Obsolete and replace terms 2

[jamesaoverton]

• Add obsolete.tsv and dron-obsolete.owl
• Report on common problems, e.g. use of obsolete
• Use obsolete.tsv to replace terms
• Results of obsolete-and-replace for one ingredient
• Obsolete-and-replace DrOn ingredients with non-obsolete labels in ChEBI
• Obsolete-and-replace ~8000 DrOn terms where the pair of the label+RXCUI duplicates another DrOn term -- keep the DrOn term with the lowest ID number

[jamesaoverton]

@hoganwr When you have time, please start reviewing this PR. I suggest working through the commits in order.

My next step is to obsolete about 8000 duplicate DrOn terms.

[jamesaoverton]

After obsoleting the ~8000 DrOn terms with duplicate label+RxCUI pairs, I still have about 16 DrOn terms with duplicate labels but differing RxCUIs (some obsolete). I also have 668 duplicate RxCUIs in DrOn. Most seem to be obsolete or remapped by RxNorm. We'll discuss those on the next call.

[hoganwr]

I have completed a build in commit 3af928b and it looks good. I have the build going on the subsequent commit.

[hoganwr]

I'm up to commit 4e8a376

The new ChEBIs, which are referred to via term_replaced_by on obsoleted DrOn terms, are showing up at the top level. But I think that's easily fixed by updating the ChEBI import, and perhaps the subsequent commits accomplish that.

I'm going to go ahead and move to the next commit.

[jamesaoverton]

The new ChEBIs, which are referred to via term_replaced_by on obsoleted DrOn terms, are showing up at the top level. But I think that's easily fixed by updating the ChEBI import, and perhaps the subsequent commits accomplish that.

Ok, we'll be sure that's cleaned up before we commit.

[hoganwr]

I've finished going through the commits one by one. Everything looks good.