#10840 Taxon rules for several terms

None
closed-accepted
5
2014-06-16
2014-05-09
Michael E Rice
No

Request taxon constraint for:
GO:000865 lipopolysaccharide metabolic process
GO:0008917 lipopolysaccharide N-acetylglucosaminyltransferase activity
GO:0009103 lipopolysaccharide biosynthetic process
GO:0008919 lipopolysaccharide glucosyltransferase I activity
GO:0047270 lipopolysaccharide glucosyltransferase II activity
only occurs in Gram negative bacteria; the terms have been assigned to non-bacterial species because of the similarity to the name of the enzyme e.g. it has been assigned to human UniProtKB:C9IYY0 which is Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase

GO:0060157 urinary bladder development
GO:0014832 urinary bladder smooth muscle contraction
does not occur in birds excepting ostrich and rhea

GO:0060067 cervix development
does not occur in birds; this term refers to the cervix of the female reproductive system, not the cervical vertebrae. The term has been incorrectly assigned to proteins of birds.

GO:0001740 Barr body
definition states "A structure found in a female mammalian cell..." Barr body is also found in non-mammalian cells.

Related

Ontology requests: #10840

Discussion

    • labels: --> Taxon restriction
    • summary: IEA annotation issues assigned by Ensembl Compara --> Taxon rules for several terms
    • assigned_to: Paola Roncaglia
     
  • (Was: "IEA annotation issues assigned by Ensembl Compara")

     
  • Hi Mike,

    Thanks for spotting these. A few notes on the lipopolysaccharide terms:

    1) I can't make GO:000865 lipopolysaccharide metabolic process only_in Bacteria, because the rule would be inherited by its child lipopolysaccharide catabolic process, which is potentially untrue (organisms other than bacteria may be able to break down the outer membrane of Gram-negative bacteria). Other than that, I applied a taxon restriction to all the other terms you listed.

    2) Gram-negative bacteria are not a monophyletic group (see http://en.wikipedia.org/wiki/Gram_negative), therefore they're not represented in the NCBI taxonomy classification that we refer to. I restricted the terms to 'Bacteria'.

    3) I applied the taxon rule also to GO:0008918 lipopolysaccharide 3-alpha-galactosyltransferase activity
    (see http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/4/1/44.html)

    I'll look into the other terms soon, thanks for your patience.

    Paola

    P.S. Note for self: see if 'lipopolysaccharide biosynthetic process' can be modeled to link to the 4 activity terms.

     
    • Michael E Rice
      Michael E Rice
      2014-05-12

      Paola,

      Thank you for catching the metabolic/catabolic rule; I got a little carried away. If I want to know if there have been any new discussions concerning changing
      GO:0006915 apoptotic process never_in Viridiplantae, could you please tell me how to do that? Thanks

      Mike


      Michael E. Rice AgBase biocurator
      School of Animal and Comparative Biomedical Science
      Thomas W. Keating Bioresearch Building
      1657 E. Helen St.
      Tucson, AZ 85721
      The College of Agriculture and Life Sciences
      The University of Arizona
      520 955-2745
      mrice@email.arizona.eduhttp://mrice@email.arizona.edu


      From: Paola Roncaglia [paolaroncaglia@users.sf.net]
      Sent: Monday, May 12, 2014 1:26 PM
      To: [geneontology:ontology-requests]
      Subject: [geneontology:ontology-requests] #10840 Taxon rules for several terms

      Hi Mike,

      Thanks for spotting these. A few notes on the lipopolysaccharide terms:

      1) I can't make GO:000865 lipopolysaccharide metabolic process only_in Bacteria, because the rule would be inherited by its child lipopolysaccharide catabolic process, which is potentially untrue (organisms other than bacteria may be able to break down the outer membrane of Gram-negative bacteria). Other than that, I applied a taxon restriction to all the other terms you listed.

      2) Gram-negative bacteria are not a monophyletic group (see http://en.wikipedia.org/wiki/Gram_negative), therefore they're not represented in the NCBI taxonomy classification that we refer to. I restricted the terms to 'Bacteria'.

