Difference between revisions of "Gene Regulation"

Revision as of 23:51, 24 May 2012

Types of fields Juancarlos can implement:

text : text
bigtext : like longtext, but makes the text box expand when you click in it so you can see everything you've written
dropdown : few values
ontology : controlled vocabulary (tell me where they come from)
multiontology / multidropdown : (allows multiple values)
toggle : on / off, yes/no etc.

Interaction Model as of WS231

The current ?Interaction model now consolidates ?Gene_regulation objects, ?YH objects, and ?Interaction objects into a single class, ?Interaction. The proposed ?Physical_interaction model has also been consolidated into this larger model. Note that #Interaction_info and #Interaction_type have been deprecated.

?Interaction	Interaction_type Physical
				 Predicted
				 Regulatory	Change_of_localization	    // Indicates regulation of localization
						Change_of_expression_level  // Indicates regulation of expression level (RNA, protein)
				 Genetic	Genetic_interaction	    // Indicates a generic genetic interaction that may not be accurately captured by any other term
						Negative_genetic	    // General case in which one genetic perturbation exacerbates the effects of second perturbation
						Synthetic		    // Two genetic perturbations are individually wild type but produce a phenotype when combined
						Enhancement		    // One genetic perturbation exacerbates the effects of second perturbation
						Unilateral_enhancement	    // One genetic perturbation exacerbates the effects of a second perturbation, which is otherwise wild type
						Mutual_enhancement	    // Two genetic perturbations individually result in a phenotype and combine to result in a more severe phenotype than either individual perturbation
						Suppression		    // One genetic perturbation suppresses the effects of second perturbation
						Unilateral_suppression	    // One genetic perturbation suppresses the effects of second perturbation, which is otherwise wild type
						Mutual_suppression	    // Two genetic perturbations individually result in a phenotype and combine to result in a less severe phenotype than either individual perturbation
						Asynthetic		    // Two genetic perturbations individually result in an identical phenotype which is also identical to the phenotype of their combination
						Suppression_enhancement	    // A double genetic perturbation yields a phenotype intermediate to that of either individual perturbation
						Epistasis		    // The phenotype of one genetic perturbation masks the phenotype of a second perturbation
						Maximal_epistasis	    // The more severe phenotype exhibited by two genetic perturbations is observed when both perturbations are combined
						Minimal_epistasis	    // The less severe phenotype exhibited by two genetic perturbations is observed when both perturbations are combined
						Suppression_epistasis	    // One genetic perturbation results in a phenotype which is suppressed back to wild type when combined with a second (wild type) perturbation
						Agonistic_epistasis	    // Combined phenotype is identical to the the single perturbation which is closer to the expected phenotype as determined by the neutrality function
						Antagonistic_epistasis	    // Two genetic perturbations each result in opposite phenotypes and the combined phenotype is identical to the the single perturbation which is furthest from the expected phenotype as determined by the neutrality function
						Oversuppression		// One genetic perturbation suppresses the phenotype of a second perturbation beyond wild type (producing an opposite phenotype)
						Unilateral_oversuppression	// One genetic perturbation suppresses the phenotype of a second (wild type) perturbation beyond wild type (producing an opposite phenotype)
						Mutual_oversuppression		// Two genetic perturbations individually result in a similar phenotype but result in an opposite phenotype when combined
						Complex_oversuppression		// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is (relative to expectation) suppressed beyond wild type, resulting in a phenotype opposite to that expected
						Oversuppression_enhancement	// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is oversuppressed relative to one perturbation and enhanced relative to the other perturbation
						Phenotype_bias			// " is less severe than either original phenotype, but deviates from expectation
						Biased_suppression		// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is less severe than either original phenotype, and less severe than expected
						Biased_enhancement		// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is less severe than either original phenotype, but more severe than expected
						Complex_phenotype_bias		// Two genetic perturbations each result in opposite phenotypes, and although the combined phenotype is expected to be wild type, the actual combined perturbations result in a phenotype less severe than either original phenotype
						No_interaction			// Negative data; no interaction was observed after testing

		Interactor	PCR_interactor UNIQUE ?PCR_product	#Interactor_info	// PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
				Sequence_interactor UNIQUE ?Sequence 	#Interactor_info	// Sequence of the interacting gene or protein
				Interactor_overlapping_CDS ?CDS		#Interactor_info	// CDS of the interacting gene or protein (or related sequence)
				Interactor_overlapping_gene ?Gene XREF Interaction #Interactor_info	// Gene (or portion of gene) involved in the interaction
				Interactor_overlapping_protein ?Protein XREF Interaction 	#Interactor_info	// Protein (or portion of protein) involved in the interaction
				Molecule_regulator      ?Molecule  XREF    Interaction	#Interactor_info	// Molecule that regulates a gene or protein (ported from Gene_regulation class)
				Other_regulator         ?Text	#Interactor_info	// Free text describing a regulator entity or condition that does not fall into a standard WormBase category
				Other_regulated         ?Text	#Interactor_info	// Free text describing a regulated entity or condition that does not fall into a standard WormBase category

