http://wiki.thebiogrid.org/ 2026-10-16T10:49:38-0400 http://wiki.thebiogrid.org/ http://wiki.thebiogrid.org/lib/tpl/biogrid3/images/favicon.ico text/html 2018-08-06T09:18:38-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:biochemical_experimental_systems?rev=1533561518&do=diff Physical Experimental Systems For each interaction entered in the tool, an experimental system must be selected. The different types of physical experimental systems are described in the table below. Physical Interactions Type Description text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:direction_of_interactions?rev=1502211168&do=diff Direction of Interactions (Bait/Hit) Bait-Hit Curation When curating the interactions, we are applying a “spoke” model that directly pairs bait proteins with associated proteins (like the spokes of a wheel). Using this bait-hit approach, we are also providing some directionality to the interactions. The bait can be entered in the 'bait' column of the tool, and any relevant interacting protein(s) can be listed in the 'hit' column separated by a return. There are different options for the bait-h… text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:editing_submitted_interactions?rev=1502211168&do=diff Editing Submitted Interactions Submitted interactions can be edited by selecting the interaction in the left hand column of the IMS and clicking on the “Modify Annotation on Checked” button at the bottom of the entry form. This will pull up a menu that will allow the curator to select one of the following: text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:genetic_experimental_systems?rev=1502211168&do=diff Genetic Experimental Systems For each interaction entered in the tool, an experimental system must be selected. The experimental systems include genetic analyses. The different types of genetic experimental systems are described in the table below. text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:htp_ltp_interaction_tags?rev=1502211168&do=diff HTP and LTP Interaction Tags 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 sc… text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:modifications?rev=1502211168&do=diff Modifications A modification should only be entered in the context of an interaction, i.e. the modification occurs during an interaction, not that a previously modified protein is involved in an interaction. For this particular curation system, the 'modification' option can be applied using only the following combination: text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:phenotype_curation?rev=1502211168&do=diff Phenotype Curation 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 ( text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:qualification?rev=1502211168&do=diff Qualifications The qualification option allows you to add relevant free-text information, if necessary. For example, it can be used to specify the correct genetic context, such as gene A is synthetic lethal with gene B only when gene C is overexpressed. There are often triple mutants that show a synthetic phenotype only when all three genes are deleted. This can be noted using the text box so that users are not mislead about the interaction. However, some papers will show very complicated genet… text/html 2017-08-08T12:52:48-0400 Anonymous (anonymous@undisclosed.example.com) http://wiki.thebiogrid.org/doku.php/curation_guide:submission_and_verification?rev=1502211168&do=diff Submission and Verification 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 m…