      3) I applied the taxon rule also to GO:0008918 lipopolysaccharide 3-alpha-galactosyltransferase activity
      (see http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/4/1/44.html)

      I'll look into the other terms soon, thanks for your patience.

      Paola

      P.S. Note for self: see if 'lipopolysaccharide biosynthetic process' can be modeled to link to the 4 activity terms.


      [ontology-requests:#10840]http://sourceforge.net/p/geneontology/ontology-requests/10840/ Taxon rules for several terms

      Status: open
      Group: None
      Labels: Taxon restriction
      Created: Fri May 09, 2014 11:24 PM UTC by Michael E Rice
      Last Updated: Sun May 11, 2014 05:06 PM UTC
      Owner: Paola Roncaglia

      Request taxon constraint for:
      GO:000865 lipopolysaccharide metabolic process
      GO:0008917 lipopolysaccharide N-acetylglucosaminyltransferase activity
      GO:0009103 lipopolysaccharide biosynthetic process
      GO:0008919 lipopolysaccharide glucosyltransferase I activity
      GO:0047270 lipopolysaccharide glucosyltransferase II activity
      only occurs in Gram negative bacteria; the terms have been assigned to non-bacterial species because of the similarity to the name of the enzyme e.g. it has been assigned to human UniProtKB:C9IYY0 which is Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase

      GO:0060157 urinary bladder development
      GO:0014832 urinary bladder smooth muscle contraction
      does not occur in birds excepting ostrich and rhea

      GO:0060067 cervix development
      does not occur in birds; this term refers to the cervix of the female reproductive system, not the cervical vertebrae. The term has been incorrectly assigned to proteins of birds.

      GO:0001740 Barr body
      definition states "A structure found in a female mammalian cell..." Barr body is also found in non-mammalian cells.


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      Ontology requests: #10840

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  • Hi Mike,

    About the taxon rules, please note that it will take some time for these to be applied, but the erroneous annotations will eventually be flagged. (The more complete explanation for this delay is that we've recently implemented addition of taxon rules directly into the file that GO editors edit, rather than via an external file. This makes the process less error-prone and quicker. However, the taxon rules need to be 'translated' into specific IDs that are then fed to the checking scripts. This task is currently underway but not completed yet. Once it is, the checking scripts will flag erroneous annotations (e.g. human annotations to 'lipopolysaccharide biosynthetic process' if any), and the databases responsible for those annotations will be notified.)

    As for your question:
    "If I want to know if there have been any new discussions concerning changing GO:0006915 apoptotic process never_in Viridiplantae, could you please tell me how to do that?"
    In general, a good way to keep up-to-date on proposed ontology changes is to keep an eye on the daily email with subject "[go] SourceForge Ontology Tracker Update" sent from BBOP-Jenkins to the general GO mailing list. If you don't already subscribe to that, I'd encourage you to (see https://mailman.stanford.edu/mailman/listinfo/go-consortium). We editors try to keep the titles of ontology SF tickets as informative as possible. If you notice a ticket whose outcome you're interested in, you can 'subscribe' to the single ticket by clicking on the 'envelope' icon, and you'll receive an email every time someone comments on that ticket. Apologies if any of this is redundant.
    More specifically for your question, I happen to be the reference editor for the apoptosis project :-)
    The discussion behind making 'apoptotic process' never_in_Viridiplantae is in an old SF ticket here - I just copied at its bottom the original email exchange that supported the taxon rule: https://sourceforge.net/p/geneontology/ontology-requests/8690/
    If you wish to suggest any revision to this taxon rule, possibly supported by references, please open a new SF ticket and assign it to me (or just leave it as is, I'll pick it up when I get the daily SF email). Of course you could just tell me, but we prefer to keep these type of requests in SF so everyone is aware and able to comment (I'm not a plant expert), and also for tracking purposes.

