Add taxon restriction for "regulation of cell migration"

[ValWood]

regulation of cell migration GO:0030334 regulation of phagocytosis GO:0050764 https://github.com/geneontology/go-annotation/issues/1421

never in yeast? exceptions?

[ukemi]

PMID:27072657?

[ValWood]

I think we discussed this in another ticket, this growing towards another cell during mating isn't really migration (which is a type of 'movement'). The cell doesn't move from one place to another, it just grows a projection towards a mating partner.

[ValWood]

this says its done? https://github.com/geneontology/go-ontology/issues/12410

[ukemi]

I see locomotion never in Dikarya.

[ValWood]

OK that shpuld do it...this is probably a time issue, although I thought the taxon offending annotations were dropped in-between proper updates @mah11 ? maybe not

[ukemi]

There is also a phagocytosis never in Fungi restriction. Should I close this or leave it open for you to investigate further?

[mah11]

I thought the taxon offending annotations were dropped in-between proper updates

I don't understand exactly what you mean by "dropped in-between proper updates", but there is a Jenkins check that uses taxon constraints:

http://geneontology.org/page/annotation-quality-control-checks#0000013

[ValWood]

so it there a warning on our file right now? I forget where I can see this...

[ValWood]

Found it. http://build.berkeleybop.org/view/GAF/

So I don't understand:

The taxon check is implemented. Our GAF is passing jenkins chacks. The taxon restricted annotation is in the GO database

[ukemi]

I think the issue is that in this ticket you want the restriction on the regulation terms. Do they also never regulate these processes, even when the process is occurring in another organism?

[ValWood]

Doesn't restriction on the regulation term happen automatically (I thought all descendants were restricted).

even when the process is occurring in another organism?

Er wouldn't that be a multi organism process if it occurs? I think for fission yeast we wouldn't expect to see this node annotated at all....not sure if other yeast want to keep the option open....

[ukemi]

Doesn't restriction on the regulation term happen automatically (I thought all descendants were restricted).

It doesn't seem like that would always be true for regulates. What about parasites that control process in their hosts, but don't carry out those processes themselves?

even when the process is occurring in another organism?

Er wouldn't that be a multi organism process if it occurs? I think for fission yeast we wouldn't expect to see this node annotated at all....not sure if other yeast want to keep the option open....

Yes, but not all regulation would be. Let's keep this open for a few more days. If no one complains, I will add the restriction.

[ValWood]

I guess they could regulate migration.... I forgot about this change. We no longer have parasite specific terms do we?.... this will be very confusing to distinguish parasite specific process from host-parasite interactions.

All I know is, we would not expect pombe to be annotated to "cell migration" terms... and based on this ticket yesterday https://github.com/geneontology/go-annotation/issues/1424 I don't think SGD would expect saccharomyces to be annotated to these terms either....

[ValWood]

We might later need cleverer taxon restrictions, where you can only use certain terms with a certain species if you specify a host......

[dosumis]

Doesn't restriction on the regulation term happen automatically (I thought all descendants were restricted).

Not how OWL works. Inheritance only works down the class (is_a) hierarchy. A property chain is needed for restrictions to carry over relationships - but this is probably not possible for never_in_taxon as it needs expansion (to a GCI) to work.

[ukemi]

Hi Val,

I will go ahead and add these restrictions can you look at the taxon hierarchy and tell me exactly where to make them?

-D

[ValWood]

Go with regulation of cell migration GO:0030334 regulation of phagocytosis GO:0050764

never in yeast for now, can refine later....

[ukemi]

Done.

[selewis]

Do you know which families are affected? We should update these to make sure all the taxon constraints are still satisfied.

Looks okay when jenkins runs the validator, so I will assume we're clear.

[dianeoinglis]

Sorry to not have commented sooner.

This taxon restriction should not apply to all Fungi. Fungal pathogens are able to alter neutrophil and macrophage cell migration and chemotaxis during infection.

Diane

[dianeoinglis]

Hi Susanna,

I added a late stage comment about fungal pathogens altering immune cell chemotaxis and cell migration but I am not sure if the ticket has to be reopened for the comment to be seen.

Best,

Diane

On Sat, Aug 13, 2016 at 1:01 PM, Suzanna Lewis notifications@github.com wrote:

Do you know which families are affected? We should update these to make sure all the taxon constraints are still satisfied.

Looks okay when jenkins runs the validator, so I will assume we're clear.

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[selewis]

@ValWood

We need you to chime in on this issue which arose in PAINT. https://github.com/geneontology/paint/issues/25

Perhaps you could start watching the PAINT list, your expertise would be appreciated.

[ukemi]

Hi Diana,

I made the restriction never in Saccharomycotina. Is that ok?

-D

[dianeoinglis]

Hi David,

No, that will not work because Candida is included in the Saccharomycotina

Saccharomycetes > Saccharomycetales > Debaromycaceae.

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1535326

Basically, any effective pathogen of animals will encounter host immune cells that migrate to either phagocytose the invading fungus or will migrate to the lymphatic tissues with an engulfed fungus. Intracellular fungal pathogens, such as Histoplasma love riding inside macrophages as vehicles for dissemination. Extracellularly, pathogenic fungi can alter chemotaxis, whether they alter the migration as intracellular passengers is less certain.

Perhaps this taxon restriction should be specific to yeast and S. pombe. It would be preferable to apply phylogenetically but the animal pathogens seem to dispersed among phyla.

I do have some important comments to contribute to the ticket on PAINT/yeast annotations.

Diane

On Mon, Aug 15, 2016 at 4:15 AM, David Hill notifications@github.com wrote:

Hi Diana,

I made the restriction never in Saccharomycotina. Is that ok?

-D

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[ukemi]

Thanks Diane. If you read above, you can see that I was originally concerned about this possibility. I have removed the taxon constraint.

-D

[ValWood]

OK, we can deal with this http://www.pombase.org/spombe/result/SPAC2F7.16c by getting the mapping updated. val

[ValWood]

It was already done https://github.com/geneontology/go-annotation/issues/1421

[ValWood]

@cmungall should this link work, I get access denied:

http://geneontology.org/page/annotation-quality-control-checks#0000013

[ValWood]

ignore..I presume they are in another location? I loose track....

[cmungall]

Rules are here: https://github.com/geneontology/go-site/tree/master/metadata/rules