http://wiki.thebiogrid.org/ 2012-02-06T06:52:41-05:00 http://wiki.thebiogrid.org/ http://wiki.thebiogrid.org/lib/tpl/biogrid3/images/favicon.ico text/html 2012-02-02T18:46:56-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/curationguide_phenotype_curation?rev=1328226416&do=diff Yeast Phenotype Curation Here are the instructions for adding phenotypes to genetic interactions using the experimental systems and the 'observables' from the Yeast Phenotype Ontology (YPO). Please note that the YPO is still evolving, and if we come across missing terms we can request them by sending an email to SGD (<pheno-curator@genome.stanford.edu>). Selecting a genetic interaction type will open up tree display of SGD's observable ontology in the lower left corner of the curator form. Clic… text/html 2012-02-01T22:36:21-05:00 rose http://wiki.thebiogrid.org/doku.php/results?rev=1328153781&do=diff The following is an example layout viewed when searching for your protein of interest within the BioGRID. We've outlined all areas of interest with yellow letters, and defined what each area represents in the definitions at the bottom of the page. Layout Legend * A - Standard annotation data for search results including official name, synonyms, organism name, and description. * B - Gene Ontology summary for the search result. If you're interested in seeing the full details for this resul… text/html 2012-02-01T22:28:03-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/identifiers?rev=1328153283&do=diff While we do support a wide variety of identifiers, our goal of limiting redundancy in our search results means that several large sequence databases such as Genbank and Ensembl do not have all their ID's available in the BioGRID. With each annotation update, our coverage increases by hundreds of thousands of new identifiers so please be patient if your ID is not currently supported. If you have a suggestion for a new identifier type, please let us know at <biogridadmin@gmail.com>. text/html 2012-02-01T18:39:45-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/aboutus?rev=1328139585&do=diff The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org). BioGRID currently holds over 460 000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 30 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission… text/html 2012-02-01T06:28:23-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/build_3.1.85?rev=1328095703&do=diff Organism Experiment Type Raw Interactions Non-Redundant Interactions Unique Proteins Unique Publications Arabidopsis thaliana PHYSICAL 14935 12459 5446 986 GENETIC 185 126 103 60 COMBINED 15120 12567 5487 1035 Bacillus subtilis 168 PHYSICAL 1 1 2 1 GENETIC 0 0 0 0 COMBINED 1 1 2 1 Bos taurus PHYSICAL 123 109 136 50 GENETIC 0 0 0 0 COMBINED 123 1… text/html 2012-02-01T04:14:57-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/statistics?rev=1328087697&do=diff This page shows the latest snapshot of statistics for the BioGRID database. All previous snapshots are archived below separated by year. * Raw Interactions - Each unique combination of interactors A and B, experimental system and publication is counted as a single interaction. Reciprocal interactions (A → B and B → A) are counted twice. * Non-Redundant Interactions - Each unique combination of interactors A and B are counted as a single interaction, regardless of directionality, experime… text/html 2012-01-23T23:58:08-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/curation_guide?rev=1327381088&do=diff Introduction The Biological General Repository for Interaction Datasets (BioGRID) is a database of physical and genetic interactions developed by Mike Tyers' group. It contains high-throughput (HTP) interaction data for Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and other organisms. For yeast, BioGRID also contains many genetic and protein interactions curated from the primary literature. SGD has incorporated BioGRID's interaction data and will also… text/html 2012-01-23T23:43:29-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/curationguide_submission_and_verification?rev=1327380209&do=diff Submit the entry by clicking the 'Add as Interactions' or 'Add as Complex' button, as appropriate. Submitted interactions are listed below the interaction form in the tool. It is a good idea to review any interaction(s) you have added to make sure everything is correct. An error log is provided on the right hand side of the curation form indicating any errors, duplicated entries, and so forth. If there is an error message showing that a bait or hit is unknown, then make sure it's the systematic … text/html 2012-01-23T23:41:15-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/curationguide_htp_ltp_interaction_tags?rev=1327380075&do=diff Once you have entered all of the necessary interaction information, select one of two interaction tags: 'High Throughput' or 'Low Throughput' to specify the type of experiment. The default is LTP unless the curator makes a call that a dataset is HTP. The HTP tag should be used for experiments involving over 100 interactions using a high-throughput method like affinity capture-MS, SGA, etc.. However, if a small set of interactions is clearly generated by a primary screen and not validated in any … text/html 2011-01-23T09:14:40-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=qtip.jpg&ns=&rev=1295792080&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/qtip.jpg?w=125&h=60t=1327362501" alt="qtip.jpg" /> text/html 2010-12-11T12:02:42-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=mgi.jpg&ns=&rev=1292086962&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/mgi.jpg?w=125&h=60t=1327362502" alt="mgi.jpg" /> text/html 2010-12-11T12:01:28-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=zfin.jpg&ns=&rev=1292086888&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/zfin.jpg?w=125&h=60t=1327362502" alt="zfin.jpg" /> text/html 2010-11-01T12:26:26-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=mi_biogrid_participant_map.xls&ns=&rev=1288628786&tab_details=history&mediado=diff&do=media text/html 2010-11-01T12:26:08-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=mi_biogrid_experiment_map.xls&ns=&rev=1288628768&tab_details=history&mediado=diff&do=media text/html 2010-09-13T15:07:30-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=irefweb.jpg&ns=&rev=1284404850&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/irefweb.jpg?w=125&h=60t=1327362501" alt="irefweb.jpg" /> text/html 2010-04-21T09:48:56-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=biogrid_data_submission_form.xls&ns=&rev=1271857736&tab_details=history&mediado=diff&do=media text/html 2010-04-19T11:22:23-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=genemania.jpg&ns=&rev=1271690543&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/genemania.jpg?w=125&h=60t=1327362501" alt="genemania.jpg" /> text/html 2010-04-19T11:06:18-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=mpact.jpg&ns=&rev=1271689578&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/mpact.jpg?w=125&h=60t=1327362502" alt="mpact.jpg" /> text/html 2010-04-19T11:02:58-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=mpidb.jpg&ns=&rev=1271689378&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/mpidb.jpg?w=125&h=60t=1327362502" alt="mpidb.jpg" /> text/html 2010-04-19T10:58:57-05:00 biogridadmin http://wiki.thebiogrid.org/doku.php/?image=matrixdb.jpg&ns=&rev=1271689137&tab_details=history&mediado=diff&do=media <img src="/lib/exe/fetch.php/matrixdb.jpg?w=125&h=60t=1327362501" alt="matrixdb.jpg" />