Processing NBP alleles

From WormBaseWiki
Jump to: navigation, search

created 16/07/08

Problems

  • 20151013 /home/acedb/karen/mid_release_scripts/nbp_maryann/parse_maryann.pl has been updated to remove any \ from the input data before processing.
  • 20151012 parsed NBP_latest but get JSON parse failure when querying for curator Mary Ann, normally, should be able to find all changed and new NBP allele entries through querying Mary Ann as curator.
    • problem was single quotes in the app_nbp tables from the script were backslashed out. These single quotes come from apostrophes within the NBP_latest file. Need to remove all \ from \' within NBP_latest before running.
  • 20140911 file was converted from rtf to txt changing the <degree> symbol to "\'c5\'e3C" and apostrophes to "/'"caused problems in the upload
21775   | homozygous viable. Dr. B. Conradt: slow growth at 15 \'c5\'e3C (possibly lethal). Dr. L. Mathies: fertile, locomotion normal, no obvious morphological defects. Dr. O. Hobert: ASE & AIY fate markers normal. Dr. J. Kaplan: non-Egl, non-Unc. | 2014-09-11 13:54:50.898092-07
 9030    | homozygous viable. Dr. B. Conradt: slow growth at 15 \'c5\'e3C (possibly lethal). Dr. L. Mathies: fertile, locomotion normal, no obvious morphological defects. Dr. O. Hobert: ASE & AIY fate markers normal. Dr. J. Kaplan: non-Egl, non-Unc. | 2014-09-11 13:54:51.025047-07
 22808   | homozygous viable. Dr. B. Conradt: slow growth at 15 \'c5\'e3C (possibly lethal). Dr. L. Mathies: fertile, locomotion normal, no obvious morphological defects. Dr. O. Hobert: ASE & AIY fate markers normal. Dr. J. Kaplan: non-Egl, non-Unc. | 2014-09-11 13:54:50.956765-07
 14772   | homozygous viable. Dr. B. Conradt: slow growth at 15 \'c5\'e3C (possibly lethal). Dr. L. Mathies: fertile, locomotion normal, no obvious morphological defects. Dr. O. Hobert: ASE & AIY fate markers normal. Dr. J. Kaplan: non-Egl, non-Unc. | 2014-09-11 13:54:50.783743-07
 14773   | homozygous viable. Dr. B. Conradt: slow growth at 15 \'c5\'e3C (possibly lethal). Dr. L. Mathies: fertile, locomotion normal, no obvious morphological defects. Dr. O. Hobert: ASE & AIY fate markers normal. Dr. J. Kaplan: non-Egl, non-Unc. | 2014-09-11 13:54:50.821237-07
 14774   | homozygous viable. Dr. B. Conradt: slow growth at 15 \'c5\'e3C (possibly lethal). Dr. L. Mathies: fertile, locomotion normal, no obvious morphological defects. Dr. O. Hobert: ASE & AIY fate markers normal. Dr. J. Kaplan: non-Egl, non-Unc. | 2014-09-11 13:54:50.865642-07
 22807   | homozygous viable. Dr. B. Conradt: slow growth at 15 \'c5\'e3C (possibly lethal). Dr. L. Mathies: fertile, locomotion normal, no obvious morphological defects. Dr. O. Hobert: ASE & AIY fate markers normal. Dr. J. Kaplan: non-Egl, non-Unc. | 2014-09-11 13:54:50.926202-07

problem solved, backslashes were removed for these objects, now postgres shows them as 15°C. Don't know if there was a change to the script to remove these types of specific backslashes; however, the

  • 20110809 curator changes to Mary Ann when no changes in the NBP comments are apparent, curator should not change
    • 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)

Updates on kyook_github_wiki --kjy 21:24, 09 July 2013 (UTC)

Parsing new NBP data into Postgres

.rtf or .txt file is received by email, usually from Mary Ann:

*Move and rename file onto tazendra to /home/acedb/karen/mid_release_scripts/nbp_maryann/NBP_latest
*Run parsing script on tazendra parse_maryann.pl*

The script should overwrite old NBP data and enter new data into the NBP field of the app_ postgres tables of the Phenotype OA.

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.

Delete the 'sterile' annotation line for that allele and check NOT for the lethal phenotype.

Change the phenotype remark to read: "Classified as homozygous viable by the National BioResource Project of Japan (NBP); originally classified as lethal or sterile."

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.

Classified as homozygous viable by the National BioResource Project of Japan. Originally classified as lethal OR sterile by the NBRP.
--kjy 22:45, 11 August 2010 (UTC)