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The Ontology for Biomedical Investigations
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In vivo, ex vivo #69

Closed obi-bot closed 1 year ago

obi-bot commented 16 years ago

AI from Vancouver workshop:

Biomaterial will attempt define in vivo, ex vivo etc as a defined class and see if this works, these may be at assay level not material level, and these will likely be processes. Assigned to: PRS

Reported by: jamesmalone

Original Ticket: "obi/obi-terms/69":https://sourceforge.net/p/obi/obi-terms/69

obi-bot commented 15 years ago

Came up again in the context of neuroscience use case spike train assay - requirement to represent in vivo and in vitro assays, still needs to be resolved, likely at the level of assay.

Original comment by: helenp

obi-bot commented 9 years ago

Discussed on OBI-dev call 2015-03-16

in vivo has different meanings, one is in an alive organism, the other is in live cell. See: http://en.wikipedia.org/wiki/In_vivo

It's better to avoid 'in vivo' in the label. We may add terms, like assay 'performing in living multi-cellular organism' (in vivo assay), 'performing in living cell'.

IEDB people will work on it.

Original comment by: zhengj2007

obi-bot commented 9 years ago

Original comment by: zhengj2007

obi-bot commented 9 years ago

Original comment by: jamesaoverton

obi-bot commented 9 years ago

Bjoern, Randi, and I discussed this further. We propose the following.

OBI already has an 'in live organism assay' that we should improve: http://purl.obolibrary.org/obo/OBI_0000966

The label and definition should be updated to specify that we're explicitly talking about multicellular organisms (animals or plants), and that the participation of an investigator does not make the assay an in vivo assay, which the current logical definition allows.

1) change label: 'assay performed on living multicellular organism' 2) keep synonym 'in vivo assay' 3) import 'animalia' and 'higher plant' from NCBI into OBI

Although the proposed label is 'living multicellular organism', we don't want to include all Eukaryota. It seems wrong to say we're doing an in vivo assay on yeast, for example. Maybe we could say 'living higher organism'.

Original comment by: jamesaoverton

obi-bot commented 9 years ago

My immediate reaction is not to use "alive" as a quality because, well, I don't think it is.

I will discuss this with Barry and get back with a concrete proposal. On Fri, Mar 20, 2015 at 10:35 AM James A. Overton < jamesaoverton@users.sf.net> wrote:

  • Group: bfo --> general
  • Comment:

Bjoern, Randi, and I discussed this further. We propose the following.

OBI already has an 'in live organism assay' that we should improve: http://purl.obolibrary.org/obo/OBI_0000966

The label and definition should be updated to specify that we're explicitly talking about multicellular organisms (animals or plants), and that the participation of an investigator does not make the assay an in vivo assay, which the current logical definition allows.

1) change label: 'assay performed on living multicellular organism' 2) keep synonym 'in vivo assay' 3) import 'animalia' and 'higher plant' from NCBI into OBI

  • http://purl.obolibrary.org/obo/NCBITaxon_33208 Metazoa (aka 'Animalia')
  • http://purl.obolibrary.org/obo/NCBITaxon_3193 Embryophyta (aka 'higher plants') 4) use these and PATO_0001421 'alive' to define 'living multicellular organism' as equivalent to: "(Metazoa or Embryophyta) and ('has quality' some alive)" 5) change textual definition to: "An assay in which a whole living multicellular organism, such as an animal or a plant, is an evaluant." 6) change logical definition to equivalent to: "assay and ('has participant' some 'living multicelluar organism' and has_role some 'evaluant role')"

Although the proposed label is 'living multicellular organism', we don't want to include all Eukaryota. It seems wrong to say we're doing an in vivo assay on yeast, for example. Maybe we could say 'living higher organism'.