    I hope this answered your question!
    Thanks,
    Paola

     
  • Back to my comment
    "Note for self: see if 'lipopolysaccharide biosynthetic process' can be modeled to link to the 4 activity terms."
    Looking at the KEGG entry for 'lipopolysaccharide biosynthesis' (http://www.genome.jp/kegg-bin/show_pathway?map00540), I think it would be correct to add the following links:

    GO:0008918 lipopolysaccharide 3-alpha-galactosyltransferase activity [EC 2.4.1.44]
    GO:0008917 lipopolysaccharide N-acetylglucosaminyltransferase activity [EC 2.4.1.56]
    GO:0008919 lipopolysaccharide glucosyltransferase I activity [EC 2.4.1.58]
    all part_of GO:0009103 lipopolysaccharide biosynthetic process (with dbxref KEGG:00540)
    but not GO:0009103 lipopolysaccharide biosynthetic process has_part those enzymatic activities because they don't seem to be necessary in some bacterial species.

    Also, I think that a link could be added:
    GO:0047270 lipopolysaccharide glucosyltransferase II activity [EC 2.4.1.73]
    part_of GO:0009103 lipopolysaccharide biosynthetic process
    this is not shown in the KEGG diagram (and I can't access details on MetaCyc; any other resource I should try?) but it makes sense based on http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/4/1/73.html

    I'll ask Jim Hu if he has any comments before I add these links.
    Paola

     
  • Hi again Mike,

    As for your taxon rule request:
    "GO:0060157 urinary bladder development
    GO:0014832 urinary bladder smooth muscle contraction
    does not occur in birds excepting ostrich and rhea"

    Bit tricky but I think I figured it out -
    ostrich, rhea, chicken and turkey are all Aves, but ostrich and rhea are Palaeognathae, while chicken and turkey are Neognathae.
    So I'd make the taxon rules apply to never_in_Neognathae. Could you please confirm that this is the higher taxon group I can safely refer to, and check that no violations would be generated to your knowledge, referring to the NCBI taxon entry for Aves? The link should be this one if it works:
    http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=8782&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&keep=1&srchmode=1&unlock

    Also, would you have any reference (PMID or ISBN or reliable web resource e.g. wikipedia) that I can support these taxon rules with?

    Thanks,
    Paola

     
    • Michael E Rice
      Michael E Rice
      2014-05-13

      Paola,

      that's cool; great work figuring out the taxons, it looks correct to me. here are some papers and web sites for supporting information
      http://en.wikipedia.org/wiki/Rhea_(bird)
      http://www.beautyofbirds.com/rheas.html
      PMID:538956
      PMID:11768524
      PMID:18276178

      Thanks

      Mike


      Michael E. Rice AgBase biocurator
      School of Animal and Comparative Biomedical Science
      Thomas W. Keating Bioresearch Building
      1657 E. Helen St.
      Tucson, AZ 85721
      The College of Agriculture and Life Sciences
      The University of Arizona
      520 955-2745
      mrice@email.arizona.eduhttp://mrice@email.arizona.edu


      From: Paola Roncaglia [paolaroncaglia@users.sf.net]
      Sent: Tuesday, May 13, 2014 3:42 AM
      To: [geneontology:ontology-requests]
      Subject: [geneontology:ontology-requests] #10840 Taxon rules for several terms

      Hi again Mike,

      As for your taxon rule request:
      "GO:0060157 urinary bladder development
      GO:0014832 urinary bladder smooth muscle contraction
      does not occur in birds excepting ostrich and rhea"

      Bit tricky but I think I figured it out -
      ostrich, rhea, chicken and turkey are all Aves, but ostrich and rhea are Palaeognathae, while chicken and turkey are Neognathae.
      So I'd make the taxon rules apply to never_in_Neognathae. Could you please confirm that this is the higher taxon group I can safely refer to, and check that no violations would be generated to your knowledge, referring to the NCBI taxon entry for Aves? The link should be this one if it works:
      http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=8782&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&keep=1&srchmode=1&unlock

      Also, would you have any reference (PMID or ISBN or reliable web resource e.g. wikipedia) that I can support these taxon rules with?

