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[go-friends] [go-discuss] Announcement: three new relationship types to be added to core GO file

Erick Antezana erick.antezana at gmail.com
Tue May 14 23:46:32 PDT 2013


Hi Jane,

thanks for the clarification.

cheers,
Erick


On 14 May 2013 23:13, Jane Lomax <jane at ebi.ac.uk> wrote:

>  Hi Erick - good news on the pipeline.
>
> I don't even think we'd need these new relations to model mitotic cell
> cycle variants - the variants would just be subclasses of mitotic cell
> cycle e.g.
>
> mitotic cell cycle
> ---[i] endocycle ---[has part]---> endoreduplication
>
> (or part_of - not sure of endoreduplication would occur outside of an
> endocycle)
>
> We concentrated on the canonical cell cycle when we worked on these terms,
> but I don't see why we couldn't also add these if they would be useful.
>
> cheers,
>
> Jane
>
>
> On 13/05/2013 14:36, Erick Antezana wrote:
>
> Hi  Jane,
>
>  thanks for the test file. I can confirm that syntactically there are no
> issues (it can be digested by my pipeline  ;-) )
>
>  however, I was wondering whether these set of new relationships would
> support the "modelling"  of variants of the mitotic cell cycle (e.g.
> endocycle -> endoreduplication)?
>
>  cheers,
> Erick
>
>
> On 10 May 2013 15:02, Robinson, Peter <peter.robinson at charite.de> wrote:
>
>>  What are, then, the parts of puberty?
>>
>>
>>
>> It would be nice to see a bunch of examples of the intended use cases of
>> the new relations. I would imagine that
>>
>>
>>
>> processA happensDuring process
>>
>> would be most common (e.g., anaphase happensDuring Mitosis)
>>
>>
>>
>> In this case it is not incorrect to have happensDuring be a SubPropertyOf
>> part_of
>>
>>
>>
>> Therefore, it would be important to know if there are range/domain
>> restrictions on happensDuring.
>>
>>
>>
>> -Peter
>>
>>
>>
>> Dr. med. Peter N. Robinson, MSc.
>>
>> Professor of Medical Genomics
>> Institut für Medizinische Genetik und Humangenetik
>> Charité - Universitätsmedizin Berlin
>> Augustenburger Platz 1
>> 13353 Berlin
>> Germany
>> +4930 450566006 <%2B4930%20450566006>
>> Mobile: 0160 93769872
>> peter.robinson at charite.de
>> http://compbio.charite.de
>> http://www.human-phenotype-ontology.org
>> Introduction to Bio-Ontologies:
>> http://www.crcpress.com/product/isbn/9781439836651
>>
>>
>>
>> *Von:* go-friends-bounces at lists.stanford.edu [mailto:
>> go-friends-bounces at lists.stanford.edu] *Im Auftrag von *David
>> Osumi-Sutherland
>> *Gesendet:* Freitag, 10. Mai 2013 13:30
>> *An:* Alan Ruttenberg
>> *Cc:* Jane Lomax; go-discuss at lists.stanford.edu; Phillip Lord; Chris
>> Mungall; go-friends at mailman.stanford.edu
>> *Betreff:* Re: [go-friends] [go-discuss] Announcement: three new
>> relationship types to be added to core GO file
>>
>>
>>
>>
>>
>> On 10 May 2013, at 10/May/2013 12:12:19, Alan Ruttenberg wrote:
>>
>>
>>
>>
>>
>> On Friday, May 10, 2013, Phillip Lord wrote:
>>
>>
>>
>> Like "Wearing long trousers" happens_during "puberty", but is not
>> part_of it.
>>
>> Phil
>>
>>
>>
>> Nice example...
>>
>>
>>  Not like. (Or bug)
>>
>>
>>
>> name: happens_during
>>
>> ...
>>
>> is_a: BFO:0000050 ! part of
>>
>>
>>
>> bug.  Should be fixed ASAP.  This probably comes from ro as I just
>> checked in ro-edit.owl and found it had accidentally gotten into there (in
>> OWLish: happens_during SubPropertyOf part_of). I have deleted this axiom.
>>
>>
>>
>> - David
>>
>>
>>
>>  -Alan
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Chris Mungall <cjmungall at lbl.gov> writes:
>> > We're currently separating out cell cycle phases from biological
>> processes
>> > proper. We don't consider the processes to be part of the stage. We
>> would use
>> > the happens_during relation to connect processes to stages.
>> >
>> > This is all consistent with release 2 of the Basic Formal Ontology
>> (BFO), the
>> > relation can be defined in terms of a chain of the ''occupies
>> spatiotemporal
>> > region' relation with part_of between occurrents.
>> >
>> > On May 7, 2013, at 9:14 AM, Alan Ruttenberg wrote:
>> >
>> >> How does happens_during differ from part_of?
>> >>
>> >> Thanks,
>> >> Alan
>> >>
>> >>
