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#117 PR:Trembl records to allow in files

None
accepted
Cecilia Arighi
None
3
2019-03-25
2017-05-31
Harold J. Drabkin
No

This is mostly a list of ids that UniProt uses in their mouse. GAF for isoforms. The ids are in PRO but are "dynamic", and not in any of the files (working version or full).

I have attached the file along with a PMID to the reference that was used to make the annotation as proof of existence.
Adding them to the obo files will allow us to convert the ids to PRO ids as we load the annotations.

A few of the ids have been used by our curators (old), but the id is a UniProt ID; once the PRO equivalent is released to the obo files we can have these in our GPI files, and then convert them to PRO ids in our interfaces

1 Attachments
DynamicPRO.txt

Discussion

  • Darren Natale

    Darren Natale - 2017-06-01
    • status: open --> accepted
    • assigned_to: Cecilia Arighi
    • Group: -->
     

    • Cecilia Arighi

      Cecilia Arighi - 2017-06-02

      The first example (PR:Q9ERP2) in the file need review by MGI.
      Q9ERP2 corresponds to the N terminus of the Short isoform, it has a distinct N terminal fragment, and could correspond to isoform 1 or 2 (see Figure 1 attached). Also the PMID:64996 provided is incorrect

      If the intent is to annotate the short isoform, a union term should be created. encompassing isoform 1 and 2

      For the other isoform the long, this is the term

      [Term]
      id: PR:M0QWP1
      name: agrin isoform m4 (mouse)
      def: "An agrin (mouse) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:M0QWP1." [PRO:CNA, PMID:11018052]
      comment: Category=organism-sequence.
      synonym: "mAGRN/iso:m4" EXACT PRO-short-label [PRO:DNx]
      synonym: "LN-agrin (mouse)" EXACT [PMID:11018052]
      synonym: "agrin long NH2 terminus isoform (mouse)" EXACT []
      xref: UniProtKB:M0QWP1
      is_a: PR:A2ASQ1 ! agrin (mouse)
      relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

      From: "Darren Natale" darren_natale@users.sf.net
      To: "[pro-obo:term-requests]" 117@term-requests.pro-obo.p.re.sf.net
      Sent: Thursday, June 1, 2017 11:51:10 AM
      Subject: [pro-obo:term-requests] #117 PR:Trembl records to allow in files 

      * status : open --> accepted 
* assigned_to : Cecilia Arighi 
* Group : -->

      [term-requests:#117] PR:Trembl records to allow in files

      Status: accepted
      Group:
      Created: Wed May 31, 2017 08:28 PM UTC by Harold J. Drabkin
      Last Updated: Wed May 31, 2017 08:28 PM UTC
      Owner: Cecilia Arighi
      Attachments: 

      * DynamicPRO.txt (2.2 kB; text/plain)

      This is mostly a list of ids that UniProt uses in their mouse. GAF for isoforms. The ids are in PRO but are "dynamic", and not in any of the files (working version or full).

      I have attached the file along with a PMID to the reference that was used to make the annotation as proof of existence.
      Adding them to the obo files will allow us to convert the ids to PRO ids as we load the annotations.

      A few of the ids have been used by our curators (old), but the id is a UniProt ID; once the PRO equivalent is released to the obo files we can have these in our GPI files, and then convert them to PRO ids in our interfaces

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/pro-obo/term-requests/117/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       
      alternate
      Thumbnail
      fig1splicing agrn.png

      • Cecilia Arighi

        Cecilia Arighi - 2017-06-02

        Here is a look at the first few
        data is as follows:
        MGI column data|name&PMID|PR assigned by PRO|PRO assessment|HIERARCHY term level
        The last three columns are my edits

