BioGRID Curation Guide
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curation_guide [2013/02/11 18:40] biogridadmin [Adding Interactions] |
curation_guide [2013/11/06 19:24] jenn [Curation Questions and Answers] |
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| - **What about genes that are 'not physically mapped' in SGD or genes that only encode RNA products?** | - **What about genes that are 'not physically mapped' in SGD or genes that only encode RNA products?** | ||
| * Currently, the tool will not allow you to enter genes that are 'not physically mapped' in SGD. This is also true for genes that only encode RNA products (e.g. Tlc1, Snr1). However, you can use the "force interactions" option to enter the gene names for now. The IMS system will eventually be updated to recognize these features. | * Currently, the tool will not allow you to enter genes that are 'not physically mapped' in SGD. This is also true for genes that only encode RNA products (e.g. Tlc1, Snr1). However, you can use the "force interactions" option to enter the gene names for now. The IMS system will eventually be updated to recognize these features. | ||
| + | - **What is the difference between “Affinity Capture-MS/Western” and “Reconstituted Complex"?** | ||
| + | * If the relevant proteins are co-expressed in the cell, then the interaction is considered to occur //in vivo// and can be classified as "Affinity Capture-Western" or "Affinity Capture-MS". If the bait is not co-expressed in the cell, but merely purified and incubated with a cell lysate //in vitro// or even purified recombinant proteins (e.g. GST pull-down), then we use the //in vitro// option of "Reconstituted Complex". | ||
| - **What if an interaction can't be assigned one of the available experimental system categories?** | - **What if an interaction can't be assigned one of the available experimental system categories?** | ||
| * Occasionally, an interaction cannot be readily assigned a protein or genetic interaction category, in which case, the closest substitute should be chosen and an explanation of the exact experimental context should be given in the qualification text box. | * Occasionally, an interaction cannot be readily assigned a protein or genetic interaction category, in which case, the closest substitute should be chosen and an explanation of the exact experimental context should be given in the qualification text box. | ||
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| - ** Do we curate cross-species interactions?** | - ** Do we curate cross-species interactions?** | ||
| * We curate cross-species interactions, e.g. between a yeast and a human protein. The curation tool allows us to select separate species for the bait and hit using the relevant pulldown menus. However, this does not include cross-species complementation experiments because they are not really genetic interactions between two genes, but rather a test to determine functional orthologs in other species. | * We curate cross-species interactions, e.g. between a yeast and a human protein. The curation tool allows us to select separate species for the bait and hit using the relevant pulldown menus. However, this does not include cross-species complementation experiments because they are not really genetic interactions between two genes, but rather a test to determine functional orthologs in other species. | ||
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| ===== BioGRID Team Members, References, and Funding Details ===== | ===== BioGRID Team Members, References, and Funding Details ===== | ||
| For more information on the BioGRID and the history of the BioGRID, a full list of our publications, team members, and funding sources can be found on our [[aboutus|About Us Page]]. | For more information on the BioGRID and the history of the BioGRID, a full list of our publications, team members, and funding sources can be found on our [[aboutus|About Us Page]]. | ||