Taxon-GO Checks and Commentary - Response to GOA - Part 5

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Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB

Q/ Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this.

Line 19: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009775 "photosynthetic electron transport in cytochrome b6/f" only_in ID:0000000 "Viridiplantae or Bacteria" :: Swiss-Prot P31480 petB GO:0009775 PMID:12837550 NAS P protein NCBITaxon:3039 20031120 UniProtKB

A/ New union term made and rule corrected.

Line 21: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83687 PSBP GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB

A/ New union term made for Viridiplantae and Euglenozoa.

Line 22: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot Q8GZR2 petA GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB Line 23: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83688 P83688 GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB

A/ As above.

Line 25: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot Q84TU6 petD GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20040507 UniProtKB

A/ Changed to Viridiplantae or bacteria or Euglenozoa.

Line 26: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot P31480 petB GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB

A/ As above.

Line 36: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54714 cpcB GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB

A/ This rule is not present. Perhaps it was previously corrected.

Line 37: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54715 cpcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB

A/ As above.

Line 38: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q01951 apcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB

A/ As above.

Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB

A/ This is a problem in the graph. We need generic and cellular versions of DNA replication.

Line 52: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP1 Q9XHP1 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB

A/ This rule appears to be gone already.

Line 53: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9SPL3 AMP2-3 GO:0045735 PMID:10571855 NAS F protein NCBITaxon:60698 20060904 UniProtKB

A/ As above.

Line 54: TAXON RULE INCORRECT. (annotation to a major plant storage protein)GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP0 Q9XHP0 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB

A/ As above.

Line 55: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q39649 Q39649 GO:0045735 PMID:8275099 TAS F protein NCBITaxon:3661 20050516 UniProtKB

A/ As above.

Line 82: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q95K09 TUBGCP5 GO:0008274 PMID:11694571 ISS UniProtKB:Q96RT8 C protein NCBITaxon:9541 20041006 UniProtKB

A/ Rule deleted.

Line 84: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q9GKK8 BRCA1 GO:0008274 PMID:12214252 NAS C protein NCBITaxon:9598 20021218 UniProtKB

A/ Rule deleted.

Line 97: TAXON RULE INCORRECT.GO:0042475 "odontogenesis of dentine-containing tooth" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:104659 Dll1 GO:0042475 MGI:MGI:1327472|PMID:9882480 NAS P gene NCBITaxon:10090 20021218 UniProtKB

A/ Bumped this up to Chordata from the current position under Vertebrate to see if that solves the problem.

Line 98: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:1914505 Zfp422 GO:0042476 MGI:MGI:2449683|PMID:12489153 NAS P gene NCBITaxon:10090 20040226 UniProtKB

A/ Deleted rule

Line 99: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: RGD 620229 Zfp422 GO:0042476 RGD:14706453 NAS P gene NCBITaxon:10116 20040226 UniProtKB

A/ Deleted rule.

Ontology Corrections

DNA Replication

Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB

A/ This is a problem in the graph. We need generic and cellular versions of DNA replication.

Terms created:

> id: GO:0055132
> name: cellular DNA metabolic process

> id: GO:0055133
> name: cellular DNA replication

> id: GO:0055134
> name: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
 


Viral annotations to non-cellular terms with cellular ancestors

Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB

Q/ Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this.

- Removed the rule that locomotion (GO:0040011) is only in cellular organisms.

- Removed link from membrane organization (GO:0016044) to cellular process.

Viruses and response to stimulus

GO:0052085 "negative regulation by symbiont of host T-cell mediated immune response" only_in NCBITaxon:131567 "cellular organisms"

From checking with Jane it appears that a symbiont can also be a virus, so this taxon rule should be removed

A/

I have removed this rule:

[Term]
id: GO:0050896
name: response to stimulus
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms

This does not hold true as viruses also respond to the stimuli produced by their hosts.

For similar reasons I have removed these links:

[Term] id: GO:0051179 name: localization relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms

[Term] id: GO:0032502 name: developmental process relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms

Cellular process only_in_taxon cellular organisms?

id: GO:0009987
name: cellular process
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms

I have removed this rule for the reasons stated in my proposal.