099519 "dense core granule cytoskeletal transport"
GO:0099520 "ion antiporter activity involved in regulation of presynaptic membrane potential"
GO:0099521 "ATPase coupled ion transmembrane transporter activity involved in regulation of presynaptic membrane potential"
GO:0099526 "presynapse to nucleus signaling pathway"
GO:0099530 "G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential"
GO:0099532 "synaptic vesicle endosomal processing"
GO:0099533 "positive regulation of presynaptic cytosolic calcium concentration"
GO:0099534 "calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration"
GO:0099544 "perisynaptic space"
GO:0099558 "maintenance of synapse structure"
GO:0099559 "maintenance of alignment of postsynaptic density and presynaptic active zone"
GO:0099560 "synaptic membrane adhesion"
GO:0099561 "synaptic membrane adhesion to extracellular matrix"
GO:0099562 "maintenance of postsynaptic density structure"
GO:0099563 "modification of synaptic structure"
GO:0099566 "regulation of postsynaptic cytosolic calcium ion concentration"
GO:0099567 "calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration"
GO:0099580 "ion antiporter activity involved in regulation of postsynaptic membrane potential"
GO:0099581 "ATPase coupled ion transmembrane transporter activity involved in regulation of postsynaptic membrane potential"
GO:0099582 "neurotransmitter receptor activity involved in regulation of presynaptic cytosolic calcium ion concentration"
GO:0099585 "release of sequestered calcium ion into presynaptic cytosol"
GO:0099586 "release of sequestered calcium ion into postsynaptic cytosol"
GO:0099588 "positive regulation of postsynaptic cytosolic calcium concentration"
GO:0099612 "protein localization to axon"
GO:0099626 "voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels"
GO:0099630 "postsynaptic neurotransmitter receptor cycle"
GO:0099633 "protein localization to postsynaptic specialization membrane"
GO:0099640 "axo-dendritic protein transport"
GO:0099641 "anterograde axonal protein transport"
GO:0099642 "retrograde axonal protein transport"
GO:0099644 "protein localization to presynaptic membrane"
GO:0099645 "neurotransmitter receptor localization to postsynaptic specialization membrane"
GO:0106003 "amyloid-beta complex"
GO:0106027 "neuron projection organization"
GO:0106028 "neuron projection retraction"
GO:0106069 "synapsis initiation complex"
GO:0106093 "EDS1 disease-resistance complex"
GO:0106104 "regulation of glutamate receptor clustering"
GO:0106137 "IkappaB kinase complex binding"
GO:0106336 "yolk syncytial layer development"
GO:0110011 "regulation of basement membrane organization"
GO:0110140 "flagellum attachment zone organization"
GO:0120039 "plasma membrane bounded cell projection morphogenesis"
GO:0120145 "protein localization to basal ectoplasmic specialization"
GO:0120158 "positive regulation of collagen catabolic process"
GO:0120160 "intraciliary transport particle A binding"
GO:0120170 "intraciliary transport particle B binding"
GO:0120180 "cell-substrate junction disassembly"
GO:0120181 "focal adhesion disassembly"
GO:0120182 "regulation of focal adhesion disassembly"
GO:0120183 "positive regulation of focal adhesion disassembly"
GO:0120184 "negative regulation of focal adhesion disassembly"
GO:0120193 "tight junction organization"
GO:0140231 "anterograde axonal transport of neurotransmitter receptor complex"
GO:0140235 "RNA polyadenylation at postsynapse"
GO:0140334 "lipopolysaccharide localization to cell outer membrane"
GO:0140509 "epithelium-like organization"
GO:0140633 "CARD8 inflammasome complex assembly"
GO:0140634 "CARD8 inflammasome complex"
GO:0140738 "NLRP6 inflammasome complex"
GO:0140739 "NLRP6 inflammasome complex assembly"
GO:0140748 "positive regulation of regulation of ascospore wall (1->3)-beta-D-glucan biosynthetic process"
GO:0150031 "regulation of protein localization to lysosome"
GO:0150032 "positive regulation of protein localization to lysosome"
GO:0150033 "negative regulation of protein localization to lysosome"
GO:0150043 "structural constituent of synapse-associated extracellular matrix"
GO:0150047 "G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential"
GO:0150054 "regulation of postsynaptic neurotransmitter receptor diffusion trapping"
GO:0150062 "complement-mediated synapse pruning"
