Source and maintenance of non-WBGene info

Caltech_documentation

Geneace dump from Hinxton

Information for gene, variation, clone, strain, rearrangement, and laboratory are provided in a nightly json dump from Hinxton. The gene information is discussed over here. This current page outlines the processing of all non gene information supplied through the dump.

nightly_geneace.pl

/home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/nightly_geneace.pl

For variations:
-populates obo_name/data_<datatype> tables where <datatype> is variation, clone, strain, or rearrangement 
-adds any WBVarID not in the geneace nightly dump but on obo_tempfile at /home/azurebrd/public_html/cgi-bin/data/obo_tempfile and 
-compares WBVar to Public_name mapping in both files by both public_name and WBVar, emails curator (Karen) if it's different. The curator needs to edit the obo_tempfile to resolve the differences, otherwise an email will continue to be sent.
-NOTE: objects added to obo_tempfile are immediately available in the variation dropdown and will remain on obo_tempfile until the object shows up in the nightly geneace dump. 

For Clone:
-script extracts Type: plasmid only from ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/clones2.ace.gz
-Need to change this to take all clones.  Construct curation will require annotating using cDNAs, Fosmids, Cosmids, etc. 

Variations

For each variation with specific Method (listed in table below), the following information will be retrieved:

• WBVar ID
• public_name
• gene association
• references
• method
• status

If the variation does not have one of the following attached methods, it is not retrieved. 
   Allele
   Deletion_allele
   Deletion_and_insertion_allele
   Deletion_polymorphism
   Insertion_allele
   Insertion_polymorhism
   KO_consortium_allele
   Mos_insertion
   NBP_knockout_allele
   NemaGENETAG_consortium_allele
   Substitution_allele
   Transposon_insertion
   Engineered_allele

These data will populate /home/postgres/work/pgpopulation/obo_oa_ontologies/geneace files
obo_name_variation
obo_data_variation

in obo_name_variation, entries are like:

WBVar00000020	ad487	2015-11-30 20:01:08

in obo_data_variation, entries are like:

WBVar00088136	id: WBVar00088136\nname: "ju2"\nspecies: "Caenorhabditis elegans"\nstatus: "Live"\ngene: "WBGene00006363 syd-1"\nreference: "WBPaper00005543"	2015-11-30 20:01:08

If a variation does not exist in the geneace dump, and hence not in obo_name/data_variation tables

Option 1: Two-steps to add variation to OA table

• Retrieve WBVarID from the variation nameserver https://names.wormbase.org/ (note: sanger/Worm_NameServer was retired in 2020). Requires log in.
• Enter the public name and WBVarId, separated by a space OR tab, into the TempVariationObo http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo * * note: The form can take columns of data as long as it is in the format of <allele public name> <WBVarID>.

The information is added immediately to the obo_name_variation and should be available through the OA variation field (a form reload may be necessary).

Option 2: One step to add variation to OA table

• Login with WormBase.org account: http://tazendra.caltech.edu/~postgres/cgi-bin/temp_objects.cgi
• Choose datatype, enter details, ID will be retrieved from new name server and object will be added to OA tables

If the allele already has a WBVarID but does not exist in the nightly geneace dump, curators should still enter the object through the generic.cgi.
When the object comes through during the geneace dump,

• the objects in geneace are compared against the objects on the obo_temp_variation
• if there is no discrepancy the information will be captured and overwritten in obo_data_variation.
• if there is a discrepancy, that is the WBVarID and public name on obo_temp_variation does not match the WBVarID and mapped public_name from geneace an alert will be sent with the discrepancy

 nightly_geneace.pl@tazendra.caltech.edu
 8:01 PM (19 hours ago)
 to kyook 
 WBVar00604189 in obo_tempfile_variation says mn688 geneace says m688
 WBVar00296275 in obo_tempfile_variation says otn567 geneace says ot567

• If a variation needs correcting, go to /home/azurebrd/public_html/cgi-bin/data/obo_tempfile_variation

Clone

• clone
• type
• strain
• general_remark
• location
• accession_number

Strain

• strain
• genotype
• location

Laboratory

• laboratory
• representative
• registered_lab_members
• allele_designation
• strain_designatin
• mail*