		Interaction_summary ?Text #Evidence

		Detection_method		Affinity_capture_luminescence			// A physical interaction detection technique
						Affinity_capture_MS				// A physical interaction detection technique
						Affinity_capture_RNA				// A physical interaction detection technique
						Affinity_capture_Western			// A physical interaction detection technique
						Cofractionation					// A physical interaction detection technique
						Colocalization					// A physical interaction detection technique
						Copurification					// A physical interaction detection technique
						Fluorescence_resonance_energy_transfer		// A physical interaction detection technique
						Protein_fragment_complementation_assay		// A physical interaction detection technique
						Yeast_two_hybrid				// A physical interaction detection technique (Protein-protein)
						Biochemical_activity				// A physical interaction detection technique
						Cocrystal_structure				// A physical interaction detection technique
						Far_western					// A physical interaction detection technique
						Protein_peptide 				// A physical interaction detection technique
						Protein_RNA 					// A physical interaction detection technique
						Reconstituted_complex				// A physical interaction detection technique
						Yeast_one_hybrid  				// A physical interaction detection technique (Protein-DNA)
						Directed_yeast_one_hybrid			// A physical interaction detection technique (Protein-DNA)
						Antibody			// A regulatory interaction detection technique; Antibody name and details captured in Interactor_info hash
						Reporter_gene  ?Text		// A regulatory interaction detection technique
						Transgene			// A regulatory interaction detection technique; Trasnsgene name and details captured in Interactor_info hash
						In_situ        Text		// A regulatory interaction detection technique
						Northern       Text		// A regulatory interaction detection technique
						Western        Text		// A regulatory interaction detection technique
						RT_PCR         Text		// A regulatory interaction detection technique
						Other_method   ?Text		// A regulatory interaction detection technique

//Physical interaction-specific tag

		Library_info 	Library_screened Text INT	// In the context of Yeast Two Hybrid or Yeast One Hybrid screens, for example, the library may have been cDNA library or some other pool of clones
				Origin  From_laboratory UNIQUE ?Laboratory 	// A library generated at an academic laboratory
					From_company UNIQUE ?Text		// A library generated at a company

//Genetic interaction-specific tags

		Deviation_from_expectation	Text	// A text description of the way in which the phenotype deviated from expectation in genetic interactions
			
		Neutrality_function UNIQUE	Multiplicative		// The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type) 
						Additive		// The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type) 
						Minimal			// The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type) 

//Gene regulation-specific tags

		Regulation_level	Transcriptional		// Regulation occurs at the transcriptional level
					Post_transcriptional	// Regulation occurs at the post-transcriptional level
					Post_translational	// Regulation occurs at the post-translational level

		Interaction_associated_feature ?Feature XREF Associated_with_gene_regulation #Evidence //to curate sequence feature connection [ar2]

		Regulation_result	Positive_regulate #GR_condition
					Negative_regulate #GR_condition
					Does_not_regulate #GR_condition // added to capture negative data [040220 krb]

//General tags

		Confidence	Description	Text		// Free text description of the confidence, e.g. "Core" vs "Noncore" (Vidal Interactome terms)
				P_value		  UNIQUE Float	// P-value confidence of interaction, if given
				Log_likelihood_score    UNIQUE Float	// Only used for Predicted interactions


		Throughput	UNIQUE	High_throughput //See BioGRID curation criteria for discussion:  http://www.yeastgenome.org/help/BiogridCuration.html
					Low_throughput
		Interaction_RNAi	?RNAi XREF Interaction		// RNAi experiment associated with the interaction
		Interaction_phenotype	?Phenotype XREF Interaction	// Phenotype associated with a genetic interaction
                Antibody_remark    ?Text       // Free text description of the antibody used to detect a regulation event //removed XREF from proposal
		WBProcess	?WBProcess	XREF	Interaction	// WormBase biological process associated with the interaction
		DB_info 	Database 	?Database 	?Database_field 	?Accession_number	// Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
		Paper 		?Paper		XREF	Interaction
		Remark 		?Text 		#Evidence


#Interactor_info       Interactor_type Non_directional		   // An interactor that has no inherent directionality
				       Bait			   // The interactor of interest or focus; the focus/starting point of an interaction screen
				       Target			   // The discovered interactor; interactors found as a result of an interaction screen
				       Effector			   // In a genetic interaction, the perturbation that affects the phenotype of the other perturbation
				       Affected			   // In a genetic interaction, the perturbation whose phenotype is affected by the other perturbation
				       Trans_regulator		   // A trans-acting regulator, e.g. a transcription factor
				       Cis_regulator		   // A cis-acting regulator, e.g. an enhancer element
				       Trans_regulated		   // A gene regulated in trans, e.g. by a transcription factor
				       Cis_regulated		   // A gene regulated in cis, e.g. by an enhancer element
		       Expr_pattern ?Expr_pattern		   // An expression pattern altered to indicate 
		       Variation ?Variation XREF Interactor	   // (allele, polymorphism, etc.) involved in the interaction //removed XREF from proposal
		       Transgene ?Transgene XREF Interactor	   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
		       Antibody ?Antibody XREF Interactor	   // Antibody used to detect a regulation event
		       Remark ?Text #Evidence			   // Info about reagents that the model can't capture (e.g. co_suppression, RNA_reagent, etc.)

#GR_condition          Life_stage               ?Life_stage      
                       Cell                     ?Cell
                       Cell_group               ?Cell_group
		       Anatomy_term		?Anatomy_term //Added by wen 02132006
                       Subcellular_localization ?Text

In the adoption of this new ?Interaction model in WS231, we have consolidated the ?YH and ?Gene_regulation class into the ?Interaction class. As of WS231, there were 3831 ?Gene_regulation objects, which were then converted to ?Interaction objects with IDs WBInteraction000501384 through WBInteraction000505214.