GO:0150089 "multiple spine synapse organization"
GO:0150090 "multiple spine synapse organization, single dendrite"
GO:0150091 "multiple spine synapse organization, multiple dendrites"
GO:0150098 "glial cell-neuron signaling"
GO:0150099 "neuron-glial cell signaling"
GO:0150105 "protein localization to cell-cell junction"
GO:0150106 "regulation of protein localization to cell-cell junction"
GO:0150107 "positive regulation of protein localization to cell-cell junction"
GO:0150111 "regulation of transepithelial transport"
GO:0150115 "cell-substrate junction organization"
GO:0150116 "regulation of cell-substrate junction organization"
GO:0150117 "positive regulation of cell-substrate junction organization"
GO:0150118 "negative regulation of cell-substrate junction organization"
GO:0150119 "negative regulation of protein localization to cell-cell junction"
GO:0150146 "cell junction disassembly"
GO:0150147 "cell-cell junction disassembly"
GO:1900024 "regulation of substrate adhesion-dependent cell spreading"
GO:1900025 "negative regulation of substrate adhesion-dependent cell spreading"
GO:1900026 "positive regulation of substrate adhesion-dependent cell spreading"
GO:1900225 "regulation of NLRP3 inflammasome complex assembly"
GO:1900226 "negative regulation of NLRP3 inflammasome complex assembly"
GO:1900227 "positive regulation of NLRP3 inflammasome complex assembly"
GO:1900383 "regulation of synaptic plasticity by receptor localization to synapse"
GO:1900447 "regulation of cell morphogenesis involved in phenotypic switching"
GO:1901613 "negative regulation of terminal button organization"
GO:1901614 "positive regulation of terminal button organization"
GO:1901626 "regulation of postsynaptic membrane organization"
GO:1901627 "negative regulation of postsynaptic membrane organization"
GO:1901628 "positive regulation of postsynaptic membrane organization"
GO:1901629 "regulation of presynaptic membrane organization"
GO:1901630 "negative regulation of presynaptic membrane organization"
GO:1901631 "positive regulation of presynaptic membrane organization"
GO:1901632 "regulation of synaptic vesicle membrane organization"
GO:1901633 "negative regulation of synaptic vesicle membrane organization"
GO:1901634 "positive regulation of synaptic vesicle membrane organization"
GO:1901922 "regulation of sclerotium development"
GO:1901923 "negative regulation of sclerotium development"
GO:1901924 "positive regulation of sclerotium development"
GO:1901950 "dense core granule transport"
GO:1901951 "regulation of anterograde dense core granule transport"
GO:1901952 "negative regulation of anterograde dense core granule transport"
GO:1901953 "positive regulation of anterograde dense core granule transport"
GO:1901954 "regulation of retrograde dense core granule transport"
GO:1901955 "negative regulation of retrograde dense core granule transport"
GO:1901956 "positive regulation of retrograde dense core granule transport"
GO:1901965 "endoplasmic reticulum to chloroplast transport"
GO:1902080 "regulation of calcium ion import into sarcoplasmic reticulum"
GO:1902081 "negative regulation of calcium ion import into sarcoplasmic reticulum"
GO:1902082 "positive regulation of calcium ion import into sarcoplasmic reticulum"
GO:1902396 "protein localization to bicellular tight junction"
GO:1902414 "protein localization to cell junction"
GO:1902473 "regulation of protein localization to synapse"
GO:1902474 "positive regulation of protein localization to synapse"
GO:1902483 "cytotoxic T cell pyroptotic process"
GO:1902547 "regulation of cellular response to vascular endothelial growth factor stimulus"
GO:1902548 "negative regulation of cellular response to vascular endothelial growth factor stimulus"
GO:1902683 "regulation of receptor localization to synapse"
GO:1902684 "negative regulation of receptor localization to synapse"
GO:1902685 "positive regulation of receptor localization to synapse"
GO:1902774 "late endosome to lysosome transport"
GO:1902803 "regulation of synaptic vesicle transport"
GO:1902804 "negative regulation of synaptic vesicle transport"
GO:1902805 "positive regulation of synaptic vesicle transport"
GO:1902822 "regulation of late endosome to lysosome transport"
GO:1902823 "negative regulation of late endosome to lysosome transport"
GO:1902824 "positive regulation of late endosome to lysosome transport"
