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I am trying to put a GOslim ontology into ClueGO on Cytoscape to analyze my data. I have found where I can import the ontology and a databased with the ontology (http://geneontology.org/docs/download-ontology/); however, the OBO file (the file described to be needed by Cytoscape) is not downloadable. Is there different way to get the ontology into Cytoscape? or a different database to download an ontology from?

lauren melissa
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  • Which ontology are you looking for? The link you provided has the slim OBO files, they are just text files which can be saved locally and then provided to Cytoscape. – Maximilian Peters Sep 23 '20 at 07:58

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ClueGo itself contains the latest, updated and manually annotated public databases that you can check as options (checkbox with update links). The renowned public databases that can be queried through clueGo are Gene Ontology (GO - that contains subgroups such as biological processes, cellular locations and molecular modules), Reactome (for molecular, immune pathways and chemical processes), KEGG and WikiPathways. All of these would serve you the same advantages as DAVID and GoSlim.

Another addition that ClueGo and team provides is interacting binding partners (or PPI) to be visualized as Subgraphs within a molecular/immune pathway. It’s an add-on plugin called cluepedia and you should check that out if possible!

Best,

Aks

A1aks
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