Model Relevant to Gene Regulation OA

The portions of this Interaction model that are relevant for the Gene_regulation OA are as follows:

?Interaction	Interaction_type Regulatory	Change_of_localization	    // Indicates regulation of localization
						Change_of_expression_level  // Indicates regulation of expression level (RNA, protein)

		Interactor	Interactor_overlapping_gene ?Gene XREF Interaction #Interactor_info	// Gene (or portion of gene) involved in the interaction
				Molecule_regulator      ?Molecule  XREF    Interaction	#Interactor_info	// Molecule that regulates a gene or protein (ported from Gene_regulation class)
				Other_regulator         ?Text	#Interactor_info	// Free text describing a regulator entity or condition that does not fall into a standard WormBase category
				Other_regulated         ?Text	#Interactor_info	// Free text describing a regulated entity or condition that does not fall into a standard WormBase category

		Interaction_summary ?Text #Evidence

		Detection_method		Antibody			// A regulatory interaction detection technique; Antibody name and details captured in Interactor_info hash
					Reporter_gene  ?Text		// A regulatory interaction detection technique
					Transgene			// A regulatory interaction detection technique; Trasnsgene name and details captured in Interactor_info hash
					In_situ        Text		// A regulatory interaction detection technique
					Northern       Text		// A regulatory interaction detection technique
					Western        Text		// A regulatory interaction detection technique
					RT_PCR         Text		// A regulatory interaction detection technique
					Other_method   ?Text		// A regulatory interaction detection technique

//Gene regulation-specific tags

		Regulation_level	Transcriptional		// Regulation occurs at the transcriptional level
					Post_transcriptional	// Regulation occurs at the post-transcriptional level
					Post_translational	// Regulation occurs at the post-translational level

		Interaction_associated_feature ?Feature XREF Associated_with_gene_regulation #Evidence //to curate sequence feature connection [ar2]

		Regulation_result	Positive_regulate #GR_condition
					Negative_regulate #GR_condition
					Does_not_regulate #GR_condition // added to capture negative data [040220 krb]

//General tags

		Interaction_RNAi	?RNAi XREF Interaction		// RNAi experiment associated with the interaction
		Interaction_phenotype	?Phenotype XREF Interaction	// Phenotype associated with a genetic interaction
                Antibody_remark    ?Text       // Free text description of the antibody used to detect a regulation event //removed XREF from proposal
		WBProcess	?WBProcess	XREF	Interaction	// WormBase biological process associated with the interaction
		DB_info 	Database 	?Database 	?Database_field 	?Accession_number	// Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
		Paper 		?Paper		XREF	Interaction
		Remark 		?Text 		#Evidence


#Interactor_info       Interactor_type Trans_regulator		   // A trans-acting regulator, e.g. a transcription factor
				       Cis_regulator		   // A cis-acting regulator, e.g. an enhancer element
				       Trans_regulated		   // A gene regulated in trans, e.g. by a transcription factor
				       Cis_regulated		   // A gene regulated in cis, e.g. by an enhancer element
		       Expr_pattern ?Expr_pattern		   // An expression pattern altered to indicate 
		       Variation ?Variation XREF Interactor	   // (allele, polymorphism, etc.) involved in the interaction //removed XREF from proposal
		       Transgene ?Transgene XREF Interactor	   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
		       Antibody ?Antibody XREF Interactor	   // Antibody used to detect a regulation event

#GR_condition          Life_stage               ?Life_stage      
                       Cell                     ?Cell
                       Cell_group               ?Cell_group
		       Anatomy_term		?Anatomy_term //Added by wen 02132006
                       Subcellular_localization ?Text

Gene_regulation OA

OA fields

Xiaodong, I've moved the fields around in the OA, if they're correct, please reorder them in the wiki. If they're not correct, let me know here, or put them in the right order in the wiki and put a bold comment to reorder them. I've left the old result / anatomy / lifestage / subcellloc in for now to compare the transferred data, later we'll remove them. I've also shortened the names of the new fields because they were too long and taking up a lot of space, if you really want the old names let me know, otherwise change the wiki to match the names in the OA -- J

All the gene regulation tables as of 4/18/2012 have been backed up at: /home/postgres/work/pgpopulation/grg_generegulation/20120402_newOA/backup/-X 4/19/2012

I've dumped .ace file for WS232 on tazendra: /home/acedb/xiaodong/gene_regulation/gene_regulation.ace.20120419 -X 04/19/2012

J will delete postgres tables: grg_result/grg_anat_term/grg_lifestage/grg_subcellloc/grg_subcellloc_text -X 04/19/2012

Pgdbid - postgras database ID, entered automatically
Reference - WBPaperID paper ontology - will you ever need to enter more than one paper? No
Interaction ID - need to be fixed, so that autocomplete will not only look for IDs from interaction OA but also from gene regulation OA autocomplete now works off of the int_index table from the interaction_ticket.cgi and the Term Info will mention the source as interaction OA, gene regulation OA, or existing as an ID but not having any data. Also, let me know where to get the Term Info for IntIDs and what to display -- J -3/28/2012 when duplicate, it will always duplicate same ID. In order to get new ID, hit 'New', and change ID in duplicated object by selecting both objects, clicking in ID field in new object, and click off the field. The duplicated object will get new ID. You can change other fields as you want then.