GO:1902897 "regulation of postsynaptic density protein 95 clustering"
GO:1902908 "regulation of melanosome transport"
GO:1902909 "negative regulation of melanosome transport"
GO:1902910 "positive regulation of melanosome transport"
GO:1902917 "positive regulation of mating projection assembly"
GO:1902950 "regulation of dendritic spine maintenance"
GO:1902951 "negative regulation of dendritic spine maintenance"
GO:1902952 "positive regulation of dendritic spine maintenance"
GO:1903023 "regulation of ascospore-type prospore membrane formation"
GO:1903024 "positive regulation of ascospore-type prospore membrane formation"
GO:1903056 "regulation of melanosome organization"
GO:1903057 "negative regulation of melanosome organization"
GO:1903058 "positive regulation of melanosome organization"
GO:1903361 "protein localization to basolateral plasma membrane"
GO:1903415 "flavonoid transport from endoplasmic reticulum to plant-type vacuole"
GO:1903429 "regulation of cell maturation"
GO:1903430 "negative regulation of cell maturation"
GO:1903431 "positive regulation of cell maturation"
GO:1903539 "protein localization to postsynaptic membrane"
GO:1903540 "establishment of protein localization to postsynaptic membrane"
GO:1903742 "regulation of anterograde synaptic vesicle transport"
GO:1903743 "negative regulation of anterograde synaptic vesicle transport"
GO:1903744 "positive regulation of anterograde synaptic vesicle transport"
GO:1903844 "regulation of cellular response to transforming growth factor beta stimulus"
GO:1903845 "negative regulation of cellular response to transforming growth factor beta stimulus"
GO:1903846 "positive regulation of cellular response to transforming growth factor beta stimulus"
GO:1903982 "negative regulation of microvillus length"
GO:1903983 "positive regulation of microvillus length"
GO:1904072 "presynaptic active zone disassembly"
GO:1904106 "protein localization to microvillus"
GO:1904107 "protein localization to microvillus membrane"
GO:1904160 "protein localization to chloroplast starch grain"
GO:1904215 "regulation of protein import into chloroplast stroma"
GO:1904216 "positive regulation of protein import into chloroplast stroma"
GO:1904275 "tricellular tight junction disassembly"
GO:1904288 "BAT3 complex binding"
GO:1904393 "regulation of skeletal muscle acetylcholine-gated channel clustering"
GO:1904394 "negative regulation of skeletal muscle acetylcholine-gated channel clustering"
GO:1904395 "positive regulation of skeletal muscle acetylcholine-gated channel clustering"
GO:1904396 "regulation of neuromuscular junction development"
GO:1904397 "negative regulation of neuromuscular junction development"
GO:1904398 "positive regulation of neuromuscular junction development"
GO:1904409 "regulation of secretory granule organization"
GO:1904410 "negative regulation of secretory granule organization"
GO:1904411 "positive regulation of secretory granule organization"
GO:1904508 "regulation of protein localization to basolateral plasma membrane"
GO:1904509 "negative regulation of protein localization to basolateral plasma membrane"
GO:1904510 "positive regulation of protein localization to basolateral plasma membrane"
GO:1904600 "actin fusion focus assembly"
GO:1904675 "regulation of somatic stem cell division"
GO:1904676 "negative regulation of somatic stem cell division"
GO:1904677 "positive regulation of somatic stem cell division"
GO:1904701 "Wnt-Frizzled-LRP5/6 complex assembly"
GO:1904702 "regulation of protein localization to adherens junction"
GO:1904703 "negative regulation of protein localization to adherens junction"
GO:1904704 "positive regulation of protein localization to adherens junction"
GO:1904711 "regulation of Wnt-Frizzled-LRP5/6 complex assembly"
GO:1904712 "positive regulation of Wnt-Frizzled-LRP5/6 complex assembly"
GO:1904714 "regulation of chaperone-mediated autophagy"
GO:1904715 "negative regulation of chaperone-mediated autophagy"
GO:1904716 "positive regulation of chaperone-mediated autophagy"
GO:1904717 "regulation of AMPA glutamate receptor clustering"
GO:1904718 "negative regulation of AMPA glutamate receptor clustering"
GO:1904719 "positive regulation of AMPA glutamate receptor clustering"
GO:1904723 "negative regulation of Wnt-Frizzled-LRP5/6 complex assembly"
