Displaying 'part of' subclasses

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Displaying 'part of' subclasses

John Williams
Hi all,

I am fairly new to using Protege. I would like to view some anatomical ontologies which use ‘part of’ relations. When I view the Brenda Tissue Ontology in EBI’s Ontology Lookup Service, I see the following structure:

tissues, cell types, and enzyme sources
animal
whole body
head
brain

nervous system
central nervous system
brain
etc

In Protege after reasoning with HermiT, while ‘brain’ is a subclass of:

‘part of’ some ‘central nervous system’
and ‘part of’ some ‘head’

which echoes the above.

When viewing the class hierarchy under “Entities” in Protege, brain appears to be a child of only ‘owl:Thing’.

Also, f I copy the sub-hierarcy of ‘brain’ in Protege via Edit -> ‘Copy sub-hierarchy as tab indented text' only ‘embryonic brain’ and ‘larval brain’ copy over. But in OLS, 18 children are seen in the tree, including cell lines and brain regions. The entry for ‘brain’ also has the same 18 named subclasses listed under “Class Usage” in Protege.

Is there something I’m missing, or is there a way to display and extract the hierarchy with these sub classes shown?

Thanks for your help,

John

John Williams
PhD Student, MRC Harwell Institute and University of Birmingham
[hidden email]


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Re: Displaying 'part of' subclasses

Michael DeBellis-2
John, I'm not sure about all your issues, it's hard to say without looking at the specific ontology. So, this will be fairly generic and you may know all of the following already but here are a few basic points that may help: 

1) Remember to distinguish between Part-of hierarchies and Subclass hierarchies. Part-of hierarchies are compositional. So a Brain is PartOf a CentralNervousSystem and a CentralNervousSystem and a CirculatorySystem are PartOf a Body.  I.e., bigger things that decompose into smaller things. Where as a subclass hierarchy is about sets, general things (starting with Thing the most general category of all) that get more specific, e.g., Human is a subclass of Mammal which is a subclass of Animal. It could be that the Bioportal browser is showing things via PartOf hierarchies and Protege is showing you subclass hierarchies. (FYI, there is a way in Protege to see PartOf hierarchies with one of the Plug Ins). 

2) Class usage and subclasses are not the same thing. Class usage shows you all the ways that class is used in the ontology. The subclasses will show up in class usage but other things will as well. E.g., if the class is the domain or range of a property. 

3) There is a distinction between the Asserted view and the Inferred view in Protege. On many Protege windows there is a little drop down menu that you can toggle between Asserted and Inferred. Asserted shows the definitions explicitly defined by the user. Inferred shows the revised definitions after the Reasoner has been run. For example, when you say that it looks as if Brain is just a subclass of Thing you may be looking at the Asserted view where as if you looked at the Inferred view it might look different. 

4) There may be more to class definitions than can be represented by indented text. The indented text just shows the subclass links but it's possible to have classes defined by more than just direct subclass relations. For example, the definition you gave above for brain: " ‘part of’ some ‘central nervous system’ and ‘part of’ some ‘head’ " is not something that could be represented that way. The simple example I used: Human is a subclass of Mammal is a subclass of Animal can be represented that way but things that use DL to define classes can't be.

I hope that was helpful. Feel free to follow up if you have more questions. 

Michael

On Wed, Nov 8, 2017 at 2:43 AM, John Williams <[hidden email]> wrote:
Hi all,

I am fairly new to using Protege. I would like to view some anatomical ontologies which use ‘part of’ relations. When I view the Brenda Tissue Ontology in EBI’s Ontology Lookup Service, I see the following structure:

tissues, cell types, and enzyme sources
animal
whole body
head
brain

nervous system
central nervous system
brain
etc

In Protege after reasoning with HermiT, while ‘brain’ is a subclass of:

‘part of’ some ‘central nervous system’
and ‘part of’ some ‘head’

which echoes the above.

When viewing the class hierarchy under “Entities” in Protege, brain appears to be a child of only ‘owl:Thing’.

Also, f I copy the sub-hierarcy of ‘brain’ in Protege via Edit -> ‘Copy sub-hierarchy as tab indented text' only ‘embryonic brain’ and ‘larval brain’ copy over. But in OLS, 18 children are seen in the tree, including cell lines and brain regions. The entry for ‘brain’ also has the same 18 named subclasses listed under “Class Usage” in Protege.

Is there something I’m missing, or is there a way to display and extract the hierarchy with these sub classes shown?

Thanks for your help,

John

John Williams
PhD Student, MRC Harwell Institute and University of Birmingham
[hidden email]


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Re: Displaying 'part of' subclasses

Matthew Horridge-2
Administrator
In reply to this post by John Williams
Hi John,

OLS displays partOf relationships in the hierarchy.  The current version of Protege does not do this.  However, the next version of Protege will display other relationships in the hierarchy, like partOf.  

