pre-import PAINT checks, PAINT IGNORING TAXON RESTRICTIONS #1873

ValWood · 2018-03-13T16:22:42Z

this batch should be taxonomically restricted:

~~fhl1 forkhead transcription factor Fhl1 cell differentiation GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN001371846 PAINT_REF:11829 20170427~~
see #1873
~~fhl1 forkhead transcription factor Fhl1 anatomical structure morphogenesis GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN001371846~~
see #1873

map1 MADS-box transcription factor Map1 multicellular organism development GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000235373 PAINT_REF:11945 20170427

MULTICELLULAR ORGANISM DEVELOPMENT IS TAXONOMICALLY RESTRICTED FOR YEAST

nup61 nucleoporin Nup61 positive regulation of mitotic centrosome separation GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000566604
(I would question this annotation more generally anyway)

THIS TERM SHOULD BE TAXONOMICALLY RESTICTED ITS PARENTS ARE
geneontology/go-ontology#15685

rho4 Rho family GTPase Rho4 regulation of cell migration GO_Central Schizosaccharomyces pombe

THIS TERM SHOULD BE TAXONOMICALLY RESTICTED ITS PARENTS ARE

shk2 PAK-related kinase Shk2 cell migration GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000686326

CELL MIGRATION IS ALREADY TAXONOMICALLY RESTRICTED, IGNORED BY PAINT???
GO:0040011 | locomotion | Never in Taxon | 451864

spn1 mitotic septin Spn1 cilium assembly GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000430231 PAINT_REF:18884 20170427

CILLIUM ASSEMBLY IS ALREADY TAXONOMICALLY RESTRICTED, IGNORED BY PAINT???
GO:0060271 | cilium assembly | Never in Taxon | 4890 | Ascomycota

ValWood · 2018-03-13T16:30:30Z

PANTHER family issue ?

ssn6 transcriptional corepressor Ssn6 histone demethylase activity (H3-K27 specific) GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000361179
This one is a bit strange,
it isn't a demethylase, but it also isn't the ortholog of the other family members in PANTHER:PTN000361179 which are. These are jmJC, and pombe ssn6 is a TRP repeat (panther family
http://www.pantherdb.org/panther/family.do?clsAccession=PTHR14017

see
#1951

ValWood · 2018-03-13T16:36:33Z

tos4 transcription factor, FHA domain protein Tos4 (predicted) translation GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000559990
(Is a transcription factor)

#1952

ValWood · 2018-03-13T16:46:44Z

#1953

rmt3 type I ribosomal protein arginine N-methyltransferase Rmt3 histone arginine methylation GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000109455 PAINT_REF:11006 20170427
rmt3 type I ribosomal protein arginine N-methyltransferase Rmt3 histone-arginine N-methyltransferase activity GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000109455

I don't think that histone is the physiological substrate here?
This is characterised in pombe as colocalizing with and methylating ribosomes
see
https://www.pombase.org/gene/SPBC8D2.10c

ValWood · 2018-03-13T16:54:36Z

#1962

not enough information to make these inferences (transport inferences are dangerous across species, because substrates change but to the best of our knowledge this is a sulfate transporter)
SPCC320.05 sulfate transmembrane transporter (predicted) regulation of intracellular pH GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000212047 PAINT_REF:11814 20170427
SPCC320.05 sulfate transmembrane transporter (predicted) bicarbonate transport GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000212047 PAINT_REF:11814 20170427
SPCC320.05 sulfate transmembrane transporter (predicted) chloride transmembrane transport GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000212047 PAINT_REF:11814 20170427
SPCC320.05 sulfate transmembrane transporter (predicted) oxalate transport

cmungall · 2018-03-13T17:04:51Z

@ValWood - are all of these for the attention of the PAINT team (assigning @huaiyumi for now)? Are some for new TCs in GO?

selewis · 2018-03-13T17:11:39Z

Does this mean that the taxon checking code was removed from PAINT? It use to be built-in.

ValWood · 2018-03-13T18:07:00Z

I guess some will be for checking the PAINT annotation.

I think ssn6 is a panther family issue?

The taxon checks don't appear to be working. I think this might be a general GO issue now I think about it. Let me know if you want these 2 split out into different tickets.

