Difference between revisions of "Data mining:WormMart:Example 6"
Line 1: | Line 1: | ||
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. | ||
− | < | + | <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><br><br>2. get a list of all anatomy terms<br><http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term><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."touch%20receptor%20neuron"&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