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<html><head><meta http-equiv="content-type" content="text/html; charset=UTF-8"><title>Conflict Resolution</title>

<link rel='stylesheet' title='help' href='css/help.css' type='text/css'>
</head>

<body bgcolor="#FFFFFF" text="#000000" link="#0000FF">

<h1>Conflict resolution tools in SEED</h1>

<p>This was written by SvetaG, March, 2005.</p>


<p>
In order for a protein/gene (PEG) in SEED to be connected to a Subsystem (SS) it's annotation must exactly match the name of a corresponding functional role as it appears in the table of Functional Roles in a SS.  Therefore, for a PEG to be connected to multiple SSs, their authors should agree on the name of the corresponding functional role.  The general philosophy in SEED (especially Annotators' SEED) is to build Pythagorean/Kepler's Harmony of the Spheres  - Subsystems that is, meaning that each Subsystem has to be encoded such as not to crash into any other (and ideally - to nicely cover metabolic space leaving minimal holes between them).  To do so, a number of naming conflict prevention and conflict resolution tools have been implemented:
</p>
<ol type="i" style="margin-left: 5em">
	<li>for use during initial SS encoding</li>
	<li>for use during uploading//installation of SSs developed elsewhere</li>
</ol>

<ol type="I">
	<li class="major">Tools for conflict prevention during construction of a new SS</li>

<ol type="1">
	<li>During the ground stage of SS development - putting the list of functional roles together - make sure you consult the tool:  <b>Locate PEGs in Subsystems</b> - found at the very bottom of the main <a href="/FIG/index.cgi">FIG search page</a>.  This great tool is the front line of defense against potential naming conflicts (in additions to it's many other uses).</li>

<img src="locatepegs.jpg" alt="Locate Pegs in index.cgi" width="476" height="113">



<p>
The easiest way to find out if a particular functional role has been already named and used in other SSs, type the corresponding EC number into the <b>Search</b> box.  In the absence of EC number, search can be performed using a COMPLETE role name as a query.  However, PEGs with annotations deviating even slightly from the query text (e.g. by capitalization or a space) will not be identified.
<br />
Alternatively, naming conflict prevention can be done one step further into SS development,  after the initial limited set of PEGs in a handful of genomes have been connected to a Spreadsheet.  Using PEG ID as a query, it's homologs (in a specified genome) connected to other SSs can be identified.  Note, that a genome must be denoted by it's SEED ID number, not it's name.
If search results are negative you are free to name the functional role as you like (however, see SEED naming conventions here) .  If it has been used in at least one other SSs, you must either use the exact role name or negotiate its name change with the author via E-mail.  An author's name appears at the top of each SS page.  For SEED annotators' contact info write to:  <a href="mailto:sveta@thefig.info">Sveta</a>.  
</p>

<li>
While projecting PEG annotations via homology using Similarities page, please note the "<b>In Sub</b>" column.  It shows the number of other SSs that each homolog is already connected to, warning you not to rename such PEGs lightly.  This tool doesn't tell you, which SS the homolog occurs in.  Please open the corresponding PEG page to see the list of "<b>Subsystems in which this peg is present</b>".  If in conflict - negotiate the PEG(s) name change with the SS author via E-mail.
</li>


<li>
Before renaming any functional roles in your existing SS, please check if any of them have been adopted by other SEED users.  To do so, to open your SS using the "old code":
</li>

<img src="workonss.jpg" alt="Work on subsystems menu" width="477" height="124">



<p>
It will take longer to open, but when it finely comes up -  you'll see by each role name a list of other SSs that use the same name.  Please, notify//negotiate with the authors possibility of a name change.
</p>


<li>
Finally, every "master" should shepherd his/her flock of SSs on Annotator's SEED carefully, checking periodically their integrity.  There is a great tool for that.  It can be activated from each SS page (located right above the NOTES section).  Please, use it with some regularity. 
</li>

<img src="checkss.jpg" alt="Check subsystems link" width="482" height="107">
 


<p>
When activated, this tool creates two lists of PEGs:

<div class="multipleimages">
	<img src="annotation.jpg" alt="Annotation choices from sims" width="479" height="114">
	<img src="assign.jpg" alt="Assignment buttons" width="244" height="33">
</div>

<img src="notinss.jpg" alt="Pegs not in subsystems options" width="476" height="84">