ValWood · 2018-03-13T18:11:14Z

see #1954

~~tra2 NuA4 complex phosphatidylinositol pseudokinase complex subunit Tra2 kinase activity GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000124197~~

(Tra2 in NuA4 is a pseudo-kinase, I think this is a general across species thing but I'm not sure)

ValWood · 2018-03-13T18:16:25Z

we wouldn't make these annotations:

~~nup211 nucleoporin nup211 mitotic spindle assembly checkpoint GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN001052033~~
#1955

nup61 nucleoporin Nup61 spindle organization GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000566604
see above
#1956

~~npp106 nucleoporin Npp106 nuclear pore complex assembly GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000131983 PAINT_REF:11225~~
#1957

ValWood · 2018-03-13T18:26:25Z

#1960

~~sec21 coatomer gamma subunit Sec21 (predicted) organelle transport along microtubule GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000029440~~

ValWood · 2018-03-13T18:30:25Z

see
#1958

positive and negitive annotation from the sme family
arg6 acetylglutamate synthase Arg6 acetylglutamate kinase activity GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000597373 PAINT_REF:23342 20170427
arg6 acetylglutamate synthase Arg6 NOT acetylglutamate kinase activity GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000597386 PAINT_REF:23342 20170427
it isn't acetylglutamate kinase activity, it's acetyl-CoA:L-glutamate N-acetyltransferase activity
(this might be becaue its a multi domain protein in higher eukaryotes?)
Actually there might be an amino acid kinase domain below threshold, but should there be both a positive and a negative annotation?

ValWood · 2018-03-13T18:35:58Z

#1959

incorrect annotations
See
#31
for some history
transport, NADH to ubiquinone GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000042666 PAINT_REF:10371
SPAC11E3.12 mitochondrial thioredoxin family protein respiratory electron transport chain GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000042665 PAINT_REF:10371 20170427
SPAC11E3.12 mitochondrial thioredoxin family protein NADH dehydrogenase (ubiquinone) activity GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN000042665 PAINT_REF:10371 20170427

ValWood · 2018-03-13T18:37:22Z

#1961

sil1 nucleotide exchange factor for the ER lumenal Hsp70 chaperone, Sil1 (predicted) cytoplasmic translation GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN001062524 PAINT_REF:19316 20170427
is involved in
SRP-dependent cotranslational protein targeting to membrane, translocation

ValWood · 2018-03-13T18:41:36Z

snd302 SRP-independent ER targeting protein Snd3b (predicted) phosphate ion transport GO_Central Schizosaccharomyces pombe IBA PANTHER:PTN001999322 PAINT_REF:28112 20170427

see InterPRo summary
http://www.ebi.ac.uk/interpro/entry/IPR012098

the phosphate transport is from some old 1996 genetics, indirect
https://www.yeastgenome.org/reference/S000051002

(queried original annotation with SGD)

2/Apr/2018, I followed this up with SGD, the original annotation was deleted

ValWood · 2018-03-13T19:05:37Z

I scanned the first 1000 they look pretty good!)
Once these are fixed I'll try a real import against our filtering (most will hopefully be duplicates so they will be filtered from PomBase as redundant).

It would be really helpful to suppress redundant annotation more generally .....

ValWood · 2018-04-02T19:53:20Z

We can't import the PAINT annotations into PomBase until these are fixed. However, the pombe annotations are now in AMiGO. Because they have the incorrect gene ID in the db object symbol column they are also causing problems for downstream softwares (see helpdesk ticket).

selewis · 2018-04-02T19:53:39Z

Right, I forwarded your message to Anushya and Huaiyu to draw their attention to this.

…

On Mon, Apr 2, 2018 at 12:48 PM, Val Wood ***@***.***> wrote: some of these will need to be addressed by PAINT curators. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1873 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABcuENlWRWf_h3HX67at8OT5PDTL15JXks5tkoCOgaJpZM4So_9y> .

ValWood · 2018-04-02T20:01:15Z

Other than the taxon restriction issue I think they are mostly annotation problems. ....

ValWood · 2018-04-26T15:21:40Z

@pgaudet this is an earlier batch. Do you want these into separate tickets?

pgaudet · 2018-05-02T08:23:12Z

@ValWood

Please create separate tickets.
Taxon constraints should go in the go-ontology tracker.

Thanks !

Pascale

mah11 · 2018-05-02T09:58:55Z

Taxon constraints should go in the go-ontology tracker.

Is that applicable to these reports? As I understand it, the taxon constraints are already present in the ontology, but annotations that should be flagged or blocked are getting through. Is that still an ontology issue?

ValWood · 2018-05-02T10:12:53Z

yes I think in many cases the taxon restrictions are present but the taxon restrictions are not in place. I have asked about this in multiple tickets.
@cmungall ?

anyway I'll start by separating this list out.

ValWood · 2018-05-02T10:14:21Z

ticket about taxon checks (and other QC checks)
#1928

ValWood · 2018-05-02T10:34:41Z

There are 2 issues really......

