Gene Regulation

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.

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", 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_anat_term>"
• Positive_regulate Life_stage "<grg_lifestage>"
• Positive_regulate Subcellular_localization "<grg_subcellloc>"
• Negative_regulate Anatomy_term "<grg_anat_term>"
• Negative_regulate Life_stage "<grg_lifestage>"
• Negative_regulate Subcellular_localization "<grg_subcellloc>"
• Does_not_regulate Anatomy_term "<grg_anat_term>"
• Does_not_regulate Life_stage "<grg_lifestage>"
• Does_not_regulate Subcellular_localization "<grg_subcellloc>"
• Type "<grg_type>"
• Regulation_level "<grg_regulationlevel>"
• Remark "<grg_remark>"
• Reference "<grg_paper>"

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 :

• 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>
• Antibody Info -> grg_antibody Dumps as: Interactor_overlapping_gene <Mapped Gene> 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)
• 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)
• Allele -> grg_allele Dumps as: Interactor_overlapping_gene <Mapped Gene> Variation <Allele>
• RNAi -> grg_rnai Dumps as: Interaction_RNAi <RNAi>
• Type -> grg_type Dumps as: <Type>
• Regulation Level -> grg_regulationlevel Dumps as: <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
• Expression Pattern -> grg_exprpattern Dumps as: Interactor_overlapping_gene <Mapped Gene> Expr_pattern <Expr_pattern>
• NO DUMP -> grg_nodump Dumps as: N/A
• Positive_regulate Anatomy_term - grg_pos_anatomy Dumps as: Positive_regulate Anatomy_term <Anatomy_term>
• Positive_regulate Life_stage - grg_pos_lifestage Dumps as: Positive_regulate Life_stage <Life_stage>
• Positive_regulate Subcellular_localization - grg_pos_scl / grg_pos_scltext Dumps as: Positive_regulate Subcellular_localization <SCL Text>
• Negative_regulate Anatomy_term - grg_neg_anatomy Dumps as: Negative_regulate Anatomy_term <Anatomy_term>
• Negative_regulate Life_stage - grg_neg_lifestage Dumps as: Negative_regulate Life_stage <Life_stage>
• Negative_regulate Subcellular_localization - grg_neg_scl / grg_neg_scltext Dumps as: Negative_regulate Subcellular_localization <SCL Text>
• Does_not_regulate Anatomy_term - grg_not_anatomy Dumps as: Does_not_regulate Anatomy_term <Anatomy_term>
• Does_not_regulate Life_stage - grg_not_lifestage Dumps as: Does_not_regulate Life_stage <Life_stage>
• Does_not_regulate Subcellular_localization - grg_not_scl / grg_not_scltext Dumps as: Does_not_regulate Subcellular_localization <SCL Text>
• 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.

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