Processing NBP alleles

created 16/07/08

Problems with scripts

• curator changes to Mary Ann when no changes in the NBP comments are apparent
  • tm1108, tm1485, tm1497, tm1524, tm2179
• curator changes for lines with WBPaper evidence - script should not touch these lines, while NBP data is not entered into the NBP comment table for these lines, the curator changes

--kjy 20:24, 9 August 2011 (UTC)

Parsing new NBP data into Postgres

.ace file is received by email, usually from Mary Ann:

*Move and rename .ace file onto tazendra to NBP_latest
*Run parsing script on tazendra  /karen/phenote/nbp_maryann/parse_maryann.pl

The script should overwrite old NBP data and enter new data into the NBP field of the phenote (variation) postgres table.

Annotating NBP data in Phenote

Retrieve new/changed NBP characters

When the NBP data are entered into postgres, Mary Ann is assigned as curator. You can retrieve all new NBP records by retrieving lines based on Mary Ann.

Or search for one of the alleles you know to be part of the new NBP phenotype batch. Once that record is retrieved in the table, you can retrieve the remaining records by NBP date.

NBP Comment of 'lethal or sterile'

Allele gets annotated for sterile and separately as lethal. In both phenotype remarks, put: -->" Classified as lethal OR sterile by the National Bioresource Project of Japan. "

NBP Comment of 'homozygous viable'

Allele gets annotated with NOT lethal -->" Classified as homozygous viable by the National Bioresource Project of Japan. "

NBP Comment changes to 'homozygous viable'

If an allele was originally classified as lethal or sterile and is now changed to homozygous viable, the new comment is only appended to one of the remarks.

You will need to retrieve the 'sterile' annotation line for that allele and check NOT for the sterile phenotype.

The phenotype remark should also be changed to "Homozygous viable; originally classified as lethal or sterile by the National Bioresource Project of Japan."

Source info

Use the NBP remark as the basis for phenotype annotations. If the comment is only from the NBP, annotate the Laboratory field with FX. If the comment is from a known lab, use the laboratory field from that lab. If there is no laboratory associated with the comment, use nothing, we do not use the Person as a reference, currently.

-cut and paste comment templates-

Comments to the National Bioresource Project of Japan:

Comment from Dr. R. Waterston to the National Bioresource Project of Japan: Dead eggs =

Originally Classified as 'homozygous viable' by the National Bioresource Project of Japan.

Classified as lethal OR sterile by the National Bioresource Project of Japan.

Classified as homozygous viable by the National Bioresource Project of Japan.
--kjy 22:45, 11 August 2010 (UTC)