Status: open Group: general

Created: Tue May 06, 2008 10:37 AM UTC by JMalone

Last Updated: Mon Mar 16, 2015 04:29 PM UTC Owner: bjoernpeters

AI from Vancouver workshop:

Biomaterial will attempt define in vivo, ex vivo etc as a defined class and see if this works, these may be at assay level not material level, and these will likely be processes. Assigned to: PRS

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/obi/obi-terms/69/

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Original comment by: alanruttenberg

obi-bot commented 9 years ago

Given that we have used the 'alive' quality before in this exact definition, I would keep it for now. We should replace throughout. We had talked about that before, something along the lines that 'living' should be replace by an organism that participates in its own life_course, but given that we don't have anything implemented, we should stick to what we have.

----- Original Message -----

My immediate reaction is not to use "alive" as a quality because, well, I don't think it is. I will discuss this with Barry and get back with a concrete proposal. On Fri, Mar 20, 2015 at 10:35 AM James A. Overton jamesaoverton@users.sf.net wrote:

  • Group : bfo --> general

  • Comment :

Bjoern, Randi, and I discussed this further. We propose the following.

OBI already has an 'in live organism assay' that we should improve:

http://purl.obolibrary.org/obo/OBI_0000966

The label and definition should be updated to specify that we're

explicitly talking about multicellular organisms (animals or plants), and

that the participation of an investigator does not make the assay an in

vivo assay, which the current logical definition allows.

1) change label: 'assay performed on living multicellular organism'

2) keep synonym 'in vivo assay'

3) import 'animalia' and 'higher plant' from NCBI into OBI

plants')

4) use these and PATO_0001421 'alive' to define 'living multicellular

organism' as equivalent to: "(Metazoa or Embryophyta) and ('has quality'

some alive)"

5) change textual definition to: "An assay in which a whole living

multicellular organism, such as an animal or a plant, is an evaluant."

6) change logical definition to equivalent to: "assay and ('has

participant' some 'living multicelluar organism' and has_role some

'evaluant role')"

Although the proposed label is 'living multicellular organism', we don't

want to include all Eukaryota. It seems wrong to say we're doing an in vivo

assay on yeast, for example. Maybe we could say 'living higher organism'.

Status: open

Group: general

Created: Tue May 06, 2008 10:37 AM UTC by JMalone

Last Updated: Mon Mar 16, 2015 04:29 PM UTC

Owner: bjoernpeters

AI from Vancouver workshop:

Biomaterial will attempt define in vivo, ex vivo etc as a defined class

and see if this works, these may be at assay level not material level, and

these will likely be processes. Assigned to: PRS

Sent from sourceforge.net because you indicated interest in

https://sourceforge.net/p/obi/obi-terms/69/

To unsubscribe from further messages, please visit

https://sourceforge.net/auth/subscriptions/

[obi-terms:#69] In vivo, ex vivo Status: open Group: general Created: Tue May 06, 2008 10:37 AM UTC by JMalone Last Updated: Fri Mar 20, 2015 02:35 PM UTC Owner: bjoernpeters AI from Vancouver workshop: Biomaterial will attempt define in vivo, ex vivo etc as a defined class and see if this works, these may be at assay level not material level, and these will likely be processes. Assigned to: PRS

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/obi/obi-terms/69/ To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/ --

Bjoern Peters Associate Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

Original comment by: bpeters42

obi-bot commented 9 years ago

Discussed on the OBI call 2015-03-23:

Chris and Jie would like to see us keep the notion of “located in”, in order to distinguish this from cases such counting/observing animals or trees. These are “vivo” assays but not “in vivo” assays.

Original comment by: jamesaoverton

obi-bot commented 9 years ago

Original comment by: bpeters42

obi-bot commented 9 years ago

Bjoern + IEDB team agrees; this can be figured out in detail in OBI, and should be as part of the assay remodeling. The distincitno in vivo / ex vivo / in vitro primarily (or exclusively) applies to organism parts; Observing time to death of an animal doesn't seem to be an 'in vivo' but a 'vivo' assay.

Original comment by: bpeters42

obi-bot commented 9 years ago

Not only organims parts, but also pathogens that can be studied within our outside of a host.

Original comment by: bpeters42

jamesaoverton commented 1 year ago

This should be resolved by the 'target environment' PR #1516