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make the small pathogen-host interaction phenotypes avaiable in obo format #1350

Closed ValWood closed 6 years ago

ValWood commented 7 years ago

This might already be available as part of previous work?

CuzickA commented 7 years ago

I have added the most recent versions from Alistair's files into the Dropbox 'PHI-base' folder created by Kim R. These include the 9 high level phenotype terms and working progress on lower level terms.

ValWood commented 7 years ago

From the discussion It is required that all pathogen host interactions map to one of the "high level terms" for export to other resources

This could be achieved by making these " a subset/ or slim" Terms where a more specific annotation is required in order for an annotation to be made under one of the high level terms could be flagged as "do not annotate" so that a more specific annotation under the appropriate high level terms is always obtained.

We use a very similar procedure with GO to force annotation specificity.

the example we discussed was "penetration" PHI phenotypes reduced virulence (quantitative, some disease) —- penetration reduced —loss of pathogenicity (qualitative no disease) —- penetration abolished altered penetration

ValWood commented 7 years ago

I do not see the dropbox PHI-base folder Could you send me a link?

ValWood commented 7 years ago

I was going to look at your ontology. Do you have textual definitions for all of the terms yet?

To make development easier you will need "logical definitions" and @mah11 will be able to advise you on this soon. It will be helpful if you have "textual definitions" in place, and if these could follow standard design patterns. You can look at FYPO to see how Midori has constructed these.

It should not be too big a task whilst your ontology is still small.

ValWood commented 6 years ago

transferred to https://github.com/PHI-base/PHI-base_ontologies/issues/4