defining different life stages of a single speciaes of organism

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defining different life stages of a single speciaes of organism

Julian Vincent-4
I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?

Julian Vincent
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Re: defining different life stages of a single speciaes of organism

mhaendel
Hi Julian,
You will likely want to define a population that is a member of a taxon based on whatever your differentia are (here stage). 
See the following paper for relevant examples:

Organismal stage ontology repo has some doc:

And the Uberon anatomy repo on modeling stages:

As there are seemingly two different groups of organisms of the same taxon at different stages, that are the subject of the experiment, you would use two different URIs for these populations, where the taxon would be the same URI in the class definition.

Cheers,
Melissa



On Jan 21, 2017, at 2:01 PM, Julian Vincent <[hidden email]> wrote:

I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?

Julian Vincent
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Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology 
[hidden email]
503-407-5970

Appointments: Shanez De Silva 





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Re: defining different life stages of a single speciaes of organism

Julian Vincent-4
Yes - I’ve got that far (not difficult, really). I have separated out various stages of life cycles and separated out the various instars as subclasses.
But when I want to say that (as an example) Manduca adult is ecologically different from Manduca larva (referring to them in two different studies), but then come to do the ‘proper’ thing and give both of them the same NCBI Taxon reference, the problem occurs. What taxon label can I give the larva?

Julian

On 21 Jan 2017, at 22:39, Melissa Haendel <[hidden email]> wrote:

Hi Julian,
You will likely want to define a population that is a member of a taxon based on whatever your differentia are (here stage). 
See the following paper for relevant examples:

Organismal stage ontology repo has some doc:

And the Uberon anatomy repo on modeling stages:

As there are seemingly two different groups of organisms of the same taxon at different stages, that are the subject of the experiment, you would use two different URIs for these populations, where the taxon would be the same URI in the class definition.

Cheers,
Melissa



On Jan 21, 2017, at 2:01 PM, Julian Vincent <[hidden email]> wrote:

I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?

Julian Vincent
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Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology 
[hidden email]
503-407-5970

Appointments: Shanez De Silva 




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Re: defining different life stages of a single speciaes of organism

Chris Mungall-2

Hi Julian,

Are you making your statements in a database, or in OWL?

If the former, then it's fairly straightforward. You just have a column for the stage and a column for the species.

If the latter, it helps to be more specific about the semantics of your statement. Is this a statement about a particular specimen? About a population? A generalization that spans all instances of a species at a stage?

Either way it's likely your statement will involve either an anonymous individual or class, or minting an IRI.

For example

Individual: specimen1234
Types: NCBITaxon:nnn, existence-starts-and-ends-during some <StageClass>
Facts: ....

Note these questions don't really pertain to the Protege tool, you may want to ask these on an owl list, or for modeling using OBO ontologies on obo-discuss

On 22 Jan 2017, at 11:50, Julian Vincent wrote:

Yes - I’ve got that far (not difficult, really). I have separated out various stages of life cycles and separated out the various instars as subclasses.
But when I want to say that (as an example) Manduca adult is ecologically different from Manduca larva (referring to them in two different studies), but then come to do the ‘proper’ thing and give both of them the same NCBI Taxon reference, the problem occurs. What taxon label can I give the larva?

Julian

On 21 Jan 2017, at 22:39, Melissa Haendel <[hidden email]> wrote:

Hi Julian,
You will likely want to define a population that is a member of a taxon based on whatever your differentia are (here stage). 
See the following paper for relevant examples:

Organismal stage ontology repo has some doc:

And the Uberon anatomy repo on modeling stages:

As there are seemingly two different groups of organisms of the same taxon at different stages, that are the subject of the experiment, you would use two different URIs for these populations, where the taxon would be the same URI in the class definition.

Cheers,
Melissa



On Jan 21, 2017, at 2:01 PM, Julian Vincent <[hidden email]> wrote:

I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?

Julian Vincent
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Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology 
[hidden email]
503-407-5970

Appointments: Shanez De Silva 




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Re: defining different life stages of a single species of organism

Julian Vincent-4
Ah . . . I’d supposed that since I’m writing to a Protege group that it would be assumed I’m writing about Protege!  i.e. OWL.

