From EcoliWiki
Jump to: navigation, search


The EcoliWiki team strives to make the Wiki better. To that end, we are asking for your opinion. If there is a feature not currently available in EcoliWiki that you would like to see, describe it here. Extended discussion of different requested features can go on the discussion page.

More filamentous phages

  • M13 is up, f1, all those!

how to annotate/easier annotation

  • what do you annotate, quickview, gene, gene product?
  • does information ever flow from gene or gene-product to quickview (it doesn't look like it)
  • need a much better way to pick categories, both GO and keyword. it looks pretty haphazard now and new overlapping categories seem to be arising
  • can the damn boxes be wider?
  • why do we need two saves for table edit (update and save) isn't one enough?

Gribskov 16:32, 13 November 2008 (UTC)

Note info.jpg

In answer to your questions:

  • In the strict sense of the word, we annotate to the Gene Product. On each Product page there is a table for annotations using the GO. In the broad sense of the word, you can annotate anything, anywhere - it is a wiki!
  • The information previously did not flow from the Gene or Product pages to the Quickview pages. We have since taken your advice and made the Quickview table mirror information from the other two, in addition to providing some user-editable fields.
  • I agree with the category picking comment. Categorizing pages based on GO term happens automatically, but not by keyword. It is very easy to add a category to a page, you can view the help page here.
  • I'm not sure what you mean by "damn boxes." The tables? The size of the browser window delimits how wide the tables can be - you can try reducing the font to see if things arrange themselves better.
  • You need two saves because the table you are editing doesn't get saved when you save a row. If it did, the wiki would create a revision for every row-change, and it would seriously clog the database with revisions. As of now, you edit a copy of the table until you are done editing, and then save it back to the wiki.

I hope this helped clarify some questions. Please feel free to contact me with others.

--Daniel 15:55, 15 April 2009 (UTC)

Subunit Composition

  • Component term could be more descriptive with addition of subunit compositions (ie homomultimer/heteromultimer)

What's up and coming for EcoliWiki v2

  • Searching for information present in the tables specifically
  • If I search for multiple genes in EcoliWiki, it would be nice for the output to be given in some delimited form.

What we would like to see?

  • Search and type greek and non-English characters or some toolbar for it (lambda vs. the symbol, delta, sigma, etc.)
  • Search for phenotype and output is a list of genes
  • References- Pubmed Central IDs (for things w/o PMIDs)
  • A "Go To" alphabet to organize the category pages
  • RNAs in W3110
    • links to RFAM
    • pulldown menus for RNAs in Gbrowse
  • synthetic lethal databaseSmrlab
  • interactome data baseSmrlab-Butland, Mori, other studies you had in mind
  • Have the "edit toolbar" visible when editing tables
  • Info on or list of compounds that can be taken up by coli e.g. cAMP?
  • Make TMHMM available to users on this site
  • Promoter prediction tools
  • A tool to map genes and/or proteins from a large data set onto pathways.


  • Make TMHMM predictions and put that information on the gene products page
  • Find based on three letter gene name prefix
  • List of Essential genes
  • CGSC Strain list - we now have all the mutant alleles from CGSC in the allele tables, along with links to CGSC.
  • References- Automatic DOI's for all PMID articles. DOI's are available from PubMed/MEDLINE and hopefully can be automatically imported when the article abstract is imported. Prepending "" to a DOI gives a URL that takes the user directly to the journal's version of the online article. See, e.g, the Links section of the table on the PMID:17244358 page.
    • DOI links will be created on all new PMID pages.
  • Video clip upload
    • Not exactly upload, but you can upload to YouTube or Google Video and embed the videos here.