*** Andrei Petcherski SOPs: ***
Updated: August 1, 2002


How to get the latest PMIDs.

Currently, Wormbase curates CGC and PMID papers about C. elegans.
Below is the description of how PMID papers relevant to C. elegans are
selected.  The list of CGC papers is compiled by CGC and the
corresponding protocol is not described here.

1. Go to Pubmed
   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed and search
   for "elegans".  Set up the limits by choosing an Entrez date
   (e.g. 60 days or 90 days depending on when the last search was
   done) under 'Ages'.

2. Copy the results to the Clipboard using ClipAdd command.

3. Go through the abstracts one by one to determine which ones do not
   deal with C. elegans (could deal with other species with elegans in
   their names, for example).  Select these and remove them from the
   clipboard.

4. Save the remaining abstracts in the clipboard.  To do this, display
   the abstracts in ASN.1 format and push 'Save' to save the file to
   the local hardrive.

5. Email the file as an attachment to Juancarlos Chan
   (azurebrd@lek.ugcs.caltech.edu).

_______________________________________________________________________

Description of the first-pass curation.

First-pass curation is intended to extract/mark the information from
the primary research literature.  Some of the information is marked
(flagged) simply to indicate the fact that a particular type of the
information is present in the paper (e.g. gene expression data).
Later this paper will be looked at and the data extracted, but this is
outside the scope of the first-pass curation.  Other types of the
information are directly extracted during the first-pass, though some
modification of the extracted data can still occur before it is
deposited into the database (e.g. gene function description).

Description of the curation fields.

General Public
ID number:	Filled in automatically
PDF file name:	Filled in automatically
Curator:	Filled in automatically
Reference:	Filled in automatically
(Title, Journal, Year, Volume, Pages, Authors)

Full Author Names: Filled by curator if familiar with the full author
name (if known)

Gene Info: 
    Gene Symbol:
Enter new gene symbol, synonyms associated with it and CDS name if any
e.g. lag-3=sel-8=C32A3.1
Mail cgc@wormbase.org

    Mapping Data: 
Enter the mapping data from the paper.  Typically
done by cutting and pasting a paragraph with data from the pdf file.
If can't be done (e.g. the pdf is copy protected) than flag the paper
by clicking the button next to the field.  
Mail cgc@wormbase.org

    Gene Function: 
Enter a short 1-3 sentence description of the gene
product function/homology.  e.g. glp-1 encodes a protein similar to
the family of Notch receptors in fly and humans.  
Mail emsch@its.caltech.edu, ranjana@its.caltech.edu
    
    Expression Data: 
If any data describing gene expression (spacial or temporal) is
mentioned than flag the paper by clicking on the button next to the
field.  Examples of gene expression: protein expression pattern
detected by Abs, gene expression pattern as determined by a gfp or
LacZ reporter, developmental western blot analysis, developmental
northern blot analysis, RT-PCR at variuos developmental stages.
Microarray data also goes into this field.  In this case "microarray
data" should be typed in the field. 
Mail wchen@its.caltech.edu
   
    RNAi: 
Any RNAi experiment including feeding, RNAi induced by
transgenes etc. is flagged.  
Mail raymond@its.caltech.edu

    Transgene: 
Flag if an integrated transgene is used in the paper.  Typically,
don't flag if the transgene in question is a common marker like an
integrated ajm-1-gfp.
Mail wchen@its.caltech.edu

    Overexpression: 
Enter the name of the gene overexpressed followed
by semi-colon followed by the phenotype.  glp-1: Muv 
Mail emsch@its.caltech.edu

    Mosaic Analysis: 
Enter gene name followed by semi-colon followed
by the tissue where it opperates.  e.g. glp-1: germ line 
Mail raymond@its.caltech.edu

    Site of Action:
Enter gene name followed by semi-colon followed by the tissue where it
operates.
e.g. glp-1: germ line 
Mail raymond@its.caltech.edu

    Extract Antibody:
Enter the protein name to which the antibodies were made.  If the
antibodies were raise against a peptide, enter its sequence. Also enter
the type of animal in which the antibodies were raised.
e.g. Antibody to XXX-1 were raised against the C-terminal
peptide YETTIYETTIYETTI in rabbits.
Mail to no one
    
    Covalent Modification:
Flag the paper if examples of covalent modifications (experimentally
defined or predicted) are mentioned.
Mail to no one

    Allele Info: 
    New Allele: 
Enter gene name followed by semi-colon followed by new allele names.
e.g. glp-1: q224, q231, q35
Mail raymond@its.caltech.edu
    
    New Mutant Phenotype:

Enter a short 1-3 sentence description of a new mutant phenotype.
This only relates to the "genetic mutants" and not to the RNAi-induced
phenotypes.  All RNAi induced phenotypes go into the RNAi field.

e.g. glp-1(q35) mutants are Muv 
Mail emsch@its.caltech.edu
    
    Sequence Change
Flag if there are sequenced mutations in the paper.
e.g. Mutations in glp-1 in fig 1
Mail to no one

Interactions:
 
    Gene Symbols: 
Enter either one-sentence statements characterizing
gene-gene interactions or simply list the genes involved if there are
many interaction instances.  This only relates to "genetic mutants",
interaction involving RNAi are flagged in the RNAi field.  
e.g. sog-1 enhances glp-1(q231) 
Mail emsch@its.caltech.edu

    Gene Product Interaction: 
Enter one sentence descriptions for gene product interactions or list
gene/products involved.  Examples of gene-product interactions that go
into this field are: protein-protein interactions, gene regulation,
RNA-protein interactions, DNA-protein interactions.
e.g. LAG-1 binds GLP-1 (y2h and in vitro)
Mail emsch@its.caltech.edu

Sequence:
 
    Gene Structure Correction:

Compare gene structures reported in the paper with those in wormbase.
Flag if there are differences in gene structure.  Most common are
exon-intron structure discrepancies.  Indicate Genbank accession
number for the sequence if known.  Depending on the source of the
sequence enter the info either in the Sanger or the St. Louis field.
The source of the sequence is indicated in wormbase on the sequence
report page.

Sanger
Mail worm@sanger.ac.uk
St. Louis
Mail worm@sanger.ac.uk
    
    Sequence Features:
Flag if any sequence features are present.  These include:
transcription factor DNA binding sites, enhancer and promoter
elements, RNA-binding sites, DNA repeats, and transposons.  Include a
short statement about the interaction.
Mail emsch@its.caltech.edu, worm@sanger.ac.uk

Cell: 
      Cell Name:
Flag if a new cell name is used.  Indicate the name used. 
Mail raymond@its.caltech.edu
      
      Cell Function:
Flag if a novel function is described for a particular cell.  Indicate
the cell/function.  
Mail raymond@its.caltech.edu

      Ablation Data:
Flag if any cell ablation is described.
Mail raymond@its.caltech.edu

SNP: 
     New SNP:
Flag if new SNP is mentioned.
Mail to no one

     Verified SNP:
Flag if a predicted SNP was experimentally verified.
Mail to no one

Good Photo: 
Flag if there is a good photo or a drawing.
Mail to no one

Comments: 
Indicate if the paper has no curatable information.  Specifically
indicate if it is a review.  Make any other comments that are
relevant.
e.g. no curatable
Mail to no one