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.<br> | 1. get a list of terms that include "touch receptor neuron" and all <br>children terms.<br> | ||
| − | <http:// | + | <http://caprica.caltech.edu:9002/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:// | + | <br>2. get a list of all anatomy terms<br><http://caprica.caltech.edu:9002/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://caprica.caltech.edu:9002/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://caprica.caltech.edu:9002/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>4. get a list of all 'live' Ce genes, 2nd dataset of anatomy terms in <br>anatomy_terms | ||
Latest revision as of 10:39, 31 January 2013
Links on this page are out of date.
1. get a list of terms that include "touch receptor neuron" and all
children terms.
2. get a list of all anatomy terms
<http://caprica.caltech.edu:9002/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://caprica.caltech.edu:9002/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
