BioGRID TAB File Loader Plugin for Cytoscape
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biogrid_tab_file_loader_plugin [2010/04/15 22:45] biogridadmin |
biogrid_tab_file_loader_plugin [2010/05/10 10:41] biogridadmin |
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| ====== BioGRID TAB File Loader Plugin for Cytoscape ====== | ====== BioGRID TAB File Loader Plugin for Cytoscape ====== | ||
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| + | ===== Version 0.2 ===== | ||
| + | Update to accommodate new evidence codes 'Positive Genetic' and 'Negative Genetic'. | ||
| ===== Version 0.1 ===== | ===== Version 0.1 ===== | ||
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| **ID:** the IDs of the connected nodes separated by "(pp)".\\ | **ID:** the IDs of the connected nodes separated by "(pp)".\\ | ||
| - | **biogrid.EXPERIMENTAL_SYSTEM:** a list of values corresponding to the EXPERIMENTAL_SYSTEM column of the .tab file (see www.wiki.thebiogrid.org/#evidence_codes).\\ | + | **biogrid.EXPERIMENTAL_SYSTEM:** a list of values corresponding to the EXPERIMENTAL_SYSTEM column of the .tab file (see www.wiki.thebiogrid.org/doku.php/#evidence_codes).\\ |
| **biogrid.PUBMED_ID:** a list of values corresponding to the PUBMED_ID column of the .tab file.\\ | **biogrid.PUBMED_ID:** a list of values corresponding to the PUBMED_ID column of the .tab file.\\ | ||
| **biogrid.SOURCE:** a list of values corresponding to the SOURCE column of the .tab file.\\ | **biogrid.SOURCE:** a list of values corresponding to the SOURCE column of the .tab file.\\ | ||
| - | **biogrid.INTERACTION_TYPE:** set to the value 'Physical' if the EXPERIMENTAL_SYSTEM list has only physical experimental systems, 'Genetic' if the list has only genetic experimental systems, and 'PhysicalANDGenetic' if the list has both physical and genetic experimental systems. Experimental systems are defined as physical or genetic according to www.wiki.thebiogrid.org/#evidence_codes.\\ | + | **biogrid.INTERACTION_TYPE:** set to the value 'Physical' if the EXPERIMENTAL_SYSTEM list has only physical experimental systems, 'Genetic' if the list has only genetic experimental systems, and 'PhysicalANDGenetic' if the list has both physical and genetic experimental systems. Experimental systems are defined as physical or genetic according to www.wiki.thebiogrid.org/doku.php/#evidence_codes.\\ |
| **biogrid.NUMBER_OF_EXPERIMENTAL_SYSTEMS:** the number of values in the EXPERIMENTAL_SYSTEM list.\\ | **biogrid.NUMBER_OF_EXPERIMENTAL_SYSTEMS:** the number of values in the EXPERIMENTAL_SYSTEM list.\\ | ||
| **biogrid.NUMBER_OF_PMIDS:** the number of values in the PUBMED_ID and SOURCE lists.\\ | **biogrid.NUMBER_OF_PMIDS:** the number of values in the PUBMED_ID and SOURCE lists.\\ | ||
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| Edge colors are green for edges with biogrid.INTERACTION_TYPE=Genetic, orange for edges with biogrid.INTERACTION_TYPE=Physical, and blue for edges with biogrid.INTERACTION_TYPE=PhysicalANDGenetic.\\ | Edge colors are green for edges with biogrid.INTERACTION_TYPE=Genetic, orange for edges with biogrid.INTERACTION_TYPE=Physical, and blue for edges with biogrid.INTERACTION_TYPE=PhysicalANDGenetic.\\ | ||
| Edge thicknesses are the default thickness of 1 for edges with biogrid.NUMBER_OF_EXPERIMENTAL_SYSTEMS=1, and 3 for edges with biogrid.NUMBER_OF_EXPERIMENTAL_SYSTEMS>1.\\ | Edge thicknesses are the default thickness of 1 for edges with biogrid.NUMBER_OF_EXPERIMENTAL_SYSTEMS=1, and 3 for edges with biogrid.NUMBER_OF_EXPERIMENTAL_SYSTEMS>1.\\ | ||
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