Rearrangement

• rearrangenment
• gene_inside
• gene_outside
• map

Non-WBGene objects retrieved through geneace

AceDB tag	Postgres table	Current - Nameserver nightly dump	Current - WS bimonthly release	Future - Geneace nightly dump	Future - WS bimonthly release	Use - Paper or meeting abstract gene connection	Use - OA data type curation	Use - OA term info	Use - Dumping scripts	Use -Text mining/SVM	Use - Updating GSA Lexicon	Comment
Variation	obo_name_variation obo_data_variation	yes	yes	yes	no	no	yes	yes	yes	no	no	WBVariationID
Variation public_name	obo_name_variation obo_data_variation	no	yes	yes	no	no	yes	yes	no	For Mary Ann's Variation first pass/SVM	For Variation lexicon	In multiple OAs
Variation- Gene	obo_data_variation	no	yes	yes	no	no	no	yes Display WBGeneID and gin_locus	no	no	no
Variation -Reference	obo_data_variation	no	yes	yes	no	no	no	yes	no	yes? for MA's scripts??	no
Variation -Method	obo_data_variation	no	no used to query for Variation type Allele and Transposon	yes	no	no	no	yes	no	no	no	Only take in data from Variation objects with these Methods: "Allele" "Deletion_allele" "Deletion_and_insertion_allele" "Deletion_polymorphism "Insertion_allele" "Insertion_polymorhism" "KO_consortium_allele" "Mos_insertion" "NBP_knockout_allele" "NemaGENETAG_consortium_allele" "Substitution_allele" "Transposon_insertion" "Engineered_allele"
Status	obo_data_variation	yes	yes	yes	no	no	no	yes	no	no	no
Rearrangement	obo_name_rearrangement obo_data_rearrangement	no	yes	yes	no	no	yes	yes	no	no	yes
Rearrangement -map	obo_data_rearrangement	no	yes	yes	no	no	no	yes	no	no	no
gene_inside	obo_data_rearrangement	no	yes	yes	no	no	no	yes display gin_locus (do not need WBGeneID)	no	no	no
gene_outside	obo_data_rearrangement	no	yes	yes	no	no	no	yes display gin_locus (do not need WBGeneID)	no	no	no
Strain	obo_name_strain obo_data_strain	no	yes	yes	no	no	yes	yes	no	no	yes
Strain -genotype	obo_data_strain	no	yes	yes	no	no	no	yes	no	no	no
Strain- location	obo_data_strain	no	yes	yes	no	no	no	yes	no	no	no
Clone	obo_name_clone obo_data_clone	no	yes	yes	no	no	yes (expr_pattern)	yes	no?	no	yes
Clone -Type	Not sure you need a table for this. All clones that populate the clone tables will be of one type = PLASMID	no	yes	yes	no	no	no	yes	no	no	no
Clone -Transgene	obo_data_clone	no	yes	yes	no	no	no	yes	no	no	no	I don't think there is any data in this tag in the ftp cloness.ace
Clone -strain	obo_data_clone	no	yes	yes	no	no	no	yes	no	no	no
Clone -general_remark	obo_data_clone	no	yes	yes	no	no	no	yes	no	no	no
Clone -location	obo_data_clone	no	yes	yes	no	no	no	yes	no	no	no
Clone -accession_number	obo_data_clone	no	yes	yes	no	no	no	yes	no	no	no
Laboratory	obo_name_laboratory obo_data_laboratory	no	yes	yes	no	no	yes	yes	no	no	no
Laboratory -Representative	obo_name_laboratory obo_data_laboratory	no	yes	yes	no	no	yes	yes	no	no	no
Laboratory -Registered_lab_members	obo_data_laboratory - actually I don't know if this needs to be displayed in the term info	no	yes	yes	no	no	no	yes	no	no	no
Laboratory - allele_designation	obo_data_laboratory	no	yes	yes	no	no	no	yes	no	yes MA's script	yes? use for text markup regex?
Laboratory - strain_designation	obo_data_laboratory	no	yes	yes	no	no	no	yes	no	no	no
Laboratory -Mail	obo_data_laboratory	no	yes	yes	no	no	no	yes	no	no	no