necessarily is_part violations

[gocentral]

There are many part_of relationships in the ontologies that don't adhere to 'necessarily is_part'. In other words, these are terms that have multiple part_of parents.

We need to look through these terms and assess whether we can remove the extra part_of parentage, and try and get a sense of any underlying problems e.g. multiple part_of where a gp exists in multiple cellular locations.

AP-2 adaptor complex ; GO:0030122 apical cortex ; GO:0045179 axonemal dynein complex ; GO:0005858 axoneme ; GO:0005930 basal cortex ; GO:0045180 cellulose microfibril ; GO:0009549 conoid ; GO:0020010 cytosolic small ribosomal subunit (sensu Eukarya) ; GO:0005843DASH complex ; GO:0042729 DASH complex ; GO:0042729 dynactin complex ; GO:0005869 dystrophin-associated glycoprotein complex ; GO:0016010 endoplasmic reticulum membrane ; GO:0005789 epsilon DNA polymerase complex ; GO:0008622 external side of plasma membrane ; GO:0009897 flagellar membrane ; GO:0020017 gamma-tubulin large complex (sensu Schizosaccharomyces) ; GO:0000929 GARP complex ; GO:0000938 Golgi membrane ; GO:0000139 hemicellulose network ; GO:0048223 lamin filament ; GO:0005638 MCM complex ; GO:0042555 mRNA editing complex ; GO:0045293 Noc1p-Noc2p complex ; GO:0030690 Noc2p-Noc3p complex ; GO:0030691 Noc4p-Nop14p complex ; GO:0030692 nuclear membrane ; GO:0005635 nuclear origin of replication recognition complex ; GO:0005664 pectic matrix ; GO:0048217 photosystem I (sensu Cyanobacteria) ; GO:0030094 photosystem II (sensu Cyanobacteria) ; GO:0030096 phycobilisome ; GO:0030089 polarisome ; GO:0000133 proteasome complex (sensu Eukarya) ; GO:0000502 snRNP U5 ; GO:0005682 striated muscle thin filament ; GO:0005865

(35)

1-aminocyclopropane-1-carboxylate catabolism ; GO:0042217 aortic cell fate commitment (sensu Drosophila) ; GO:0035052 ATP synthesis coupled electron transport ; GO:0042773 attenuation of antimicrobial humoral response (sensu Invertebrata) ; GO:0042154 attenuation of antimicrobial humoral response (sensu Vertebrata) ; GO:0042155 cell plate formation (sensu Magnoliophyta) ; GO:0009920 cinnamic acid biosynthesis ; GO:0009800 clathrin coating of Golgi vesicle ; GO:0048202 COPI coating of Golgi vesicle ; GO:0048205 COPII coating of Golgi vesicle ; GO:0048208 DNA double-strand break processing ; GO:0000729 DNA ligation ; GO:0006266 DNA recombinase assembly ; GO:0000730 DNA repair synthesis ; GO:0000731 DNA replication ; GO:0006260 ectoderm cell fate determination ; GO:0001713 endoderm cell fate determination ; GO:0007493 establishment of lymphocyte polarity ; GO:0001767 female gametophyte egg cell differentiation ; GO:0009560 female germ-line cyst encapsulation ; GO:0048139 female germ-line cyst encapsulation (sensu Insecta) ; GO:0030708 formation of immunological synapse ; GO:0001771 germ-line cyst encapsulation ; GO:0048138 germ-line stem cell division ; GO:0048131 heart proper cell fate commitment (sensu Drosophila) ; GO:0035053 heteroduplex formation ; GO:0030491 imaginal disc morphogenesis ; GO:0007560 induction of non-apoptotic programmed cell death by pathogen ; GO:0012504 interpretation of external signals that regulate cell growth ; GO:0001560 lactosylceramide biosynthesis ; GO:0001572 luteinization ; GO:0001553 luteolysis ; GO:0001554 male germ-line cyst encapsulation ; GO:0048140 megasporogenesis ; GO:0009554 meiotic chromosome movement ; GO:0016344 meiotic DNA double-strand break formation ; GO:0042138 meiotic DNA double-strand break processing ; GO:0000706 meiotic DNA recombinase assembly ; GO:0000707 meiotic DNA repair synthesis ; GO:0000711 meiotic mismatch repair ; GO:0000710 meiotic strand invasion ; GO:0000708 menopause ; GO:0042697 mesoderm cell fate determination ; GO:0007500 microsporogenesis ; GO:0009556 morphogenesis of larval imaginal disc epithelium ; GO:0016335 mRNA catabolism\, exonucleolytic ; GO:0000291 muscle cell fate determination ; GO:0007521 nuclear localization of viral capsid precursors ; GO:0046752 oocyte microtubule cytoskeleton polarization ; GO:0008103 oocyte microtubule cytoskeleton polarization (sensu Insecta) ; GO:0048129 ossification ; GO:0001503 ovarian cumulus cell differentiation ; GO:0001549 ovarian cumulus expansion ; GO:0001550 ovarian follicle antrum/follicular fluid formation ; GO:0001548 ovarian follicle development ; GO:0001541 ovarian ring canal formation ; GO:0007301 photoreceptor pigment granule morphogenesis ; GO:0008059 pollen recognition ; GO:0009857 preantral ovarian follicle growth ; GO:0001546 primary ovarian follicle growth ; GO:0001545 proboscis morphogenesis ; GO:0016349 proprioception ; GO:0019230 R3/R4 cell fate commitment ; GO:0007464 radial axis specification ; GO:0009945 regulation of asymmetric cytokinesis ; GO:0009786 regulation of CDK activity ; GO:0000079 regulation of cytokine biosynthesis ; GO:0042035 regulation of cytokine secretion ; GO:0050707 regulation of eye photoreceptor development (sensu Drosophila) ; GO:0045314 regulation of fibroblast proliferation ; GO:0048145 regulation of hair cell differentiation ; GO:0045607 regulation of juvenile hormone metabolism ; GO:0007556 regulation of long-term neuronal synaptic plasticity ; GO:0048169 regulation of natural killer cell activity ; GO:0045845 regulation of synapse structure ; GO:0050807 replication of extrachromosomal circular DNA during replicative cell aging ; GO:0001314 retinal cone cell fate commitment ; GO:0046551 S-adenosylmethionine biosynthesis ; GO:0006556 sperm ejaculation ; GO:0042713 strand invasion ; GO:0042148 synaptic vesicle docking ; GO:0016081 synaptic vesicle endocytosis ; GO:0008099 synaptic vesicle exocytosis ; GO:0016079 trans assembly of SL containing precatalytic spliceosome ; GO:0000352

