- 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
#Address hash - Cecilia
Remove UNIQUE so that multiple affiliations can be stored along with a single address??
#Address Institution UNIQUE Text
GO_annotation class - Kimberly
Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event.
Feature unused tag removal - M.A.
Can we remove Annotation and Defined_by_author
Tag additions for connecting ?Picture to ?WBProcess (Topic)
?Picture Depict WBProcess ?WBProcess XREF Picture
?WBProcess Picture ?Picture #Evidence
?WBProcess Picture ?Picture XREF WBProcess #Evidence
Unique -> UNIQUE housekeeping change
Corresponding_transgene Unique ?Transgene XREF Corresponding_variation
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
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
Under ?Expression_cluster model
Regulation Regulated_by_gene ?Gene // Wen WS228 Regulated_by_treatment Text // Wen WS228 Regulated_by_molecule ?Molecule // Wen WS228
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.
?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.
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
Transgene - tag removal
Remove Historical_gene from ?Transgene