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

Jane Lomax jane at ebi.ac.uk
Tue May 14 14:13:36 PDT 2013


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 
> <mailto: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 <tel:%2B4930%20450566006>
>     Mobile: 0160 93769872
>     peter.robinson at charite.de <mailto: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>
>     [mailto: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
>     <mailto:go-discuss at lists.stanford.edu>; Phillip Lord; Chris
>     Mungall; go-friends at mailman.stanford.edu
>     <mailto: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 <mailto: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
>         <mailto: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 <tel:%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
>
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>
>     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
>     <tel:%2B44%20%280%291223%20333%20963>, Fax: +44 (0)1223 766 732
>     <tel:%2B44%20%280%291223%20766%20732>
>
>     http://www.virtualflybrain.org
>
>
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