So I have classes of insects, such as Manduca. But in the cases that I’m classifying (research papers) it’s sometimes the adult that’s used, sometimes the larva, sometimes the egg.
I have classes defined for all the instars, so as a subclass of Manduca I have Manduca caterpillar and Manduca egg. Thus I can query the ontology to see which papers are talking about Manduca as a species, but also which install they are using (adult is the default case). So I now have 3 Manduca classes, all the same species, but only one taxon identifier (IRI) (figs 1 and 2). What can I do? I might keep species and instar separate and have two entries (Species - Manduca - and instar - caterpillar) for the research paper, but that won’t work if I have two species of insect only one of which is present as a larva (Fig 3)

Any ideas?
Thanks
Julian






On 22 Jan 2017, at 21:18, Chris Mungall <[hidden email]> wrote:

Hi Julian,

Are you making your statements in a database, or in OWL?

If the former, then it's fairly straightforward. You just have a column for the stage and a column for the species.

If the latter, it helps to be more specific about the semantics of your statement. Is this a statement about a particular specimen? About a population? A generalization that spans all instances of a species at a stage?

Either way it's likely your statement will involve either an anonymous individual or class, or minting an IRI.

For example

Individual: specimen1234
Types: NCBITaxon:nnn, existence-starts-and-ends-during some <StageClass>
Facts: ....

Note these questions don't really pertain to the Protege tool, you may want to ask these on an owl list, or for modeling using OBO ontologies on obo-discuss

On 22 Jan 2017, at 11:50, Julian Vincent wrote:


Yes - I’ve got that far (not difficult, really). I have separated out various stages of life cycles and separated out the various instars as subclasses.
But when I want to say that (as an example) Manduca adult is ecologically different from Manduca larva (referring to them in two different studies), but then come to do the ‘proper’ thing and give both of them the same NCBI Taxon reference, the problem occurs. What taxon label can I give the larva?

Julian

On 21 Jan 2017, at 22:39, Melissa Haendel <[hidden email]> wrote:

Hi Julian,
You will likely want to define a population that is a member of a taxon based on whatever your differentia are (here stage). 
See the following paper for relevant examples:

Organismal stage ontology repo has some doc:

And the Uberon anatomy repo on modeling stages:

As there are seemingly two different groups of organisms of the same taxon at different stages, that are the subject of the experiment, you would use two different URIs for these populations, where the taxon would be the same URI in the class definition.

Cheers,
Melissa



On Jan 21, 2017, at 2:01 PM, Julian Vincent <[hidden email]> wrote:

I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?

Julian Vincent
_______________________________________________
protege-user mailing list
[hidden email]
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Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology 
[hidden email]
503-407-5970

Appointments: Shanez De Silva 




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Re: defining different life stages of a single species of organism

Chris Mungall-2

What you have now seems valid. You may want to add equivalence axioms for the two subclasses to make the model more complete and add inferential power. But what you have is valid.

Not sure what the problem is?

You may want to coordinate what URIs you use for stage-specific subclasses with others doing similar work. You're free to use whatever URIs you like here. But if you wanted to publish your ontology on the OBO library we'd want to make sure that we had a plan for this. But this isn't a modeling issue.

On 22 Jan 2017, at 13:47, Julian Vincent wrote:

Ah . . . I’d supposed that since I’m writing to a Protege group that it would be assumed I’m writing about Protege!  i.e. OWL.

So I have classes of insects, such as Manduca. But in the cases that I’m classifying (research papers) it’s sometimes the adult that’s used, sometimes the larva, sometimes the egg.
I have classes defined for all the instars, so as a subclass of Manduca I have Manduca caterpillar and Manduca egg. Thus I can query the ontology to see which papers are talking about Manduca as a species, but also which install they are using (adult is the default case). So I now have 3 Manduca classes, all the same species, but only one taxon identifier (IRI) (figs 1 and 2). What can I do? I might keep species and instar separate and have two entries (Species - Manduca - and instar - caterpillar) for the research paper, but that won’t work if I have two species of insect only one of which is present as a larva (Fig 3)

Any ideas?
Thanks
Julian






On 22 Jan 2017, at 21:18, Chris Mungall <[hidden email]> wrote:

Hi Julian,

Are you making your statements in a database, or in OWL?

If the former, then it's fairly straightforward. You just have a column for the stage and a column for the species.

If the latter, it helps to be more specific about the semantics of your statement. Is this a statement about a particular specimen? About a population? A generalization that spans all instances of a species at a stage?