      Thanks,
      Paola


      [ontology-requests:#10840]http://sourceforge.net/p/geneontology/ontology-requests/10840/ Taxon rules for several terms

      Status: open
      Group: None
      Labels: Taxon restriction
      Created: Fri May 09, 2014 11:24 PM UTC by Michael E Rice
      Last Updated: Tue May 13, 2014 10:23 AM UTC
      Owner: Paola Roncaglia

      Request taxon constraint for:
      GO:000865 lipopolysaccharide metabolic process
      GO:0008917 lipopolysaccharide N-acetylglucosaminyltransferase activity
      GO:0009103 lipopolysaccharide biosynthetic process
      GO:0008919 lipopolysaccharide glucosyltransferase I activity
      GO:0047270 lipopolysaccharide glucosyltransferase II activity
      only occurs in Gram negative bacteria; the terms have been assigned to non-bacterial species because of the similarity to the name of the enzyme e.g. it has been assigned to human UniProtKB:C9IYY0 which is Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase

      GO:0060157 urinary bladder development
      GO:0014832 urinary bladder smooth muscle contraction
      does not occur in birds excepting ostrich and rhea

      GO:0060067 cervix development
      does not occur in birds; this term refers to the cervix of the female reproductive system, not the cervical vertebrae. The term has been incorrectly assigned to proteins of birds.

      GO:0001740 Barr body
      definition states "A structure found in a female mammalian cell..." Barr body is also found in non-mammalian cells.


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      Ontology requests: #10840

      Attachments
    • labels: Taxon restriction --> Taxon restriction, enzymes, metabolism
     
  • Thanks Mike.

    Note for self:
    Just requested NCBITaxon:8825 ! Neognathae in imports_request.
    When it's in, I can add taxon rules:

    GO:0060157 urinary bladder development
    GO:0014832 urinary bladder smooth muscle contraction
    both never_in_taxon Neognathae

    both supported by these dbxrefs:
    GOC:mr
    http://en.wikipedia.org/wiki/Rhea_(bird)
    PMID: 538956
    PMID: 11768524
    PMID: 18276178

     
  • Jim Hu
    Jim Hu
    2014-05-14

    I'll try to read some literature and also consult my bacterial surface experts.

     
  • Many thanks Jim!

     
  • Mike,

    Wtr your last request (I'm still working on the cervix one)
    "GO:0001740 Barr body
    definition states "A structure found in a female mammalian cell..." Barr body is also found in non-mammalian cells."
    As a matter of fact, the term is not formally restricted to mammals; only to eukaryotes.
    So it would be enough to remove the 'mammalian' in 'female mammalian cell' from the definition.
    Would you have any references handy that show Barr bodies in non-mammalian species please? Not strictly required in this case, but helpful.

    Thanks,
    Paola

     
    • Michael E Rice
      Michael E Rice
      2014-05-14

      Paola,

      I believe I am wrong about this. I did not read carefully the information, but going back over it, I cannot find any mention of Barr bodies occurring outside of mammals; I think I confused it with the sex chromosome which I see is an ancestor to Barr body. I am very sorry and I will be more careful in the future. I hope I did not create unnecessary work for you. However, I see that GO:0001740 Barr body has been assigned to chicken and turkey by IEA so perhaps these need to be corrected as well as any other non mammalian species. Please let me know, thanks for your help,

      Mike


      Michael E. Rice AgBase biocurator
      School of Animal and Comparative Biomedical Science
      Thomas W. Keating Bioresearch Building
      1657 E. Helen St.
      Tucson, AZ 85721
      The College of Agriculture and Life Sciences
      The University of Arizona
      520 955-2745
      mrice@email.arizona.eduhttp://mrice@email.arizona.edu


      From: Paola Roncaglia [paolaroncaglia@users.sf.net]
      Sent: Wednesday, May 14, 2014 4:01 AM
      To: [geneontology:ontology-requests]
      Subject: [geneontology:ontology-requests] #10840 Taxon rules for several terms

      Mike,

      Wtr your last request (I'm still working on the cervix one)
      "GO:0001740 Barr body
      definition states "A structure found in a female mammalian cell..." Barr body is also found in non-mammalian cells."
      As a matter of fact, the term is not formally restricted to mammals; only to eukaryotes.
      So it would be enough to remove the 'mammalian' in 'female mammalian cell' from the definition.
      Would you have any references handy that show Barr bodies in non-mammalian species please? Not strictly required in this case, but helpful.

