TreeGrafter motivated Taxon constraint: Restrict for yeast/fungi

[ValWood]

TreeGrafter motivated

Please provide as much information as you can:

• GO term ID label:

lysosomal =never in fungi (or suggest)

• [x] GO:0007041 lysosomal transport
• [x] GO:0007040 lysosome organization

~GO:0008333 endosome to lysosome transport~ covered by GO:0007041 ~GO:0098943 neurotransmitter receptor transport, postsynaptic endosome to lysosome~ covered by GO:0007041 ~GO:0032510 endosome to lysosome transport via multivesicular body sorting pathway~ covered by GO:0007041 ~GO:0007042 lysosomal lumen acidification~ covered by lysosome organization

• [x] GO:0009725 response to hormone never in fungi ~GO:0032869 cellular response to insulin stimulus ONLY IN METAZOA?~ will be covered by "response to hormone"

~GO:0048499    synaptic vesicle membrane organization~ see https://github.com/geneontology/go-ontology/issues/27280 ~GO:0008088 axo-dendritic transport~ see https://github.com/geneontology/go-ontology/issues/27280 ~GO:0097479 synaptic vesicle localization~ see https://github.com/geneontology/go-ontology/issues/27280 ~GO:0048490 anterograde synaptic vesicle transport~ covered by GO:0008088 ~GO:0048489 synaptic vesicle transport~ covered by GO:0097479

• [x] GO:1990428 miRNA transport NEVER IN YEAST? (weird term?) ~GO:0043032 positive regulation of macrophage activation ONLY IN METAZOA~ covered by GO:0050865

• [x] GO:0050865 regulation of cell activation this one is tricky because there are 8 non metazoan annotations for suppression of cell activation by bacteria, virus etc. I can add never in pombe/cerevisiae

[ValWood]

~GO:0098974 postsynaptic actin cytoskeleton organization~ see https://github.com/geneontology/go-ontology/issues/27280 GO:1901029 negative regulation of mitochondrial outer membrane permeabilization involved in involved in apoptotic signaling pathway (I'll level this because 'involved_in' will be obsoleted)

[ValWood]

~GO:0010807 regulation of synaptic vesicle priming~ see https://github.com/geneontology/go-ontology/issues/27280

[ValWood]

tau-protein kinase activity (GO:0050321) (should this even exist?)

[ValWood]

I would like to block all circadian rhythm. terms for fission yeast GO:0009649 entrainment of circadian clock but possibly others from current evidence https://pubmed.ncbi.nlm.nih.gov/25239547/

I can't block "fungi" or even yeast because Neurospora have circadian rythms but it might be possible to broaden the clade.

[ValWood]

• [x] GO:0045335 phagocytic vesicle

since immune cells and protists can do phagocytosis, I'll just add "never in fungi" for this one

[ValWood]

• [x] GO:2000636 positive regulation of primary miRNA processing

[ValWood]

• [x] GO:0070877 microprocessor complex GO:0070877

[ValWood]

• [x] GO:0030097 | hemopoiesis ADD only in metazoa
• [x] ~GO:0048671 | negative regulation of collateral sprouting~ GO:0051960 regulation of nervous system development ADD only in metazoa

~GO:0045773 | positive regulation of axon extension add to GO:0010975
regulation of neuron projection development but note that this term has no connection to regulation of neurogenesis~ covered by https://github.com/geneontology/go-ontology/issues/27280

[ValWood]

These terms also need taxon resticting, OR taxon restricted ontology ancestors should be already present, so maybe missing a parent?

• [x] GO:0010736 serum response element binding GO:0009887 animal organ morphogenesis (higher term needs restricting (GO:0048856 anatomical structure development) ~GO:0009652 thigmotropism (plants and fungi, but not yeast~ done in another ticket GO:0009649 entrainment of circadian clock

• [x] GO:0010236  plastoquinone biosynthetic process ADD only in photosynthesising species

• [x] ~GO:0009736 cytokinin-activated signaling pathway~ GO:0009755

• [x] hormone-mediated signaling pathway? add "NEVER IN FUNGI"

• [x] GO:0016444 somatic cell DNA recombination (weird term probably has the same meaning as GO:0006312) will add "NEVER IN FUNGI" for now to block predictions

• [x] GO:0015127 bilirubin transmembrane transporter activity (also process bilirubin transport) ~GO:0099563 modification of synaptic structure (GO:0034330 cell junction organization)~ covered by https://github.com/geneontology/go-ontology/issues/27280

  • [x] ~GO:0030032 lamellipodium assembly~ add NEVER IN FUNGI to GO:0097581 lamellipodium organization
  • [x] ~GO:0045724 positive regulation of cilium assembly~ add NEVER IN FUNGI to GO:1902017 regulation of cilium assembly

• [x] GO:0051489 regulation of filopodium assembly add NEVER IN FUNGI ~GO:0010975 regulation of neuron projection development~ (positive) see https://github.com/geneontology/go-ontology/issues/27280