Either way it's likely your statement will involve either an anonymous individual or class, or minting an IRI.

For example

Individual: specimen1234
Types: NCBITaxon:nnn, existence-starts-and-ends-during some <StageClass>
Facts: ....

Note these questions don't really pertain to the Protege tool, you may want to ask these on an owl list, or for modeling using OBO ontologies on obo-discuss

On 22 Jan 2017, at 11:50, Julian Vincent wrote:


Yes - I’ve got that far (not difficult, really). I have separated out various stages of life cycles and separated out the various instars as subclasses.
But when I want to say that (as an example) Manduca adult is ecologically different from Manduca larva (referring to them in two different studies), but then come to do the ‘proper’ thing and give both of them the same NCBI Taxon reference, the problem occurs. What taxon label can I give the larva?

Julian

On 21 Jan 2017, at 22:39, Melissa Haendel <[hidden email]> wrote:

Hi Julian,
You will likely want to define a population that is a member of a taxon based on whatever your differentia are (here stage). 
See the following paper for relevant examples:

Organismal stage ontology repo has some doc:

And the Uberon anatomy repo on modeling stages:

As there are seemingly two different groups of organisms of the same taxon at different stages, that are the subject of the experiment, you would use two different URIs for these populations, where the taxon would be the same URI in the class definition.

Cheers,
Melissa



On Jan 21, 2017, at 2:01 PM, Julian Vincent <[hidden email]> wrote:

I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?

Julian Vincent
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology 
[hidden email]
503-407-5970

Appointments: Shanez De Silva 




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Re: defining different life stages of a single species of organism

Julian Vincent-4
The problem is that I can’t give the Manduca larva and egg subclasses the same IRI as the Manduca adult, yet they are all the same species and so (presumably) have to have the same NCBI identifier. If this isn’t necessary, what should the identifier be? Or can I just make one up? What would the equivalence statement look like? I already have the caterpillar stage defined (Fig 4) 

Many thanks
Julian



On 22 Jan 2017, at 21:59, Chris Mungall <[hidden email]> wrote:


What you have now seems valid. You may want to add equivalence axioms for the two subclasses to make the model more complete and add inferential power. But what you have is valid.

Not sure what the problem is?

You may want to coordinate what URIs you use for stage-specific subclasses with others doing similar work. You're free to use whatever URIs you like here. But if you wanted to publish your ontology on the OBO library we'd want to make sure that we had a plan for this. But this isn't a modeling issue.

On 22 Jan 2017, at 13:47, Julian Vincent wrote:

Ah . . . I’d supposed that since I’m writing to a Protege group that it would be assumed I’m writing about Protege!  i.e. OWL.

So I have classes of insects, such as Manduca. But in the cases that I’m classifying (research papers) it’s sometimes the adult that’s used, sometimes the larva, sometimes the egg.
I have classes defined for all the instars, so as a subclass of Manduca I have Manduca caterpillar and Manduca egg. Thus I can query the ontology to see which papers are talking about Manduca as a species, but also which install they are using (adult is the default case). So I now have 3 Manduca classes, all the same species, but only one taxon identifier (IRI) (figs 1 and 2). What can I do? I might keep species and instar separate and have two entries (Species - Manduca - and instar - caterpillar) for the research paper, but that won’t work if I have two species of insect only one of which is present as a larva (Fig 3)

Any ideas?
Thanks
Julian



<Fig 2.tiff>
<Fig 1.tiff><Fig 3.tiff>



On 22 Jan 2017, at 21:18, Chris Mungall <[hidden email]> wrote:

Hi Julian,

Are you making your statements in a database, or in OWL?

If the former, then it's fairly straightforward. You just have a column for the stage and a column for the species.

If the latter, it helps to be more specific about the semantics of your statement. Is this a statement about a particular specimen? About a population? A generalization that spans all instances of a species at a stage?

Either way it's likely your statement will involve either an anonymous individual or class, or minting an IRI.

For example

Individual: specimen1234
Types: NCBITaxon:nnn, existence-starts-and-ends-during some <StageClass>
Facts: ....

