edOTTs

JSON edits usable as inputs to otcetera otc-taxonomy-patcher tool (currently on the taxonomy-diff-maker branch) for editing the Open Tree of Life Taxonomy (ott).

Provenance will later be inlined. Currently:

1. edott-000001.json - Homo sapiens sapiens should no longer be hidden. See OpenTreeOfLife/reference-taxonomy#374

2. edott-000002.json - flagging extinct and extinct_inherited as incertae_sedis, which is how the synthesis algorithm treats them.

3. edott-000003.json - simple taxon additions taken from the commits between 12c810f5da4cc4c32ea2f6e3c6993eb18b0d2586 and 77292e0e8f31ae3f4266531ee4ec14e1c5562a74 in https://github.com/OpenTreeOfLife/amendments-1

The next 5 edits are from the taxon amendments that fall within the range included in edott-000003.json, but they required some hand editing.

1. edott-000004.json - Bucco noanamae is the preferred name, but an unrecognized synonym of the genus name Nystactes caused this bird species to be in the Heteroconger eels in OTT 3.2

2. edott-000005.json - Cirrhilabrus briangreenei was assigned 2 IDs because the taxon additions are not live in the TNRS.

3. edott-000006.json - Celeus ochraceus was assigned 2 IDs because the taxon additions are not live in the TNRS.

4. edott-000007.json - Alopochen mauritiana was assigned 2 IDs because the taxon additions are not live in the TNRS.

5. edott-000008.json - Poospiza nigrorufa is not an synonym of Sporophila nigrorufa

6. edott-000009.json No hand edits recorded

7. edott-000010.json No hand edits recorded

More automatic updates:

1. edott-000011.json amendment-1 sha = 5f4764d6f0f4b2908465100fae724640b6306153

2. semanticize_amendments.py amendments-1 5f4764d6f0f4b2908465100fae724640b6306153 > edott-000012.json while amendments-1 was at 2faeefa1549ad7c231533528d1ec1dc1420060bd

3. edott-000013 is still in progress, but started via running semanticize_amendments.py amendments-1 2faeefa1549ad7c231533528d1ec1dc1420060bd > edott-000013.json while amendments-1 was at 09800651d3bef9f335fe663951cdc9d857ffa084 see notes/edott-000013-notes.md for some notes.