GO:1904764 "chaperone-mediated autophagy translocation complex disassembly"
GO:1904779 "regulation of protein localization to centrosome"
GO:1904780 "negative regulation of protein localization to centrosome"
GO:1904781 "positive regulation of protein localization to centrosome"
GO:1904784 "NLRP1 inflammasome complex assembly"
GO:1904809 "regulation of dense core granule transport"
GO:1904810 "negative regulation of dense core granule transport"
GO:1904811 "positive regulation of dense core granule transport"
GO:1904837 "beta-catenin-TCF complex assembly"
GO:1904863 "regulation of beta-catenin-TCF complex assembly"
GO:1904864 "negative regulation of beta-catenin-TCF complex assembly"
GO:1904865 "positive regulation of beta-catenin-TCF complex assembly"
GO:1904887 "Wnt signalosome assembly"
GO:1904904 "regulation of endothelial cell-matrix adhesion via fibronectin"
GO:1904905 "negative regulation of endothelial cell-matrix adhesion via fibronectin"
GO:1904906 "positive regulation of endothelial cell-matrix adhesion via fibronectin"
GO:1904916 "transmembrane L-lysine transport from lysosomal lumen to cytosol"
GO:1904917 "L-arginine transmembrane transport from lysosomal lumen to cytosol"
GO:1904918 "transmembrane L-histidine transport from lysosomal lumen to cytosol"
GO:1904919 "transmembrane L-cystine transport from lysosomal lumen to cytosol"
GO:1904962 "plastid to vacuole vesicle-mediated transport"
GO:1904987 "regulation of endothelial cell activation"
GO:1904988 "negative regulation of endothelial cell activation"
GO:1904989 "positive regulation of endothelial cell activation"
GO:1905054 "calcium-induced calcium release activity involved in regulation of presynaptic cytosolic calcium ion concentration"
GO:1905055 "calcium:cation antiporter activity involved in regulation of presynaptic cytosolic calcium ion concentration"
GO:1905056 "P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration"
GO:1905057 "voltage-gated calcium channel activity involved in regulation of postsynaptic cytosolic calcium levels"
GO:1905058 "calcium-induced calcium release activity involved in regulation of postsynaptic cytosolic calcium ion concentration"
GO:1905059 "P-type calcium transporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration"
GO:1905060 "calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration"
GO:1905071 "tight junction disassembly"
GO:1905073 "regulation of tight junction disassembly"
GO:1905074 "negative regulation of tight junction disassembly"
GO:1905075 "positive regulation of tight junction disassembly"
GO:1905126 "regulation of axo-dendritic protein transport"
GO:1905127 "negative regulation of axo-dendritic protein transport"
GO:1905128 "positive regulation of axo-dendritic protein transport"
GO:1905146 "lysosomal protein catabolic process"
GO:1905165 "regulation of lysosomal protein catabolic process"
GO:1905166 "negative regulation of lysosomal protein catabolic process"
GO:1905167 "positive regulation of lysosomal protein catabolic process"
GO:1905178 "regulation of cardiac muscle tissue regeneration"
GO:1905179 "negative regulation of cardiac muscle tissue regeneration"
GO:1905180 "positive regulation of cardiac muscle tissue regeneration"
GO:1905244 "regulation of modification of synaptic structure"
GO:1905274 "regulation of modification of postsynaptic actin cytoskeleton"
GO:1905383 "protein localization to presynapse"
GO:1905384 "regulation of protein localization to presynapse"
GO:1905385 "negative regulation of protein localization to presynapse"
GO:1905386 "positive regulation of protein localization to presynapse"
GO:1905413 "regulation of dense core granule exocytosis"
GO:1905414 "negative regulation of dense core granule exocytosis"
GO:1905415 "positive regulation of dense core granule exocytosis"
GO:1905516 "positive regulation of fertilization"
GO:1905671 "regulation of lysosome organization"
GO:1905672 "negative regulation of lysosome organization"
GO:1905673 "positive regulation of lysosome organization"
GO:1905684 "regulation of plasma membrane repair"
GO:1905685 "negative regulation of plasma membrane repair"
GO:1905686 "positive regulation of plasma membrane repair"
GO:1905708 "regulation of cell morphogenesis involved in conjugation with cellular fusion"
GO:1905741 "calcium export from the mitochondrion involved in positive regulation of presynaptic cytosolic calcium concentration"
