Difference between revisions of "Data mining:WormMart:Example 6"

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1. get a list of terms that include "touch receptor neuron" and all <br>children terms.  
 
1. get a list of terms that include "touch receptor neuron" and all <br>children terms.  
  
&lt;[http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options."touch receptor neuron";ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term]&gt;<br><br>2. get a list of all anatomy terms<br>&lt;http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&amp;ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term&gt;<br>remove the 9 terms from above, save as anatomy_terms<br><br>3. get a list of all 'live' Ce genes, 2nd dataset of anatomy term "touch <br>receptor neuron" incl. child terms.<br><br>4. get a list of all 'live' Ce genes, 2nd dataset of anatomy terms in <br>anatomy_terms<br><br>5. find any gene that is in gene list 3 but not in gene list 4.<br><br>as of WS189, this results in four genes WBGene00000548 (removed in WS190), WBGene00003168, WBGene00003471, WBGene00003179<br>
+
&lt;http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&amp;FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options.&amp;quot;touch%20receptor%20neuron&amp;quot;&amp;ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term&gt;<br><br>2. get a list of all anatomy terms<br>&lt;http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&amp;ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term&gt;<br>remove the 9 terms from above, save as anatomy_terms<br><br>3. get a list of all 'live' Ce genes, 2nd dataset of anatomy term "touch <br>receptor neuron" incl. child terms.<br><br>4. get a list of all 'live' Ce genes, 2nd dataset of anatomy terms in <br>anatomy_terms<br><br>5. find any gene that is in gene list 3 but not in gene list 4.<br><br>as of WS189, this results in four genes WBGene00000548 (removed in WS190), WBGene00003168, WBGene00003471, WBGene00003179<br>

Revision as of 00:56, 8 May 2008

1. get a list of terms that include "touch receptor neuron" and all
children terms.

<http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options.&quot;touch%20receptor%20neuron&quot;&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term>

2. get a list of all anatomy terms
<http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term>
remove the 9 terms from above, save as anatomy_terms

3. get a list of all 'live' Ce genes, 2nd dataset of anatomy term "touch
receptor neuron" incl. child terms.

4. get a list of all 'live' Ce genes, 2nd dataset of anatomy terms in
anatomy_terms

5. find any gene that is in gene list 3 but not in gene list 4.

as of WS189, this results in four genes WBGene00000548 (removed in WS190), WBGene00003168, WBGene00003471, WBGene00003179