<ol type="i">
	<li><b>PEGs in Subsystem with MISMATCHING Functions</b> are PEGs that still appear connected to this SS, but which have been renamed recently by someone.  Note that "Role name" and "Function name"  columns do not match any more - hence these PEGs will be lost if you do "<b>refill from scratch</b>".  To prevent this, you can reannotate them inside this tool - using <b>Assign Roles to Selected PEGs</b> button.  As always, before doing this negotiate the change with other SEED "masters".  </li>
	<li><b>PEGs NOT in Subsystem with MATCHING Functions</b>.  Those PEGs will automatically associate with this SS when the corresponding genomes will be added to it.  For PEGs in the genomes already connected to SS use "<b>refill from scratch</b>" function on a SS page (you'll need to exit <b>Check Subsystem</b> window to use it).</li>
</ol>
</p>
</ol>

<li class="major">Conflict resolution during SS uploading and installation</li>
	
	<p>
	Often Subsystems created on different SEED servers by different curators can contain identical functional roles (and PEG assigned with these roles) named slightly differently.  When a SS from a remote server is uploaded into your version of SEED recklessly, these 'shared' PEGs are automatically renamed in your SEED, and therefore are disconnected from resident SS(s.)  To prevent or resolve these naming conflicts, every incoming SS should pass through a series of checks.  To activate them, do the following:
	</p>
	
	
	<ol type="1">
		<li>On the <a href="/FIG/p2p/new_seed_update_page.cgi">SEED Peer to Peer Updates</a> page mark the check-box near the SS you need to upload.  Scroll all the way to the bottom of this page, make sure that the <b>Enqueue Subsystems check-box is marked</b>, and press the <b>Install Checked Subsystems button</b>.  Then follow the link called <a href="/FIG/p2p/show_queue.cgi?user=None">subsystem update queue</a> located in the middle of the same page:</li>

<img src="enqueue.jpg" alt="Link to Enqueue Installations" width="482" height="107">



		<li>There you'll see many SSs in queue - wait until yours (the bottom one) is processed - then click on <b>Show analysis</b> - and you'll see in minute detail all the terrible harm to resident SSs you were about to cause by uploading the new one:  </li>

<img src="overlap.jpg" alt="Overlap between subsystems" width="481" height="277">

		<li>If it looks benign - press <b>Install subsystem</b> button, then <b>delete SS from queue</b>.  </li>
		<li>If it looks horrible - it is your responsibility to contact the author ("master") of each SS, which the incoming SS is trespassing into - and to resolve naming conflicts with them by E-mail.  To find out the authorship of affected SSs - click on each <b>Local Subsystem</b> name to open it - the author's name appears at the top of each SS page. For the authors' contact info write to: <a href="mailto:sveta@thefig.info">Sveta</a>.  </li>
		<li>In the meantime:</li>
	
		<ol type="i">
			<li>register all the conflicts and planned changes in Word or any other format</li>
			<li>check <b>skip PEG</b> boxes for all the PEGs that require attention of other SEED annotators </li>
			<li>press <b>Install subsystem</b> button.  Do not <b>delete SS from queue</b> if there are unresolved naming conflicts left.</li>
		</ol>
	
	
		<li>Generate E-mails to the authors of all affected SSs.</li>
		<li>Depending on their responses you will need either:</li>
	
		<ol type="i">
			<li>to change the names of affected roles in the newly installed SS to match the resident ones, or </li>
			<li>to rename all the affected resident PEGs to match the role in the new SS (if all the authors of affected SSs have found the role names in the newly installed SS superior) </li>
		</ol>
	
	
		<li>To change the naming of functional role(s), open the newly installed SS, delete the old name and type in the new.  Now check <b>refill from scratch</b> check-box (located under the spreadsheet) and press <b>update spreadsheet</b> button.  </li>
	
		<li>To rename affected resident PEGs in batch, use <b>Generate Assignments via Translation</b> tool.  It can be activated from the SEED main <a href="/FIG/index.cgi">FIG search page</a> (located mid-page):</li>
	 
<img src="assviat.jpg" alt="Assignments via translation" width="479" height="214">
	 
