View source for Source and maintenance of non-WBGene info

__TOC__
==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. 

<pre>

The script 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.

</pre>
QUES: what is the name of the script that populates the tables (is this a separate script from the one that will be populating 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 [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo 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==
{| class="wikitable" border="1"
!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<br>obo_data_variation
|yes
|yes
|yes
|no
|no
|yes
|yes
|yes
|no
|no
|WBVariationID
|-
|Variation public_name
|obo_name_variation<br>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 <br>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 <br>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:<br>"Allele"<br>"Deletion_allele"<br>"Deletion_and_insertion_allele"<br>"Deletion_polymorphism<br>"Insertion_allele"<br>"Insertion_polymorhism"<br>"KO_consortium_allele"<br>"Mos_insertion"<br>"NBP_knockout_allele"<br>"NemaGENETAG_consortium_allele"<br>"Substitution_allele"<br>"Transposon_insertion"
|-
|Status 
|obo_data_variation
|yes
|yes
|yes
|no
|no
|no
|yes
|no
|no
|no
|
|-
|Rearrangement
|obo_name_rearrangement<br>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 <br>display gin_locus (do not need WBGeneID)
|no
|no
|no
|
|-
|gene_outside
|obo_data_rearrangement
|no
|yes
|yes
|no
|no
|no
|yes <br>display gin_locus (do not need WBGeneID)
|no
|no
|no
|
|-
|Strain
|obo_name_strain<br>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<br>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<br>obo_data_laboratory
|no
|yes
|yes
|no
|no
|yes
|yes
|no
|no
|no
|
|-
|Laboratory -Representative
|obo_name_laboratory<br>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
|
|-
|}