in vitro model and in vivo model

masciam commented 4 years ago

I need a 'in vitro and in vivo model role'. I searched and I could not find any term in any of the ontologies except that in the NCIT but it is no listed as role and does not have a definition. I thought this should belong to OBI since it is refer to experiment. Let me know if you agree

bpeters42 commented 4 years ago

Hi Anna Maria,

We have done some (minimal) work on 'animal models of disease', which is highly related to your 'in vivo model role' I guess. It will be important to what you 'model', for example there are plenty of in vivo and in vitro toxicology models, which would not be considered 'diseases'.

Also, what is bearing the role? In some cases you have an inbred mouse strain, or a cell line, created specifically to serve as a model. But I think more often you have a whole protocol (e.g. injection of mice with OVA peptides to simulate allergy sensitization). So it is more that the data generated is considered a proxy for what happens in a disease?

Can you give a list of specific examples for things that should have the in vivo and in vitro model roles in your experience, so that we can coordinate?

On Wed, Sep 30, 2020 at 1:33 PM Anna Maria Masci notifications@github.com wrote:

I need a 'in vitro and in vivo model role'. I searched and I could not find any term in any of the ontologies except that in the NCIT but it is no listed as role and does not have a definition. I thought this should belong to OBI since it is refer to experiment. Let me know if you agree

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masciam commented 4 years ago

Bjoern I am working on toxic compound and cardiovascular failure modes. This involves many diverse mechanisms that are studied in different models: in animals (in vivo) on cell lines and on chips ( in vitro). The main goal is to be able to compare the mechanisms from different models for the same failure mode.

If you have worked on the animal model I think that will solve the in vivo issue. For the in vitro I know you have all the in vitro assay but I do not think this is what I really need. The effect of toxic compounds in different models ( in vivo and in vitro) for the same failure mode is what I would like to be able to capture.

I hope this clarifies more.

All the best AM

On Wed, Sep 30, 2020 at 6:32 PM bpeters42 notifications@github.com wrote:

Hi Anna Maria,

We have done some (minimal) work on 'animal models of disease', which is highly related to your 'in vivo model role' I guess. It will be important to what you 'model', for example there are plenty of in vivo and in vitro toxicology models, which would not be considered 'diseases'.

Also, what is bearing the role? In some cases you have an inbred mouse strain, or a cell line, created specifically to serve as a model. But I think more often you have a whole protocol (e.g. injection of mice with OVA peptides to simulate allergy sensitization). So it is more that the data generated is considered a proxy for what happens in a disease?

Can you give a list of specific examples for things that should have the in vivo and in vitro model roles in your experience, so that we can coordinate?

On Wed, Sep 30, 2020 at 1:33 PM Anna Maria Masci <notifications@github.com

wrote:

I need a 'in vitro and in vivo model role'. I searched and I could not find any term in any of the ontologies except that in the NCIT but it is no listed as role and does not have a definition. I thought this should belong to OBI since it is refer to experiment. Let me know if you agree

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bpeters42 commented 4 years ago

That is what I assumed Anna Maria, and it makes perfect sense. I meant that we should have some kind of relation ship between the model, and the thing that is being modeled. So for example, RIP-GP transgenic mice are used as a model for diabetes. Balb/c mice injected with OVA are used as models of allergy and many other things, dependent on the timing and route of administration and readouts.

So I am wondering if what we are really saying by 'model' is that the data generated in an in vivo or in vitro system is expected to inform us about something else (e.g. diabetes, cardiovascular failure, or drug toxicity typically in humans). In OBI we have the relationship: "is_proxy_for" which is similar but meant to be tighter. I think there is an implicit 'we know this is data from a model, so take it with a grain of salt'. While the 'is proxy for' is meant to connect e.g. the position of a band on a gel with the molecular weight of the substance being run, which everyone would expect to be truthful.

So I would suggest adding a relationship 'is model output for' between a data item (domain) and an entity (range). And then we can classify in vivo model vs. in vitro model based on the data item being generated using in vivo assays / manipulations or in vitro assays. Does that make sense?

On Fri, Oct 2, 2020 at 7:40 AM Anna Maria Masci notifications@github.com wrote:

Bjoern I am working on toxic compound and cardiovascular failure modes. This involves many diverse mechanisms that are studied in different models: in animals (in vivo) on cell lines and on chips ( in vitro). The main goal is to be able to compare the mechanisms from different models for the same failure mode.