GO:1905743 "calcium import into the mitochondrion involved in negative regulation of presynaptic cytosolic calcium concentration"
GO:1905793 "protein localization to pericentriolar material"
GO:1905805 "excitatory synapse pruning"
GO:1905806 "regulation of synapse pruning"
GO:1905807 "negative regulation of synapse pruning"
GO:1905808 "positive regulation of synapse pruning"
GO:1905809 "negative regulation of synapse organization"
GO:1905810 "regulation of excitatory synapse pruning"
GO:1905811 "negative regulation of excitatory synapse pruning"
GO:1905874 "regulation of postsynaptic density organization"
GO:1905875 "negative regulation of postsynaptic density organization"
GO:1905876 "positive regulation of postsynaptic density organization"
GO:1990019 "protein storage vacuole organization"
GO:1990036 "calcium ion import into sarcoplasmic reticulum"
GO:1990045 "sclerotium development"
GO:1990048 "anterograde neuronal dense core vesicle transport"
GO:1990049 "retrograde neuronal dense core vesicle transport"
GO:1990052 "ER to chloroplast lipid transport"
GO:1990146 "protein localization to rhabdomere"
GO:1990227 "paranodal junction maintenance"
GO:1990252 "Syp1 complex"
GO:1990255 "subsynaptic reticulum organization"
GO:1990349 "gap junction-mediated intercellular transport"
GO:1990413 "eyespot apparatus"
GO:1990500 "eif4e-cup complex"
GO:1990504 "dense core granule exocytosis"
GO:1990512 "Cry-Per complex"
GO:1990513 "CLOCK-BMAL transcription complex"
GO:1990522 "tail spike morphogenesis"
GO:1990523 "bone regeneration"
GO:1990535 "neuron projection maintenance"
GO:1990586 "divisome complex"
GO:1990587 "FtsQBL complex"
GO:1990588 "FtsBL complex"
GO:1990620 "ANPR-A receptor complex"
GO:1990633 "mutator focus"
GO:1990660 "calprotectin complex"
GO:1990661 "S100A8 complex"
GO:1990662 "S100A9 complex"
GO:1990709 "presynaptic active zone organization"
GO:1990713 "survivin complex"
GO:1990722 "DAPK1-calmodulin complex"
GO:1990724 "galectin complex"
GO:1990779 "glycoprotein Ib-IX-V complex"
GO:1990798 "pancreas regeneration"
GO:1990832 "slow axonal transport"
GO:1990851 "Wnt-Frizzled-LRP5/6 complex"
GO:1990907 "beta-catenin-TCF complex"
GO:1990909 "Wnt signalosome"
GO:2000027 "regulation of animal organ morphogenesis"
GO:2000035 "regulation of stem cell division"
GO:2000100 "regulation of establishment or maintenance of bipolar cell polarity regulating cell shape"
GO:2000115 "regulation of maintenance of bipolar cell polarity regulating cell shape"
GO:2000247 "positive regulation of establishment or maintenance of bipolar cell polarity regulating cell shape"
GO:2000331 "regulation of terminal button organization"
GO:2000359 "regulation of binding of sperm to zona pellucida"
GO:2000360 "negative regulation of binding of sperm to zona pellucida"
GO:2000392 "regulation of lamellipodium morphogenesis"
GO:2000393 "negative regulation of lamellipodium morphogenesis"
GO:2000394 "positive regulation of lamellipodium morphogenesis"
GO:2000489 "regulation of hepatic stellate cell activation"
GO:2000490 "negative regulation of hepatic stellate cell activation"
GO:2000491 "positive regulation of hepatic stellate cell activation"
GO:2000750 "negative regulation of establishment or maintenance of bipolar cell polarity regulating cell shape"
GO:2000769 "regulation of establishment or maintenance of cell polarity regulating cell shape"
GO:2000770 "negative regulation of establishment or maintenance of cell polarity regulating cell shape"
GO:2000771 "positive regulation of establishment or maintenance of cell polarity regulating cell shape"
GO:2000782 "regulation of establishment of cell polarity regulating cell shape"
GO:2000783 "negative regulation of establishment of cell polarity regulating cell shape"
GO:2000784 "positive regulation of establishment of cell polarity regulating cell shape"
GO:2001017 "regulation of retrograde axon cargo transport"
GO:2001018 "negative regulation of retrograde axon cargo transport"
GO:2001019 "positive regulation of retrograde axon cargo transport"
GO:2001112 "regulation of cellular response to hepatocyte growth factor stimulus"
GO:2001113 "negative regulation of cellular response to hepatocyte growth factor stimulus"
GO:2001114 "positive regulation of cellular response to hepatocyte growth factor stimulus"