Name (free text) - this gets appended to the reference to be the object name. usually a WBPaperID followed by regulated gene name, i.e.WBPaper00036472_dod-3.a
Summary (long text) - most of time copy and paste from paper directly with curator's slight modifications do you actually want a big text box, i.e., something that expands to see all the info when you click in the box? yes, that's what I want. Then, I should say 'Big Text'

Antibody Info - antibody multiontology, fill the field with existing antibody, inform the curator (myself) to curate non-existing antibody objects otherwise you could have this work the way Molecule works, when you need a new antibody, you go to the Antibody OA and create, then update the ontology so you can use the new antibody right away. yes, I would like to do so. Autocomplete on abp_ antibody table -> name. in term information show -> original publication, location. .ace -> Antibody_info move this field to a new tab2, rename old tab2 and 3 as tab3 and 4. In new tab2, make four multiontology fields, 'transgene', 'antibody_info', 'allele' and 'expr_pattern', with three ontology fields: 'gene', 'protein' and 'sequence' (from gin_sequence). -X, 3/28/2012 Instead of creating each combination field, we will map antibodies to genes with the following steps: 1. If antibodies exist, look up "Gene" for each antibody, 2. Compare list of Antibody->"Gene" genes to Trans_regulator_gene and Trans_regulated_gene genes, 3. Place each antibody in the Interactor_info hash of the associated gene -- C 4/2/2012

Antibody Remark (free text). .ace -> Antibody If data exactly matches abp_name then put in Antibody info. -move this field to new tab2. X 3/28/2012

Reporter_gene (free text)
- move this field to new tab2. X 3/28/2012
- need to change dumper to separate multiple entries with pipe. -X 3/28/2012 done

Transgene - transgene multiontology, move this field to a new tab2, rename old tab2 and 3 as tab3 and 4. In new tab2, make four multiontology fields, 'transgene', 'antibody_info', 'allele' and 'expr_pattern', with three ontology fields: 'gene', 'protein' and 'sequence' (from gin_sequence). -X, 3/28/2012 Instead of creating each combination field, we will map transgenes to genes with the following steps: 1. If transgenes exist, look up "Driven_by_gene" for each transgene, 2. Compare list of "Driven_by_gene" genes to Trans_regulator_gene and Trans_regulated_gene genes, 3. Place each transgene in the Interactor_info hash of the associated gene -- C 4/2/2012

I'm not sure about what you need for these following method fields, would it work to have one field called Method and then a drop down list? or would you like to have a toggle (yes/no with default of no) for each of these values? I thought about the dropdown list for method first, then later I think, sometimes, I will need to comment in some fields. i.e. For 'RT_PCR', I will need to write ' semi-quantitative'. so a toggle with yes/no will not be enough, right?

In_situ (toggle text) - don't have to write anything in the field, but will need method (In_situ) shown.
Northern (toggle text) - don't have to write anything in the field, but will need method (Northern) shown.
Western (toggle text) - don't have to write anything in the field, but will need method (Western) shown.
RT_PCR (toggle text) - don't have to write anything in the field, but will need method (RT_PCR) shown.
Other_method (toggle text)

Type - multidropdown list with 'Change_of_localization' and 'Change_of_level'
Regulation_level - multidropdown list with 'Transcriptional', 'Post_transcriptional' and 'Post_translational'
Allele - variation multiontology - move this field to a new tab2, rename old tab2 and 3 as tab3 and 4. In new tab2, make four multiontology fields, 'transgene', 'antibody_info', 'allele' and 'expr_pattern', with three ontology fields: 'gene', 'protein' and 'sequence' (from gin_sequence). -X, 3/28/2012 Instead of creating each combination field, we will map alleles to genes with the following steps: 1. If alleles exist, look up "Gene" for each allele, 2. Compare list of Allele->"Gene" genes to Trans_regulator_gene and Trans_regulated_gene genes, 3. Place each allele in the Interactor_info hash of the associated gene -- C 4/2/2012

RNAi - text with pipes. need a way to inform RNAi curators (Chris and Gary) about new RNAi id requirement. there need to be a way they can come in later and fill the field. I'm not sure how Juancarlos will deal with this. This will need to change to multiontology working off of RNAi OA when that's live -- the dumper is currently spliting on pipes -- J To transfer from pipe data to multiontology use script /home/postgres/work/pgpopulation/grg_generegulation/20120406_rnaiToOnt/convert_grg_rnai_to_ont.pl -- J
- will be multi-ontology field when RNAi OA is done
From RNAi - grg_fromrnai - toggle field. is on, when RNAi curator flags the object needs to be curated by GR. Run /home/postgres/work/pgpopulation/grg_generegulation/20120323_fromrnai/create_grg_tables.pl to make the tables on tazendra when going live. Live 2012 03 26 -- J -need to go live on tazendra-X, 3/28/2012 when I checked it was already there, you probably need to shift-reload the browser -- J
- should be able to query new objects from RNAi by RNAi curator names and toggle on field
No Dump - need to add no dump field under 'From RNAi' -X 3/28/12 moved to be right below it -- J
Trans_regulator_gene - (multiontology on gene) I will enter gene by public/sequence name, please autocomplete with WBGeneID
Molecule_regulator - (multiontology like app_molecule) Karen's molecule ontology, and a way to inform her non-existing molecules. you will be able to create add new molecules or synonyms to molecules and update the postgres list.
Trans_regulator_seq
- field is now 'text', need to change dumper to separate multiple entries with pipe. -X 3/28/2012 if it's going to be multiontology (the data already is in that format) it shouldn't split on pipes -- J
- change the field to multiontology of sequence objects off of gin_sequence done -- J

Other_regulator- free text separate by pipe for multivalues, but if any match mop_publicname, put them in Molecule_regulator. -need to change dumper to separate multiple entries with pipe. -X 3/28/2012 done

Expr_pattern - move this field to a new tab2, rename old tab2 and 3 as tab3 and 4. In new tab2, make four multiontology fields, 'transgene', 'antibody_info', 'allele' and 'expr_pattern', with three ontology fields: 'gene', 'protein' and 'sequence' (from gin_sequence). -X, 3/28/2012 Instead of creating each combination field, we will map Expr_patterns to genes with the following steps: 1. If Expr_patterns exist, look up "Gene" and "Sequence" for each Expr_pattern, 2. Compare list of Expr_pattern->"Gene"/"Sequence" to Trans_regulator_gene/Trans_regulator_seq and Trans_regulated_gene/Trans_regulated_seq, 3. Place each Expr_pattern in the Interactor_info hash of the associated gene/Sequence -- C 4/2/2012

