Difference between revisions of "Expression pattern remodel"
(5 intermediate revisions by the same user not shown) | |||
Line 143: | Line 143: | ||
</pre> | </pre> | ||
− | |||
− | |||
==model of the future (WS2XX??)== | ==model of the future (WS2XX??)== | ||
Line 207: | Line 205: | ||
[[.ace examples]] | [[.ace examples]] | ||
+ | |||
+ | |||
+ | ==cell cycle specificity== | ||
+ | |||
+ | One way to go and add cell cycle specificity could be to add the ?CCO (cell cycle ontology, http://www.ebi.ac.uk/ontology-lookup/) | ||
+ | |||
+ | The Cell cycle ontology has XREFs to ?GO biological_process. A mapping could provide GO cc curators the info needed to fill in the Annotation_extension | ||
+ | |||
+ | |||
+ | Detected_in ?Anatomy_term ?Life_stage ?GO_term ?CCO ?float #Qualifier | ||
+ | |||
+ | |||
+ | ==open questions== | ||
+ | * does ?float have to be always populated? If so, how? | ||
+ | * how do we deal with male/hermaphrodite | ||
+ | |||
+ | e.g. 'expressed in the tail in males' we have occurrence of 2 anatomy terms | ||
+ | |||
+ | |||
+ | ==additional changes== | ||
+ | |||
+ | Not_detected_in ?Anatomy_term | ||
+ | Not_detected_during ?Life_stage | ||
+ | |||
+ | combine the 2? | ||
+ | |||
+ | add ubiquitous tag? | ||
Back to | Back to | ||
[[Expression Pattern]] | [[Expression Pattern]] | ||
+ | |||
+ | |||
+ | ==the ?Descriptor proposal== | ||
+ | |||
+ | <pre> | ||
+ | Changes that should affect expr_pattern model | ||
+ | |||
+ | ?Expression_pattern Expression_of ?Gene .. | ||
+ | ... | ||
+ | Detected_in ?Descriptor XREF Expr_pattern | ||
+ | Not_Detected_in ?Descriptor XREF Expr_pattern
.. | ||
+ | |||
+ | Algorithm ?Text //for quantitative expression | ||
+ | |||
+ | |||
+ | |||
+ | ?Gene GO_term ?GO_term XREF Gene GO_code ?GO_code ?Descriptor | ||
+ | Expr_pattern ?Expr_pattern XREF Gene | ||
+ | ************************************************************************************************************************************************************************************************************************************************************** | ||
+ | |||
+ | ?Expression_pattern Expression_of ?Gene .. | ||
+ | ... | ||
+ | Detected_in ?Descriptor XREF Expr_pattern | ||
+ | Not_Detected_in ?Descriptor XREF Expr_pattern | ||
+ | |||
+ | ************************************************************************************************************************************************************************************************************************************************************** | ||
+ | |||
+ | ?Descriptor Annotation_relation UNIQUE Relation ?Relation //Used to capture the explicit relation between the gene/gene product and the ontology term. | ||
+ | Annotation_made_with Interactor_overlapping_gene ?Gene //Annotation_made_with captures entries in the With/From column used for IGI, IPI, IMP, ISS, and IC GO annotations. | ||
+ | Interactor_overlapping_protein ?Protein | ||
+ | IC_GO_term ?GO_term | ||
+ | Motif ?Motif | ||
+ | RNAi ?RNAi | ||
+ | Variation ?Variation | ||
+ | Phenotype ?Phenotype | ||
+ | Database ?Database ?Database_field ?Text | ||
+ | Annotation_extension Life_stage_Relation ?Relation ?Life_stage XREF Descriptor #Qualifier //Annotation_extension captures the information describing the specific contextual details of a single experiment. | ||
+ | Gene_Relation ?Relation ?Gene | ||
+ | Protein_Relation ?Relation ?Protein | ||
+ | Molecule_Relation ?Relation ?Molecule | ||
+ | Anatomy_Relation ?Relation ?Anatomy_term XREF Descriptor #Qualifier | ||
+ | GO_term_Relation ?Relation ?GO_term XREF Descriptor #Qualifier | ||
+ | Quantitative_expression UNIQUE Float | ||
+ | Annotation_isoform Protein ?Protein //This tag is used when the annotation refers to a specific gene product isoform, e.g. one isoform localizes to the plasma membrane, while another localizes to the cytoplasm. | ||
+ | Transcript ?Transcript | ||
+ | Interacting_taxon NCBITaxonomyID UNIQUE Int //This tag captures Taxon IDs when the GO term used refers to a multi-organism process, e.g. defense response to Gram negative bacterium. | ||
+ | Reference ?Paper XREF GO_annotation #Evidence //This tag captures the Reference used for an annotation when that reference is a published paper. | ||