(84)

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/1580":https://sourceforge.net/p/geneontology/ontology-requests/1580

[gocentral]

Logged In: YES user_id=516865

blimey, I won't be looking through all these but I think DASH complex is always a aprt of condensed nuclear chromosome kinetochore, kinetochore microtubule and microtubule associated complex is true, I dont think they are mutually exclusive, are they?

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=451873

Yeah - this is one of the main problems we've got, how we represent entities that occur all over the place. The way we've typically done it is to have:

DASH complex ---%condensed nuclear chromosome kinetochore DASH complex ---%kinetochore microtubule DASH complex ---%microtubule associated complex DASH complex

with all the children copied as part_of to the correct location e.g.

condensed nuclear chromosome ---<condensed nuclear chromosome kinetochore DASH complex

And the lazy way to do it is to look for the nearest common ancestor, which in this case is 'cytoplasm', and just plonk the term there:

cytoplasm ---%DASH complex

but you lose some information that way.

Original comment by: jl242

[gocentral]

Logged In: YES user_id=516865

the 3 locations here are referring to the same place does that make a difference...its slightly different from a complex like the proteasome which can be nuclear or cytoplasmic.

This is at the same time associated with these 3 locations the microtubules referred to are the kinetochore microtubules ..perhaps though in this case a single parentage of cytoplasm is sufficient because the complex is 'associated with' these other component terms not part of them. A curator can specify the localization terms for kinetochore and condensed nuclear chromosome with separate annotations and the new associated_with qualifier

Original comment by: ValWood

[gocentral]

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Right - cyoplasm it is then. That's one down...;)

Original comment by: jl242

[gocentral]

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See also SF item [ 1007061 ] tpv: polarisome from Val (now closed).

Original comment by: jl242

[gocentral]

Logged In: YES user_id=436423

Val submitted polarisome again in SF 1029845.

Original comment by: mah11

[gocentral]

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I fixed this one: mRNA editing complex ; GO:0045293 see SF 991827

Original comment by: mah11

[gocentral]

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This list is totally out of date now.

Original comment by: jl242

[gocentral]

• status: open --> closed-out-of-date

Original comment by: jl242