• [x] GO:0030027 lamellipodium add NEVER IN FUNGI

• [x] GO:2000036 regulation of stem cell population maintenance add NEVER IN FUNGI

• [x] GO:0030330 DNA damage response, signal transduction by p53 class mediator Add to GO:0072331 signal transduction by p53 class mediator ONLY IN METAZOA ~GO:0031643 positive regulation of myelination. Add to GO:0031641 regulation of myelination~ covered by GO:0051960

• [x] GO:0042541 hemoglobin biosynthetic process ONLY IN METAZOA GO:0035196 miRNA processing GO:0035198 miRNA binding ~GO:0033211 adiponectin-activated signaling pathway~ covered by https://github.com/geneontology/go-ontology/issues/27099
  GO:0035329 hippo signaling

• [x] GO:0046850 regulation of bone remodeling ONLY IN METAZOA

• [x] GO:0055120 striated muscle dense body ONLY IN METAZOA ~GO:0030018 Z disc (add to sarcomere)~ see https://github.com/geneontology/go-ontology/issues/27281 ~GO:0050770 regulation of axonogenesis add to GO:0010975 regulation of neuron projection development~ see https://github.com/geneontology/go-ontology/issues/27280 ~GO:0060998 regulation of dendritic spine development~ see https://github.com/geneontology/go-ontology/issues/27280 ~GO:0097271 protein localization to bud neck (only in budding yeast)~ see https://github.com/geneontology/go-ontology/issues/27092 GO:1990220 GroEL-GroES complex only in bacteria GO:2000630 positive regulation of miRNA metabolic process (at regulation)

~GO:0050870 positive regulation of T cell activation~ (at regulation) covered by GO:0002682

• [x] GO:0042417 dopamine metabolic process add NEVER IN FUNGI ~GO:0032727 positive regulation of interferon-alpha production (at regulation)~ see below ~GO:0032729 positive regulation of type I interferon production (at regulation)~ see below ~GO:0032755 positive regulation of interleukin-6 production (at regulation)~ see below GO:0035060 brahma complex (check first if this is "RSC-type complex" ) ~GO:0030016 myofibril only in metazoan (or stricter, cardiac muscle specific)~ see https://github.com/geneontology/go-ontology/issues/27281

[ValWood]

• [x] these are tricky, GO:0032727 positive regulation of interferon-alpha production (at regulation) GO:0032729 positive regulation of type I interferon production (at regulation) GO:0032755 positive regulation of interleukin-6 production (at regulation)

because I guess pathogens can "regulate" cytokines? for now will add

GO:0001817 regulation of cytokine production never in S. pombe never in S. cerevisiae

and to GO:0050870 regulation of immune system process

[ValWood]

Outstanding:

• [ ] GO:0035060 brahma complex (check first if this is "RSC-type complex" )
• [x] GO:1990220 GroEL-GroES complex only in bacteria

miRNA related- tricky, may need to be pombe/cerevisiae

• [x] GO:1990428 miRNA transport

• [x] GO:2000630 positive regulation of miRNA metabolic process (at regulation)

• [x] GO:0035196 miRNA processing

• [x] GO:0035198 miRNA binding

• [x] GO:0010736 serum response element binding (this is actually SRE response element which is a TF binding sequence, it is present in yeast, but this def is too narrow, and it seems to be out or scope, more SO territory? (there are 2 promoters called SRE, serum response and sterol response)

• [x] GO:0009887 animal organ morphogenesis (higher term needs restricting (GO:0048856 anatomical structure development)

• [x] GO:0009652 thigmotropism (plants and fungi, but not yeast

• [x] GO:0009649 entrainment of circadian clock (need to look into this)

• [x] GO:0010236 plastoquinone biosynthetic process ADD only in photosynthesising species

• [x] GO:0050865 regulation of cell activation this one is tricky because there are 8 non metazoan annotations for suppression of cell activation by bacteria, virus etc. I can add never in pombe/cerevisiae

• [ ] GO:0050321 tau-protein kinase activity (should this even exist?)

• [ ] GO:0035329 hippo signaling (yeast probably have this, but they don't call it hippo)

• [ ] GO:1901029 negative regulation of mitochondrial outer membrane permeabilization involved in involved in apoptotic signaling pathway (obsoletion?)

• [x] GO:0051960 regulation of nervous system development ADD only in metazoa

• [x] GO:0070877 microprocessor complex GO:0070877

• [x] GO:2000636 positive regulation of primary miRNA processing

[ValWood]

@pgaudet should these be obsoleted? If so I will just filter them from Pombase rather than add restrictions GO:1901029 negative regulation of mitochondrial outer membrane permeabilization involved in involved in apoptotic signaling pathway (obsoletion?) GO:0050321 tau-protein kinase activity (should this even exist?)

[ValWood]

A couple of outstanding questions moved to https://github.com/geneontology/go-ontology/issues/27589

leaving circadian rhythm until I'm sure yeast don't have it