+ | GO_reference ?Database ?Database_field ?Text #Evidence //This tag captures the reference used for an annotation when that reference is one of the GO references (e.g., GO_REF:0000015) | ||
+ | Annotation_properties Text //This tag will use a controlled vocabulary for meta-data about the annotation. GO may populate this in the future - we could wait to add it, if needed. | ||
+ | |||
+ | |||
+ | //GOC wiki page for description of GPAD file format (the format in which we get annotations from Protein2GO): http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format. | ||
+ | //What will the XREFs in ?Life_stage, etc. look like? Would the Descriptor tag in Life_stage, etc., then hold a mix of Descriptors from Expr_pattern and GO curation (all ontologies)? | ||
+ | ************************************************************************************************************************************************************************************************************************************************************** | ||
+ | //This is just a brainstorm about what we might want to include in a ?Relation class. If a relation was part of the RO, then we could also include the parent-child relationships, if we wanted, but I haven't included them in this draft yet. | ||
+ | |||
+ | ?Relation | ||
+ | Public_name ?Text | ||
+ | Definition Text | ||
+ | Relation_ontology_id UNIQUE ?Text | ||
+ | Synonym ?Text | ||
+ | |||
+ | |||
+ | Possible relations to include (will likely be expanded): involved_in | ||
+ | enables | ||
+ | contributes_to | ||
+ | part_of | ||
+ | colocalizes_with | ||
+ | exists_during | ||
+ | happens_during | ||
+ | has_regulation_target | ||
+ | has_input | ||
+ | has_direct_input | ||
+ | in_the_presence_of | ||
+ | in_the_absence_of | ||
+ | dependent_on | ||
+ | |||
+ | and the equivalent nots, e.g., not_involved_in | ||
+ | |||
+ | |||
+ | </pre> |
Latest revision as of 08:29, 12 May 2014
This is a proposal for changing the current ?Expr_pattern model in order to capture
- quantitative expression
- life_stage, cellular_compartment expression specificity
we will also take the opportunity to clean up some unused tags
- CDS: no objects
- Sequence: 8 objects I could consolidate with other classes -e.g. clone
- Pseudogene: no objects
- Protein: 1 object, found by Paul D should figure out where it comes from
- Cell: no objects
- Cell_group: no objects
Contents
Current model (WS242)
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence CDS ?CDS XREF Expr_pattern // for coding genes Sequence ?Sequence XREF Expr_pattern // for clones??? Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb] Clone ?Clone XREF Expr_pattern Protein ?Protein XREF Expr_pattern Protein_description Text // stores information for Expr_patterns with unknown antigens [031105 krb] Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2] Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier Cell_group ?Cell_group XREF Expr_pattern #Qualifier Life_stage ?Life_stage XREF Expr_pattern #Qualifier Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier GO_term ?GO_term XREF Expr_pattern #GR_condition Subcellular_localization ?Text Type Reporter_gene ?Text In_situ Text Antibody ?Text Northern Text // Wen [krb 030425] Western Text // Wen RT_PCR Text // Wen Localizome ?Text //added by Wen Microarray ?Microarray_experiment Tiling_array ?Analysis EPIC ?Text Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome Pattern ?Text Picture ?Picture XREF Expr_pattern MovieURL Text //Added by wen for link to movie URLs. Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video Remark ?Text #Evidence DB_info ?Database ?Database_field Text Experiment Laboratory ?Laboratory Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern Transgene ?Transgene XREF Expr_pattern Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining // added [031120 krb] Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb] Historical_gene ?Gene #Evidence //Qualifer hash will be used for Expr_pattern curation to specify the reliability of data. #Qualifier Certain Text Uncertain Text //For faint or variable expression Partial Text //For expression of unidentified cell in a cell group
Proposed model (WS244?)
