Chris-Evelo
commented
4 years ago These are probably stubs. We even have a tool to create these pathways automatically from the Gene Ontology themselves. That can be useful in case you want enrichment analysis to include a part of the gene ontology that is not covered by a real pathway yet. In that case, it could also serve as the start of a real pathway (which obviously didn't really work then). Note that using a few of these pathways is more integrated than doing GO analysis separately, although that often is the reason to find them in the first place.
I would: 1) Check for each of these whether we have a real pathway that covers the same process. If that is the case just delete the "table" pathway" 2) Check out that tool (sorry can't think of the name right now) and add some documentation so people that really want more pathways like that can just generate them "locally" 3) If there are any of these tables that you want to keep, because they really describe a field not covered by a current pathway update them using that same tool (simply create a new one) and also add them to the wishlist. Like "we would really want a real pathway for this, currently we only have GO based table). Maybe also add that to descriptions?
During the Curation Cafe (2020-01-30); we found quite some (old) PWs which are "annotated lists". Do we want to keep these, or should we make this data available in another manner? Quite some of these have been made based on "Gene Ontologies", so I think there are better alternatives to perform PW/network analysis on them. Besides, these PWs are not well maintained, often missing lit.refs/description/proper IDs (or all of the above), and we don't have a curation protocol for them...