If you have worked on the animal model I think that will solve the in vivo issue. For the in vitro I know you have all the in vitro assay but I do not think this is what I really need. The effect of toxic compounds in different models ( in vivo and in vitro) for the same failure mode is what I would like to be able to capture.

I hope this clarifies more.

All the best AM

On Wed, Sep 30, 2020 at 6:32 PM bpeters42 notifications@github.com wrote:

Hi Anna Maria,

We have done some (minimal) work on 'animal models of disease', which is highly related to your 'in vivo model role' I guess. It will be important to what you 'model', for example there are plenty of in vivo and in vitro toxicology models, which would not be considered 'diseases'.

Also, what is bearing the role? In some cases you have an inbred mouse strain, or a cell line, created specifically to serve as a model. But I think more often you have a whole protocol (e.g. injection of mice with OVA peptides to simulate allergy sensitization). So it is more that the data generated is considered a proxy for what happens in a disease?

Can you give a list of specific examples for things that should have the in vivo and in vitro model roles in your experience, so that we can coordinate?

On Wed, Sep 30, 2020 at 1:33 PM Anna Maria Masci < notifications@github.com

wrote:

I need a 'in vitro and in vivo model role'. I searched and I could not find any term in any of the ontologies except that in the NCIT but it is no listed as role and does not have a definition. I thought this should belong to OBI since it is refer to experiment. Let me know if you agree

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masciam commented 4 years ago

That is what I assumed Anna Maria, and it makes perfect sense. I meant that we should have some kind of relation ship between the model, and the thing that is being modeled. So for example, RIP-GP transgenic mice are used as a model for diabetes. Balb/c mice injected with OVA are used as models of allergy and many other things, dependent on the timing and route of administration and readouts. YES

So I am wondering if what we are really saying by 'model' is that the data generated in an in vivo or in vitro system is expected to inform us about something else (e.g. diabetes, cardiovascular failure, or drug toxicity typically in humans). In OBI we have the relationship: "is_proxy_for" which is similar but meant to be tighter. I think there is an implicit 'we know this is data from a model, so take it with a grain of salt'. While the 'is proxy for' is meant to connect e.g. the position of a band on a gel with the molecular weight of the substance being run, which everyone would expect to be truthful.

YES YOUR ARGUMENT IS CORRECT and is proxy for is to tight

So I would suggest adding a relationship 'is model output for' between a data item (domain) and an entity (range). And then we can classify in vivo model vs. in vitro model based on the data item being generated using in vivo assays / manipulations or in vitro assays. Does that make sense? I AGREE

On Fri, Oct 2, 2020 at 12:25 PM bpeters42 notifications@github.com wrote:

That is what I assumed Anna Maria, and it makes perfect sense. I meant that we should have some kind of relation ship between the model, and the thing that is being modeled. So for example, RIP-GP transgenic mice are used as a model for diabetes. Balb/c mice injected with OVA are used as models of allergy and many other things, dependent on the timing and route of administration and readouts.

So I am wondering if what we are really saying by 'model' is that the data generated in an in vivo or in vitro system is expected to inform us about something else (e.g. diabetes, cardiovascular failure, or drug toxicity typically in humans). In OBI we have the relationship: "is_proxy_for" which is similar but meant to be tighter. I think there is an implicit 'we know this is data from a model, so take it with a grain of salt'. While the 'is proxy for' is meant to connect e.g. the position of a band on a gel with the molecular weight of the substance being run, which everyone would expect to be truthful.

So I would suggest adding a relationship 'is model output for' between a data item (domain) and an entity (range). And then we can classify in vivo model vs. in vitro model based on the data item being generated using in vivo assays / manipulations or in vitro assays. Does that make sense?

On Fri, Oct 2, 2020 at 7:40 AM Anna Maria Masci notifications@github.com wrote:

Bjoern I am working on toxic compound and cardiovascular failure modes. This involves many diverse mechanisms that are studied in different models: in animals (in vivo) on cell lines and on chips ( in vitro). The main goal is to be able to compare the mechanisms from different models for the same failure mode.

If you have worked on the animal model I think that will solve the in vivo issue. For the in vitro I know you have all the in vitro assay but I do not think this is what I really need. The effect of toxic compounds in different models ( in vivo and in vitro) for the same failure mode is what I would like to be able to capture.

