Gene Regulation

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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.

Updated for WS249 - CG 3-19-2015


?Interaction	Interaction_type Physical
				 Predicted
				 Regulatory Change_of_localization
					    Change_of_expression_level
				 Genetic Genetic_interaction
					 Neutral_genetic
					 Synthetic
					 Enhancement
					 Unilateral_enhancement
					 Mutual_enhancement
					 Positive_genetic
					 Suppression
					 Complete_suppression
					 Partial_suppression
					 Unilateral_suppression
					 Complete_unilateral_suppression
					 Partial_unilateral_suppression
					 Mutual_suppression
					 Complete_mutual_suppression
					 Partial_mutual_suppression
					 Suppression_enhancement
					 Asynthetic
					 Negative_genetic
					 Oversuppression	
					 Unilateral_oversuppression
					 Mutual_oversuppression		
					 Oversuppression_enhancement
       					 Phenotype_bias				
					 No_interaction				// Negative data; no interaction was observed after testing
					 Epistasis
					 Positive_epistasis
					 Maximal_epistasis
					 Minimal_epistasis
					 Neutral_epistasis
					 Qualitative_epistasis
					 Opposing_epistasis
					 Quantitative_epistasis
		Interactor PCR_interactor ?PCR_product  XREF Interaction #Interactor_info	// PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
			   Sequence_interactor ?Sequence  XREF Interaction #Interactor_info	// Sequence of the interacting gene or protein
			   Feature_interactor ?Feature  XREF Associated_with_Interaction  #Interactor_info  // New as of WS241
			   Interactor_overlapping_CDS ?CDS XREF Interaction #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_interactor ?Text #Interactor_info	// Free text describing an interactor entity or condition that does not fall into a standard WormBase category
			   Rearrangement  ?Rearrangement XREF Interactor #Interactor_info
		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
				 Electrophoretic_mobility_shift_assay         // 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
		Library_info Library_screened Text INT			  // In the context of Y2H or YH screens, for example, the library may have been cDNA library or a 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
		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
		Regulation_result Positive_regulate #GR_condition
				  Negative_regulate #GR_condition
				  Does_not_regulate #GR_condition // added to capture negative data [040220 krb]
		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
				  Low_throughput
		Interaction_RNAi ?RNAi XREF Interaction			// RNAi experiment associated with the interaction
		Interaction_phenotype ?Phenotype XREF Interaction	// Phenotype associated with a genetic interaction
		Unaffiliated_variation   ?Variation
		Unaffiliated_transgene   ?Transgene
                Unaffiliated_construct    ?Construct    //New, XW 7-8-2014
		Unaffiliated_antibody    ?Antibody
		Unaffiliated_expr_pattern   ?Expr_pattern
		WBProcess ?WBProcess XREF Interaction			// WormBase biological process associated with the interaction
		DB_info Database ?Database ?Database_field ?Text	// Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
		Paper ?Paper XREF Interaction
		Antibody_remark ?Text
		Historical_gene   ?Gene Text
		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 
		       Transgene ?Transgene XREF Interactor	   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
		       Construct ?Construct XREF Interactor     //Construct used as interactor - New, XW 7-8-2014
                       Antibody ?Antibody XREF Interactor	   // Free text description of the antibody used to detect a regulation event //removed XREF from proposal
		       Inferred_automatically Text                 // a script has updated this connection

#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
				Feature_interactor ?Feature  XREF Associated_with_Interaction  #Interactor_info
				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
				Variation_interactor   ?Variation   #Interactor_info

		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

		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
		Historical_gene   ?Gene Text
		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 
		       Transgene ?Transgene XREF Interactor	   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
                       Construct ?Construct XREF Interactor     //Construct used as interactor - New, XW 7-8-2014
                       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
  • Construct - construct used as interactor, multiontology - XW 7-8-2014



