BioGRID Curation Guide
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curation_guide [2013/02/11 18:40] biogridadmin [Adding Interactions] |
curation_guide [2015/05/20 18:07] christie [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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| - **When is a protein considered to interact with itself as a bait and hit?** | - **When is a protein considered to interact with itself as a bait and hit?** | ||
| * This type of interaction is reserved for situations where clear evidence has been shown for the presence of a dimer or multimer. The most common experiment involves tagging a single protein with two different tags, pulling down with one and then blotting for the other. "Affinity Capture-Western" applies if it's an //in vivo// experiment and "Reconstituted Complex" if it's an //in vitro// one. Crystal structures may also show dimerization. | * This type of interaction is reserved for situations where clear evidence has been shown for the presence of a dimer or multimer. The most common experiment involves tagging a single protein with two different tags, pulling down with one and then blotting for the other. "Affinity Capture-Western" applies if it's an //in vivo// experiment and "Reconstituted Complex" if it's an //in vitro// one. Crystal structures may also show dimerization. | ||
| + | - **If I have to arbitrarily choose a directionality for an interaction should I enter the interaction twice (once in each direction)?** | ||
| + | *No, we curate using a spoke model and entering interactions in both directions will artificially inflate the number of interactions in the database (making it appear as if an interaction has been shown twice in a paper when it has not). Choose the directionality that makes the most sense based on BioGRID guidelines in the Directionality of Interactions (Baits/Hits) section and only enter the interaction once. | ||
| - **What if I'm not sure how to curate a paper?** | - **What if I'm not sure how to curate a paper?** | ||
| * If you are having trouble curating a difficult paper, then it is a good idea to email other curators for advice. | * If you are having trouble curating a difficult paper, then it is a good idea to email other curators for advice. | ||
| - **What if a paper also contains interactions for an organism I'm not working on?** | - **What if a paper also contains interactions for an organism I'm not working on?** | ||
| - | * If the paper only contains interactions from an organism that isn’t in the organism pull down menu in the IMS, then the paper can be marked as read. However, if it contains interactions in other organisms that are in the IMS, but not from the project you're working on, then switch the paper to the relevant project or "Misc". If the paper contains interactions from a variety of organisms, then go ahead and curate all of the interactions for all relevant organisms if they're straightforward. However, if there's any confusion about the genes/proteins involved, then it is best to only curate the relevant interactions for your organism of interest. When you are finished, mark the paper as read and select the 'Full Text' option for the project you're in, then email the PubMed ID to other curators who may be able to help out with the curation of interactions from other organisms in that paper. | + | * If the paper only contains interactions from an organism that isn’t in the organism pull down menu in the IMS, then move it to the "Miscellaneous curation" project. If the paper contains interactions from a variety of organisms, then go ahead and curate all of the interactions for all relevant organisms if they're straightforward. However, if there's any confusion about the genes/proteins involved, then it is best to only curate the relevant interactions for your organism of interest. When you are finished, mark the paper as read and select the 'Full Text' option for the project you're in, then email the PubMed ID to other curators who may be able to help out with the curation of interactions from other organisms in that paper. |
| - **If a paper shows that the presence of a protein is required for the formation of a protein complex, is this enough evidence to enter an interaction between the required protein and all the subunits of the complex (e.g. Fig. 1, [[http://www.jbc.org/cgi/content/full/277/50/48484|PMID: 12377768]])?** | - **If a paper shows that the presence of a protein is required for the formation of a protein complex, is this enough evidence to enter an interaction between the required protein and all the subunits of the complex (e.g. Fig. 1, [[http://www.jbc.org/cgi/content/full/277/50/48484|PMID: 12377768]])?** | ||
| * In Fig. 1 of this example, the authors show that Tim11p is required for dimerization of the FIFO-ATP synthase dimer, but they only immunoblotted with an antibody against one subunit of the F1 sector of the complex. This would not warrant entering an interaction with all of the subunits of the complex because we are not going to add inferences based on this type of in vivo data. It is also important to note that none of the existing experimental systems in the curation tool would apply to this type of experiment. | * In Fig. 1 of this example, the authors show that Tim11p is required for dimerization of the FIFO-ATP synthase dimer, but they only immunoblotted with an antibody against one subunit of the F1 sector of the complex. This would not warrant entering an interaction with all of the subunits of the complex because we are not going to add inferences based on this type of in vivo data. It is also important to note that none of the existing experimental systems in the curation tool would apply to this type of experiment. | ||
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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]]. | ||