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DataONEorg / sem-prov-ontologies

Ontologies focused on scientific observations and scientific workflow provenance.
https://ontologies.dataone.org
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clean up new ENVO import #35

Open mobb opened 7 years ago

mobb commented 7 years ago

New mireot export for ENVO has lots of bare classes. these come from the includeAllIntermediates directive. But if we leave this out (ie, includeNoIntermediates), we lose lots of axioms, and the classes they reference. So might be better to gather up those unclassified classes. could be similar to what foodon did.

At first, I think we should treat them all the same (not prune selectively). Some of these we are already importing (BFO, PATO, CHEBI) and some we are likely to want later, eg PCO. For some features that we would miss (eg, connecting diatomite to diatoms) we could later decide to selectively prune and then reproduce them in ECSO. (ENVO did this for some classes)

The 7 trees in the ENVO import have relations to ~200 classes from these ontologies: BFO CHEBI FOODON (1) GO (40) NCBITaxon (2) PATO (77) PCO (4) PO (5) UBERON (32)

Process: Step 0. Compare mob's and eolson's exports Step 1. gather foodon, go, ncbitaxon, pco, po, uberon first. Step 2. bring into ECSO and see how the classes from CHEBI, BFO, PATO look.

mobb commented 7 years ago

Step 0 done. see issue #36

mobb commented 7 years ago

new process:

  1. duplicate eolson's ENVO import (ie, w/o CHEBI)
  2. commit ontofox file for ENVO
  3. gather classes for foodon, go, ncbitaxon, pco, po, uberon ontologies in ECSO