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>"
  • Construct "<grg_construct>"
  • 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>"
  • Trans Regulator Allele "<grg_transregulatorallele>"
  • Cis Regulator Allele "<grg_cisregulatorallele>"
  • RNAi "<grg_rnai>"
  • Molecule_regulator "<grg_moleculeregulator>"
  • Trans_regulator_seq "<grg_transregulatorseq>" Deprecated December 2018
  • Other_regulator "<grg_otherregulator>"
  • Trans_regulator_gene "<grg_transregulator>"
  • Expr_pattern "<grg_exprpattern>"
  • Trans_regulated_gene "<grg_transregulated>"
  • Trans_regulated_seq "<grg_transregulatedseq>" Deprecated December 2018
  • Cis Regulator Feature "<grg_cisregulatorfeature>"
  • Cis Regulated Gene "<grg_cisregulated>"
  • Other_regulated "<grg_otherregulated>"
  • Anatomy "<grg_anatomy>" Added December 2018
  • Life Stage "<grg_lifestage>" Added December 2018
  • SCL "<grg_scl>" Added December 2018
  • SCL Text "<grg_scltext>" Added December 2018
  • Positive_regulate Anatomy_term "<grg_pos_anatomy>" Deprecated December 2018
  • Positive_regulate Life_stage "<grg_pos_lifestage>" Deprecated December 2018
  • Positive_regulate Subcellular_localization "<grg_pos_scl>" Deprecated December 2018
  • Positive_regulate Subcellular_localization_text "<grg_pos_scltext>" Deprecated December 2018
  • Negative_regulate Anatomy_term "<grg_neg_anatomy>" Deprecated December 2018
  • Negative_regulate Life_stage "<grg_neg_lifestage>" Deprecated December 2018
  • Negative_regulate Subcellular_localization "<grg_neg_scl>" Deprecated December 2018
  • Negative_regulate Subcellular_localization_text "<grg_neg_scltext>" Deprecated December 2018
  • Does_not_regulate Anatomy_term "<grg_not_anatomy>" Deprecated December 2018
  • Does_not_regulate Life_stage "<grg_not_lifestage>" Deprecated December 2018
  • Does_not_regulate Subcellular_localization "<grg_subcellloc>" Deprecated December 2018
  • Does_not_regulate Subcellular_localization_text "<grg_not_scltext>" Deprecated December 2018
  • Type "<grg_type>"
  • Regulation_level "<grg_regulationlevel>"
  • Remark "<grg_remark>"
  • Reference "<grg_paper>"
  • No Subdata Result Regulation result "<grg_result>" Updated field label Dec 2018

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 :


Gene Regulation OA postgres tables (grg_*)

As of December 14, 2018

postgres tables
grg_anatomy grg_insitu_text grg_otherregulator grg_scltext
grg_anatomy_hst grg_insitu_text_hst grg_otherregulator_hst grg_scltext_hst
grg_antibody grg_intid grg_paper grg_sentid
grg_antibody_hst grg_intid_hst grg_paper_hst grg_sentid_hst
grg_antibodyremark grg_lifestage grg_rearrangement grg_summary
grg_antibodyremark_hst grg_lifestage_hst grg_rearrangement_hst grg_summary_hst
grg_cisregulated grg_moleculeregulator grg_regulationlevel grg_transgene
grg_cisregulated_hst grg_moleculeregulator_hst grg_regulationlevel_hst grg_transgene_hst
grg_cisregulatorallele grg_name grg_remark grg_transregulated
grg_cisregulatorallele_hst grg_name_hst grg_remark_hst grg_transregulated_hst
grg_cisregulatorfeature grg_nodump grg_reportergene grg_transregulator
grg_cisregulatorfeature_hst grg_nodump_hst grg_reportergene_hst grg_transregulatorallele
grg_construct grg_northern grg_result grg_transregulatorallele_hst
grg_construct_hst grg_northern_hst grg_result_hst grg_transregulator_hst
grg_curator grg_northern_text grg_rnai grg_type
grg_curator_hst grg_northern_text_hst grg_rnai_hst grg_type_hst
grg_exprpattern grg_othermethod grg_rtpcr grg_western
grg_exprpattern_hst grg_othermethod_hst grg_rtpcr_hst grg_western_hst
grg_fromrnai grg_othermethod_text grg_rtpcr_text grg_western_text
grg_fromrnai_hst grg_othermethod_text_hst grg_rtpcr_text_hst grg_western_text_hst
grg_insitu grg_otherregulated grg_scl
grg_insitu_hst grg_otherregulated_hst grg_scl_hst