        PR:Q9ERP2; Agrn; dynamic PMID:64996 incorrect PMID, should be union of isoform 1 and isoform 2
        PR:M0QWP1 Agrn dynamic PMID:11018052 PR:M0QWP1 done organism-sequence
        UniProtKB:A0A0R4J0I9 Lrp1 dynamic PR:Q91ZX7 PMID missing, sequence is identical to SP entry. organism-gene
        UniProtKB:A8R0T9 Esp6 PR version dynamic PMID:17935991 WRONG ACCESSION, ESP6 is A8R0U0 (see suppl material seq S.1)
        UniProtKB:A8R0U0 Esp6 PR version dynamic PMID:17935991 PR:A8R0U0 DONE organism-gene
        UniProtKB:B8QI33 Ppfia1 dynamic; PMID:19013515 PR:B8QI33 DONE, seq fig 2 organism-gene
        UniProtKB:B8QI36 Ppfia4 dynamic PMID:19013515 PR:B8QI36 DONE, seq fig 2 organism-gene
        UniProtKB:D3Z2B1 Lrp11 PMID:25262641 why this Accession over the SP Q8CB67?
        UniProtKB:D3Z3A7 Lrp11 PMID:25262641 why this Accession over the SP Q8CB67?

        From: "Cecilia Arighi" arighi@users.sf.net
        To: "[pro-obo:term-requests]" 117@term-requests.pro-obo.p.re.sf.net
        Sent: Friday, June 2, 2017 9:19:21 AM
        Subject: [pro-obo:term-requests] Re: #117 PR:Trembl records to allow in files

        The first example (PR:Q9ERP2) in the file need review by MGI.
        Q9ERP2 corresponds to the N terminus of the Short isoform, it has a distinct N terminal fragment, and could correspond to isoform 1 or 2 (see Figure 1 attached). Also the PMID:64996 provided is incorrect

        If the intent is to annotate the short isoform, a union term should be created. encompassing isoform 1 and 2

        For the other isoform the long, this is the term

        [Term]
        id: PR:M0QWP1
        name: agrin isoform m4 (mouse)
        def: "An agrin (mouse) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:M0QWP1." [PRO:CNA, PMID:11018052]
        comment: Category=organism-sequence.
        synonym: "mAGRN/iso:m4" EXACT PRO-short-label [PRO:DNx]
        synonym: "LN-agrin (mouse)" EXACT [PMID:11018052]
        synonym: "agrin long NH2 terminus isoform (mouse)" EXACT []
        xref: UniProtKB:M0QWP1
        is_a: PR:A2ASQ1 ! agrin (mouse)
        relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

        From: "Darren Natale" darren_natale@users.sf.net
        To: " [pro-obo:term-requests] " 117@term-requests.pro-obo.p.re.sf.net
        Sent: Thursday, June 1, 2017 11:51:10 AM
        Subject: [pro-obo:term-requests] #117 PR:Trembl records to allow in files
        status : open --> accepted
        assigned_to : Cecilia Arighi
        * Group : -->

        [term-requests:#117] PR:Trembl records to allow in files

        Status: accepted
        Group:
        Created: Wed May 31, 2017 08:28 PM UTC by Harold J. Drabkin
        Last Updated: Wed May 31, 2017 08:28 PM UTC
        Owner: Cecilia Arighi
        Attachments:
        * DynamicPRO.txt (2.2 kB; text/plain)

        This is mostly a list of ids that UniProt uses in their mouse. GAF for isoforms. The ids are in PRO but are "dynamic", and not in any of the files (working version or full).

        I have attached the file along with a PMID to the reference that was used to make the annotation as proof of existence.
        Adding them to the obo files will allow us to convert the ids to PRO ids as we load the annotations.

        A few of the ids have been used by our curators (old), but the id is a UniProt ID; once the PRO equivalent is released to the obo files we can have these in our GPI files, and then convert them to PRO ids in our interfaces

        Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/pro-obo/term-requests/117/

        To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

        [term-requests:#117] PR:Trembl records to allow in files

        Status: accepted
        Group:
        Created: Wed May 31, 2017 08:28 PM UTC by Harold J. Drabkin
        Last Updated: Thu Jun 01, 2017 09:48 PM UTC
        Owner: Cecilia Arighi
        Attachments: 

        * DynamicPRO.txt (2.2 kB; text/plain)

        This is mostly a list of ids that UniProt uses in their mouse. GAF for isoforms. The ids are in PRO but are "dynamic", and not in any of the files (working version or full).

