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

David Osumi-Sutherland djs93 at gen.cam.ac.uk
Thu May 9 15:10:54 PDT 2013


On 9 May 2013, at 22:16, Alan Ruttenberg wrote:

> Hi,
> Thanks. 
> 
> There are three words you use here. Phases stages and processes. I can  look up biological process. Can you tell me where I can find the other two please?

From a paper I've been working on:

For any single species, many events during development occur in an invariant order.  Developmental biologists, particularly those working on model organisms, traditionally measure the progress of development in a single species relative to the occurrence of some standard series of easily and reliably score-able events whose order is invariant [1, 4, 5]. These events are commonly the beginning, end or some easily score-able key point during a major developmental process, but may also simply be an easily score-able conjunction of morphological features. These events define boundaries between developmental stages, relative to which the timing of gene expression, developmental processes and the birth, death or transformation of anatomical structures can be recorded.

Stage series are not limited to development of a whole animal.  They can be used for any developmental process with events that occur in an invariant order.  Drosophila oogenesis, for example, has a well defined stage series [6], and named, rather than numbered stages have been defined for wing development [7] and the development of ommatidia from clusters of precursors [8].

Here are some examples:

A standard stage series for Xenopus leavis development:
http://www.xenbase.org/anatomy/alldev.do

oogenesis stages
http://ars.els-cdn.com/content/image/1-s2.0-S1097276500800817-gr1.jpg

Cell cycle phases:
http://en.wikipedia.org/wiki/Cell_cycle#Phases

(I think it is reasonable to thing of cell cycle phases as stages.  The term phase is presumably preferred over stage for dividing a cycle.)

BTW - I think all of these are subclasses of BFO:process, as currently defined in BFO2.  But this may reflect a difference between the BFO2 conception of process and the usage of this term by biologists.

Cheers,
David



> 
> -Alan
> 
> On Thursday, May 9, 2013, Chris Mungall wrote:
> Hi Alan,
> 
> 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_during
>> 
>> 
>> 
>> 
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