Difference between revisions of "Data mining:WormMart:Example 6"
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<http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options.%22touch%20receptor%20neuron%22&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term> | <http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options.%22touch%20receptor%20neuron%22&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term> | ||
| − | <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><[http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options.%22touch%20receptor%20neuron%22%7Cwormbase_gene.default.filters.identity_status.%22Live%22%7Cwormbase_gene.default.filters.species_selection.%22Caenorhabditis%20elegans%22&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term%7Cwormbase_gene.default.attributes.gene http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options."touch receptor neuron"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.species_selection."Caenorhabditis elegans"&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term|wormbase_gene.default.attributes.gene]> | + | <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 (lines of anatomy term ID ONLY).<br><br>3. get a list of all 'live' Ce genes, 2nd dataset of anatomy term "touch <br>receptor neuron" incl. child terms.<br><[http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options.%22touch%20receptor%20neuron%22%7Cwormbase_gene.default.filters.identity_status.%22Live%22%7Cwormbase_gene.default.filters.species_selection.%22Caenorhabditis%20elegans%22&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term%7Cwormbase_gene.default.attributes.gene http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options."touch receptor neuron"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.species_selection."Caenorhabditis elegans"&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term|wormbase_gene.default.attributes.gene]> |
| − | <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> | + | <br>4. get a list of all 'live' Ce genes, 2nd dataset of anatomy terms in <br>anatomy_terms |
| + | |||
| + | (second Dataset Filters-><span style="display: inline;">Identification-></span>[Anatomy Term] ID(s)->Browse to upload the file anatomy_terms (a list of IDs only).<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 17:06, 8 May 2008
1. get a list of terms that include "touch receptor neuron" and all
children terms.
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 (lines of anatomy term ID ONLY).
3. get a list of all 'live' Ce genes, 2nd dataset of anatomy term "touch
receptor neuron" incl. child terms.
<http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options."touch receptor neuron"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.species_selection."Caenorhabditis elegans"&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term|wormbase_gene.default.attributes.gene>
4. get a list of all 'live' Ce genes, 2nd dataset of anatomy terms in
anatomy_terms
(second Dataset Filters->Identification->[Anatomy Term] ID(s)->Browse to upload the file anatomy_terms (a list of IDs only).
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