Note these questions don't really pertain to the Protege tool, you may want to ask these on an owl list, or for modeling using OBO ontologies on obo-discuss

On 22 Jan 2017, at 11:50, Julian Vincent wrote:


Yes - I’ve got that far (not difficult, really). I have separated out various stages of life cycles and separated out the various instars as subclasses.
But when I want to say that (as an example) Manduca adult is ecologically different from Manduca larva (referring to them in two different studies), but then come to do the ‘proper’ thing and give both of them the same NCBI Taxon reference, the problem occurs. What taxon label can I give the larva?

Julian

On 21 Jan 2017, at 22:39, Melissa Haendel <[hidden email]> wrote:

Hi Julian,
You will likely want to define a population that is a member of a taxon based on whatever your differentia are (here stage). 
See the following paper for relevant examples:

Organismal stage ontology repo has some doc:

And the Uberon anatomy repo on modeling stages:

As there are seemingly two different groups of organisms of the same taxon at different stages, that are the subject of the experiment, you would use two different URIs for these populations, where the taxon would be the same URI in the class definition.

Cheers,
Melissa



On Jan 21, 2017, at 2:01 PM, Julian Vincent <[hidden email]> wrote:

I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?

Julian Vincent
_______________________________________________
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Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology 
[hidden email]
503-407-5970

Appointments: Shanez De Silva 




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Re: defining different life stages of a single species of organism

Chris Mungall-2
Some background for anyone else following. The NCBITaxon class URIs
referred to here come from:
http://obofoundry.org/ontology/ncbitaxon.html

Each class URI corresponds to an NCBI Taxonomy ID for a taxon, and the
class is interpreted as a class of organism instances belonging to a
taxon.

Comments below:

On 22 Jan 2017, at 14:08, Julian Vincent wrote:

> The problem is that I can’t give the Manduca larva and egg
> subclasses the same IRI as the Manduca adult, yet they are all the
> same species and so (presumably) have to have the same NCBI
> identifier.

I think this is where the confusion lies. These would necessarily have
different URIs from their superclass parent, so the presumption isn't
correct.

(we are talking about class URIs here. There is no first-class property
of 'identifier' in OWL. You're welcome to link your classes to NCBI
identifiers using your own annotation property in a many-to-one fashion
if you like, but this is separate from the issue of what the class URI
is. But IMO there is no need for this separate level of linkage here).

> If this isn’t necessary, what should the identifier be?

See my previous email. You're free to assign whatever URI you like.
However, with my OBO hat on I would say that you would want to
coordinate on a strategy such that there are not competing URIs for
stage-specific taxa. Thus far most ontologies have used anonymous
classes here.

> Or can I just make one up?

You're free to

> What would the equivalence statement look like? I already have the
> caterpillar stage defined (Fig 4)

In protege you can just select both superclasses and turn into an
equivalence axiom. MSC EquivalentTo MS and in-instar some CS.

Again, with my OBO hat on I would say to reuse an existing RO relation
(see my previous email) so that you get intended inferences with
ontologies such as uberon, but you're free to use whatever OPs you like
here for your own purposes.

