Check annotations to 'cell envelope' and children #1636
Comments
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Hi Pascale, |
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Maybe the part_of relationship between "cell envelope" and "cell outer membrane" is an error? |
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Then again, maybe not. It looks like "plasma membrane" is the term eukaryotes should use rather than cell outer membrane? |
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Hi @cerivs UniProtKB A4IGB6 part_of GO:0045203 PMID:27563101 ECO:0000314 20161110 ZFIN goEvidence=IDA ps...I think we need to look at our expression and phenotype annotations as well. I think there might be expression data related to this prokaryote only term...I'm not sure about phenotypes. |
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Hi @doughowe
Thanks, |
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I have changed two of the mouse annotations, but the third: UniProtKB Q8BVC1 part_of GO:0030112 PMID:18787081 ECO:0000314 20110323 MGI part_of(CL:0000019) goEvidence=IDA to glycocalyx, is valid based on the definition of the term and a quick search of the literature. We either need to change the parentage or create a separate class for things like sperm/epithelial glycocalyx and the ones found in fish, although the fish one might be considered an anatomical structure. |
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Or remove the taxon constriction of the cell envelope. |
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Hi @ukemi Thanks, Pascale |
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Still, editing the ontology will still leave the annotation pointed out by Pascale as needing to be cleaned up in mouse and zebrafish, right? |
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Not to glycocalyx. I think the mouse annotation is ok. I'm not sure about fish. I think moving to cell periphery will at least fix the issue for the glycocalyx that surrounds certain types of eukaryotic cells. |
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@cerivs |
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I fixed the Zebrafish annotations. It would be really helpful if the taxon limitation was propagated down tree since I had to go up a fair way until the in bacteria showed up. Perhaps prokaryotic could be added to the text definition of the branch for curator convenience. |
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?Hi Ceri,
The best we have at the moment is that, at least in this case, the terms are part of the prokaryote slim. That info is available near the bottom (might have to scroll the window) of our term details window. So there's a clue..but easy to miss.
D
…--
Doug Howe, Ph.D.
ZFIN Data Curation Manager
Zebrafish Model Organism Database
University of Oregon
541-346-2355
________________________________
From: cerivs <[email protected]>
Sent: Tuesday, September 26, 2017 4:11 PM
To: geneontology/go-annotation
Cc: Doug Howe; Mention
Subject: Re: [geneontology/go-annotation] Check annotations to 'cell envelope' and children (#1636)
I fixed the Zebrafish annotations. It would be really helpful if the taxon limitation was propagated down tree since I had to go up a fair way until the in bacteria showed up. Perhaps prokaryotic could be added to the text definition of the branch for curator convenience.
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You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#1636 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AGz6vViLaJORQxlnyvnsq4928h1C-3nfks5smYSTgaJpZM4PkLY5>.
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?...and ps...I don't know if the prokaryote slim IS a manifestation directly of the taxon constraint, or if inclusion in the slim was just circumstantial.? Anyone know? If it results from the taxon constraint, then its an indication not to use it in fish. If its circumstantial..well...it's a clue...but maybe not much use really for this issue.
…--
Doug Howe, Ph.D.
ZFIN Data Curation Manager
Zebrafish Model Organism Database
University of Oregon
541-346-2355
________________________________
From: Doug Howe <[email protected]>
Sent: Monday, October 2, 2017 10:12 AM
To: geneontology/go-annotation; geneontology/go-annotation
Cc: Doug Howe; Mention
Subject: Re: [geneontology/go-annotation] Check annotations to 'cell envelope' and children (#1636)
?Hi Ceri,
The best we have at the moment is that, at least in this case, the terms are part of the prokaryote slim. That info is available near the bottom (might have to scroll the window) of our term details window. So there's a clue..but easy to miss.
D
--
Doug Howe, Ph.D.
