Difference between revisions of "WS247 Models.wrm"
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__TOC__ | __TOC__ | ||
+ | |||
+ | == Analysis class - Gary == | ||
+ | Add Independent_variable for storing the condition of interest so that it is easy to find out what are the experimental variables that are being varied in an experiment | ||
+ | |||
+ | '''Done''' | ||
+ | |||
+ | == #Address hash - Cecilia == | ||
+ | |||
+ | Remove UNIQUE so that multiple affiliations can be stored along with a single address?? | ||
+ | |||
+ | #Address | ||
+ | Institution UNIQUE Text | ||
+ | |||
+ | '''Done''' | ||
== GO_annotation class - Kimberly == | == GO_annotation class - Kimberly == | ||
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Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event. | Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event. | ||
− | == Feature - M.A.== | + | '''Done''' |
+ | |||
+ | == Feature unused tag removal - M.A.== | ||
Can we remove Annotation and Defined_by_author | Can we remove Annotation and Defined_by_author | ||
+ | |||
+ | '''Done''' | ||
== Tag additions for connecting ?Picture to ?WBProcess (Topic) == | == Tag additions for connecting ?Picture to ?WBProcess (Topic) == | ||
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?WBProcess | ?WBProcess | ||
− | Picture ?Picture XREF WBProcess #Evidence | + | Picture ?Picture XREF WBProcess #Evidence |
+ | |||
+ | |||
+ | '''Done''' | ||
== Unique -> UNIQUE housekeeping change == | == Unique -> UNIQUE housekeeping change == | ||
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Corresponding_transgene Unique ?Transgene XREF Corresponding_variation | Corresponding_transgene Unique ?Transgene XREF Corresponding_variation | ||
− | == Expr_patter - Daniela == | + | also |
+ | |||
+ | Add UNIQUE to the second text value as it should be a single pair of values and not 1 to many which could be stored (and a couple were there in error) | ||
+ | |||
+ | ?Variation | ||
+ | Type_of_mutation Substitution UNIQUE Text Text #Evidence // wild type and mutant sequence | ||
+ | Type_of_mutation Substitution UNIQUE Text UNIQUE Text #Evidence // wild type and mutant sequence | ||
+ | |||
+ | |||
+ | '''Done''' | ||
+ | |||
+ | == Expr_patter Microarray_results connection - Daniela == | ||
I would like to add | I would like to add | ||
Line 46: | Line 78: | ||
this will allow to map graphs for expression for remanei, briggsae and japonica to 'gene' through already existing probe-to-genome mappings | this will allow to map graphs for expression for remanei, briggsae and japonica to 'gene' through already existing probe-to-genome mappings | ||
− | == | + | '''Done''', fixed typo in the class name ?Expr_Pattern/pattern |
+ | |||
+ | == Expr_pattern Species tag - Daniela == | ||
I would also like to add a Species tag in the Expr_pattern class | I would also like to add a Species tag in the Expr_pattern class | ||
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Species UNIQUE ?Species | Species UNIQUE ?Species | ||
− | + | '''Done''' | |
− | |||
− | |||
− | |||
− | |||
+ | == ?Expression_cluster Wen == | ||
− | + | Under ?Expression_cluster model | |
Please change: | Please change: | ||
− | |||
Regulation Regulated_by_gene ?Gene // Wen WS228 | Regulation Regulated_by_gene ?Gene // Wen WS228 | ||
Regulated_by_treatment Text // Wen WS228 | Regulated_by_treatment Text // Wen WS228 | ||
Regulated_by_molecule ?Molecule // Wen WS228 | Regulated_by_molecule ?Molecule // Wen WS228 | ||
− | |||
into | into | ||
− | |||
Regulation Regulated_by_gene ?Gene XREF Regulate_expr_cluster | Regulation Regulated_by_gene ?Gene XREF Regulate_expr_cluster | ||
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Regulated_by_molecule ?Molecule XREF Regulate_expr_cluster | Regulated_by_molecule ?Molecule XREF Regulate_expr_cluster | ||
+ | Corresponding XREF already exist in ?Gene and ?Molecule class, the XREFs in Expression_cluster were probably forgotten when I proposed them for WS228. | ||
+ | |||
+ | '''Done''' | ||
− | + | == ?Position_Matrix - Xiaodong == | |
+ | I would like to propose a model change for ?Position_matrix: | ||
+ | |||
+ | ?Position_Matrix Description ?Text #Evidence | ||
+ | Brief_id UNIQUE ?Text // Addition Xiaodong | ||
+ | Type UNIQUE Frequency | ||
+ | Weight | ||
+ | Background_model Text UNIQUE Float | ||
+ | Site_values Text UNIQUE Float REPEAT | ||
+ | Threshold Float | ||
+ | Consensus Text #Evidence | ||
+ | Associated_feature ?Feature XREF Associated_with_Position_Matrix #Evidence | ||
+ | Sites_used UNIQUE Int | ||
+ | Derived_from_matrix ?Position_Matrix | ||
+ | Bound_by_gene_product ?Gene XREF Product_binds_matrix #Evidence | ||
+ | Transcription_factor UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3 | ||
+ | Remark ?Text #Evidence | ||
+ | |||
+ | I would like to remove UNIQUE for Transcription_factor tag. In some PFM/PWM cases, motifs can be bound by multiple TFs. | ||
+ | |||
+ | '''Done''' | ||
+ | |||
+ | == Associations between Genes and Transcription_factor objects - Gary == | ||
+ | |||
+ | Tag additions to hold information on associations between Genes and Transcription_factor objects. Often these associations are based on very weak evidence that would not be suitable for justifying the use of Interaction objects to link them. The primary example I have would be using proximity of a transcription factor binding site to a gene. We have an explicit request from a user (Oliver Hobart) to be able to give the name of a transcription factor and be able to pull out all genes that are near to the binding sites based on ChIP-Seq evidence. This would be facilitated by holding information on this proximity in the Transcription_factor object. | ||
+ | |||
+ | The type of association (e.g. proximity, etc.) would be specified by an appropriate Analysis object in the #Evidence | ||
− | + | Additional tag in ?Transcription_factor to hold further information on the type of that factor. | |
− | + | ?Gene | |
+ | Associated_transcription_factor ?Transcription_factor XREF Associated_with_gene #Evidence | ||
− | + | ?Transcription_factor | |
+ | Associated_with_gene ?Gene XREF Associated_transcription_factor #Evidence | ||
+ | Type Text #Evidence | ||
− | + | '''Done''' | |
− | + | == Transgene - tag removal == | |
− | + | Remove Historical_gene from ?Transgene | |
− | + | '''Done''' |
Latest revision as of 16:47, 5 December 2014
Contents
- 1 Analysis class - Gary
- 2 #Address hash - Cecilia
- 3 GO_annotation class - Kimberly
- 4 Feature unused tag removal - M.A.