No Dump - toggle to prevent dumping object if it should have expr_pattern but doesn't yet. -Remove this field. -X 3/28/2012
Trans_regulated_gene - I will enter gene by public/sequence name, please autocomplete with WBGeneID
Trans_regulated_seq
- field is now 'text', need to change dumper to separate multiple entries with pipe. -X 3/28/2012 if it's going to be multiontology (the data already is in that format) it shouldn't split on pipes -- J
- change the field to multiontology of sequence objects off of gin_sequence done -- J

Other_regulated - free text separate by pipe for multivalues -need to change dumper to separate multiple entries with pipe. -X 3/28/2012 done

~~Rather than having a "Result" dropdown with "Positive_regulate", "Negative_regulate" and "Does_not_regulate"~~

In addition to the 9 fields below, we will bring back the "Result" dropdown menu with : "Positive_regulate", "Negative_regulate" and "Does_not_regulate" - CG 5-17-2012

we will have 9 individual fields that accommodate these and their associated data fields, as such:

Positive_regulate Anatomy_term - grg_pos_anatomy - (Multiontology) anatomy ontology
Positive_regulate Life_stage - grg_pos_lifestage - (Multiontology) life stage
Positive_regulate Subcellular_localization - grg_pos_scl / grg_pos_scltext - (toggletext)
Negative_regulate Anatomy_term - grg_neg_anatomy - (Multiontology) anatomy ontology
Negative_regulate Life_stage - grg_neg_lifestage - (Multiontology) life stage
Negative_regulate Subcellular_localization - grg_neg_scl / grg_neg_scltext - (toggletext)
Does_not_regulate Anatomy_term - grg_not_anatomy - (Multiontology) anatomy ontology
Does_not_regulate Life_stage - grg_not_lifestage - (Multiontology) life stage
Does_not_regulate Subcellular_localization - grg_not_scl / grg_not_scltext - (toggletext)

Remark (long text) perhaps big text? yes

Not Using

Result - dropdown of Positive_regulate, Negative_regulate, Does_not_regulate - change dropdown to six fields, as 'does_not_regulate life_stage anatomy_term', 'positive_regulated life_stage anatomy_term', and 'negative_regulated life_stage anatomy_term' -X 03/28/2012 We need to replace the two fields below too -- J
Anatomy_term - (multiontology app_anatomy) anatomy ontolgy This field needs to be merged with above -- J
Life_stage - (multiontology app_lifestage - check the names) life_stage ontology This field needs to be merged with above -- J
Subcellular_localization (toggle text) wouldn't this be a cell component GO term? , so could be the GO cell component Ontology. The model was designed to enter the free text - need to change dumper to separate multiple entries with pipe. -X 3/28/2012 done

.ace template

different OA rows will have the same object, so dump like phenotype does, grouping all rows with the same name into a single .ace object.

postgres table fields <> corresponding to .ace tag -X 11/05 added

//Template for Gene_regulation

~~Gene_regulation : "<grg_name>"~~
Summary "<grg_summary>
Antibody "<grg_antibodyremark>"
Antibody_info "<grg_antibody>"
Reporter_gene "<grg_reportergene>"
Transgene "<grg_transgene>"
In_situ "<grg_insitu>" (toggle just writes In_situ toggle + text or just text write In_situ "text")
Northern "<grg_northern>"
Western "<grg_western>"
RT_PCR "<grg_rtpcr">
Other_method "<grg_othermethod>"
Allele "<grg_allele>"
RNAi "<grg_rnai>"
Molecule_regulator "<grg_moleculeregulator>"
Trans_regulator_seq "<grg_transregulatorseq>"
Other_regulator "<grg_otherregulator>"
Trans_regulator_gene "<grg_transregulator>"
Expr_pattern "<grg_exprpattern>"
Trans_regulated_gene "<grg_transregulated>"
Trans_regulated_seq "<grg_transregulatedseq>"
Other_regulated "<grg_otherregulated>"
Positive_regulate Anatomy_term "<grg_pos_anatomy>"
Positive_regulate Life_stage "<grg_pos_lifestage>"
Positive_regulate Subcellular_localization "<grg_pos_scl>"
Positive_regulate Subcellular_localization_text "<grg_pos_scltext>"
Negative_regulate Anatomy_term "<grg_neg_anatomy>"
Negative_regulate Life_stage "<grg_neg_lifestage>"
Negative_regulate Subcellular_localization "<grg_neg_scl>"
Negative_regulate Subcellular_localization_text "<grg_neg_scltext>"
Does_not_regulate Anatomy_term "<grg_not_anatomy>"
Does_not_regulate Life_stage "<grg_not_lifestage>"
Does_not_regulate Subcellular_localization "<grg_subcellloc>"
Does_not_regulate Subcellular_localization_text "<grg_not_scltext>"
Type "<grg_type>"
Regulation_level "<grg_regulationlevel>"
Remark "<grg_remark>"
Reference "<grg_paper>"
No Subdata Result "<grg_result>"

Populating postgres

- source file for GR_OA.ace are WS223

- On mangolassi at /home/postgres/work/pgpopulation/grg_generegulation/ create tables with create_grg_tables.pl populate tables based on GR_OA.ace , CellAO.txt , obo_ and other postgres tables. Errors at populate_pg.err (there's a few check them out, need to fix the source file at /home/acedb/xiaodong/gene_regulation/GR_OA.ace ) DONE on tazendra, live on 2010 11 08 -- J.