I hope this clarifies more.

All the best AM

On Wed, Sep 30, 2020 at 6:32 PM bpeters42 notifications@github.com wrote:

Hi Anna Maria,

We have done some (minimal) work on 'animal models of disease', which is highly related to your 'in vivo model role' I guess. It will be important to what you 'model', for example there are plenty of in vivo and in vitro toxicology models, which would not be considered 'diseases'.

Also, what is bearing the role? In some cases you have an inbred mouse strain, or a cell line, created specifically to serve as a model. But I think more often you have a whole protocol (e.g. injection of mice with OVA peptides to simulate allergy sensitization). So it is more that the data generated is considered a proxy for what happens in a disease?

Can you give a list of specific examples for things that should have the in vivo and in vitro model roles in your experience, so that we can coordinate?

On Wed, Sep 30, 2020 at 1:33 PM Anna Maria Masci < notifications@github.com

wrote:

I need a 'in vitro and in vivo model role'. I searched and I could not find any term in any of the ontologies except that in the NCIT but it is no listed as role and does not have a definition. I thought this should belong to OBI since it is refer to experiment. Let me know if you agree

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handemcginty commented 4 years ago

for @apmody to finalize and process.

apmody commented 4 years ago

There is very similar term https://www.ebi.ac.uk/ols/ontologies/stato/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fstato.owl%23is_model_for

How does this fit in with everything?

bpeters42 commented 4 years ago

Discussed on the call 10/19: To clearly differentiate from STATO term and make OBI specific, the relationship label should be tightened to be 'is experimental model output for', and the domain being 'measurement datum'

jamesaoverton commented 4 years ago

@bpeters42 Do we have a definition for this?

bpeters42 commented 4 years ago

Here is an attempt at a definition. I forgot if/how we were trying to have 'aristotelian' style definitions for relationships, but I tried:

Definition: a relationship between a data item (domain) and an entity (range), where the data item 'is about' the entity in the sense that the data item is the output of an experimental assay that has been designed to enable studying the entity without directly involving it.

Examples of usage: The breakpoint data from a 1:1000 model of a bridge is a model for the maximum load the actual bridge can carry. IC50 data from a compound screening assay of ACE2 receptor inhibition to SARS-2 spike protein is an experimental model for inhibition of infectivity by the compound in human infection.

linikujp commented 4 years ago

What I read is that Anna Maria wants a mouse to bear the role of animal model. Besides the model output that is data, what about connecting the model organism to the animal itself? ( Anna, please let me know if this is what you are looking for.)

This is similar with cell line story The cell line is a disease model. There is a connection from cell line to disease.

RIKEN Dr. Masuya(cced) may have explored, as he maintains database for those models.

Thanks, Asiyah

On Fri, Oct 23, 2020, 23:10 bpeters42 notifications@github.com wrote:

Here is an attempt at a definition. I forgot if/how we were trying to have 'aristotelian' style definitions for relationships, but I tried:

Definition: a relationship between a data item (domain) and an entity (range), where the data item 'is about' the entity in the sense that the data item is the output of an experimental assay that has been designed to enable studying the entity without directly involving it.

Examples of usage: The breakpoint data from a 1:1000 model of a bridge is a model for the maximum load the actual bridge can carry. IC50 data from a compound screening assay of ACE2 receptor inhibition to SARS-2 spike protein is an experimental model for inhibition of infectivity by the compound in human infection.

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hiroshi-masuya commented 4 years ago

Hi all,

I'm not familiar with BFO’s role, but I've been working on a database of model animals for a long time.

My understanding is that what you are discussing is the definition of "model organism" that is an organism plays “model role" of disease or something.

“Model” may be an entity that show a similar attribute to the target as an "imitation". Therefore, I think that a model organism is "a biological entity that has attribute/characteristeic and/or participate in the phenomena similar to the target attribute/phenomena/entity".

I think that the model role needs to link between 1) the target attribute/phenomena and the model organism, and 2) the target attribute/phenomena and attribute/phenomena which the model organism has.