>
> Many thanks
> Julian
>
>
>
>
>> On 22 Jan 2017, at 21:59, Chris Mungall <[hidden email]> wrote:
>>
>>
>> What you have now seems valid. You may want to add equivalence axioms
>> for the two subclasses to make the model more complete and add
>> inferential power. But what you have is valid.
>>
>> Not sure what the problem is?
>>
>> You may want to coordinate what URIs you use for stage-specific
>> subclasses with others doing similar work. You're free to use
>> whatever URIs you like here. But if you wanted to publish your
>> ontology on the OBO library we'd want to make sure that we had a plan
>> for this. But this isn't a modeling issue.
>>
>> On 22 Jan 2017, at 13:47, Julian Vincent wrote:
>>
>> Ah . . . I’d supposed that since I’m writing to a Protege group
>> that it would be assumed I’m writing about Protege!  i.e. OWL.
>>
>> So I have classes of insects, such as Manduca. But in the cases that
>> I’m classifying (research papers) it’s sometimes the adult
>> that’s used, sometimes the larva, sometimes the egg.
>> I have classes defined for all the instars, so as a subclass of
>> Manduca I have Manduca caterpillar and Manduca egg. Thus I can query
>> the ontology to see which papers are talking about Manduca as a
>> species, but also which install they are using (adult is the default
>> case). So I now have 3 Manduca classes, all the same species, but
>> only one taxon identifier (IRI) (figs 1 and 2). What can I do? I
>> might keep species and instar separate and have two entries (Species
>> - Manduca - and instar - caterpillar) for the research paper, but
>> that won’t work if I have two species of insect only one of which
>> is present as a larva (Fig 3)
>>
>> Any ideas?
>> Thanks
>> Julian
>>
>>
>>
>> <Fig 2.tiff>
>> <Fig 1.tiff><Fig 3.tiff>
>>
>>
>>
>>> On 22 Jan 2017, at 21:18, Chris Mungall <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>> Hi Julian,
>>>
>>> Are you making your statements in a database, or in OWL?
>>>
>>> If the former, then it's fairly straightforward. You just have a
>>> column for the stage and a column for the species.
>>>
>>> If the latter, it helps to be more specific about the semantics of
>>> your statement. Is this a statement about a particular specimen?
>>> About a population? A generalization that spans all instances of a
>>> species at a stage?
>>>
>>> Either way it's likely your statement will involve either an
>>> anonymous individual or class, or minting an IRI.
>>>
>>> For example
>>>
>>> Individual: specimen1234
>>> Types: NCBITaxon:nnn, existence-starts-and-ends-during some
>>> <StageClass>
>>> Facts: ....
>>> Note these questions don't really pertain to the Protege tool, you
>>> may want to ask these on an owl list, or for modeling using OBO
>>> ontologies on obo-discuss
>>>
>>> On 22 Jan 2017, at 11:50, Julian Vincent wrote:
>>>
>>>
>>> Yes - I’ve got that far (not difficult, really). I have separated
>>> out various stages of life cycles and separated out the various
>>> instars as subclasses.
>>> But when I want to say that (as an example) Manduca adult is
>>> ecologically different from Manduca larva (referring to them in two
>>> different studies), but then come to do the ‘proper’ thing and
>>> give both of them the same NCBI Taxon reference, the problem occurs.
>>> What taxon label can I give the larva?
>>>
>>> Julian
>>>
>>>> On 21 Jan 2017, at 22:39, Melissa Haendel <[hidden email]
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>> Hi Julian,
>>>> You will likely want to define a population that is a member of a
>>>> taxon based on whatever your differentia are (here stage).
>>>> See the following paper for relevant examples:
>>>> https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-30 
>>>> <https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-30>
>>>>
>>>> Organismal stage ontology repo has some doc:
>>>> https://github.com/obophenotype/developmental-stage-ontologies 
>>>> <https://github.com/obophenotype/developmental-stage-ontologies>
>>>>
>>>> And the Uberon anatomy repo on modeling stages:
>>>> https://github.com/obophenotype/uberon/wiki/Modeling-developmental-stages 
>>>> <https://github.com/obophenotype/uberon/wiki/Modeling-developmental-stages>
>>>>
>>>> As there are seemingly two different groups of organisms of the
>>>> same taxon at different stages, that are the subject of the
>>>> experiment, you would use two different URIs for these populations,
>>>> where the taxon would be the same URI in the class definition.
>>>>
>>>> Cheers,
>>>> Melissa
>>>>
>>>>
>>>>
>>>>> On Jan 21, 2017, at 2:01 PM, Julian Vincent
>>>>> <[hidden email] <mailto:[hidden email]>>
>>>>> wrote:
>>>>>
>>>>> I want to distiguish between adult and larval stages of a single
>>>>> species since sometimes experiments are performed on the adult (a
>>>>> moth, which feeds on nectar) and sometimes on a caterpillar (which
>>>>> feeds on leaves). Unfortunately the NCBI Taxon is the same for
>>>>> both stages, as is right and proper, since they are both the same
>>>>> species. But when I try to define the larval stage as a subclass
>>>>> of the imaginal stage, and give them the same NCBI Taxon ID, the
>>>>> two classes are fused into one. How can I keep them separate but
>>>>> with the same  ID?
>>>>>
>>>>> Julian Vincent
>>>>> _______________________________________________
>>>>> protege-user mailing list
>>>>> [hidden email]
>>>>> <mailto:[hidden email]>
>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-user 
>>>>> <https://mailman.stanford.edu/mailman/listinfo/protege-user>
>>>>
>>>> Melissa Haendel, PhD
>>>> Associate Professor
>>>> Library & Dept. of Medical Informatics and Clinical Epidemiology
>>>> [hidden email] <mailto:[hidden email]>
>>>> 503-407-5970
>>>> www.monarchinitiative.org <http://www.monarchinitiative.org/>
>>>>
>>>> Appointments: Shanez De Silva
>>>> [hidden email] <mailto:[hidden email]>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> protege-user mailing list
>>>> [hidden email]
>>>> <mailto:[hidden email]>
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>>>> <https://mailman.stanford.edu/mailman/listinfo/protege-user>
>>>
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>>
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Re: defining different life stages of a single species of organism