ZFIN Data Curation Manager
Zebrafish Model Organism Database
University of Oregon
541-346-2355
________________________________
From: cerivs <[email protected]>
Sent: Tuesday, September 26, 2017 4:11 PM
To: geneontology/go-annotation
Cc: Doug Howe; Mention
Subject: Re: [geneontology/go-annotation] Check annotations to 'cell envelope' and children (#1636)
I fixed the Zebrafish annotations. It would be really helpful if the taxon limitation was propagated down tree since I had to go up a fair way until the in bacteria showed up. Perhaps prokaryotic could be added to the text definition of the branch for curator convenience.
-
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#1636 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AGz6vViLaJORQxlnyvnsq4928h1C-3nfks5smYSTgaJpZM4PkLY5>.
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The offending annotations have gone, but there are new ones, despite the taxon constraint: 
Not sure who to tag for these. |
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@pgaudet we could close since these are taxon restricted. |
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@uliboehme one of these is an IDA to GAMA, Plasmodium falciparum 3D7 @jlewsmith the others are CGD but are IEAs, can you just check that these aren't being generated or passed through anymore by CGD? |
Technically they are filtered, but it looks like this is not applied here. I opened a ticket in the go-site repo: |
Hello,
Cell envelope applies to prokaryotes only. We noticed a few EXP annotations in eukaryotes:
@doughowe @hdrabkin (who can I ask for GeneDB?)
Can you please have a look?
UniProtKB A0A0R4IZH2 part_of GO:0045203 PMID:21773621 ECO:0000314 20110913 ZFIN goEvidence=IDA
UniProtKB A4IGB6 part_of GO:0045203 PMID:27563101 ECO:0000314 20161110 ZFIN goEvidence=IDA
UniProtKB B3DK48 part_of GO:0045203 PMID:27628598 ECO:0000314 20161121 ZFIN goEvidence=IDA
UniProtKB F1QPL3 part_of GO:0045203 PMID:27784684 ECO:0000314 20170406 ZFIN goEvidence=IDA
UniProtKB F1RAX4 part_of GO:0045203 PMID:27563101 ECO:0000314 20161110 ZFIN goEvidence=IDA
UniProtKB F8W297 part_of GO:0045203 PMID:27628598 ECO:0000314 20161121 ZFIN goEvidence=IDA
UniProtKB F8W4J6 part_of GO:0045203 PMID:27628598 ECO:0000314 20161121 ZFIN goEvidence=IDA
UniProtKB P41251 part_of GO:0009279 PMID:10065630 ECO:0000314 20090803 MGI goEvidence=IDA
UniProtKB P51576 part_of GO:0031240 PMID:11570704 ECO:0000314 20080512 MGI part_of(EMAPA:18321),part_of(CL:0000192) goEvidence=IDA
UniProtKB Q1ECX5 part_of GO:0045203 PMID:27563101 ECO:0000314 20161110 ZFIN goEvidence=IDA
UniProtKB Q4V9K3 part_of GO:0045203 PMID:27784684 ECO:0000314 20170406 ZFIN goEvidence=IDA
UniProtKB Q563W7 part_of GO:0045203 PMID:27628598 ECO:0000314 20161121 ZFIN goEvidence=IDA
UniProtKB Q6DGZ6 part_of GO:0045203 PMID:27563101 ECO:0000314 20161110 ZFIN goEvidence=IDA
UniProtKB Q7T3Q4 part_of GO:0045203 PMID:21773621 ECO:0000314 20110913 ZFIN goEvidence=IDA
UniProtKB Q8BVC1 part_of GO:0030112 PMID:18787081 ECO:0000314 20110323 MGI part_of(CL:0000019) goEvidence=IDA
UniProtKB Q8IBB9 part_of GO:0031244 PMID:19820120 ECO:0000314 20091019 GeneDB goEvidence=IDA
UniProtKB Q9PTQ8 part_of GO:0045203 PMID:27784684 ECO:0000314 20170406 ZFIN goEvidence=IDA
UniProtKB S5UFQ9 part_of GO:0045203 PMID:27628598 ECO:0000314 20161121 ZFIN goEvidence=IDA
Thanks, Pascale
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