Hiroshi,

===== Hiroshi Masuya Ph.D Integrated Bioresource Information Division RIKEN BioResource Research Center hiroshi.masuya@riken.jp http://info.brc.riken.jp/en/

masciam commented 4 years ago

This is what I am thinking In the study I am working on I have : study to address the effect of compounds on the human health The study could be measure the same type of evaluant but using different "experimental models" in vivo using different organisms, different cell types in vitro using specific devices such as microchip or assays

The definition that Bjoern has given for the relation "is experimental model output for" is general to link to the data. Bjoern example below: IC50 data from a compound screening assay of ACE2 receptor inhibition to SARS-2 spike protein is an experimental model for inhibition of infectivity by the compound in human infection.

BUT how can I capture the fact that the same IC50 data has been measured in 3 different animals or using a microchip? We need to capture the environment from where those data have been produced. In the ICD50 example is the animal the specified input? Does it have an evaluant role? Can this be answered with an "experimental model role" in addition to the relation that Bjoern has created?

On Tue, Oct 27, 2020 at 2:21 AM Hiroshi Masuya notifications@github.com wrote:

Hi all,

I'm not familiar with BFO’s role, but I've been working on a database of model animals for a long time.

My understanding is that what you are discussing is the definition of "model organisms" that is an organism having “model” role of disease or something.

“Model” may be an entity that show a similar attribute to the target work as a "imitation". Therefore, I think that a model organism is a "biological entity that has attribute/characteristeic or participate in the phenomena similar to the target attribute/phenomena/entity".

I think that the model role needs to link between 1) the target attribute/phenomena and the model organism, and 2) the target attribute/phenomena and attribute/phenomena which the model organism has.

Hiroshi,

===== Hiroshi Masuya Ph.D Integrated Bioresource Information Division RIKEN BioResource Research Center hiroshi.masuya@riken.jp http://info.brc.riken.jp/en/

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hiroshi-masuya commented 4 years ago

I'm sorry. I was completely misunderstood. The relationship between model animals and diseases does not contribute your problem.

Is this what you want to capture? 3 instances of experimental action using 3 different individuals (instances) of animal were work out. Data from these instances of experiment show the same values.

masciam commented 4 years ago

the relation between model animals and disease is what i need to capture

An assay is performed to evaluate different failure mode (e.g. cardiovascular failure )

Cardiovascular failure can have different phenotypes depending on model used it could be myocarditis or myocardial infraction etc.

I need to link these information The assay type the failure mode the phenotype depending on the model so that i could be able to query: which phenotype is associated with this specific failure mode in this animal model and which assay type I can run

I hope this clarify what I am trying to do

linikujp commented 4 years ago

@masciam based on your query, the disease is not what you want to link to. You want to link to failure mode -- I think that fits into the "target attribute/phenomena" from Dr. Hiroshi's comment.

hectorguzor commented 3 years ago

Discussed on OBI call 2021-06-14: @masciam it would be helpful if you could let us know that if the proposed relationship addresses your original issue or further discussion is needed?

linikujp commented 3 years ago

Discussed with Anna Maria on 7/7/2021: The request/use case is: in vivo/in vitro model - can be a cell line, animal, tissue sample, or single cell. [The definition of this model is needed: the definition Hiroshi was given can be a start point: ""a biological entity that has attribute/characteristeic and/or participate in the phenomena similar to the target attribute/phenomena/entity"] The needs for relationships:

in vivo/in vitro model links to disease or conditions.
in vivo/in vitro model links to the assay that is used to test the research theory within this model system.

bpeters42 commented 3 years ago

Asiyah, did you review at all what I wrote previously? Has Anna Maria completely changed her mind from the previous email where she agreed with what I had written?

On Wed, Jul 7, 2021 at 10:21 AM Asiyah Yu Lin @.***> wrote:

Discussed with Anna Maria on 7/7/2021: The request/use case is: in vivo/in vitro model - can be a cell line, animal, tissue sample, or single cell. [The definition of this model is needed: the definition Hiroshi was given can be a start point: ""a biological entity that has attribute/characteristeic and/or participate in the phenomena similar to the target attribute/phenomena/entity"] The needs for relationships:

in vivo/in vitro model links to disease or conditions.

in vivo/in vitro model links to the assay that is used to test the research theory within this model system.

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linikujp commented 3 years ago

Hi Bjoern, The data portion is fine. We could use that. But additionally, what I just summarized is the current use case.Please let me know what other actions we need to take.