1 . Why aren't the taxon restrictions being included more generally (i.e when a gene products is annotated to a taxonomically restricted term, why isn't it flagged in the logs.

but
2. Why is PAINT ignoring the taxon restrictions and making annotations to them
For example, pombe and cerevisiae should not get any annotation via PAINT to
"multicellular organism development"

Both of these problems need resolving. The taxon checks not working issue is already reported to @cmungall

The entries in this ticket related to taxon checks is about PAINT ignoring taxon restrictions....

ValWood · 2018-05-02T10:49:53Z

It seems to be a mixture.
I renamed this ticket
pre-import PAINT checks, PAINT IGNORING TAXON RESTRICTIONS

I'll move any queries that do not appear to be this particular problem to separate tickets

pgaudet · 2018-05-02T12:14:44Z

@ValWood
The fact that taxon restrictions are ignored for PAINT annotations is a known issue. So you can skip creating new tickets if this is the problem. I'm investigating this with @cmungall @huaiyumi and @dougli1sqrd to see why some PAINT annotations are not exported/displayed correctly.

Thanks, Pascale

ValWood · 2018-05-02T12:21:40Z

OK this particular ticket is now only about PAINT ignoring taxon restrictions.

pgaudet · 2018-05-02T12:22:48Z

Thanks !

ValWood · 2018-05-02T12:38:00Z

If it helps, taxon restrictions are being ignored for everything, and have been for a while. Not just for PAINT (although I had assumed that there would be an extra upstream step to prevent PAINT annotations being created if a taxon restriction exists?)

ValWood · 2018-05-16T16:02:53Z

GO:0060271 | cilium assembly | Never in Taxon | 4890 | Ascomycota
we get 8 pombe genes annotated to this term

via
PANTHER:PTN000430231
PANTHER:PTN000223362
PANTHER:PTN000223485

selewis · 2018-05-17T17:32:32Z

There ought to be (and indeed use to be) at least two built-in checks for passing the taxon constraints. First during PAINT handling and second during the standard pipeline

Built-in to PAINT itself so that the annotations aren't created in the first place. 3 possible things could happen at this stage. 1.a code-rot resulting in this functionality being lost. -- @huaiyumi would you please check that. -- 1.b older PAINT annotations prior to current checks, but these could be caught when the PAINT gafs are generated by @huaiyumi, again @huaiyumi to check-- and last 1.c the taxon checker service that PAINT uses is down -- @kltm or @dougli1sqrd can determine that.
The pipeline should be checking all submissions to ensure they obey the taxon constraints. This would deal with any failures in the above. Really though these should ideally be caught at inception

kltm · 2018-08-09T23:56:27Z

Moved to implementation ticket here: geneontology/go-site#758

pgaudet · 2018-08-10T07:18:07Z

We should leave this ticket open as it provides nice examples to do QC.

kltm · 2018-08-10T14:30:26Z

@pgaudet If they are to be implemented, they should go with the ticket; if they are documentation, the wiki may be a more appropriate place.

pgaudet · 2019-08-19T13:02:05Z

I think this is all done. Please reopen if not.

cmungall added the PAINT annotation label Mar 13, 2018

cmungall assigned huaiyumi Mar 13, 2018

ValWood mentioned this issue Apr 2, 2018

PAINT annotations do not use the correct primary name in GAF field for DB object symbol geneontology/helpdesk#112

Closed

ValWood assigned pgaudet Apr 2, 2018

ValWood changed the title ~~pre-import PAINT checks~~ pre-import PAINT checks, PAINT IGNORING TAXON RESTICTIONS May 2, 2018

ValWood changed the title ~~pre-import PAINT checks, PAINT IGNORING TAXON RESTICTIONS~~ pre-import PAINT checks, PAINT IGNORING TAXON RESTRICTIONS May 2, 2018

This was referenced May 2, 2018

PANTHER:PTN001062524 #1961

Closed

PTN000212047 sulphate transport #1962

Closed

selewis assigned dougli1sqrd and kltm May 17, 2018

ValWood mentioned this issue May 30, 2018

Which annotation validation rules are currently implemented? (e.g Taxon checks are not running) #1928

Closed

kltm mentioned this issue Aug 9, 2018

Implement taxon checks in pipeline against PAINT data geneontology/go-site#758

Closed

kltm closed this as completed Aug 9, 2018

pgaudet reopened this Aug 10, 2018

pgaudet unassigned kltm and dougli1sqrd Aug 10, 2018

pgaudet closed this as completed Aug 19, 2019

pre-import PAINT checks, PAINT IGNORING TAXON RESTRICTIONS #1873

pre-import PAINT checks, PAINT IGNORING TAXON RESTRICTIONS #1873

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