        I have attached the file along with a PMID to the reference that was used to make the annotation as proof of existence.
        Adding them to the obo files will allow us to convert the ids to PRO ids as we load the annotations.

        A few of the ids have been used by our curators (old), but the id is a UniProt ID; once the PRO equivalent is released to the obo files we can have these in our GPI files, and then convert them to PRO ids in our interfaces

        Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/pro-obo/term-requests/117/

        To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

         
        alternate

  • Darren Natale

    Darren Natale - 2017-06-01

    Looking at a few of these, I note that they cannot be made automatically, and cannot be simply imported from the dynamic term maker.

     

    • Cecilia Arighi

      Cecilia Arighi - 2017-06-01

      Ok Will look at this tomorrow
      Ceci
      ----- Original Message -----
      From: Darren Natale darren_natale@users.sf.net
      To: [pro-obo:term-requests] 117@term-requests.pro-obo.p.re.sf.net
      Sent: Thu, 01 Jun 2017 17:48:20 -0400 (EDT)
      Subject: [pro-obo:term-requests] #117 PR:Trembl records to allow in files

      Looking at a few of these, I note that they cannot be made automatically, and cannot be simply imported from the dynamic term maker.

      [term-requests:#117] PR:Trembl records to allow in files

      Status: accepted
      Group:
      Created: Wed May 31, 2017 08:28 PM UTC by Harold J. Drabkin
      Last Updated: Thu Jun 01, 2017 03:51 PM UTC
      Owner: Cecilia Arighi
      Attachments:

      This is mostly a list of ids that UniProt uses in their mouse. GAF for isoforms. The ids are in PRO but are "dynamic", and not in any of the files (working version or full).

      I have attached the file along with a PMID to the reference that was used to make the annotation as proof of existence.
      Adding them to the obo files will allow us to convert the ids to PRO ids as we load the annotations.

      A few of the ids have been used by our curators (old), but the id is a UniProt ID; once the PRO equivalent is released to the obo files we can have these in our GPI files, and then convert them to PRO ids in our interfaces

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/pro-obo/term-requests/117/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

      Cecilia Arighi, PhDORCID:0000-0002-0803-4817Research Associate Professor
      Center of Bioinformatics and Computational Biology
      Department of Computer and Information Sciences
      University in Delaware

      UniProt: http://www.uniprot.orgBioCreative: http://www.biocreative.orgProtein Ontology: http://proconsortium.org/
      PIR: http://proteininformationresource.org/International Society for Biocuration: http://biocuration.org

       

  • Darren Natale

    Darren Natale - 2017-06-02

    I should probably add my notes to this thread. I formatted an Excel spreadsheet. I find that at least one gene is likely incorrect, and there are some surprises because of a bug in the dynamic generator that fails to report when the term already exists in PRO but under a different accession. I would check all these by hand, including alignments and checks of UniParc.

     
    Harolds trembl.xlsx

  • Harold J. Drabkin

    Harold J. Drabkin - 2019-03-22

    I still need an id for the SN form for PMID:11018052 of Agrn (SN form)

     

  • Darren Natale

    Darren Natale - 2019-03-25

    SN-agrin is just the canonical isoform. I added the reference and synonym.

    [Term]
    id: PR:A2ASQ1-1
    name: agrin isoform m1 (mouse)
    def: "An agrin (mouse) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:A2ASQ1-1." [PRO:DNx, UniProtKB:A2ASQ1, PMID:11018052]
    comment: Category=organism-sequence.
    synonym: "mAGRN/iso:m1" EXACT PRO-short-label [PRO:DNx]
    synonym: "agrin isoform TM-agrin (mouse)" EXACT [UniProtKB:A2ASQ1]
    synonym: "SN-agrin (mouse)" EXACT [PRO:DAN, PMID:11018052]
    synonym: "agrin isoform Transmembrane agrin (mouse)" EXACT [UniProtKB:A2ASQ1]
    xref: UniProtKB:A2ASQ1-1
    is_a: PR:A2ASQ1 ! agrin (mouse)
    relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

     

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