	<li>To use this tool:</li>
	 
		<ol type="a">
			<li>type in your user name in the Section: <b>Exporting Assignments</b> in the box <b>Save as user</b></li>
			<li>to the <b>From</b> box paste "Branched-chain amino acid aminotransferase (EC 2.6.1.42)" from an example above</li>
			<li>to the <b>To</b> box paste "D-alanine aminotransferase (EC 2.6.1.21)"</li>
			<li>click on the <b>Generate Assignments via Translation</b> button  </li>
			<li>when the job is done, go to <b>Process Saved Assignments Sets</b> section down the same <a href="/FIG/index.cgi">FIG search page</a>:</li>

<img src="processsavedassign.jpg" alt="Process Saved Assignments" width="482" height="129">

			<li>type in your user name WITH master:____ and click on '<b>Process Assignments Sets</b> button</li>
			<li>examine, accept (if OK) and delete (!!!) the set.</li>
		</ol>
	</ol>
</ol>



<a name="conflicts"><h2>Conflicts</h2></a>

<p>Please also see the <a href="/FIG/Html/conflict_resolution.html">Conflict Resolution</a> help page.</p>

<p>A new tool to straighten out conflicts in peg assignments.  If you use the URL:</p>

<div class="code" style="text-align:center">          
<a href="http://yersinia.uchicago.edu/FIG/conflicted_pegs.cgi?user=master:" target="_blank">http://yersinia.uchicago.edu/FIG/conflicted_pegs.cgi?user=master:XXXXXX</A>
</div>

<p>where XXXXXX is your user name, you should get a summary of your conflicts.</p>

<p>For example,</p> 

<div class="code" style="text-align:center">          
<a href="http://yersinia.uchicago.edu/FIG/conflicted_pegs.cgi?user=master:RobE" target="_blank">http://yersinia.uchicago.edu/FIG/conflicted_pegs.cgi?user=master:RobE </a>
</div>

<p>would produce a short report for RobE.</p>

<div class="example">
<div style="font-size:150%; font-weight: stronger">Sulfate_to_Sulfide</div>
<ul>
<li> 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase
<ul><br>
<li> <a href=http://yersinia.uchicago.edu/FIG/protein.cgi?prot=fig|633.2.peg.468&user=master:RobE>fig|633.2.peg.468</a> &nbsp; 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase
<br>
<br>
<table border>
	<caption><b>In These Subsystems</b></caption>

	<tr>
				<th>subsystem</th>
		<th>role</th>
		<th>curator</th>
	</tr>
	<tr>
		<td>cysteine_biosynthesis</td>

		<td>3'-phosphoadenoside 5'-phosphosulfate metabolism (cysQ)</td>
		<td>RobE</td>
	</tr>
</table>
<br><br><br>
<li> <a href=http://yersinia.uchicago.edu/FIG/protein.cgi?prot=fig|12149.1.peg.4378&user=master:RobE>fig|12149.1.peg.4378</a> &nbsp; 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase
<br>
<br>

<table border>
	<caption><b>In These Subsystems</b></caption>
	<tr>
				<th>subsystem</th>
		<th>role</th>
		<th>curator</th>
	</tr>

	<tr>
		<td>cysteine_biosynthesis</td>
		<td>3'-phosphoadenoside 5'-phosphosulfate metabolism (cysQ)</td>
		<td>RobE</td>
	</tr>
</table>
<br><br><br>
<li> <a href=http://yersinia.uchicago.edu/FIG/protein.cgi?prot=fig|83333.1.peg.4124&user=master:RobE>fig|83333.1.peg.4124</a> &nbsp; 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase

<br>
<br>
<table border>
	<caption><b>In These Subsystems</b></caption>
	<tr>
				<th>subsystem</th>
		<th>role</th>
		<th>curator</th>

	</tr>
	<tr>
		<td>cysteine_biosynthesis</td>
		<td>3'-phosphoadenoside 5'-phosphosulfate metabolism (cysQ)</td>
		<td>RobE</td>
	</tr>
</table>
<br><br><br>

<li> <a href=http://yersinia.uchicago.edu/FIG/protein.cgi?prot=fig|83334.1.peg.5171&user=master:RobE>fig|83334.1.peg.5171</a> &nbsp; 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase
<br>
<br>
<table border>
	<caption><b>In These Subsystems</b></caption>
	<tr>
				<th>subsystem</th>
		<th>role</th>

		<th>curator</th>
	</tr>
	<tr>
		<td>cysteine_biosynthesis</td>
		<td>3'-phosphoadenoside 5'-phosphosulfate metabolism (cysQ)</td>
		<td>RobE</td>
	</tr>

</table>
</div>


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