Deprecated Postgres tables

Data from deprecated grg tables stored here on Tazendra/Mangolassi:

/home/postgres/work/pgpopulation/grg_generegulation/20181210_anatomy_lifestage_scl_scltext/backup/

Deprecated tables (with backup):

  • grg_pos_anatomy
  • grg_pos_lifestage
  • grg_pos_scl
  • grg_pos_scltext
  • grg_neg_anatomy
  • grg_neg_lifestage
  • grg_neg_scl
  • grg_neg_scltext
  • grg_not_anatomy
  • grg_not_lifestage
  • grg_not_scl
  • grg_not_scltext

Deprecated tables (without backup; unused):

  • grg_transregulatorseq
  • grg_transregulatedseq

OA field to Postgres table mapping

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 <RP Text> (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 of the associated ?Construct in the Construct OA) 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>
    • Since all three fields (Driven_by_gene, Gene, and 3'UTR) are moved to construct model, don't need to check transgene against these field anymore. Jucarlose removed scripts of checking from gene regulation dumper.- XW 7-9-2014
  • Construct -> grg_construct Dumps as: Interactor_overlapping_gene <Mapped Gene> Construct <Construct> AND Construct (on a new line) -XW 7-9-2014
    • When mapping constructs to genes, compare construct-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 Construct that don't map to a gene in the interaction, dump as: Unaffiliated_construct <construct>
  • Trans Regulator Allele -> grg_transregulatorallele Dumps as: Variation_interactor <Allele> Trans_regulator
  • Cis Regulator Allele -> grg_cisregulatorallele Dumps as: Variation_interactor <Allele> Cis_regulator
  • 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>
  • Sentence ID -> grg_sentid Dumps as: N/A
  • 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_interactor <Molecule> Trans_regulator
  • Trans Regulator Seq -> grg_transregulatorseq Deprecated December 2018
  • Cis Regulator Feature -> grg_cisregulatorfeature Dumps as: Feature_interactor <Feature> Cis_regulator
  • Other Regulator -> grg_otherregulator Dumps as: Other_interactor <Text> Trans_regulator
  • Trans Regulated Gene -> grg_transregulated Dumps as: Interactor_overlapping_gene <Gene> Trans_regulated
  • Cis Regulated Gene -> grg_cisregulated Dumps as: Interactor_overlapping_gene <Gene> Cis_regulated
  • Trans Regulated Seq -> grg_transregulatedseq Deprecated December 2018
  • Other Regulated -> grg_otherregulated Dumps as: Other_interactor <Text> Trans_regulated

TAB 4

  • Anatomy - grg_anatomy Dumps as: <Regulation_result> Anatomy_term <Anatomy_term> Added December 2018
  • Life Stage - grg_lifestage Dumps as: <Regulation_result> Life_stage <Life_stage> Added December 2018
  • SCL - grg_scl Dumps as: <Regulation_result> Subcellular_localization Added December 2018
  • SCL Text - grg_scltext Dumps as: <Regulation_result> Subcellular_localization <SCL_Text> Added December 2018
  • Positive Anatomy - grg_pos_anatomy Deprecated December 2018
  • Positive Life_stage - grg_pos_lifestage Deprecated December 2018
  • Positive SCL - grg_pos_scl Deprecated December 2018
  • Positive SCL Text - grg_pos_scltext Deprecated December 2018
  • Negative Anatomy - grg_neg_anatomy Deprecated December 2018
  • Negative Life Stage - grg_neg_lifestage Deprecated December 2018
  • Negative SCL - grg_neg_scl Deprecated December 2018
  • Negative SCL Text - grg_neg_scltext Deprecated December 2018
  • Does Not Anatomy - grg_not_anatomy Deprecated December 2018
  • Does Not Life Stage - grg_not_lifestage Deprecated December 2018
  • Does Not SCL - grg_not_scl Deprecated December 2018
  • Does Not SCL Text - grg_not_scltext Deprecated December 2018
  • Regulation 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