Julian Vincent-4
Obviously I have no idea how strict your rules are! Many thanks.
Julian



> On 23 Jan 2017, at 00:09, Chris Mungall <[hidden email]> wrote:
>
> Some background for anyone else following. The NCBITaxon class URIs referred to here come from: http://obofoundry.org/ontology/ncbitaxon.html
>
> Each class URI corresponds to an NCBI Taxonomy ID for a taxon, and the class is interpreted as a class of organism instances belonging to a taxon.
>
> Comments below:
>
> On 22 Jan 2017, at 14:08, Julian Vincent wrote:
>
>> The problem is that I can’t give the Manduca larva and egg subclasses the same IRI as the Manduca adult, yet they are all the same species and so (presumably) have to have the same NCBI identifier.
>
> I think this is where the confusion lies. These would necessarily have different URIs from their superclass parent, so the presumption isn't correct.
>
> (we are talking about class URIs here. There is no first-class property of 'identifier' in OWL. You're welcome to link your classes to NCBI identifiers using your own annotation property in a many-to-one fashion if you like, but this is separate from the issue of what the class URI is. But IMO there is no need for this separate level of linkage here).
>
>> If this isn’t necessary, what should the identifier be?
>
> See my previous email. You're free to assign whatever URI you like. However, with my OBO hat on I would say that you would want to coordinate on a strategy such that there are not competing URIs for stage-specific taxa. Thus far most ontologies have used anonymous classes here.
>
>> Or can I just make one up?
>
> You're free to
>
>> What would the equivalence statement look like? I already have the caterpillar stage defined (Fig 4)
>
> In protege you can just select both superclasses and turn into an equivalence axiom. MSC EquivalentTo MS and in-instar some CS.
>
> Again, with my OBO hat on I would say to reuse an existing RO relation (see my previous email) so that you get intended inferences with ontologies such as uberon, but you're free to use whatever OPs you like here for your own purposes.
>
>>
>> Many thanks
>> Julian
>>
>>
>>
>>
>>> On 22 Jan 2017, at 21:59, Chris Mungall <[hidden email]> wrote:
>>>
>>>
>>> What you have now seems valid. You may want to add equivalence axioms for the two subclasses to make the model more complete and add inferential power. But what you have is valid.
>>>
>>> Not sure what the problem is?
>>>
>>> You may want to coordinate what URIs you use for stage-specific subclasses with others doing similar work. You're free to use whatever URIs you like here. But if you wanted to publish your ontology on the OBO library we'd want to make sure that we had a plan for this. But this isn't a modeling issue.
>>>
>>> On 22 Jan 2017, at 13:47, Julian Vincent wrote:
>>>
>>> Ah . . . I’d supposed that since I’m writing to a Protege group that it would be assumed I’m writing about Protege!  i.e. OWL.
>>>
>>> So I have classes of insects, such as Manduca. But in the cases that I’m classifying (research papers) it’s sometimes the adult that’s used, sometimes the larva, sometimes the egg.
>>> I have classes defined for all the instars, so as a subclass of Manduca I have Manduca caterpillar and Manduca egg. Thus I can query the ontology to see which papers are talking about Manduca as a species, but also which install they are using (adult is the default case). So I now have 3 Manduca classes, all the same species, but only one taxon identifier (IRI) (figs 1 and 2). What can I do? I might keep species and instar separate and have two entries (Species - Manduca - and instar - caterpillar) for the research paper, but that won’t work if I have two species of insect only one of which is present as a larva (Fig 3)
>>>
>>> Any ideas?
>>> Thanks
>>> Julian
>>>
>>>
>>>
>>> <Fig 2.tiff>
>>> <Fig 1.tiff><Fig 3.tiff>
>>>
>>>
>>>
>>>> On 22 Jan 2017, at 21:18, Chris Mungall <[hidden email] <mailto:[hidden email]>> wrote:
>>>>
>>>> Hi Julian,
>>>>
>>>> Are you making your statements in a database, or in OWL?
>>>>
>>>> If the former, then it's fairly straightforward. You just have a column for the stage and a column for the species.
>>>>