- fixed errors from pupulated_pg.err file in GR_OA source file, except there are two valid items, WBGene00003004 (lin-15, again), and WBbt:0005118 -X. WBbt:0005118 is not in the list of valie Expr_pattern objects see the autocomplete -- J WBbt:0005118 is in autocomplete list in Anatomy Term. -X Yes, but the tag in the .ace file is for Expr_pattern -J got you. I fixed the source file in mangolassi: /home/postgres/work/pgpopulation/grg_generegulation/GR_OA.ace. -X

- run ./use_package.pl in mangolassi at:/home/acedb/xiaodong/gene_regulation, no errors out in 'err.out.20101102' file, no errors in 'populate_pg.err' show up again in 'gene_regulation.ace.20101102' (except WBGene00003004 and WBbt:0005118 are still there, since I did nothing to them in GR_OA source file in same directory). -X I don't understand this, what shows up again ? What's wrong ? -- J Nothing wrong. don't worry about this. -X

Populating postgres new pos/neg/not - anatomy/lifestage/scl/scltext tables

/home/postgres/work/pgpopulation/grg_generegulation/20120402_newOA/merge_lines_populate_new.pl

get lines with same grg name, move data from result-to-table pairs of tables to specific type-table tables (e.g. result Positive + anat_term Data into pos_anatomy Data), merging multiontology fields (anatomy and lifestage). If multiple pgids for a given genereg name, merge into the numerically lower pgid and delete the higher pgid ; for now do not delete, just set curator to WBPerson1823 to make it easier to check data.

Testing OA

Not sure where things were with the OA before, now that expr_pattern is multiontology, at least test that.

I saw it. it looks good! thanks. -X

Antibody info was storing data from Antibody OA, but it was storing the postgres ID instead of the antibody name. Double check that it works in OA and dumper after changing test data. -J

see comments in next section-X

.ace dumper script

Main code at /home/postgres/work/citace_upload/gene_regulation/ get_gene_regulation_ace.pm and use_package.pl Symlinked to be run at /home/acedb/xiaodong/gene_regulation. Copied to tazendra 2010 11 08 -- J

I'm not sure antibody / antibody_info is dumping correctly, please find example (pgid) and tell me how it is, and how it should be. 162 has both, but you can make your own. -J

They are not dumped correctly. Take the example of pgid 6 : in source file GR_OA.ace, it is Antibody "To detect GLP-1, a mixture of anti-EGFL, anti-LNG, and anti-ANK polyclonal antibodies was used.", this information got transferred into OA in Antibody Remark field, which is correct. However, later, when it is dumped in gene_regulation.ace.20111103 file, it got dumper as Antibody_info "To detect GLP-1, a mixture of anti-EGFL, anti-LNG, and anti-ANK polyclonal antibodies was used.", which is wrong. it should be under Antibody tag again as it is in the source file. Antibody in .ace and Antibody Remark in OA are equivalent fields, which is free text. Antibody_info in .ace and Antibody Info in OA are the same field, which is ontology.

This doesn't make sense to me. From above, the .ace output says :

Antibody ""
Antibody_info ""

Never mind. pgid 6 is correctly dumped in .ace now as I just checked.

There are 18 objects in OA currently which Antibody_info are mapped in Antibody Remark field mistakenly, where they should be in Antibody Info field. If you query 'Antibody_info' in Antibody Remark field, you will get them (18 values). -X The .ace data looks like this : Antibody "Antibody_info: [cgc4906]:odr-7" so it goes into the Antibody_remark field because that's the tag in the .ace field. If you want that fixed you should fix those in the .ace file and let me know to repopulate it (you probably should, rather than wait utnil the OA is live, it's only 18 of them -- J I have fixed the GR_OA.ace file in mangolassi: /home/postgres/work/pgpopulation/grg_generegulation/GR_OA.ace. you can repopulate it. I fixed WBbt:0005118 problem in source file too. -X

Please clarify which table should go in which tag. I've change the Antibody Info field to use the tag Antibody_info. Antibody Remark field now uses Antibody tag. I don't think this is correct, but I don't understand what you want. Here's the mapping of OA fields to postgres table names :

TAB 1

Interaction ID -> grg_intid Dumps as: Interaction: <Interaction ID>
Curator -> grg_curator Dumps as: N/A
Reference -> grg_paper Dumps as: Paper <WBPaper ID>
Name -> grg_name Dumps as: N/A
Summary -> grg_summary Dumps as: Interaction_summary <Text>
In Situ -> grg_insitu Dumps as: In_situ <IS Text>
IS Text -> grg_insitu_text Dumps as: In_situ <IS Text> (same as above)
Northern -> grg_northern Dumps as: Northern <N Text>
N Text -> grg_northern_text Dumps as: Northern <N Text> (same as above)
Western -> grg_western Dumps as: Western <W Text>
W Text -> grg_western_text Dumps as: Western <W Text> (same as above)
RT PCR -> grg_rtpcr Dumps as: RT_PCR
RP Text -> grg_rtpcr_text Dumps as: RT_PCR (same as above)
Other Method -> grg_othermethod Dumps as: Other_method <OM Text>
OM Text -> grg_othermethod_text Dumps as: Other_method <OM Text> (same as above)
RNAi -> grg_rnai Dumps as: Interaction_RNAi <RNAi>
From RNAi -> grg_fromrnai Dumps as: N/A
NO DUMP -> grg_nodump Dumps as: N/A

