MP: latest bp_xp_cc reasoner results

[gocentral]

[ GO:0009992 ! cellular water homeostasis ] is_a [ GO:0055082 ! cellular chemical homeostasis ] [ GO:0033502 ! cellular galactose homeostasis ] is_a [ GO:0001678 ! cellular glucose homeostasis ] [ GO:0034620 ! cellular response to unfolded protein ] is_a [ GO:0033554 ! cellular response to stress ] [ GO:0034637 ! cellular carbohydrate biosynthetic process ] is_a [ GO:0044249 ! cellular biosynthetic process ] [ GO:0044247 ! cellular polysaccharide catabolic process ] is_a [ GO:0034962 ! cellular biopolymer catabolic process ] [ GO:0006622 ! protein targeting to lysosome ] is_a [ GO:0006623 ! protein targeting to vacuole ]

• [ GO:0006897 ! endocytosis ] is_a [ GO:0055085 ! transmembrane transport ] Fix 55085 xp def? [ GO:0006999 ! nuclear pore organization ] is_a [ GO:0043933 ! macromolecular complex subunit organization ] [ GO:0009663 ! plasmodesma organization ] is_a [ GO:0045216 ! cell-cell junction organization ] [ GO:0030031 ! cell projection assembly ] is_a [ GO:0022607 ! cellular component assembly ] [ GO:0033298 ! contractile vacuole organization ] is_a [ GO:0016050 ! vesicle organization ] [ GO:0034728 ! nucleosome organization ] is_a [ GO:0043933 ! macromolecular complex subunit organization ] [ GO:0043482 ! cellular pigment accumulation ] is_a [ GO:0051716 ! cellular response to stimulus ] [ GO:0051383 ! kinetochore organization ] is_a [ GO:0043933 ! macromolecular complex subunit organization ] [ GO:0000913 ! preprophase band formation ] is_a [ GO:0010926 ! anatomical structure formation ] [ GO:0001325 ! formation of extrachromosomal circular DNA ] is_a [ GO:0010926 ! anatomical structure formation ] [ GO:0001765 ! membrane raft formation ] is_a [ GO:0010926 ! anatomical structure formation ] [ GO:0001845 ! phagolysosome formation ] is_a [ GO:0010926 ! anatomical structure formation ] [ GO:0007416 ! synaptogenesis ] is_a [ GO:0022607 ! cellular component assembly ] [ GO:0009665 ! plastid inheritance ] is_a [ GO:0048308 ! organelle inheritance ] [ GO:0022617 ! extracellular matrix disassembly ] is_a [ GO:0022411 ! cellular component disassembly ] [ GO:0030031 ! cell projection assembly ] is_a [ GO:0022607 ! cellular component assembly ] [ GO:0030474 ! spindle pole body duplication ] is_a [ GO:0022607 ! cellular component assembly ] [ GO:0030994 ! primary cell septum disassembly ] is_a [ GO:0022411 ! cellular component disassembly ] [ GO:0031035 ! myosin filament disassembly ] is_a [ GO:0032988 ! ribonucleoprotein complex disassembly ] [ GO:0031321 ! ascospore-type prospore formation ] is_a [ GO:0010926 ! anatomical structure formation ] [ GO:0032964 ! collagen biosynthetic process ] is_a [ GO:0009059 ! macromolecule biosynthetic process ] [ GO:0033502 ! cellular galactose homeostasis ] is_a [ GO:0033501 ! galactose homeostasis ]

The following are suggestions for new is_a links where there already exist part_of relations or part_of paths:

[ GO:0060152 ! microtubule-based peroxisome localization ] is_a [ GO:0060151 ! peroxisome localization ] asserted: [ GO:0060152 ! microtubule-based peroxisome localization ] part_of [ GO:0060151 ! peroxisome localization ] [ GO:0019069 ! viral capsid assembly ] is_a [ GO:0022607 ! cellular component assembly ] entailed: [ GO:0019069 ! viral capsid assembly ] part_of [ GO:0022607 ! cellular component assembly ] [ GO:0051878 ! lateral element assembly ] is_a [ GO:0022607 ! cellular component assembly ] entailed: [ GO:0051878 ! lateral element assembly ] part_of [ GO:0022607 ! cellular component assembly ]

Reported by: cmungall

Original Ticket: "geneontology/ontology-requests/5961":https://sourceforge.net/p/geneontology/ontology-requests/5961

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

related: we have pilus formation but pilus is a broad synonym for fimbrium

Original comment by: cmungall

[gocentral]

yup, we know about that:

https://sourceforge.net/tracker/index.php?func=detail&aid=2149713&group\_id=36855&atid=440764

I guess I'll wait until Jane says which to use in names, and then fix xps.

m

Original comment by: mah11

[gocentral]

implemented as suggested except as noted here:

> [ GO:0033502 ! cellular galactose homeostasis ] is_a [ GO:0001678 ! cellular glucose homeostasis ]

no; galactose is not a type of glucose; corrected is_a parent of GO:0033502 (which also addresses last item on list)

> * [ GO:0006897 ! endocytosis ] is_a [ GO:0055085 ! transmembrane transport ] 
> Fix 55085 xp def?

actually, 55085 still looks ok: !! [Term] !! id: GO:0055085 ! transmembrane transport !! intersection_of: GO:0006810 ! transport !! intersection_of: OBO_REL:results_in_transport_across GO:0016020 ! membrane !! ! ok

it's 6897 that I'm having second thoughts about: !! [Term] !! id: GO:0006897 ! endocytosis !! intersection_of: GO:0016192 ! vesicle-mediated transport !! intersection_of: OBO_REL:results_in_transport_from GO:0005576 ! extracellular region !! intersection_of: OBO_REL:results_in_transport_within GO:0016023 ! cytoplasmic membrane-bounded vesicle !! intersection_of: OBO_REL:results_in_transport_across GO:0005886 ! plasma membrane !! ! ok

... topologically, the endocytosed stuff doesn't cross from one side of the membrane to the other, but it does get into the cell (so it "crosses" the plasma membrane in a woolly non-topological sense)

> [ GO:0000913 ! preprophase band formation ] is_a [ GO:0010926 ! anatomical structure formation ] > [ GO:0001765 ! membrane raft formation ] is_a [ GO:0010926 ! anatomical structure formation ]
> [ GO:0001845 ! phagolysosome formation ] is_a [ GO:0010926 ! anatomical structure formation ] for these, used is_a GO:0022607 ! cellular component assembly instead; added synonyms

> [ GO:0031035 ! myosin filament disassembly ] is_a [ GO:0032988 ! ribonucleoprotein complex disassembly ]

ack, no; fixed 31035 xp!

> [ GO:0019069 ! viral capsid assembly ] is_a [ GO:0022607 ! cellular component assembly ]

used GO:0010927 ! cellular component assembly involved in morphogenesis instead, because of current (new, I think) parent of virion assembly

I also marked that pilus biogenesis xp (GO:0009297) as ready to go.

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> TermGenie
• status: open --> closed-accepted

Original comment by: mah11