Difference between revisions of "Antibody"

From WormBaseWiki
Jump to navigationJump to search
Line 21: Line 21:
 
wen@athena:~/TextPresso/TextPressoAb$ ./TextpressoAbFinder.pl
 
wen@athena:~/TextPresso/TextPressoAb$ ./TextpressoAbFinder.pl
 
This script check the result of Textpresso, compare with the antibody paper list dumped from citace, and look For Antibody papers that were not curated.
 
This script check the result of Textpresso, compare with the antibody paper list dumped from citace, and look For Antibody papers that were not curated.
 +
 
Input file 1: anti_protein.txt  -- all antibody papers found by Textpresso
 
Input file 1: anti_protein.txt  -- all antibody papers found by Textpresso
 +
 
Input file 2: WBAbPaperList.ace  -- Antibody papers curated before Textpresso time
 
Input file 2: WBAbPaperList.ace  -- Antibody papers curated before Textpresso time
 +
 
Input file 3: CurationLog/AbCurationLog.txt  -- Antibody curation log.
 
Input file 3: CurationLog/AbCurationLog.txt  -- Antibody curation log.
 +
 
Output file 1: NewAbPaper.txt  -- New antibody papers
 
Output file 1: NewAbPaper.txt  -- New antibody papers
 +
 
Output file 2: TPAbFalsePositive.txt  -- All false positive antibody papers.
 
Output file 2: TPAbFalsePositive.txt  -- All false positive antibody papers.
 +
 
1789 papers flagged by Textpresso, 1734 curated, 55 need to be checked.
 
1789 papers flagged by Textpresso, 1734 curated, 55 need to be checked.
 
Among not curated papers, 30 has anti-XXX pattern, 25 has no anti-XXX pattern.
 
Among not curated papers, 30 has anti-XXX pattern, 25 has no anti-XXX pattern.
 
1626 papers curated in citace, 1347 found by Textpresso, 279 not found by Textpresso. Recall is 0.828413284132841.
 
1626 papers curated in citace, 1347 found by Textpresso, 279 not found by Textpresso. Recall is 0.828413284132841.
518 papers identified by Textpresso are false positive. Precision is 0.710452766908888.  
+
518 papers identified by Textpresso are false positive. Precision is 0.710452766908888.  
  
 
5. The result of the script is NewAbPaper.txt. This is the list of antibody papers that need to be curated.  
 
5. The result of the script is NewAbPaper.txt. This is the list of antibody papers that need to be curated.  
 
 
 
  
 
=== Antibody curation===
 
=== Antibody curation===
Line 41: Line 44:
  
 
Curators need to document the status of every paper from NewAbPaper.txt into the curation log file AbCurationLog.txt, so that the same paper will not appear again next time.  
 
Curators need to document the status of every paper from NewAbPaper.txt into the curation log file AbCurationLog.txt, so that the same paper will not appear again next time.  
 
 
 
  
 
===Antibody curation controlled vocabulary===
 
===Antibody curation controlled vocabulary===
  
 
+
Antibody control vocabulary
//Antibody control vocabulary
 
  
 
Remark "Commercial Antibody."
 
Remark "Commercial Antibody."
Line 55: Line 54:
 
Summary "Rabbit polyclonal peptide antibody against XXX."
 
Summary "Rabbit polyclonal peptide antibody against XXX."
 
Summary "Mouse monoclonal peptide antibody against XXX."
 
Summary "Mouse monoclonal peptide antibody against XXX."
 
 
  
 
=== Antibody curation guideline===
 
=== Antibody curation guideline===
 
  
 
WormBase requires the following information for Antibody:  
 
WormBase requires the following information for Antibody:  
  
 
1. Original reference where the antibody was first reported. For antibodies that are published for the first time, list the original publication and mark the antibody as "Original_publication" antibody (these are good and valid antibody objects in WormBase.)
 
1. Original reference where the antibody was first reported. For antibodies that are published for the first time, list the original publication and mark the antibody as "Original_publication" antibody (these are good and valid antibody objects in WormBase.)
 +
 
2. targeting gene (abc-1, xyz-1 ...), clonality (polyclonal or monoclonal) and animal (rabbit or mouse ...)
 