TAB 2

Antibody Info -> grg_antibody Dumps as: Interactor_overlapping_gene <Mapped Gene> Antibody <Antibody> AND Antibody (on a new line)
- When mapping antibodies to genes, compare antibody-affiliated genes with those in the "Trans Regulator Gene" and "Trans Regulated Gene" fields
- For Antibodies that don't map to a gene in the interaction, dump as: Unaffiliated_antibody <Antibody>
Antibody Remark -> grg_antibodyremark Dumps as: Antibody_remark <Text>
Reporter Gene -> grg_reportergene Dumps as: Reporter_gene <Text>
Transgene -> grg_transgene Dumps as: Interactor_overlapping_gene <Mapped Gene> Transgene <Transgene> AND Transgene (on a new line)
- When mapping transgenes to genes, compare transgene-affiliated genes (from the Driven_by_gene, Gene, and 3'UTR fields) with those in the "Trans Regulator Gene" and "Trans Regulated Gene" fields
- For Transgenes that don't map to a gene in the interaction, dump as: Unaffiliated_transgene <Transgene>
Allele -> grg_allele Dumps as: Interactor_overlapping_gene <Mapped Gene> Variation <Allele>
- When mapping variations to genes, compare variation-affiliated genes with those in the "Trans Regulator Gene" and "Trans Regulated Gene" fields
- For Variations that don't map to a gene in the interaction, dump as: Unaffiliated_variation <Variation>
Rearrangement -> grg_rearrangement Dumps as: Rearrangement <Rearrangement>
Expression Pattern -> grg_exprpattern Dumps as: Interactor_overlapping_gene <Mapped Gene> Expr_pattern <Expr_pattern>
- When mapping Expression patterns to genes, compare Expr-affiliated genes with those in the "Trans Regulator Gene" and "Trans Regulated Gene" fields
- For Expression patterns that don't map to a gene in the interaction, dump as: Unaffiliated_expr_pattern <Expr_pattern>

TAB 3

Type -> grg_type Dumps as: Regulatory <Type>
Regulation Level -> grg_regulationlevel Dumps as: Regulation_level <Regulation Level>
Trans Regulator Gene -> grg_transregulator Dumps as: Interactor_overlapping_gene <Gene> Trans_regulator
Molecule Regulator -> grg_moleculeregulator Dumps as: Molecule_regulator <Molecule> Trans_regulator
Trans Regulator Seq -> grg_transregulatorseq Dumps as: Sequence_interactor <Sequence> Trans_regulator
Other Regulator -> grg_otherregulator Dumps as: Other_regulator <Text> Trans_regulator
Trans Regulated Gene -> grg_transregulated Dumps as: Interactor_overlapping_gene <Gene> Trans_regulated
Trans Regulated Seq -> grg_transregulatedseq Dumps as: Sequence_interactor <Sequence> Trans_regulated
Other Regulated -> grg_otherregulated Dumps as: Other_regulated <Text> Trans_regulated

TAB 4

Positive Anatomy - grg_pos_anatomy Dumps as: Positive_regulate Anatomy_term <Anatomy_term>
Positive Life_stage - grg_pos_lifestage Dumps as: Positive_regulate Life_stage <Life_stage>
Positive SCL - grg_pos_scl Dumps as: Positive_regulate Subcellular_localization <SCL Text>
Positive SCL Text - grg_pos_scltext Dumps as: Positive_regulate Subcellular_localization <SCL Text>
Negative Anatomy - grg_neg_anatomy Dumps as: Negative_regulate Anatomy_term <Anatomy_term>
Negative Life Stage - grg_neg_lifestage Dumps as: Negative_regulate Life_stage <Life_stage>
Negative SCL - grg_neg_scl Dumps as: Negative_regulate Subcellular_localization <SCL Text>
Negative SCL Text - grg_neg_scltext Dumps as: Negative_regulate Subcellular_localization <SCL Text>
Does Not Anatomy - grg_not_anatomy Dumps as: Does_not_regulate Anatomy_term <Anatomy_term>
Does Not Life Stage - grg_not_lifestage Dumps as: Does_not_regulate Life_stage <Life_stage>
Does Not SCL - grg_not_scl Dumps as: Does_not_regulate Subcellular_localization <SCL Text>
Does Not SCL Text - grg_not_scltext Dumps as: Does_not_regulate Subcellular_localization <SCL Text>
No Subdata Result -> grg_result Dump as: Regulation_result <Result>
Remark -> grg_remark Dumps as: Remark <Text>

Please keep track of this for when you need to refer to postgres tables. For example, when dumping the .ace you should write it up something like :

RNAi<tab>"<datafrom rnai table>"

Another example, pgid 319: in GR_OA.ace source file, it is Antibody "[cgc2045]:glp-1", this infomation got transferred into OA in Antibody Remark field, which is wrong. As we stated in wiki above, if Antibody in source file exactly matches abp_name then put in Antibody info. However, later, when it is dumped in gene_regulation.ace.20111103 file, it got dumped correctly as Antibody_info "[cgc2045]:glp-1".

162 is transferred and dumped perfectly right. -X

Other_method doubling should be fixed, double check -J

it is fixed. I checked in 'gene_regulation.ace.20101102' file. -X

Notes

1. objects with trans_regulator/ed_seq - 3/16/2011

testdb=# SELECT * FROM grg_transregulatorseq; joinkey | grg_transregulatorseq | grg_timestamp

44 | "ZC404.8" | 2010-11-08 19:39:42.302809-08
45 | "K07H8.10" | 2010-11-08 19:39:42.772692-08
(2 rows)

testdb=# SELECT * FROM grg_transregulatedseq; joinkey | grg_transregulatedseq | grg_timestamp