This is an ntermediate version until all legacy objects will be remodeled accordingly. In this version of the model the 2 scenarios will coexist:
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence Clone ?Clone XREF Expr_pattern Protein_description Text // stores information for Expr_patterns with unknown antigens [031105 krb] Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2] Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression Algorithm ?Text //for quantitative expression Expressed_in Life_stage ?Life_stage XREF Expr_pattern #Qualifier Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier GO_term ?GO_term XREF Expr_pattern #GR_condition Subcellular_localization ?Text Type Reporter_gene ?Text In_situ Text Antibody ?Text Northern Text // Wen [krb 030425] Western Text // Wen RT_PCR Text // Wen Localizome ?Text //added by Wen Microarray ?Microarray_experiment Tiling_array ?Analysis EPIC ?Text Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome Pattern ?Text Picture ?Picture XREF Expr_pattern MovieURL Text //Added by wen for link to movie URLs. Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video Remark ?Text #Evidence DB_info ?Database ?Database_field Text Experiment Laboratory ?Laboratory Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern Transgene ?Transgene XREF Expr_pattern Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining // added [031120 krb] Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb] Historical_gene ?Gene #Evidence #Qualifier Certain Text Uncertain Text //For faint or variable expression Partial Text //For expression of unidentified cell in a cell group Present //for quantitative expression Absent //for quantitative expression
simplified summary of the changes for WS244
removed CDS ?CDS XREF Expr_pattern // for coding genes Sequence ?Sequence XREF Expr_pattern // for clones??? Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb] Protein ?Protein XREF Expr_pattern Cell ?Cell XREF Expr_pattern #Qualifier Cell_group ?Cell_group XREF Expr_pattern #Qualifier added Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression Algorithm ?Text //for quantitative expression #Qualifier ... Present //for quantitative expression Absent //for quantitative expression
model of the future (WS2XX??)
This will be the final version once all legacy objects will be remodeled accordingly.
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence Clone ?Clone XREF Expr_pattern Protein_description Text // stores information for Expr_patterns with unknown antigens [031105 krb] Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2] Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression Algorithm ?Text //for quantitative expression Subcellular_localization ?Text Type Reporter_gene ?Text In_situ Text Antibody ?Text Northern Text // Wen [krb 030425] Western Text // Wen RT_PCR Text // Wen Localizome ?Text //added by Wen Microarray ?Microarray_experiment Tiling_array ?Analysis EPIC ?Text Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome Pattern ?Text Picture ?Picture XREF Expr_pattern MovieURL Text //Added by wen for link to movie URLs. Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video Remark ?Text #Evidence DB_info ?Database ?Database_field Text Experiment Laboratory ?Laboratory Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern Transgene ?Transgene XREF Expr_pattern Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining // added [031120 krb] Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb] Historical_gene ?Gene #Evidence #Qualifier Certain Text Uncertain Text //For faint or variable expression Partial Text //For expression of unidentified cell in a cell group Present //for quantitative expression Absent //for quantitative expression
simplified summary of the changes for WS2XXX
removed Expressed_in Life_stage ?Life_stage XREF Expr_pattern #Qualifier Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier GO_term ?GO_term XREF Expr_pattern #GR_condition
.ace examples
cell cycle specificity
One way to go and add cell cycle specificity could be to add the ?CCO (cell cycle ontology, http://www.ebi.ac.uk/ontology-lookup/)
The Cell cycle ontology has XREFs to ?GO biological_process. A mapping could provide GO cc curators the info needed to fill in the Annotation_extension
Detected_in ?Anatomy_term ?Life_stage ?GO_term ?CCO ?float #Qualifier
open questions
- does ?float have to be always populated? If so, how?
