what would be a quality of ? I am not sure this would fit in PATO. You can get this sort of "values" from PATO but I do not think gene expression could be a quality.
What do you think ?
Best wishes,
George
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Zfin would use an expression annotation as the entity.
(Gene, environment, experiment, ZFA term).
The top level term probably should not be gene_expression because people measure protein expression too.
We would probably prefer the terms be
Increased expression - Expression of a gene or protein product that is high relative to normal.
decreased expression- Expression of a gene or protein product that is low relative to normal.
expression normal - Expression of a gene or protein product that is the same relative to normal.
expression abnormal - Expression of a gene or protein product that is the different relative to normal.
expression not detected - Expression of a gene or protein product that is not detected.
rather then upregulated and downregulated, normal/no change and abnormal.
We cover absolute expression with a database column that denotes expressed yes or expressed no in our current expression annotations.
We have talked about the fact that expression is phenotype since ~2004 when we started curating expression.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
what you are after seems reasonable and you can certainly use PATO for expressing decreased/increased etc but why would we need a quality for gene expression.... We can use GO:0010467 ! gene expression.
GO defines gene expression as a process:
The process by which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
GO:0010467 talks about the process, how a gene is expressed. That's now we are looking for. We are looking for THE expression of the THE gene as a phenotype and not necessarily what is involved (GO: process) in rendering the phenotype
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I forgot to add this to the tracker following our offline conversation a few months back.
The pattern we are using for all processes is the reuse of the GO term and a quality from PATO such as "increased/decreased rate" or "increased/decreased/ etc. I think you should follow this. We are working on these patterns for annotation since they are not ideal.
Best wishes,
George
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi George,
We (ZFIN) would like to revisit this discussion about gene expression as a phenotype. I think what we are looking for may be slightly different than what Pankaj originally was proposing. We are in the process of adding the ability to curate gene expression phenotypes, preferably in E:Q syntax with our other phenotype annotations. For example, we would be curating phenotype for statements like "pax2a expression in the hindbrain is increased in the fgf8a mutant fish". These are observations of the expression pattern and intensity, not observations about the process of gene expression. So, it is not appropriate for us to us the GO process as an entity. We would like to have anatomical terms as the entities, the bearers of the qualities. We have about 11 new expression qualities to propose.
So for example, if pax2a expression were increased in the hindbrain in a mutant, we want to curate the following in E:Q syntax:
E=hindbrain : Q=increased expression level
We would be attaching these Q's to a full expression annotation, so the gene that is exhibiting the altered expression will be known as will the assay, stage, probes, etc..
Here is a draft of the full list of new expression Q's we would like to propose. I've also attached a graph image from oboedit to visualize how these connect to the rest of PATO.
This should be feasible, yes?
[Term]
id: ID:0000000
name: expression pattern
namespace: default_namespace
def: "A physical quality inhering in a bearer by virtue of the bearer's spatiotemporal pattern of expression. Expression pattern includes the location, timing of appearance/disappearance, and quantity of a molecular entity. This can include gene expression pattern as well as antibody staining patterns, and chemical staining patterns where the staining is indicative of the presence of a known molecular entity." []
is_a: PATO:0001018 ! physical quality
creation_date: 2014-03-13T11:28:27Z
[Term]
id: ID:0000001
name: expression level
namespace: default_namespace
def: "An expression pattern quality inhering in a bearer by virtue the bearer having a qualitative expression pattern." []
is_a: ID:0000000 ! expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:29:26Z
[Term]
id: ID:0000002
name: spatial expression pattern
namespace: default_namespace
def: "An expression pattern quality inhering in a bearer by virtue of the spatial character of bearer's expression pattern." []
is_a: ID:0000000 ! expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:31:27Z
[Term]
id: ID:0000003
name: temporal expression pattern
namespace: default_namespace
def: "An expression pattern quality inhering in a bearer by virtue of the temporal character of the bearer's expression pattern." []
is_a: ID:0000000 ! expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:31:55Z
[Term]
id: ID:0000004
name: increased expression level
namespace: default_namespace
def: "An expression level that is increased in comparison to the normal expression level observed in a tissue, cell, or cellular component at a specific point in time." []
is_a: ID:0000001 ! expression level
is_a: PATO:0002305 ! increased object quality
created_by: dhowe
