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

Robinson, Peter peter.robinson at charite.de
Fri May 10 06:02:32 PDT 2013


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
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<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> _______________________________________________
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--
Phillip Lord,                           Phone: +44 (0) 191 222 7827
Lecturer in Bioinformatics,             Email: phillip.lord at newcastle.ac.uk<javascript:;>
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David Osumi-Sutherland, PhD
Ontologist at FlyBase & Virtual Fly Brain
Department of Genetics, University of Cambridge,
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