What is YIOS?
The Yeast Interaction Overlap Search Engine (YIOS) is a tool for comparing protein interaction datasets against already published interaction data.
YIOS was created as part of the Genome Canada funded Integrative Biology of Yeast Project, to help researchers generating information about molecular interactions compare the results of their experiments with previously published interaction data. Primarily, YIOS is used to determine the degree of overlap between a user's interaction set and those within YIOSs interaction database.
How do I use YIOS?
On YIOS's search interface page, enter the interactions from your dataset into the text box. Interactions are specified as space separated pairs of interactor IDs. You can specify multiple interactions in the same search by entering each interaction on its own line of the text area. If you want to limit interactor ID matching to a particular database, prefix the interactor ID with the ID of the interactor database, with a ':' in between the database ID and the interactor ID (see the "How does YIOS match IDs?" section for more details on this feature). There are also a number of additional search options which you can specify to restrict the results of your search, such as restricting to interactions which were part of a particular publication. Once you've specified all your query interactions and search parameters, press the 'Submit Form' button to launch the search.
Click the 'Example' button on the search form to see an example of a populated form, which you can submit to see example results.
You can also upload a file containing interactions to search. Hit the 'browse' button to launch a file chooser dialog, and then hit the 'Submit File' button once you've selected your interaction set file to launch the search. The file should specify interactions in the same format as you would in the text area. At present, file submission mode does not apply the additional search restriction options which are possible for the text area form.
What are these 'previously published interactions?'
There exist a number of repositories which collect and store molecular interaction data generated from experiments upon publication of that data. Many of these repositories make the interaction data they collect available over the internet. YIOS collects and aggregates the interaction data from a number of these repositories in its own local database. Running YIOS involves comparison against this local copy of those interaction datasets. Currently, YIOS incorporates the following datasets:
- BioGRID's Saccharomyces Cerevisiae data, version 2.0.26
If you have ideas for other yeast datasets to include in YIOS's interaction database, please contact the site administrator.
How does YIOS match IDs?
The original interaction repositories from which YIOS gets its data label each interactor with a short label plus various primary and secondary IDs, each from a specific database. For example, an interactor may be given the label 'YPL091W', corresponding to its standard yeast ORF name, as well as the primary reference ID 'S000006012' from the database 'SGD', and secondary references 'NREF:NF00366501' and 'PIR:S61975'. By default, YIOS will compare the identifiers you specify against all of the identifiers in the original record. You can modify this behaviour to limit results to identifiers which come from a particular database by prefixing your identifiers with a specific database name followed by a colon; if you do this, YIOS will only consider an interactor ID as matching if the database ID also matches. You can also limit to particular databases through other options in the YIOS search form.
A word of warning on using these features: different interaction repositories may give different names for the same protein database. For example, BioGRID may name the Uniprot protein database as "UNIPROT", wherease IntAct may describe it as "uniprotkb"; limiting the allowable database ID to one of these will exclude results from the other. Therefore, if it is most important to minimize the number of false negatives in your search results, you should avoid using these 'limit to database' features.