      Thanks,
      Paola


      [ontology-requests:#10840]http://sourceforge.net/p/geneontology/ontology-requests/10840/ Taxon rules for several terms

      Status: open
      Group: None
      Labels: Taxon restriction enzymes metabolism
      Created: Fri May 09, 2014 11:24 PM UTC by Michael E Rice
      Last Updated: Wed May 14, 2014 10:57 AM UTC
      Owner: Paola Roncaglia

      Request taxon constraint for:
      GO:000865 lipopolysaccharide metabolic process
      GO:0008917 lipopolysaccharide N-acetylglucosaminyltransferase activity
      GO:0009103 lipopolysaccharide biosynthetic process
      GO:0008919 lipopolysaccharide glucosyltransferase I activity
      GO:0047270 lipopolysaccharide glucosyltransferase II activity
      only occurs in Gram negative bacteria; the terms have been assigned to non-bacterial species because of the similarity to the name of the enzyme e.g. it has been assigned to human UniProtKB:C9IYY0 which is Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase

      GO:0060157 urinary bladder development
      GO:0014832 urinary bladder smooth muscle contraction
      does not occur in birds excepting ostrich and rhea

      GO:0060067 cervix development
      does not occur in birds; this term refers to the cervix of the female reproductive system, not the cervical vertebrae. The term has been incorrectly assigned to proteins of birds.

      GO:0001740 Barr body
      definition states "A structure found in a female mammalian cell..." Barr body is also found in non-mammalian cells.


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      Related

      Ontology requests: #10840

      Attachments
  • Jim Hu
    Jim Hu
    2014-05-14

    aargh. Sourceforge did it again. My session must have timed out so I lost the really long reply I was writing when I hit post. Sigh. Reconstructing…
    LPS is usually thought of as

    • Lipid A
    • Core oligosaccharide
    • O antigen - varies a lot within species, and may be completely absent

    LPS is really variable so a small number of activity terms are going to be has_part for the overall biosynthetic process. The three mentioned above participate in synthesis of the core oligosaccharide that tends to be more conserved than the outer O-antigen. However
    "more conserved is relative" This book chapter says:

    All core region chemical structures identified so far are less varied than those of O-antigens. Still, only one structural element is present in all core regions, namely that Kdo residue which links the core to the lipid A.

    The LPS biosynthetic process and related terms probably need a major overhaul at some point. Perhaps this could be a good student project for one of us here to supervise. But for now I hope this answers the query.

     
  • Hi Mike,

    I think we have grounds to restrict GO:0001740 Barr body to mammals (only_in_taxon Mammalia).
    At first I was confused by this bit in wikipedia (the only reference provided for 'Barr body):

    "A Barr body ... is the inactive X chromosome in a female somatic cell, rendered inactive in a process called lyonization, in those species in which sex is determined by the presence of the Y (including humans) or W chromosome rather than the diploidy of the X or Z." (http://en.wikipedia.org/wiki/Barr_body)

    So I was looking for species "in which sex is determined by the presence of the Y (including humans) or W chromosome rather than the diploidy of the X or Z" (which include some insects and fish, see http://en.wikipedia.org/wiki/Sex-determination_system#Chromosomal_determination). However, the process of X-inactivation or lyonization is found in mammals only, as far as I can tell:

    "Species can have different mechanisms of dosage compensation. In human females (XX), one chromosome is inactivated (see X-inactivation), resulting in a heterochromatic and largely genetically inactive Barr body. Drosophila males (XY) double the expression of genes along the X chromosome. In C. elegans hermaphrodites (XX), both X chromosomes are partially repressed. Any of these mechanisms results in balancing the relative gene expression between males and females (or, in the case of C. elegans, hermaphrodites and males)." (http://en.wikipedia.org/wiki/Dosage_compensation)

    Also reported here:

    "X-inactivation (also called lyonization) is a process by which one of the two copies of the X chromosome present in female mammals is inactivated." (http://en.wikipedia.org/wiki/X-inactivation)

    Note that we also have this term:
    GO:0009048 dosage compensation by inactivation of X chromosome
    "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex."
    with exact synonym 'X chromosome inactivation'
    This term has no taxon rules applied.
    All manual annotations are to mammals, except for 1 to Drosophila, which looks incorrect based on the paper abstract, but I'll need to check with Flybase.