Thanks, Asiyah

On Wed, Jul 7, 2021, 15:05 bpeters42 @.***> wrote:

Asiyah, did you review at all what I wrote previously? Has Anna Maria completely changed her mind from the previous email where she agreed with what I had written?

On Wed, Jul 7, 2021 at 10:21 AM Asiyah Yu Lin @.***> wrote:

Discussed with Anna Maria on 7/7/2021: The request/use case is: in vivo/in vitro model - can be a cell line, animal, tissue sample, or single cell. [The definition of this model is needed: the definition Hiroshi was given can be a start point: ""a biological entity that has attribute/characteristeic and/or participate in the phenomena similar to the target attribute/phenomena/entity"] The needs for relationships:

in vivo/in vitro model links to disease or conditions.

in vivo/in vitro model links to the assay that is used to test the research theory within this model system.

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bpeters42 commented 3 years ago

I am not getting my point across. If you simply link an organism like B6 mice to a disease, then you end up having essentially every disease known to man be linked to B6 mice. But for every disease model there is nut just the mouse strain, but a specific sets of experiments performed to do that study, e.g. for allergy using a series of inoculations with adjuvants to sensitize the mice, or alternatively to adoptively transfer Th2 cells. Or studying learning disabilities using surgically modified mice and measuring their ability to navigate a maze, or the multitude of ways to study diabetes etc.

So I would suggest that we rather define:

An experiment procedure which is the 'experimental model of disease X' by virtue of generating data that is informative about disease X, but which is not a natural occurrence of disease X.
Within that experimental procedure, there is a role for an organism (or tissue or cell) which is the 'model organism' within that experimental procedure.

That way, you can query for what model organisms X are used in experimental procedures that are models of disease Y. But the link is through the type of procedure performed.

On Wed, Jul 7, 2021 at 12:33 PM Asiyah Yu Lin @.***> wrote:

Hi Bjoern, The data portion is fine. We could use that. But additionally, what I just summarized is the current use case.Please let me know what other actions we need to take.

Thanks, Asiyah

On Wed, Jul 7, 2021, 15:05 bpeters42 @.***> wrote:

Asiyah, did you review at all what I wrote previously? Has Anna Maria completely changed her mind from the previous email where she agreed with what I had written?

On Wed, Jul 7, 2021 at 10:21 AM Asiyah Yu Lin @.***> wrote:

Discussed with Anna Maria on 7/7/2021: The request/use case is: in vivo/in vitro model - can be a cell line, animal, tissue sample, or single cell. [The definition of this model is needed: the definition Hiroshi was given can be a start point: ""a biological entity that has attribute/characteristeic and/or participate in the phenomena similar to the target attribute/phenomena/entity"] The needs for relationships:

in vivo/in vitro model links to disease or conditions.

in vivo/in vitro model links to the assay that is used to test the research theory within this model system.

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masciam commented 3 years ago

Bjoern and Asiyah Sorry for reply so late. This suggested approach should work with the type of queries I need. Do we have in addition to model organism, model tissue and model cell role or should be created? If is ok for all we can close the issue.

linikujp commented 3 years ago

Bjoern and OBI discuss,

I agree with Bjoern's solution earlier as well, and if we can create role terms Anna Maria proposed, we could close the loop. Please advise.

Thanks, Asiyah

On Tue, Jul 20, 2021, 11:47 Anna Maria Masci @.***> wrote:

Bjoern and Asiyah Sorry for reply so late. This suggested approach should work with the type of queries I need. Do we have in addition to model organism, model tissue and model cell role or should be created? If is ok for all we can close the issue.

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jamesaoverton commented 1 year ago

I believe that a solution to this longstanding issue was proposed in #1516 and implemented in #1554, so I'll close this issue.

To summarize: we added a 'has assay target context' relation defined as "A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc.", and added a 'target context' column to the assay and epitope-assay templates. For some in vitro epitope assays we have asserted that the target context is 'cell culture', and for some in vivo epitope assays we have asserted that the target context is "(Metazoa and ('has quality' some alive))". Most assays have not been updated to use this column yet, but at least we have a path forward.

hectorguzor commented 1 year ago

I will close this issue. Look at James' previous comment. If anyone wants to revisit this issue, we can reopen it later.

obi-ontology / obi

in vitro model and in vivo model #1234