Source and maintenance of non-WBGene info

Variations

Getting variations from the nightly geneace dump

Variation information is retrieved from the geneace nightly json dump provided by Hinxton. For each variation with Method listed in table below, the following information will be retrieved:

• WBVar ID
• public_name
• gene association
• references
• method (only selected Methods)

If the variation does not have an attached method, it is not retrieved. These data will populate obo_name_variation and obo_data_variation.

The script ''nightly_geneace.pl?'' that populates these tables, looks at the obo_tempfile at
/home/azurebrd/public_html/cgi-bin/data/obo_tempfile and adds any
WBVarID that are not in the geneace nightly dump.

It also compares the WBVar to Public_name mapping in both files by
both public_name and WBVar, and emails it to you if it's different.

Once it emails you, you have to edit the obo_tempfile to resolve it, 
otherwise you'll keep getting that email each time the script runs.

QUES: where is nightly_geneace.pl kept, and is this the one that will also be used to populate the gin_tables?
QUES: once I edit the obo_tempfile, do I contact you to rerun the geneace obo_data table population scripts?

When variations do not exist in the geneace dump

Variations can be temporarily added to obo_name_variation through the TempVariationObo

Curators first need to retrieve a WBVarID from the variation nameserver in Hinxton. Once a WBVarID is received, curators enter the id and the public name into the form at the link above. The information is added immediately to the obo_name_variation and is available through the OA (a reload may be necessary).

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 gets into geneace, it's information will be captured and updated in obo_data_variation.

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"
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