Missing species in the old protein tree test build
Closed this issue · 3 comments
dmx2 commented
Examples:
Gallus gallus
Fagopyrum tataricum
Hepatitis C virus
Alnus glutinosa
Likely to do with the way molecule-tree.owl file is built fromnanobot.db protein_tree_old table.
jamesaoverton commented
I don't think the conversion from "protein_tree_old" to molecule-tree.owl is the problem. On arborist-dev.lji.org in /mnt/data/arborist/build/arborist/nanobot.db for "protein_tree_old", I see a parent node:
sqlite3 build/arborist/nanobot.db "SELECT * FROM protein_tree_old WHERE subject = 'iedb-protein:9031'"but I don't see any child nodes, which should be returned by:
sqlite3 build/arborist/nanobot.db "SELECT * FROM protein_tree_old WHERE object = 'iedb-protein:9031'"So I think the necessary rows are just missing from "protein_tree_old".
jamesaoverton commented
I would also expect to see rows for particular chicken proteins in "protein_tree_old", but I don't:
sqlite3 build/arborist/nanobot.db "SELECT * FROM protein_tree_old WHERE subject = 'UP:P01012'"In contrast I get results for human insulin:
sqlite3 build/arborist/nanobot.db "SELECT * FROM protein_tree_old WHERE subject = 'UP:P01308'"