- 5 Tag additions for connecting ?Picture to ?WBProcess (Topic)
- 6 Unique -> UNIQUE housekeeping change
- 7 Expr_patter Microarray_results connection - Daniela
- 8 Expr_pattern Species tag - Daniela
- 9 ?Expression_cluster Wen
- 10 ?Position_Matrix - Xiaodong
- 11 Associations between Genes and Transcription_factor objects - Gary
- 12 Transgene - tag removal
Analysis class - Gary
Add Independent_variable for storing the condition of interest so that it is easy to find out what are the experimental variables that are being varied in an experiment
Done
#Address hash - Cecilia
Remove UNIQUE so that multiple affiliations can be stored along with a single address??
#Address Institution UNIQUE Text
Done
GO_annotation class - Kimberly
Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event.
Done
Feature unused tag removal - M.A.
Can we remove Annotation and Defined_by_author
Done
Tag additions for connecting ?Picture to ?WBProcess (Topic)
Add:
?Picture Depict WBProcess ?WBProcess XREF Picture
and change:
?WBProcess Picture ?Picture #Evidence
to:
?WBProcess Picture ?Picture XREF WBProcess #Evidence
Done
Unique -> UNIQUE housekeeping change
Corresponding_transgene Unique ?Transgene XREF Corresponding_variation
also
Add UNIQUE to the second text value as it should be a single pair of values and not 1 to many which could be stored (and a couple were there in error)
?Variation Type_of_mutation Substitution UNIQUE Text Text #Evidence // wild type and mutant sequence Type_of_mutation Substitution UNIQUE Text UNIQUE Text #Evidence // wild type and mutant sequence
Done
Expr_patter Microarray_results connection - Daniela
I would like to add
Microarray_results ?Microarray_results XREF Expr_Pattern
to the Expr_pattern class
between Expression_cluster ?Expression_cluster XREF Expr_pattern and Pattern ?Text
this will allow to map graphs for expression for remanei, briggsae and japonica to 'gene' through already existing probe-to-genome mappings
Done, fixed typo in the class name ?Expr_Pattern/pattern
Expr_pattern Species tag - Daniela
I would also like to add a Species tag in the Expr_pattern class
Species UNIQUE ?Species
Done
?Expression_cluster Wen
Under ?Expression_cluster model
Please change:
Regulation Regulated_by_gene ?Gene // Wen WS228 Regulated_by_treatment Text // Wen WS228 Regulated_by_molecule ?Molecule // Wen WS228
into
Regulation Regulated_by_gene ?Gene XREF Regulate_expr_cluster Regulated_by_treatment Text Regulated_by_molecule ?Molecule XREF Regulate_expr_cluster
Corresponding XREF already exist in ?Gene and ?Molecule class, the XREFs in Expression_cluster were probably forgotten when I proposed them for WS228.
Done
?Position_Matrix - Xiaodong
I would like to propose a model change for ?Position_matrix:
?Position_Matrix Description ?Text #Evidence Brief_id UNIQUE ?Text // Addition Xiaodong Type UNIQUE Frequency Weight Background_model Text UNIQUE Float Site_values Text UNIQUE Float REPEAT Threshold Float Consensus Text #Evidence Associated_feature ?Feature XREF Associated_with_Position_Matrix #Evidence Sites_used UNIQUE Int Derived_from_matrix ?Position_Matrix Bound_by_gene_product ?Gene XREF Product_binds_matrix #Evidence Transcription_factor UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3 Remark ?Text #Evidence
I would like to remove UNIQUE for Transcription_factor tag. In some PFM/PWM cases, motifs can be bound by multiple TFs.
Done
Associations between Genes and Transcription_factor objects - Gary
Tag additions to hold information on associations between Genes and Transcription_factor objects. Often these associations are based on very weak evidence that would not be suitable for justifying the use of Interaction objects to link them. The primary example I have would be using proximity of a transcription factor binding site to a gene. We have an explicit request from a user (Oliver Hobart) to be able to give the name of a transcription factor and be able to pull out all genes that are near to the binding sites based on ChIP-Seq evidence. This would be facilitated by holding information on this proximity in the Transcription_factor object.
The type of association (e.g. proximity, etc.) would be specified by an appropriate Analysis object in the #Evidence
Additional tag in ?Transcription_factor to hold further information on the type of that factor.
?Gene Associated_transcription_factor ?Transcription_factor XREF Associated_with_gene #Evidence
?Transcription_factor Associated_with_gene ?Gene XREF Associated_transcription_factor #Evidence Type Text #Evidence
Done
Transgene - tag removal
Remove Historical_gene from ?Transgene
Done