144 | "F47G4.3" | 2010-11-08 19:40:23.092894-08
145 | "K11H3.1a","K11H3.1b" | 2010-11-08 19:40:23.346593-08
148 | "T28C12.4a","T28C12.4b" | 2010-11-08 19:40:24.114176-08
263 | "C45G7.5" | 2010-11-08 19:41:10.204312-08
267 | "R107.1" | 2010-11-08 19:41:11.515213-08
(5 rows)

2. fixed dumper - 3/24/2011

we changed the dumper to take each moleculeregulator value and convert it from a molecule pgid to a molecule ID using the mop_molecule table to get the mappings

3. request new variation:

a. go to Sanger variation name server:

http://www.sanger.ac.uk/cgi-bin/Projects/C_elegans/scripts/variation_server.pl?action=new_var

choose 'new_var' from 'Select action to perform:' dropdown list; Enter Public name of Variation, and search. new variation will be in Sanger database.

b. run a short script to synchronize Sanger and tazendra postgress database:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=AddToVariationObo

c. refresh OA page, than new variation should be able to be autocompleted.

4. request new RNAi object IDs through RNAi OA:

click new, click 'From Genereg' and 'NO DUMP' on tab 2, enter relevant info in remark field for RNAi curator.

From BitBucket Wiki

Getting data into OA

source file GR_OA.ace and parse.pl is at mangolassi:

/home/acedb/xiaodong/gene_regulation/populate_grg

OA dumper for gene regulation

OBSOLETE: The script is at mangolassi:

/home/postgres/work/citace_upload/gene_regulation/use_package.pl

OBSOLETE: run dumper:
- ssh acedb@mangolassi.caltech.edu
- cd /home/postgres/work/citace_upload/gene_regulation/
- then : ./use_package.pl
- and it will create :

err.out.20100913 gene_regulation.ace.20100913

dumper is at tazendra:
- cd /home/acedb/xiaodong/gene_regulation
- run by: ./use_package.pl
- and it will create :

err.out.20101217 gene_regulation.ace.20101217

copy the file to citace at spica by:

scp gene_regulation.ace.20101217 citace@spica.caltech.edu:///home/citace/Data_for_citace/Data_from_Xiaodong/.

test file in empty acedb in spica by:
- open a X-termimal
- ssh -X citpub@spica.caltech.edu
- cd CitaceMirror
- ts

Plan as of 11/01/2010

need to issue a ticket on gene regulation OA change from text to ontology for expression_pattern field.
now first, I want my expression pattern field work exactly same as =

picture OA: autocomplete, and show same info in term info box. I will = test OA when data get populated in, and test .ace dumper again. if = everything goes well, we will make it live.

Changes when integrating interaction curation

we decide to keep gene regulation curation separately by keep using gene regulation OA
add interaction ID field (ontology) in gene regulation OA tab one **done -- J**
cronjob to assign interaction IDs **when verified, add code from /home/postgres/work/pgpopulation/grg_generegulation/20120221_intId/assign_grg_intid.pl to current cronjob /home/acedb/xiaodong/assigning_interaction_ids/assign_interaction_ids.pl script is on tazendra, but no cronjob is set yet 2012 02 24**

for existing gene regulation objects
- J will write a script to assign interaction IDs to grg names without IDs(taking mappings of existing grg -> intID and populating the same-named grg with the same intID, and assigning new intIDs to new grg names). **Script written on sandbox /home/postgres/work/pgpopulation/grg_generegulation/20120221_intId/assign_grg_intid.pl data populating -- J 2012 02 21 done and populated original data 2012 02 24 -- J**
  - gets data from grg_name grg_intid grg_curator
  - maps grg_name to grg_intid to get mappings of grg names to grg intIDs.
  - for each pgid in grg_name :
    - skip if already has an intid
    - if that name maps to an intid, use that intid
    - otherwise get a new intid from interaction_ticket.cgi using the curator's two#, and assign a mapping of that grg name to this new intid.
    - add these intids to grg_intid and grg_intid_hst
- X will test the current dumper dumps grg data .ace with intIDs.
- Chris can use the mapping script to convert grg data with intIDs to

new interaction .ace format and test it reads okay.

for future gene regulation objects
- X will figure out how to dump the gene regulation OA data in the new interaction ace format and talks to J so we can write a new gene regulation dumper directly into the new interaction format.
- Chris will need to update the gene regulation mapping

files

- - **He'll need to read the file through a blank acedb and redump to sanitize the format for the conversion script. use /home/postgres/work/pgpopulation/grg_generegulation/20120221_intId/get_grg_to_intid_mappings.pl to generate file grgNameToIntID and place on /home/acedb/chris/Interaction_Changes/Object_output_files/Mapping_files/ so that changeGeneRegulationInteractions.pl will generate new interaction headers. -- J**
in order to get a new interaction ID for similar grg object curation
- first hit 'new' to get a new interaction ID
- duplication old object
- replace the interaction ID in old object with new ID just got from new object
- keep the similar fields and make change in other fields

@@ Line 458: / Line 458: @@
 **'''When mapping variations to genes, compare variation-affiliated genes with those in the "Trans Regulator Gene" and "Trans Regulated Gene" fields'''
 **'''For Variations that don't map to a gene in the interaction, dump as: Unaffiliated_variation  <Variation>'''
-* Rearrangement                    ->                         '''Dumps as: Rearrangement <Rearrangement>'''
+* Rearrangement                   ->     grg_rearrangement   '''Dumps as: Rearrangement <Rearrangement>'''
 * Expression Pattern              ->       grg_exprpattern   '''Dumps as: Interactor_overlapping_gene <Mapped Gene> Expr_pattern <Expr_pattern>'''
 **'''When mapping Expression patterns to genes, compare Expr-affiliated genes with those in the "Trans Regulator Gene" and "Trans Regulated Gene" fields'''