Phenote .ace citace upload

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Dumping Phenote into .ace file

The phenote-> .ace dump script is called ./use_package.pl and is on tazendra in /home/acedb/work/allele_phenotype. This script takes about 10 minutes and will create two files: ‘allele_phenotype.ace.<date> and err.out.<date>. NOTE: these files will accumulate over time so make sure to clear them out every once in a while.

: ssh  acedb@tazendra.caltech.edu
Pswd
: cd /home/acedb/work/allele_phenotype
: ./use_package.pl 

New allele_phenotype.ace and err.out files will be created as noted by date at the end of each. Send them to your computer e.g. Allele_Phene_Dump on scoobydoo:

: scp err.out.20080407 yook@scoobydoo.caltech.edu:/Users/Yook/WS_latest/ace_phenote_dump  
pswd
: scp allele_phenotype.ace.20080407 yook@scoobydoo.caltech.edu:/Users/Yook/WS_latest/ace_phenote_dump 
pswd

Open err.out to see if any errors were generated during the dump process.

Errors in .ace file generated form should be indicated by "ERROR" in the .ace output, or as comments at the top of the form.

<left over from CGI .ace dump instructions> Is this still necessary? Make sure that there are no obsolete phenotype annotations: - Script for finding obsolete terms is find_obsolete.pl at path listed below on tazendra: /home/Postgres/work/citace_upload/allele_phenotype/

Testing Phenote .ace for upload

Evaluate how the uploaded data impacts WB by comparing object numbers before and after data upload. This means that you need access to the latest WS and have the means to edit the WS to read the .ace dump.

Test file on spica

Send new allele_phenotype.ace to kyook on spica:

: scp <.ace dump files> kyook@spica.caltech.edu:/home3/kyook/alle_phen.ace.latest

Test file locally on Acedb

This step is to test two things: First, that the file is readable. Second, that the file does not alter any objects it shouldn’t.

Launch local acedb:

$ cd Desktop/acedb
$ ./xace /Users/Yook/WS_latest/WS188

Comparing data builds: From the latest build, record

1. Number strain objects
2. Number life stage objects
3. Number anatomy terms
4. Number allele-phenotype connection

use either AQL query
select all class variation where exists_tag ->phenotype
select a, a-> variation from a in class phenotype where exists_tag a ->variation

5. Number variations that are alleles:

use WQL

find variation variation_type=allele

or AQL

select g from g in class variation where exists_tag g-> allele 

6. Number alleles with a phenotype

Find all alleles with a phenotype

select a from a in class variation where exists_tag->phenotype

Checking that the .ace dump file is readable: Load in .ace dump Hit ‘Edit..‘ button Choose ‘Read .ace file’ Accept change in write priviledges Select ‘Open ace file’ Find and select file to open Select ‘Read all’

If the .ace file is okay, then 100% of the lines will have been read in. This will be noted in the second line called ‘Line:’. If the dump produced a bad file, the read in will stop at the point where the problem occurred. You can go to that line in the .ace file and check it out.

Checking that the file does not alter any objects it shouldn’t: Once .ace dump loaded in redo counts for all objects as above. Compare object numbers between latest database and new .ace file to make sure data in the dump looks reasonable, i.e., no lost data or inflated numbers.

Uploading .ace for Wen into Citace

Deposit .ace for Wen in citace:

scp XXXXX citace@altair:~/Data_for_citace/Data_from_<YOU> /home/citace/Data_for_citace/Data_from_<YOU>/ <allele_phenotype_dump_WSxxx.ace>