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[go-helpdesk] GO Help query (from website)

Rebecca Foulger rfoulger at ebi.ac.uk
Tue Jun 14 03:25:49 PDT 2011


For archiving.


-------- Original Message --------
Subject: 	Re: GO Help query (from website)
Date: 	Tue, 14 Jun 2011 10:26:21 +0100
From: 	Samuel Croset <croset at ebi.ac.uk>
To: 	Rebecca Foulger <rfoulger at ebi.ac.uk>



Dear Rebecca,

Thank you for this comprehensive reply. It makes now actually lots of 
sense to me :-)

I will come to see you if I have further questions.

Best regards,

Samuel

On Tue, Jun 14, 2011 at 9:44 AM, Rebecca Foulger <rfoulger at ebi.ac.uk 
<mailto:rfoulger at ebi.ac.uk>> wrote:


    Dear Samuel,

    Thank you for contacting GO help.

    The part_of relationship means necessarily part_of. If B is part of
    A, where B exists it is always as part of A (for example, not all
    cells have nuclei, but where a nucleus exists, it's always part of a
    cell). Therefore it doesn't make sense to say that nucleic acid
    binding is part_of 'nucleic acid binding transcription factor
    activity' (not all gene products that bind nucleic acids are
    transcription factors).

    HAS_PART relationships are the opposite way round and are only used
    in cases where A necessarily has part B. So where A exists, B will
    also exist. So a nucleic-acid binding transcription factor will
    always have nucleic acid binding activity. The HAS_PART relationship
    is much newer in GO, so there are far fewer of them in the ontology
    at present.

    We can not assert either relationship if it is not true all the time.

    There is a more extensive description of the relation types on the
    GO webpages:
    http://www.geneontology.org/GO.ontology-ext.relations.shtml

    Do pop round to the EBI GO office (A2-04) if you have any further
    questions or want to go through it in person.

    Best wishes,
    Rebecca (GO help desk)


>
>     Subject:
>     GO Help query (from website)
>     From:
>     croset at ebi.ac.uk <mailto:croset at ebi.ac.uk>
>     Date:
>     Mon, 13 Jun 2011 08:06:18 -0700
>
>     To:
>     go-helpdesk at mailman.stanford.edu
>     <mailto:go-helpdesk at mailman.stanford.edu>
>
>
>     Email:croset at ebi.ac.uk  <mailto:croset at ebi.ac.uk>
>     Name: Ontology (from Samuel Croset)
>     Text: Dear Support Team,
>
>     In the today (Monday the 13th of June) version of GO, both "part_of" and "has_part" relations are present, in the following quantities:
>     has_part = 183
>     part_of = 6618
>
>     I was wondering whether there is particular reason for asserting a "has_part" relation instead of a "part_of" relation (as it seems to me in discord with the relation ontology).
>
>     For example, we have the following assertion:
>     "nucleic acid binding transcription factor activity" has_part "nucleic acid binding".
>
>     Would it be correct to assert it the other way round:
>
>     "nucleic acid binding" part_of "nucleic acid binding transcription factor activity" .
>
>     And if yes, would it be true at all time?
>
>     Many thanks for your help,
>
>     Samuel Croset


    -- 
    Dr Rebecca Foulger
    GO Editorial Office
    EMBL-EBI
    Wellcome Trust Genome Campus
    Hinxton
    Cambridgeshire, UK
    CB10 1SD

    p: +44 1223 492523
    f: +44 1223 494468

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