[ValWood]

@balhoff you are correct- this brings back many many terms that I previously spent a lot of time adding taxon restrictions to, so that our users would not see them in the curation tool drop down. It seems trivial but it just seems odd to implement a system that makes the taxon restrictions worse than they used to be (this seems to be a recent problem).

But I don't fully understand the situation..... I guess my question is, why use uberon for taxon restrictions if it messes things up.

Why not remove the offending relation that "anatomical structures start existing during or after zygote stage" this is just not true for many cell level anatomical structures. Or, restrict it to tissue and organ level anatomical structures in some way. Or don't rely on uberon for GO taxonomic restrictions?

[balhoff]

We're fixing the Uberon issues in parallel; I just wanted to try to give you a quicker option. Uberon provides many useful taxon constraints; I would say the problem ones here are just errors.

My new script is a bit more transparent than the owltools command, so I find it easier to understand what is happening. But I'll focus on getting the changes into Uberon and see if we can quickly get a release out.

[ValWood]

Don't worry about a quick fix especially for us if the changes are pending. I'm happy to keep sessions that I can't approve back for a while to save you doing extra work. Weeks is OK, but let me know if it is many months as we may then need an interim fix.

[ValWood]

Hi, revisiting this ticket, do you have an ETA for the fix rather than the proposed workaround?

I ask because I thought this was only preventing me re-approving curation sessions that I needed to edit. However, it just struck me that this will prevent any of our community curators from using terms in the anatomical structure branch (so anything to do with conjugation, cell polarity, sporulation etc).

I didn't really want to implement the "replacement script" because a) it isn't really clear to me what this is doing and b) would it be practical since we erimport the ontology into PomBAse every day. Would we need to do this every time we update?

So I really wanted to check when a proper fix is expected so we can get back to working as normal. It seems really (since this issue presumably affects other databases, they just haven't noticed). Would it not be more prudent NOT to use the uberon taxon constraints until this issue is resolved?

I guess really we are waiting on https://github.com/obophenotype/uberon/issues/2348 which is assigned to @cmungall

Thanks for any update you can provide so that we can decide what we need to do from a users perspective.

[balhoff]

@cmungall could you take a look at this PR? https://github.com/obophenotype/uberon/pull/2390

[ValWood]

Thanks Jim!

[ValWood]

this change should fix this issue: https://github.com/geneontology/go-ontology/issues/23445

[pgaudet]

@balhoff are these changes now in GO ?

[balhoff]

Yes, but yesterday I found there is one additional problem axiom involving 'zygote stage'. I sent @ValWood a workaround to get things working at PomBase, and I will open an issue at Uberon to fix the rest.

[ValWood]

Yay , the work-around worked, and I could approve all of the unapproved sessions. I should have listened and got Kim to do that before. It sounded complicated to me but not to @kimrutherford ! Thanks @balhoff

[pgaudet]

Excellent!