    Summing up, I think we should:
    1) Make GO:0001740 Barr body only_in_taxon Mammalia (then the chicken and turkey annotations will go away automatically within a year)
    2) Make GO:0009048 dosage compensation by inactivation of X chromosome only_in_taxon Mammalia (and notify FlyBase to move their annotation)
    I'll take care of this, but let me know if you have any comment.

    Thanks,
    Paola

     
    • Michael E Rice
      Michael E Rice
      2014-05-19

      Thanks Paola,

      That looks great. I am also looking at GO:0007565 female pregnancy; the constraint is only in Mammalia but I will try to investigate if the definition "The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth." could fit for species such as snakes and frogs that give birth to live young. I will request a ticket when I get it sorted out. Thanks again so much for all your help.

      Mike

      Michael E. Rice AgBase biocurator
      School of Animal and Comparative Biomedical Science
      Thomas W. Keating Bioresearch Building
      1657 E. Helen St.
      Tucson, AZ 85721
      The College of Agriculture and Life Sciences
      The University of Arizona
      520 955-2745
      mrice@email.arizona.eduhttp://mrice@email.arizona.edu


      From: Paola Roncaglia [paolaroncaglia@users.sf.net]
      Sent: Monday, May 19, 2014 5:25 AM
      To: [geneontology:ontology-requests]
      Subject: [geneontology:ontology-requests] #10840 Taxon rules for several terms

      Hi Mike,

      I think we have grounds to restrict GO:0001740 Barr body to mammals (only_in_taxon Mammalia).
      At first I was confused by this bit in wikipedia (the only reference provided for 'Barr body):

      "A Barr body ... is the inactive X chromosome in a female somatic cell, rendered inactive in a process called lyonization, in those species in which sex is determined by the presence of the Y (including humans) or W chromosome rather than the diploidy of the X or Z." (http://en.wikipedia.org/wiki/Barr_body)

      So I was looking for species "in which sex is determined by the presence of the Y (including humans) or W chromosome rather than the diploidy of the X or Z" (which include some insects and fish, see http://en.wikipedia.org/wiki/Sex-determination_system#Chromosomal_determination). However, the process of X-inactivation or lyonization is found in mammals only, as far as I can tell:

      "Species can have different mechanisms of dosage compensation. In human females (XX), one chromosome is inactivated (see X-inactivation), resulting in a heterochromatic and largely genetically inactive Barr body. Drosophila males (XY) double the expression of genes along the X chromosome. In C. elegans hermaphrodites (XX), both X chromosomes are partially repressed. Any of these mechanisms results in balancing the relative gene expression between males and females (or, in the case of C. elegans, hermaphrodites and males)." (http://en.wikipedia.org/wiki/Dosage_compensation)

      Also reported here:

      "X-inactivation (also called lyonization) is a process by which one of the two copies of the X chromosome present in female mammals is inactivated." (http://en.wikipedia.org/wiki/X-inactivation)

      Note that we also have this term:
      GO:0009048 dosage compensation by inactivation of X chromosome
      "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex."
      with exact synonym 'X chromosome inactivation'
      This term has no taxon rules applied.
      All manual annotations are to mammals, except for 1 to Drosophila, which looks incorrect based on the paper abstract, but I'll need to check with Flybase.

      Summing up, I think we should:
      1) Make GO:0001740 Barr body only_in_taxon Mammalia (then the chicken and turkey annotations will go away automatically within a year)
      2) Make GO:0009048 dosage compensation by inactivation of X chromosome only_in_taxon Mammalia (and notify FlyBase to move their annotation)
      I'll take care of this, but let me know if you have any comment.

