Transgene curation

Transgene Model
Transgene First Pass
Transgene Curation-OA
Transgene.ace dumper
Changes to Transgenes tables, OA and .ace dumper

Scripts

update_textpreso_transgene.pl
/postgres/work/pgpopulation/textpresso/transgene/update_textpreso_transgene.pl* - populates postgres with the results of Arun's transgene pattern matching script track down this script???
- adds new Is/In transgenes and new paper connections to pre-existing ones.
Input: C.elegans corpus
Input: /home/postgres/work/pgpopulation/textpresso/transgene/Obsolete.Tg.txt (no longer needed with switch to OA)
Note: Obsolete.Tg.txt was manually edited to store false transgene objects and paper connections that were picked up by Arun's pattern matching scripts. Obsolete objects are now tagged as 'Fails' so they will not be entered into the transgene table again as they will always be picked up by Arun's script.
Output: postgres transgene table
Runs: every morning, 4am; the textpresso transgene table is wiped clean during each run and repopulated
Written by: Juancarlos

<Arun's script >
What: Uses pattern matching to find all Is, In, transgene names, and paper
Input: C.elegans corpus
Output: http://textpresso-dev.caltech.edu/transgene/
Written by: Arun

<Arun's other script> that includes Ex and genomic expressions
What: finds all Is, In, and Ex expressions plus any possible genomic expression following the transgene regular expression name
Input: C.elegans corpus
Output: transgenes_in_regular_papers.out and transgenes_summary.out
Runs: manually
Written by: Arun

getNewTg.pl /home/citpub/Karen/TgSummary/getNewTg.pl
What: Parses output of transgenes_summary to display only those transgenes that do not exist in WS216 and displays ones that have more than one reference. All new entries will get assigned curator "Arun" and can be retrieved that way
Input 1: WSTg.ace lists all transgenes already in WormBase
Input 2: transgenes_summary.out output file from Textpresso"
Output1: NewTg.txt (all new Ex lines not in WS216.)
Output2: NewTgHighPriority.txt (all new Ex lines that has at least 2 paper entry.)
Runs: manually
Written by: Wen

transgene_dump_ace.pl -> /home/acedb/wen/phenote_transgene/transgene_dump_ace.pl
What: dumps all data in transgene postgres table into a .ace file from the phenote table (switching to the OA for WS220)
Input: transgene phenote tables
Output: /home/acedb/wen/phenote_transgene/transgene.ace.20080917
Output copy: home/citace/Data_for_citace/Data_from_Karen on citace
Runs: every Thursday at 4am
Written: Juancarlos

daily_transgene_curators.pl Added 20130513 :script for identifying objects added by curators other than Karen Yook. <br/> 0 1 * * * /home/acedb/karen/cronjobs/daily_transgene_curators.pl<br/> Runs daily and send e-mail from <br/> daily_transgene_curators.pl@tazendra.caltech.edu<br/> 18211 WBPerson4793 2013-05-20 04:00:04.501962-07<br/>

Interaction with other datatype pipelines

Transgenes are used by other datatypes: Gene_regulation, Overexpression Phenotype, Interactions, Expr_pattern

For all datatypes, requests for transgene names are made to the transgene curator or curators can create transgenes through the transgene OA themselves.

Gene_regulation:
The gene regulation curator can create new transgenes or request them from the transgene curator

Overexpression Phenotype:
Transgenes are created by the phenotype curator

Interaction;
Transgenes can be created by the interaction curator

Expr_pattern:
The expression pattern curator requires many transgene objects to be created on the fly. Rather than impeding the curation flow, when the expression pattern curator needs a transgene that has not been created already, they enter the relavant information for the transgene in their Reporter gene text box. A script that is manually run will check for lines that have text in the reporter gene field and missing a value in the transgene field. This script will create a new object in the transgene OA containing with the corresponding paper id, expression curator as curator, and the remark field populated with the reporter gene text. A synonym will be created based on the expression pattern value with an appended _Ex. This temporary name will be deposited in the synonym field of the transgene OA for that newly created object. See this wiki page for more information: http://wiki.wormbase.org/index.php/Expression_Pattern#Exporting_Reporter_Gene_description_from_Expr_pattern_OA_to_Transgene_OA

The transgene curator needs to

• verify that the object created by the expression pattern curator is not a duplicate transgene, if it is a duplicate, the transgene curator will merge the transgene into the preexisting one, this will make the new transgene invalid its information will not be dumped. The new transgene ID and other synonyms will be pipe added to the synonym list of the pre-existing object
• assign a public name if it exists or if needed
• fill in all other relevant information