- how do we deal with male/hermaphrodite
e.g. 'expressed in the tail in males' we have occurrence of 2 anatomy terms
additional changes
Not_detected_in ?Anatomy_term Not_detected_during ?Life_stage
combine the 2?
add ubiquitous tag?
Back to
Expression Pattern
the ?Descriptor proposal
Changes that should affect expr_pattern model ?Expression_pattern Expression_of ?Gene .. ... Detected_in ?Descriptor XREF Expr_pattern Not_Detected_in ?Descriptor XREF Expr_pattern .. Algorithm ?Text //for quantitative expression ?Gene GO_term ?GO_term XREF Gene GO_code ?GO_code ?Descriptor Expr_pattern ?Expr_pattern XREF Gene ************************************************************************************************************************************************************************************************************************************************************** ?Expression_pattern Expression_of ?Gene .. ... Detected_in ?Descriptor XREF Expr_pattern Not_Detected_in ?Descriptor XREF Expr_pattern ************************************************************************************************************************************************************************************************************************************************************** ?Descriptor Annotation_relation UNIQUE Relation ?Relation //Used to capture the explicit relation between the gene/gene product and the ontology term. Annotation_made_with Interactor_overlapping_gene ?Gene //Annotation_made_with captures entries in the With/From column used for IGI, IPI, IMP, ISS, and IC GO annotations. Interactor_overlapping_protein ?Protein IC_GO_term ?GO_term Motif ?Motif RNAi ?RNAi Variation ?Variation Phenotype ?Phenotype Database ?Database ?Database_field ?Text Annotation_extension Life_stage_Relation ?Relation ?Life_stage XREF Descriptor #Qualifier //Annotation_extension captures the information describing the specific contextual details of a single experiment. Gene_Relation ?Relation ?Gene Protein_Relation ?Relation ?Protein Molecule_Relation ?Relation ?Molecule Anatomy_Relation ?Relation ?Anatomy_term XREF Descriptor #Qualifier GO_term_Relation ?Relation ?GO_term XREF Descriptor #Qualifier Quantitative_expression UNIQUE Float Annotation_isoform Protein ?Protein //This tag is used when the annotation refers to a specific gene product isoform, e.g. one isoform localizes to the plasma membrane, while another localizes to the cytoplasm. Transcript ?Transcript Interacting_taxon NCBITaxonomyID UNIQUE Int //This tag captures Taxon IDs when the GO term used refers to a multi-organism process, e.g. defense response to Gram negative bacterium. Reference ?Paper XREF GO_annotation #Evidence //This tag captures the Reference used for an annotation when that reference is a published paper. GO_reference ?Database ?Database_field ?Text #Evidence //This tag captures the reference used for an annotation when that reference is one of the GO references (e.g., GO_REF:0000015) Annotation_properties Text //This tag will use a controlled vocabulary for meta-data about the annotation. GO may populate this in the future - we could wait to add it, if needed. //GOC wiki page for description of GPAD file format (the format in which we get annotations from Protein2GO): http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format. //What will the XREFs in ?Life_stage, etc. look like? Would the Descriptor tag in Life_stage, etc., then hold a mix of Descriptors from Expr_pattern and GO curation (all ontologies)? ************************************************************************************************************************************************************************************************************************************************************** //This is just a brainstorm about what we might want to include in a ?Relation class. If a relation was part of the RO, then we could also include the parent-child relationships, if we wanted, but I haven't included them in this draft yet. ?Relation Public_name ?Text Definition Text Relation_ontology_id UNIQUE ?Text Synonym ?Text Possible relations to include (will likely be expanded): involved_in enables contributes_to part_of colocalizes_with exists_during happens_during has_regulation_target has_input has_direct_input in_the_presence_of in_the_absence_of dependent_on and the equivalent nots, e.g., not_involved_in