Cheers,

Matthew


> On 8 Nov 2017, at 02:43, John Williams <[hidden email]> wrote:
>
> Hi all,
>
> I am fairly new to using Protege. I would like to view some anatomical ontologies which use ‘part of’ relations. When I view the Brenda Tissue Ontology in EBI’s Ontology Lookup Service, I see the following structure:
>
> tissues, cell types, and enzyme sources
> animal
> whole body
> head
> brain
>
> nervous system
> central nervous system
> brain
> etc
>
> In Protege after reasoning with HermiT, while ‘brain’ is a subclass of:
>
> ‘part of’ some ‘central nervous system’
> and ‘part of’ some ‘head’
>
> which echoes the above.
>
> When viewing the class hierarchy under “Entities” in Protege, brain appears to be a child of only ‘owl:Thing’.
>
> Also, f I copy the sub-hierarcy of ‘brain’ in Protege via Edit -> ‘Copy sub-hierarchy as tab indented text' only ‘embryonic brain’ and ‘larval brain’ copy over. But in OLS, 18 children are seen in the tree, including cell lines and brain regions. The entry for ‘brain’ also has the same 18 named subclasses listed under “Class Usage” in Protege.
>
> Is there something I’m missing, or is there a way to display and extract the hierarchy with these sub classes shown?
>
> Thanks for your help,
>
> John
>
> John Williams
> PhD Student, MRC Harwell Institute and University of Birmingham
> [hidden email]
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Displaying 'part of' subclasses

John Williams
Hi Matthew and Michael,

Great to know! I’ll look forward to the new version coming out.

Thanks to both for your help,

John


> On 13 Nov 2017, at 20:00, Matthew Horridge <[hidden email]> wrote:
>
> Hi John,
>
> OLS displays partOf relationships in the hierarchy.  The current version of Protege does not do this.  However, the next version of Protege will display other relationships in the hierarchy, like partOf.
>
> Cheers,
>
> Matthew
>
>
>> On 8 Nov 2017, at 02:43, John Williams <[hidden email]> wrote:
>>
>> Hi all,
>>
>> I am fairly new to using Protege. I would like to view some anatomical ontologies which use ‘part of’ relations. When I view the Brenda Tissue Ontology in EBI’s Ontology Lookup Service, I see the following structure:
>>
>> tissues, cell types, and enzyme sources
>> animal
>> whole body
>> head
>> brain
>>
>> nervous system
>> central nervous system
>> brain
>> etc
>>
>> In Protege after reasoning with HermiT, while ‘brain’ is a subclass of:
>>
>> ‘part of’ some ‘central nervous system’
>> and ‘part of’ some ‘head’
>>
>> which echoes the above.
>>
>> When viewing the class hierarchy under “Entities” in Protege, brain appears to be a child of only ‘owl:Thing’.
>>
>> Also, f I copy the sub-hierarcy of ‘brain’ in Protege via Edit -> ‘Copy sub-hierarchy as tab indented text' only ‘embryonic brain’ and ‘larval brain’ copy over. But in OLS, 18 children are seen in the tree, including cell lines and brain regions. The entry for ‘brain’ also has the same 18 named subclasses listed under “Class Usage” in Protege.
>>
>> Is there something I’m missing, or is there a way to display and extract the hierarchy with these sub classes shown?
>>
>> Thanks for your help,
>>
>> John
>>
>> John Williams
>> PhD Student, MRC Harwell Institute and University of Birmingham
>> [hidden email]
>>
>>
>> This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
>> _______________________________________________
>> protege-user mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Displaying 'part of' subclasses

Michael DeBellis-2
John, One more thing: there is a way to visualize part hierarchies in the current version of Protege. It's a plugin called the Individual Hierarchy plugin. You can follow the links of any property that has a compositional hierarchy. You get all the Object properties in a list on the left (this is the same as the Object Property tab) and then you select a property and you can see the tree formed by following the links. 

I recently created a small example car ontology and I used that to illustrate how it would look on a toy example following the hasPart property for a car to its component parts. 

Michael

On Tue, Nov 14, 2017 at 12:58 AM, John Williams <[hidden email]> wrote:
Hi Matthew and Michael,

Great to know! I’ll look forward to the new version coming out.

Thanks to both for your help,

John


> On 13 Nov 2017, at 20:00, Matthew Horridge <[hidden email]> wrote:
>
> Hi John,
>
> OLS displays partOf relationships in the hierarchy.  The current version of Protege does not do this.  However, the next version of Protege will display other relationships in the hierarchy, like partOf.
>
> Cheers,
>
> Matthew
>
>
>> On 8 Nov 2017, at 02:43, John Williams <[hidden email]> wrote:
>>
>> Hi all,
>>
>> I am fairly new to using Protege. I would like to view some anatomical ontologies which use ‘part of’ relations. When I view the Brenda Tissue Ontology in EBI’s Ontology Lookup Service, I see the following structure:
>>
>> tissues, cell types, and enzyme sources
>> animal
>> whole body
>> head
>> brain
>>
>> nervous system
>> central nervous system
>> brain
>> etc
>>
>> In Protege after reasoning with HermiT, while ‘brain’ is a subclass of:
>>
>> ‘part of’ some ‘central nervous system’
>> and ‘part of’ some ‘head’
>>
>> which echoes the above.
>>
>> When viewing the class hierarchy under “Entities” in Protege, brain appears to be a child of only ‘owl:Thing’.
>>
>> Also, f I copy the sub-hierarcy of ‘brain’ in Protege via Edit -> ‘Copy sub-hierarchy as tab indented text' only ‘embryonic brain’ and ‘larval brain’ copy over. But in OLS, 18 children are seen in the tree, including cell lines and brain regions. The entry for ‘brain’ also has the same 18 named subclasses listed under “Class Usage” in Protege.
>>
>> Is there something I’m missing, or is there a way to display and extract the hierarchy with these sub classes shown?
>>
>> Thanks for your help,
>>
>> John
>>
>> John Williams
>> PhD Student, MRC Harwell Institute and University of Birmingham
>> [hidden email]
>>
>>
>> This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
>> _______________________________________________
>> protege-user mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
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