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Add import command #75

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jamesaoverton opened this issue Mar 25, 2021 · 0 comments · Fixed by #79
Closed

Add import command #75

jamesaoverton opened this issue Mar 25, 2021 · 0 comments · Fixed by #79
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@jamesaoverton
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jamesaoverton commented Mar 25, 2021

We have Gizmos extract for getting terms out of RDFTab tables. It's close to MIREOT. That's a good start, but we want to be able to define ontology imports more concisely. In particular, given a target term, we want to be able to get sets of related terms: children, descendants, parents, ancestors.

For example:

Source ID Label Parent ID Parent Label Related
obi OBI:0000070 assay OBI:0000011 planned process children

Columns:

  • Source: optional; used to help filter which terms come from which ontologies
  • ID: required; the term ID to extract, using a prefix from the prefix table
  • Label: optional; human-readable label only for documentation purposes -- Gizmos will ignore this column
  • Parent ID: optional; assert the term as a subclass of this parent
  • Parent Label: optional; human-readable label only for documentation purposes -- Gizmos will ignore this column
  • Related: optional; can be a space-separated list of keywords: children, descendants, parents, ancestors

It's possible that we would want a "not self" keyword, but I can't think of a use case right now. We may add more keywords in the future.

The overall goal / test case is to replace OBI's OntoFox imports with a combination of this and some ROBOT commands in a Makefile recipe. We can work on higher levels of abstraction/configuration later.

Historical Notes

Ontopilot implements a version of import tables, see https://github.com/stuckyb/ontopilot/wiki/Managing-imports. This implementation inspired ROBOT remove/filter but we never followed through to provide nice import tables. OntoFox also provides similar features, but with a completely different configuration file format. All this stuff has been discussed in ontodev/robot#212.

We're trying to converge with new ODK import features, e.g.https://github.com/INCATools/ontology-development-kit/releases/tag/v.1.2.26 @matentzn Note that ODK currently includes an Entity Type column that we don't think we need here.

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