Literature Curation

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Contents

General Info

PubMed import

  • PubMed references are imported automatically once a week; this import occurs in the middle of the night, around 1:00AM Monday.
  • Every week the newly imported literature is added to an Excel file (Literature2009) in the Curators folder on cgm-1.
  • Use SQL submit to query the database for new papers
select * from reference where date_created >= to_date('03/19/2007','MM/DD/YYYY') 
and date_created < to_date('03/20/2007','MM/DD/YYYY') 
and ref_source = 'PUBMED' 
order by reference_no
  • Copy new papers in the Literature2010.xls file on cgm1.


Saving papers to dictyBase and textpresso

  1. Each paper is saved on the dicty-curators literature folder on the bioinformatics (dicty-curators.bioinformatics.northwestern.edu server.
    • Save by PMID, also save the supplemental materials in the format:PMID-supp.pdf (add numbers after 'supp' if there is more than one supplemental file)
    • Upload in textpresso: [1]

username: dicty - pw: textpresso


Associating genes and papers

  • Associate dictyBase references with all appropriate genes. Appropriate genes include any genes involved in experiments in the paper, or key genes discussed in a review.
  • Genes mentioned only in introduction/discussion sections of papers should only be associated if the curator judges it pertinent.
  • If the curator judges that users would be interested in that paper when reading about a gene, the paper should be associated.
  • See also Link a PubMed Reference in the Curation Tools.




Associating researchers and genes

  • In cases where there are multiple PIs:
  • The gene must be the main focus of the paper (for example, if they are studying how amiB regulates acaA, they are Researchers for amiB but not acaA).
  • Associate first and senior author(s) from 'significant' publications, cloning, etc.; papers that focus on THAT gene.
  • Do not associate if they used the gene as a marker or used a mutant to study another 'major' topic of the paper.
  • Associate submitters of GenBank entries.
  • Authors of "genome-wide" papers can be included, especially if no other papers exist.
  • Do not link authors of reviews, only primary research papers.
  • When authors identify a number of mutants shown in a table but do no further analyze those mutants, they should be linked as researchers on all of those genes, but only if the genes have not been previously identified. This could be useful to link them as researchers so other colleagues may contact them.
  • See also the Curation Tools.



Annotation

Annotating genes from the literature

In general
While reading a paper, take note of all possible annotations that can be extracted from the text. This includes GO terms, phenotype, description, name description, gene product, strains, and information for the summary paragraph.


Large-scale analysis
When a paper contains results from a large-scale analysis and provides gene product information for the identified genes, annotation of those genes is up to curator discretion. If a gene product assignment seems unlikely, it is acceptable to assign a different function/process based on curator analysis. The assumption is that the authors do not spend a lot of time analyzing individual proteins in a large-scale analysis. [Add a public curator note when published function/process is overwritten?]



Literature topics

The following notes are guidlines for the use of literature topics in addition to the guidelines posted here.

  • DNA/RNA Sequence Features: Use this topic for any cloning of a gene, as authors typically have the sequence even if they don't show it.
  • Protein Physical Properties: In addition to cases in which physical properties are demonstrated experimentally, use this topic if the authors state the molecular weight, number of amino acids, etc.
  • RNA Levels and Processing: When authors look at the RNA levels of other genes in a mutant background, use this topic.
  • Regulatory Role and Regulated By: These topics apply to proteins only.



Literature curation resources



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