creation_date: 2014-03-13T11:32:25Z
[Term]
id: ID:0000005
name: decreased expression level
namespace: default_namespace
def: "An expression level that is reduced in comparison to the normal expression level observed in a tissue, cell, or cellular component at a specific point in time." []
is_a: ID:0000001 ! expression level
is_a: PATO:0002303 ! decreased object quality
created_by: dhowe
creation_date: 2014-03-13T11:32:54Z
[Term]
id: ID:0000006
name: spatially expanded expression pattern
namespace: default_namespace
def: "A mislocalized expression pattern which is characterized by expression in a correct location as well as contiguous adjacent tissue in which the expression is not normally found at a specific point in time." []
is_a: ID:0000004 ! increased expression level
is_a: ID:0000009 ! mislocalized expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:33:26Z
[Term]
id: ID:0000007
name: spatially restricted expression pattern
namespace: default_namespace
def: "A spatial expression pattern characterized by decreased or absent expression in a portion of a contiguous region where expression is normally found at a specific time point." []
is_a: ID:0000002 ! spatial expression pattern
is_a: ID:0000005 ! decreased expression level
created_by: dhowe
creation_date: 2014-03-13T11:38:32Z
[Term]
id: ID:0000009
name: mislocalized expression pattern
namespace: default_namespace
def: "An spatial expression pattern which is located in whole or in part in a tissue where it is not normally found at a specific time point." []
is_a: ID:0000002 ! spatial expression pattern
is_a: PATO:0000628 ! mislocalised
created_by: dhowe
creation_date: 2014-03-13T11:42:33Z
[Term]
id: ID:0000011
name: ectopic expression pattern
namespace: default_namespace
def: "A mislocalized expression pattern which is characterized by having no spatial overlap with the normal expression pattern at a specific point in time." []
is_a: ID:0000004 ! increased expression level
is_a: ID:0000009 ! mislocalized expression pattern
created_by: dhowe
creation_date: 2014-06-02T15:45:14Z
[Term]
id: ID:0000013
name: lacks expression
namespace: default_namespace
def: "An expression pattern characterized by the complete lack of expression in an anatomical structure, cell, or subcellular component where the expression is normally found at a specific point in time." []
is_a: ID:0000005 ! decreased expression level
created_by: dhowe
creation_date: 2014-06-03T11:06:53Z
Hi Pankaj,
what would be a quality of ? I am not sure this would fit in PATO. You can get this sort of "values" from PATO but I do not think gene expression could be a quality.
What do you think ?
Best wishes,
George
Quality of 'gene expression'. we consider it a molecular phenotype.
Zfin would use an expression annotation as the entity.
(Gene, environment, experiment, ZFA term).
The top level term probably should not be gene_expression because people measure protein expression too.
We would probably prefer the terms be
Increased expression - Expression of a gene or protein product that is high relative to normal.
decreased expression- Expression of a gene or protein product that is low relative to normal.
expression normal - Expression of a gene or protein product that is the same relative to normal.
expression abnormal - Expression of a gene or protein product that is the different relative to normal.
expression not detected - Expression of a gene or protein product that is not detected.
rather then upregulated and downregulated, normal/no change and abnormal.
We cover absolute expression with a database column that denotes expressed yes or expressed no in our current expression annotations.
We have talked about the fact that expression is phenotype since ~2004 when we started curating expression.
Hi Pankaj and Ceri,
what you are after seems reasonable and you can certainly use PATO for expressing decreased/increased etc but why would we need a quality for gene expression.... We can use GO:0010467 ! gene expression.
GO defines gene expression as a process:
The process by which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
GO:0010467 talks about the process, how a gene is expressed. That's now we are looking for. We are looking for THE expression of the THE gene as a phenotype and not necessarily what is involved (GO: process) in rendering the phenotype
Hi Pankaj,
I forgot to add this to the tracker following our offline conversation a few months back.
The pattern we are using for all processes is the reuse of the GO term and a quality from PATO such as "increased/decreased rate" or "increased/decreased/ etc. I think you should follow this. We are working on these patterns for annotation since they are not ideal.
Best wishes,
George
Hi George,
We (ZFIN) would like to revisit this discussion about gene expression as a phenotype. I think what we are looking for may be slightly different than what Pankaj originally was proposing. We are in the process of adding the ability to curate gene expression phenotypes, preferably in E:Q syntax with our other phenotype annotations. For example, we would be curating phenotype for statements like "pax2a expression in the hindbrain is increased in the fgf8a mutant fish". These are observations of the expression pattern and intensity, not observations about the process of gene expression. So, it is not appropriate for us to us the GO process as an entity. We would like to have anatomical terms as the entities, the bearers of the qualities. We have about 11 new expression qualities to propose.
