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INCATools / dead_simple_owl_design_patterns

A simple system for specifying OWL class design patterns for OBO-ish ontologies.
http://incatools.github.io/dead_simple_owl_design_patterns/
GNU General Public License v3.0
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Rules for synonyms - how to cope with these? #3

Closed dosumis closed 7 years ago

cmungall commented 9 years ago

A basic synonym scope algebra for combining concepts:

E x E -> E
R x R -> R
N x N -> N
B x B -> B
anything else -> R

Rules for synonym types are other properties will likely be domain-specific. But some general ones:

I think it might be useful to have a type for trivial lexical shuffling. For example, a display may want to hide "development of lung" if the primary label is "lung development".

In general it would be useful to track evidence for a synonym, so we can do cascading deletes. I wonder how many stale synonyms we have in GO, or cases where we need to auto-fill.

dosumis commented 9 years ago

Plan to add the ability to specify regex patterns. Synonyms can the be specified by a mix of concatenation & regex given input synonyms.

dosumis commented 9 years ago

Scope algebra looks good.

hdietze commented 9 years ago

One thing we use in TG to exclude synonyms are (custom) scopes. For example PO has a custom scope for non-english translations, which should be avoided for the synonym generation. Maybe consider a white list or a black list of scopes as configuration option.

What should be included/excluded is often driven by the external ontology and how the use synonyms (i.e. ChEBI IUPAC synonyms are not useful).

cmungall commented 9 years ago

Good point

This could be configured either within the template, or as some kind of additional parameter or conf file passed in to the generator. The latter has the advantage of not complicating the pattern language. Also some rule may end up being procedural, which also points to outside configuration.

On 12 Oct 2015, at 11:28, hdietze wrote:

One thing we use in TG to exclude synonyms are (custom) scopes. For example PO has a custom scope for non-english translations, which should be avoided for the synonym generation. Maybe consider a white list or a black list of scopes as configuration option.

What should be included/excluded is often driven by the external ontology and how the use synonyms (i.e. ChEBI IUPAC synonyms are not useful).

Reply to this email directly or view it on GitHub: https://github.com/dosumis/dead_simple_owl_design_patterns/issues/3#issuecomment-147483642

dosumis commented 7 years ago

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