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
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.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
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'.
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
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:
[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
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
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'.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
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.
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:
Related
OBI Terms: #69
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 -----
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
Related
OBI Terms: #69
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'.
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.
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.
Not only organims parts, but also pathogens that can be studied within our outside of a host.