>> >> On Tue, May 7, 2013 at 8:50 AM, Jane Lomax <jane at ebi.ac.uk> wrote:
>> >> Dear GO friends - we will be adding three new relationships to this
>> core GO file:
>> >>
>> >> go.obo     http://purl.obolibrary.org/obo/go.obo
>> >> go.owl     http://purl.obolibrary.org/obo/go.owl
>> >>
>> >> For more information about the content of these and other files,
>> please see our beta ontology downloads page:
>> >>
>> >> http://beta.geneontology.org/page/download-ontology
>> >>
>> >> Note that this file is equivalent to these legacy files:
>> >>
>> >>
>> ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology.1_2.obo
>> >> ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo
>> >>
>> >> so these files will be affected too.
>> >>
>> >> The relationships are starts_with, ends_with and happens_during. Their
>> >> definitions from the OBO relations ontology are listed below.
>> >>
>> >> We'll start adding these to the file in 2 weeks, 21 May 2013. Let us
>> know if you have any questions.
>> >>
>> >> many thanks,
>> >>
>> >> GO ontology editors
>> >>
>> >>
>> >>
>> >> From: http://code.google.com/p/obo-relations/
>> >> [Typedef]
>> >> id: RO:0002224
>> >> name: starts with
>> >> def: "x starts with y if and only if x has part y and the time point at
>> >> which x starts is equivalent to the time point at which y starts.
>> Formally:
>> >> ?(y) = ?(x) ? ?(y) < ?(x), where ? is a function that maps a process
>> to a
>> >> start point, and ? is a function that maps a process to an end point."
>> []
>> >> property_value: IAO:0000112 "Every insulin receptor signaling pathway
>> starts
>> >> with the binding of a ligand to the insulin receptor" xsd:string
>> >> property_value: IAO:0000114 IAO:0000125
>> >> property_value: IAO:0000118 "started by" xsd:string
>> >> is_transitive: true
>> >> is_a: BFO:0000051 ! has part
>> >> is_a: RO:0002222 ! temporally related to
>> >> inverse_of: RO:0002223 ! starts
>> >>
>> >> [Typedef]
>> >> id: RO:0002230
>> >> name: ends with
>> >> def: "x ends with y if and only if x has part y and the time point at
>> which
>> >> x ends is equivalent to the time point at which y ends. Formally: ?(y)
>> >
>> >> ?(x) ? ?(y) = ?(x), where ? is a function that maps a process to a
>> start
>> >> point, and ? is a function that maps a process to an end point." []
>> >> property_value: IAO:0000114 IAO:0000125
>> >> property_value: IAO:0000118 "finished by" xsd:string
>> >> is_transitive: true
>> >> is_a: BFO:0000051 ! has part
>> >> is_a: RO:0002222 ! temporally related to
>> >>
>> >> [Typedef]
>> >> id: RO:0002092
>> >> name: happens_during
>> >> comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with
>> >> start(X)) AND (end(X) before_or_simultaneous_with end(Y))
>> >> property_value: IAO:0000118 "d" xsd:string
>> >> property_value: IAO:0000118 "during" xsd:string
>> >> is_transitive: true
>> >> is_a: BFO:0000050 ! part of
>> >> is_a: RO:0002093 ! ends_d>
>> _______________________________________________
>> > go-friends mailing list
>> > go-friends at lists.stanford.edu
>> > https://mailman.stanford.edu/mailman/listinfo/go-friends
>>
>> --
>> Phillip Lord,                           Phone: +44 (0) 191 222 7827<%2B44%20%280%29%20191%20222%207827>
>> Lecturer in Bioinformatics,             Email:
>> phillip.lord at newcastle.ac.uk
>> School of Computing Science,
>> http://homepages.cs.ncl.ac.uk/phillip.lord
>> Room 914 Claremont Tower,               skype: russet_apples
>> Newcastle University,                   twitter: phillord
>> NE1 7RU
>>
>> _______________________________________________
>> go-friends mailing list
>> go-friends at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/go-friends
>>
>>
>>
>> David Osumi-Sutherland, PhD
>>
>> Ontologist at FlyBase & Virtual Fly Brain
>>
>> Department of Genetics, University of Cambridge,
>>
>> Downing Street, Cambridge, CB2 3EH, UK
>>
>> Tel: +44 (0)1223 333 963 <%2B44%20%280%291223%20333%20963>, Fax: +44
>> (0)1223 766 732 <%2B44%20%280%291223%20766%20732>
>>
>> http://www.virtualflybrain.org
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
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>> https://mailman.stanford.edu/mailman/listinfo/go-friends
>>
>>
>
>
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