Gene Class Descriptions

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Gene Class Summaries

Gene class summaries are a new data type started in May 2011. The goal of this curation is to clarify what WB gene classes are, beyond a simple definition of the acronym itself. These summaries should be targeted to non-worm researchers as this is the audience that is most unfamiliar with worm biology and has the most need for a lay-person bridge to understanding the wealth of information made available through research on C. elegans and related nematodes.

Gene class summaries should contain a brief definition of the terms used in the name of the class, a brief historical note of how the genes came to be grouped together in that class, and a brief summary of the biology that is known about the members of the class or some other interesting tidbit that will entertain curiosity and further exploration into WormBase.


Number of gene classes 2270(WS225).

Tools

Textpresso: http://textpresso-dev.caltech.edu/celegans/
Do search (a good place to start is the spelled-out acronym)
Click "Use these results for sentence saver" ->needs to be fixed so all the sentences can be accessed through the sentence saver. Alternative, once a CGI/OA is built, these searches and sentences can be automatically uploaded into the curation form.
Once fixed, it should take you to the sentence saver webpage, name the file to save the textpresso results.
You should be able to access the file from the sentence saver, this will display all the textpresso results by paper.
Choose the sentences you want to use.
Name the sentence file.
That should take you to the category creator.
Name the category, choose the words to add to the category.
To see the final list, click 'Category'.
See if you can make a sentence out of it.

CGI/OA

  • Curator: drop down, add Uma. what's her person ID ? She'll get added to all the curator lists. this has been done already, she is in the curator list for the OAs. ok, then I won't add Uma.
  • Gene_class: drop down- single ontology with term info: gene_class (linkable to wormpage), description, laboratory, # of genes in class, # concise descriptions, # of cloned genes, list of all GO-bp and GO-mf associated with genes in class

AQL query used:
select a,b,c,d,e,f,g from a in class gene_class, b in a->description, c in a->designating_laboratory, d in count(select a->genes), e in count(select a->genes->concise_description), f in count(select a->genes->sequence_name), g in a->genes->GO_term
(can be limited by adding 'where e>1' for example).
where is the file ? I'm putting it in /karen/Gene_class unless you want me to put it somewhere else. that's good. You'll update it yourself with the other files ? yes, for now. I don't recall what script picks up those files. I don't think there is a script yet. well, something is parsing those files into the OA, so we'll have to change that script, which I don't recall. I don't remember if you run something manually after updating the file, or if it's a cronjob

  • Summary: big text
  • WBPaper: multi-ontology
  • Other_source: free text. just text, not bigtext ? ok, yes, big text. k
  • Summary status: dropdown- done/incomplete/recheck
  • Type of gene_class: dropdown- molecular/phenotype/phenotype-function/other

does this data get dumped in some way, and do we need to prepopulate postgres with existing data ? we won't be dumping these yet; we will manually transfer her work to postgres through the OA. cool

Gene_class term info file

Column names:

  • Gene_class
  • Description
  • Laboratory
  • Number of gene members
  • Number of gene concise desc.
  • Number of genes in class cloned
  • Associated GO terms

URL links

Please link Column -Gene class and Column -Associated GO terms to their pages in WormBase

  • Gene_class URL example for aagr

http://www.wormbase.org/db/gene/gene_class?name=aagr;class=Gene_class

  • Associated GO terms URL example for GO:0002119

http://www.wormbase.org/db/ontology/gene?name=GO%3A0002119;class=GO_term