2. targeting gene (abc-1, xyz-1 ...), clonality (polyclonal or monoclonal) and animal (rabbit or mouse ...)
 +
 
3. Antigen used to generate antibody (peptide or protein sequence)  
 
3. Antigen used to generate antibody (peptide or protein sequence)  
 +
 
4. If the antibody is from another paper, find the original antibody object and add the reference to it.  
 
4. If the antibody is from another paper, find the original antibody object and add the reference to it.  
 +
 
5. If the antibody has no original reference, create a new antibody object and mark it as "No_original_reference". If you suspect the antibody is the same as another one that was previously published, enter the "Possible_pseudonym" field.
 
5. If the antibody has no original reference, create a new antibody object and mark it as "No_original_reference". If you suspect the antibody is the same as another one that was previously published, enter the "Possible_pseudonym" field.
  

Revision as of 22:42, 22 November 2010

back to Caltech documentation

Antibody curation SOPs

Antibody first pass

These are the important files for antibody curation

1. Antibody papers are identified via a script written by Juancarlos. Here is the first pass results for antibody curation: http://textpresso-dev.caltech.edu/azurebrd/wen/anti_protein_wen The file lists paper names and the antibodies associated with them. I download the file, save it and call it: anti_protein.txt

2. Curator maintain a curation log file for all the antibody papers that were already curated. The file is called: AbCurationLog.txt

3. The curation log file listed above only document papers that were curated after Texpresso first pass was applied. Antibodies curated before that are kept in this file: WBAbPaperList.ace

4. There is a script written by Wen to screen file 1, and filter out papers in file 2 and 3 (which were already curated), then give the new paper list. The script is called: TextpressoAbFinder.pl

Here is how to use the TextpressoAbFinder.pl

wen@athena:~/TextPresso/TextPressoAb$ ./TextpressoAbFinder.pl This script check the result of Textpresso, compare with the antibody paper list dumped from citace, and look For Antibody papers that were not curated.

Input file 1: anti_protein.txt -- all antibody papers found by Textpresso

Input file 2: WBAbPaperList.ace -- Antibody papers curated before Textpresso time

Input file 3: CurationLog/AbCurationLog.txt -- Antibody curation log.

Output file 1: NewAbPaper.txt -- New antibody papers

Output file 2: TPAbFalsePositive.txt -- All false positive antibody papers.

1789 papers flagged by Textpresso, 1734 curated, 55 need to be checked. Among not curated papers, 30 has anti-XXX pattern, 25 has no anti-XXX pattern. 1626 papers curated in citace, 1347 found by Textpresso, 279 not found by Textpresso. Recall is 0.828413284132841. 518 papers identified by Textpresso are false positive. Precision is 0.710452766908888.

5. The result of the script is NewAbPaper.txt. This is the list of antibody papers that need to be curated.

Antibody curation

Curation is done via Phenote or OA.

Curators need to document the status of every paper from NewAbPaper.txt into the curation log file AbCurationLog.txt, so that the same paper will not appear again next time.

Antibody curation controlled vocabulary

Antibody control vocabulary

Remark "Commercial Antibody." Remark "Tissue Specific Antibody Marker." Summary "Rabbit polyclonal antibody against XXX recombinant protein." Summary "Rabbit polyclonal peptide antibody against XXX." Summary "Mouse monoclonal peptide antibody against XXX."

Antibody curation guideline

WormBase requires the following information for Antibody:

1. Original reference where the antibody was first reported. For antibodies that are published for the first time, list the original publication and mark the antibody as "Original_publication" antibody (these are good and valid antibody objects in WormBase.)

2. targeting gene (abc-1, xyz-1 ...), clonality (polyclonal or monoclonal) and animal (rabbit or mouse ...)

3. Antigen used to generate antibody (peptide or protein sequence)

4. If the antibody is from another paper, find the original antibody object and add the reference to it.

5. If the antibody has no original reference, create a new antibody object and mark it as "No_original_reference". If you suspect the antibody is the same as another one that was previously published, enter the "Possible_pseudonym" field.

Antibody dumper

is located in tazendra: /home/acedb/wen/phenote-antibody/dump_antibody_ace.pl

dumped out file: antibody.ace