So for example, if pax2a expression were increased in the hindbrain in a mutant, we want to curate the following in E:Q syntax:
E=hindbrain : Q=increased expression level
We would be attaching these Q's to a full expression annotation, so the gene that is exhibiting the altered expression will be known as will the assay, stage, probes, etc..
Here is a draft of the full list of new expression Q's we would like to propose. I've also attached a graph image from oboedit to visualize how these connect to the rest of PATO.
This should be feasible, yes?
[Term]
id: ID:0000000
name: expression pattern
namespace: default_namespace
def: "A physical quality inhering in a bearer by virtue of the bearer's spatiotemporal pattern of expression. Expression pattern includes the location, timing of appearance/disappearance, and quantity of a molecular entity. This can include gene expression pattern as well as antibody staining patterns, and chemical staining patterns where the staining is indicative of the presence of a known molecular entity." []
is_a: PATO:0001018 ! physical quality
creation_date: 2014-03-13T11:28:27Z
[Term]
id: ID:0000001
name: expression level
namespace: default_namespace
def: "An expression pattern quality inhering in a bearer by virtue the bearer having a qualitative expression pattern." []
is_a: ID:0000000 ! expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:29:26Z
[Term]
id: ID:0000002
name: spatial expression pattern
namespace: default_namespace
def: "An expression pattern quality inhering in a bearer by virtue of the spatial character of bearer's expression pattern." []
is_a: ID:0000000 ! expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:31:27Z
[Term]
id: ID:0000003
name: temporal expression pattern
namespace: default_namespace
def: "An expression pattern quality inhering in a bearer by virtue of the temporal character of the bearer's expression pattern." []
is_a: ID:0000000 ! expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:31:55Z
[Term]
id: ID:0000004
name: increased expression level
namespace: default_namespace
def: "An expression level that is increased in comparison to the normal expression level observed in a tissue, cell, or cellular component at a specific point in time." []
is_a: ID:0000001 ! expression level
is_a: PATO:0002305 ! increased object quality
created_by: dhowe
creation_date: 2014-03-13T11:32:25Z
[Term]
id: ID:0000005
name: decreased expression level
namespace: default_namespace
def: "An expression level that is reduced in comparison to the normal expression level observed in a tissue, cell, or cellular component at a specific point in time." []
is_a: ID:0000001 ! expression level
is_a: PATO:0002303 ! decreased object quality
created_by: dhowe
creation_date: 2014-03-13T11:32:54Z
[Term]
id: ID:0000006
name: spatially expanded expression pattern
namespace: default_namespace
def: "A mislocalized expression pattern which is characterized by expression in a correct location as well as contiguous adjacent tissue in which the expression is not normally found at a specific point in time." []
is_a: ID:0000004 ! increased expression level
is_a: ID:0000009 ! mislocalized expression pattern
created_by: dhowe
creation_date: 2014-03-13T11:33:26Z
[Term]
id: ID:0000007
name: spatially restricted expression pattern
namespace: default_namespace
def: "A spatial expression pattern characterized by decreased or absent expression in a portion of a contiguous region where expression is normally found at a specific time point." []
is_a: ID:0000002 ! spatial expression pattern
is_a: ID:0000005 ! decreased expression level
created_by: dhowe
creation_date: 2014-03-13T11:38:32Z
[Term]
id: ID:0000009
name: mislocalized expression pattern
namespace: default_namespace
def: "An spatial expression pattern which is located in whole or in part in a tissue where it is not normally found at a specific time point." []
is_a: ID:0000002 ! spatial expression pattern
is_a: PATO:0000628 ! mislocalised
created_by: dhowe
creation_date: 2014-03-13T11:42:33Z
[Term]
id: ID:0000011
name: ectopic expression pattern
namespace: default_namespace
def: "A mislocalized expression pattern which is characterized by having no spatial overlap with the normal expression pattern at a specific point in time." []
is_a: ID:0000004 ! increased expression level
is_a: ID:0000009 ! mislocalized expression pattern
created_by: dhowe
creation_date: 2014-06-02T15:45:14Z
[Term]
id: ID:0000013
name: lacks expression
namespace: default_namespace
def: "An expression pattern characterized by the complete lack of expression in an anatomical structure, cell, or subcellular component where the expression is normally found at a specific point in time." []
is_a: ID:0000005 ! decreased expression level
created_by: dhowe
creation_date: 2014-06-03T11:06:53Z
Last edit: Doug Howe 2014-06-04