Ecoliwiki is providing detailed gene reports in a community editable form. One goal for this with GMOD is to integrate annotations made in MediaWiki with a Chado database for better comprehensive genome data management. MediaWiki is a widely used wiki package and the one that backs the GMOD site, Ecoliwiki, and Wikipedia). MediaWiki is also included in the Community Annotation System.
Ecoliwiki’s Table Edit is the core for this gene-oriented community annotation database. TableEdit provides a somewhat more friendly way to edit simple tables in MediaWiki. TableEdit tables show up in a page with their own Edit link. Users who have editing privileges can add rows and columns, rename headings, and change the style of the headings row using a GUI, rather than MediaWiki’s table markup, which can be a challenge to read and update.
The TableEdit code is at http://www.mediawiki.org/wiki/Extension:TableEdit
The basic infrastructure is based on two PHP object classes, wikiBox
and TableEdit. The wikiBox object class is defined by
class.wikiBox.php in the TableEdit distribution.
wikiBoxA wikiBox object consists of a series of attributes that control the
behavior and appearance of the table and a collection of row objects
that hold the actual data. The wikiBox also has methods to manipulate
rows, serialize and unserialize its contents, and
for interacting with the MySQL database that controls
the tables.
wikiBoxRowA wikiBoxRow object holds the actual data. This is also defined in
class.wikiBox.php. The wikiBoxRow has methods for loading and saving
etc.
TableEditclass TableEdit is defined in SpecialTableEdit.body.php and is an
extension of the
MediaWiki SpecialPage
class. However, it can be invoked without generating a special page
to handle interactions between wikiBoxes and Article objects in
MediaWiki.
In constructing the first release of
EcoliWiki, we built PHP scripts to load and/or update
tables. This involved writing functions that find the box_uid of
tables of specific types on specific pages, looking for the rows that
needed updating, creating them if they did not already exist, and either
incorporating the table markup into an XML
load file for the wiki, or directly editing the page via MediaWiki’s command line utilities.
Here is a code snippet from a wrapper script
foreach ($genes as $gene){
$gene_count++;
$gene_name = $gene['feature_name'];
# require something that finds the desired page and table and edits it
require "$bot_dir/colimod_colipedia/modify_tables/test_modify.php";
if ($box){
$tableEdit = new TableEdit();
$title = Title::newFromID($box->page_uid);
$tableEdit->save_to_page($title, $box);
unset($box);
}
}
test_modify.php corrected a typo introduced by an earlier load, where
a double || was needed instead of a single | after a PMID. The
metadata is data associated with a row that is not displayed on the
page. I use this to identify rows that have been used to store a
particular kind of content. In this case, it’s rows in an allele table
that describe the availability of knockouts from a strain collection
from Hirotada Mori’s lab.
<?php
# example for modifying box without rebuilding the whole page. This example does not use metadata matching or conflict catching
$page_name = "$gene_name:Gene_Product(s)";
$template = "Gene_allele_table";
echo "$page_name\t $template\n";
$box_id = get_wikibox_id($page_name, $template);
$box_uid = get_wikibox_uid($box_id);
$box = new wikiBox();
$box->box_uid = $box_uid;
$box->template = $template;
$box->set_from_DB();
$metadata = 'keio';
$uid = 0;
$rows = get_wikibox_rows($box, $uid, $metadata);
foreach ($rows as $index=>$row){
$box->rows[$index]->row_data = preg_replace("/16738554\|\[/","16738554||[", $box->rows[$index]->row_data);
$box->rows[$index]->db_save_row();
}
?>
Making the Table Editor more useful and integrating it better with other GMOD tools was our goal for the wiki part of Hackathon 2007. See Possible TableEdit/Wiki hackathon projects for more.
Integration with Chado will require that TableEdit tables reflect data from an underlying Chado, and also that changes made in a TableEdit table be saved back to the underlying Chado. In both directions there are issues about how to handle situations where the modifications on one end might cause loss or corruption of data in the other.
This would involve:
Based on our already being able to do table insertion, row creation, row updates, and row deletion, this should be a relatively simple task of getting middleware to have Chado provide data in a form that the TableEdit can use.
This would involve:
This is a specific case of the general problem discussed at the Jan 2007 GMOD workshop - how to transform data to update Chado where the structure of the incoming data has to be manipulated to fit the Chado schema.
Some issues to discuss:
Two or more tables in a wiki could be interconnected so that updating the Table in page A triggers an update of the table in page B. Use case: GO annotations on wiki pages. If round-trips work, this should fall out of the code needed. It may then be possible to couple tables without an intermediate trip to Chado.
This one is relatively simple and we might have a prototype before the 2007 Hackathon - modify the wiki search system to restrict searching to a particular class of tables or fields.
There are many places where the TableEdit system would benefit from the addition of AJAX.
Many of the items above do not require changes to the core TableEdit extension. But we can do that too during the 2007 Hackathon, if there’s time. Some possible things to add or change