      Thanks,
      Paola


      [ontology-requests:#10840]http://sourceforge.net/p/geneontology/ontology-requests/10840/ Taxon rules for several terms

      Status: open
      Group: None
      Labels: Taxon restriction enzymes metabolism
      Created: Fri May 09, 2014 11:24 PM UTC by Michael E Rice
      Last Updated: Wed May 14, 2014 09:19 PM UTC
      Owner: Paola Roncaglia

      Request taxon constraint for:
      GO:000865 lipopolysaccharide metabolic process
      GO:0008917 lipopolysaccharide N-acetylglucosaminyltransferase activity
      GO:0009103 lipopolysaccharide biosynthetic process
      GO:0008919 lipopolysaccharide glucosyltransferase I activity
      GO:0047270 lipopolysaccharide glucosyltransferase II activity
      only occurs in Gram negative bacteria; the terms have been assigned to non-bacterial species because of the similarity to the name of the enzyme e.g. it has been assigned to human UniProtKB:C9IYY0 which is Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase

      GO:0060157 urinary bladder development
      GO:0014832 urinary bladder smooth muscle contraction
      does not occur in birds excepting ostrich and rhea

      GO:0060067 cervix development
      does not occur in birds; this term refers to the cervix of the female reproductive system, not the cervical vertebrae. The term has been incorrectly assigned to proteins of birds.

      GO:0001740 Barr body
      definition states "A structure found in a female mammalian cell..." Barr body is also found in non-mammalian cells.


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      Related

      Ontology requests: #10840

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  • Hi Jim,

    Thanks. Based on your feedback, I think it's safe to add part_of links for the time being. If/when LPS terms are thoroughly revised, has_part links may be evaluated.

    Note for self: wrapping up, make the following terms part_of GO:0009103 lipopolysaccharide biosynthetic process:
    GO:0008918 lipopolysaccharide 3-alpha-galactosyltransferase activity [EC 2.4.1.44]
    GO:0008917 lipopolysaccharide N-acetylglucosaminyltransferase activity [EC 2.4.1.56]
    GO:0008919 lipopolysaccharide glucosyltransferase I activity [EC 2.4.1.58]
    (the first three with dbxref KEGG:00540)
    GO:0047270 lipopolysaccharide glucosyltransferase II activity [EC 2.4.1.73]

    Paola

     
  • Hi Mike,

    About this portion of your request:

    "GO:0060067 cervix development
    does not occur in birds; this term refers to the cervix of the female reproductive system, not the cervical vertebrae. The term has been incorrectly assigned to proteins of birds."

    'cervix' stands for UBERON:0000002 'uterine cervix' which is part_of 'uterus'.
    In UBERON, 'uterus' is restricted to Theria (placental mammals) (see http://purl.obolibrary.org/obo/UBERON_0000995).
    Uberon has lots of taxon constraints, often much bolder than those in GO.
    To make a long story short, we're going to include logical definitions in GO that point to UBERON soon-ish. When this is done, we'll run a pipeline to bring existing taxon rules from UBERON into GO (and possibly the other way round if necessary). (We may have to manually review the newly added taxon rules.) So, while we wait for this pipeline to be in place, if we see GO terms that should have a taxon rule, and reference UBERON (or will soon), such as GO:0060067 'cervix development', where the UBERON term has its own taxon rule, we may not worry about adding the same in GO as it will be added 'automatically' later on. There is already a 'ticket' in our Jira system to carry out this task, so it won't be forgotten.

    I hope this makes sense. Thanks,
    Paola

     
  • Note to self: FlyBase agreed to move or delete their annotation to 'dosage compensation by inactivation of X chromosome'.

     
  • Hi again Mike,

    For the 'urinary bladder' terms, please note that we're discussing with UBERON whether the taxon constraint should be to all Aves (i.e. both Paleognathae and Neognathae) or just to Neognathae.

    For my own reference, this is detailed here: https://github.com/obophenotype/uberon/issues/454

    Once this is resolved, I will add the taxon rule in GO, because there's no 'never in taxon' rule for 'urinary bladder' in UBERON right now. Unless this is updated.

    Thanks
    Paola

     
    Last edit: Paola Roncaglia 2014-05-20
  • Hi Mike,

    Feedback from a UBERON curator indicates that the terms 'urinary bladder development' and 'urinary bladder smooth muscle contraction' should be restricted by 'never_in_taxon Aves (taxon ID 8782)', so I did that. The full discussion is here, let me know if you can't access it:

    https://github.com/obophenotype/uberon/issues/454

    Thanks,
    Paola

     
  • All pending items - done. Closing now.
    Thanks,
    Paola

     
    • status: open --> closed-accepted