.ACE Dumper Script Documentation

Module path on tazendra: /home/postgres/work/citace_upload/gene_regulation/get_gene_regulation_ace.pm

Script path on tazendra: /home/postgres/work/citace_upload/gene_regulation/use_package.pl

Notes (5-30-2012):

  • The Gene_regulation object "Name" will not be dumped as it is now an obsolete tag; Interaction IDs have now superseded the "Name" as the official unique identifier
  • RNAi curators: 1) If you are creating a new Gene_regulation object using the OA, make sure to select the "From RNAi" toggle and the "NO DUMP" toggle to indicate to Xiaodong that this needs to be approved/finished before being dumped. Once Xiaodong has taken a look at the new object, she will deselect the "NO DUMP" toggle, but leave the "From RNAi" toggle selected, for record keeping. 2) There is no free text field for RNAi objects and so RNAi experiments from large scale RNAi papers (WBPaper00004402, WBPaper00004403, WBPaper00004651, WBPaper00005654, WBPaper00006395, WBPaper00024497, WBPaper00025054, WBPaper00029258) cannot be used. If we need to include RNAi experiments from one of these papers, we will need to add a "Large Scale RNAi" field as a free-text field.
  • Antibodies, Transgenes, Expression patterns, and Variations will be mapped to genes as follows:
    • Antibodies
      • If a Gene_regulation object has an antibody listed in the "Antibody Info" field, the script looks in the Postgres tables abp_name and abp_gene to see if the antibody is affiliated with a gene(s) according to Postgres (Antibody OA); if a gene(s) is affiliated with that antibody, the script looks for that matching gene(s) in the grg_transregulator and grg_transregulated tables with the current Gene_regulation object's joinkey (PGID). If there is a second match, the dumper will dump the line:
        • "Interactor_overlapping_gene <Gene> Antibody <Antibody>"
      • Otherwise it will dump:
        • "Unaffiliated_antibody <Antibody>"
    • Transgenes
      • If a Gene_regulation object has an transgene listed in the "Transgene" field, the script looks in the Postgres tables trp_name, trp_driven_by_gene, trp_gene, and trp_threeutr to see if the transgene is affiliated with a gene(s) according to Postgres (Transgene OA); if a gene(s) is affiliated with that transgene, the script looks for that matching gene(s) in the grg_transregulator and grg_transregulated tables with the current Gene_regulation object's joinkey (PGID). If there is a second match, the dumper will dump the line:
        • "Interactor_overlapping_gene <Gene> Transgene <Transgene>"
      • Otherwise it will dump:
        • "Unaffiliated_transgene <Transgene>"
    • Expression patterns
      • If a Gene_regulation object has an expression pattern listed in the "Expression Pattern" field, the script looks in the Postgres tables exp_name and exp_gene to see if the expression pattern is affiliated with a gene(s) according to Postgres (Expr_pattern OA); if a gene(s) is affiliated with that expression pattern, the script looks for that matching gene(s) in the grg_transregulator and grg_transregulated tables with the current Gene_regulation object's joinkey (PGID). If there is a second match, the dumper will dump the line:
        • "Interactor_overlapping_gene <Gene> Expr_pattern <Expr_pattern>"
      • Otherwise it will dump:
        • "Unaffiliated_expr_pattern <Expr_pattern>"
    • Variations
      • If a Gene_regulation object has an variation listed in the "Allele" field, the script looks in <need to check with Juancarlos and Karen for this> to see if the variation is affiliated with a gene(s) according to <again, need to check>; if a gene(s) is affiliated with that variation, the script looks for that matching gene(s) in the grg_transregulator and grg_transregulated tables with the current Gene_regulation object's joinkey (PGID). If there is a second match, the dumper will dump the line:
        • "Interactor_overlapping_gene <Gene> Variation <Variation>"
      • Otherwise it will dump:
        • "Unaffiliated_variation <Variation>"
  • Free-text fields in which entries are to be split on pipes ("|"):
    • Reporter Gene, Positive SCL Text, Negative SCL Text, Does not SCL Text, Other Regulator, Other Regulated
    • Pipes will indicate that the separated entries should be dumped as separate lines in the .ACE file
  • No Subdata Result field:
    • This field is intended to only be filled in if there is no Anatomy, Life Stage, or Subcellular localization data associated with the gene regulation event
  • Sentence ID field
    • This is intended to only be filled in when Textpresso sentences indicate, via the Interaction OA, that a sentence may be regulatory and Xiaodong (or other curator) confirms this and copies the sentence ID over the Gene Regulation OA. The remaining object can be then deleted from the Interaction OA if there is no other interaction data in the sentence.
  • Does Not Regulate
    • In the event of a negative result (i.e. "Does Not Regulate"), curators should leave the "Type" and "Regulation Level" fields blank