>>>> If the latter, it helps to be more specific about the semantics of your statement. Is this a statement about a particular specimen? About a population? A generalization that spans all instances of a species at a stage?
>>>>
>>>> Either way it's likely your statement will involve either an anonymous individual or class, or minting an IRI.
>>>>
>>>> For example
>>>>
>>>> Individual: specimen1234
>>>> Types: NCBITaxon:nnn, existence-starts-and-ends-during some <StageClass>
>>>> Facts: ....
>>>> Note these questions don't really pertain to the Protege tool, you may want to ask these on an owl list, or for modeling using OBO ontologies on obo-discuss
>>>>
>>>> On 22 Jan 2017, at 11:50, Julian Vincent wrote:
>>>>
>>>>
>>>> Yes - I’ve got that far (not difficult, really). I have separated out various stages of life cycles and separated out the various instars as subclasses.
>>>> But when I want to say that (as an example) Manduca adult is ecologically different from Manduca larva (referring to them in two different studies), but then come to do the ‘proper’ thing and give both of them the same NCBI Taxon reference, the problem occurs. What taxon label can I give the larva?
>>>>
>>>> Julian
>>>>
>>>>> On 21 Jan 2017, at 22:39, Melissa Haendel <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>
>>>>> Hi Julian,
>>>>> You will likely want to define a population that is a member of a taxon based on whatever your differentia are (here stage).
>>>>> See the following paper for relevant examples:
>>>>> https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-30 <https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-30>
>>>>>
>>>>> Organismal stage ontology repo has some doc:
>>>>> https://github.com/obophenotype/developmental-stage-ontologies <https://github.com/obophenotype/developmental-stage-ontologies>
>>>>>
>>>>> And the Uberon anatomy repo on modeling stages:
>>>>> https://github.com/obophenotype/uberon/wiki/Modeling-developmental-stages <https://github.com/obophenotype/uberon/wiki/Modeling-developmental-stages>
>>>>>
>>>>> As there are seemingly two different groups of organisms of the same taxon at different stages, that are the subject of the experiment, you would use two different URIs for these populations, where the taxon would be the same URI in the class definition.
>>>>>
>>>>> Cheers,
>>>>> Melissa
>>>>>
>>>>>
>>>>>
>>>>>> On Jan 21, 2017, at 2:01 PM, Julian Vincent <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>>
>>>>>> I want to distiguish between adult and larval stages of a single species since sometimes experiments are performed on the adult (a moth, which feeds on nectar) and sometimes on a caterpillar (which feeds on leaves). Unfortunately the NCBI Taxon is the same for both stages, as is right and proper, since they are both the same species. But when I try to define the larval stage as a subclass of the imaginal stage, and give them the same NCBI Taxon ID, the two classes are fused into one. How can I keep them separate but with the same  ID?
>>>>>>
>>>>>> Julian Vincent
>>>>>> _______________________________________________
>>>>>> protege-user mailing list
>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-user <https://mailman.stanford.edu/mailman/listinfo/protege-user>
>>>>>
>>>>> Melissa Haendel, PhD
>>>>> Associate Professor
>>>>> Library & Dept. of Medical Informatics and Clinical Epidemiology
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> 503-407-5970
>>>>> www.monarchinitiative.org <http://www.monarchinitiative.org/>
>>>>>
>>>>> Appointments: Shanez De Silva
>>>>> [hidden email] <mailto:[hidden email]>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> protege-user mailing list
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-user <https://mailman.stanford.edu/mailman/listinfo/protege-user>
>>>>
>>>> _______________________________________________
>>>> protege-user mailing list
>>>> [hidden email] <mailto:[hidden email]>
>>>> https://mailman.stanford.edu/mailman/listinfo/protege-user <https://mailman.stanford.edu/mailman/listinfo/protege-user>
>>>> _______________________________________________
>>>> protege-user mailing list
>>>> [hidden email] <mailto:[hidden email]>
>>>> https://mailman.stanford.edu/mailman/listinfo/protege-user
>>>
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