Dumper Checks

Notes (5-31-2012):

  • when dump, the dumper should check dead/obsolete genes from field 'Trans Regulator Gene' and 'Trans Regulated Gene', and write the results in error file
  • when dump, the dumper should also check invalid WBPaper IDs from field 'Reference', and write the results in error file.


Notes (12-14-2018):

  • If an annotation (row) has an anatomy, life stage, or subcellular localization (SCL) annotation but does not have a regulation result, the annotation should be flagged as no_dump and reported in the error file
    • This is because the current ?Interaction data model (as of Dec 14, 2018) cannot support an anatomy, life stage, or SCL reference without a regulation result; we may modify the model in the future to allow such a submission

Handling Dead Genes During Dump Process

The dumper script will now (as of May, 2013) run an automatic check for dead genes in any gene field. Any genes that are considered dead that are referenced in an Gene_regulation (Interaction) object in the OA will be handled in the following manner:

1) If there is a replacement for the gene (i.e. the gene has merged into another gene), the dead gene will be dumped into a "Historical_gene" field in the .ACE file, the replacement gene will fill the original gene field. A comment will be added to the Historical_gene field via a 'Text' tag (updated as of 3-18-2015). The original gene field (now with the updated gene reference) will be printed with an "Inferred_automatically" tag after the gene. So, for example, if WBGene00001234 is now a dead gene that has been merged into WBGene00002345:

Gene  "WBGene00001234"

becomes

Gene  "WBGene00002345"  Inferred_automatically
Historical_gene  "WBGene00001234"  "Note: This object originally referred to WBGene00001234.
WBGene00001234 is now considered dead and has been merged into WBGene00002345. WBGene00002345 has 
replaced WBGene00001234 accordingly."

Also, since Antibodies, Transgenes, Expression patterns, and Variations are mapped to an interactor where possible (or else they are dumped as "Unaffiliated"), this mapping will now occur to only the newest genes that the interactor refers to.

2) If there is no replacement for the gene (Dead or Suppressed), we would dump the following:

Gene  "WBGene00001234"
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene
 (WBGene00001234) that is now considered dead. Please interpret with discretion."

OR

Gene  "WBGene00001234"
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene
 (WBGene00001234) that has been suppressed. Please interpret with discretion."

and lastly,

3) If the gene has undergone a split, such genes will be dumped as:

Gene  "WBGene00001234"
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene 
(WBGene00001234) that is now considered split. Please interpret with discretion."

and also printed out in the error output file of the dumping script for a curator to go back and manually change according to best judgement.


Gene Examples:
A split gene: WBGene00012507
A merged gene: WBGene00007524
A dead gene: WBGene00007814
A suppressed gene: WBGene00015490

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