high-level terms in paper

[alanruttenberg]

Guy: There are a total of five placeholders (high-level terms) described in our paper: ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), and small interfering RNA (siRNA). When you edit NCRO, please add them as direct children of the term “ncRNA.” Thanks!

Jingshan

[alanruttenberg]

Done. Waiting for review from Jingshan.

[Huang-OMIT]

1. How do we handle the “small_regulatory_ncRNA” tree and other child terms defined underneath "ncRNA" in SO, including lncRNA, rRNA, siRNA, snRNA, and tRNA?
2. Can we go back to original imports for "organism," "cell," and "cell line?" - from OBI (0100026), CL (0000000), and CLO (000031), respectively.
3. ontology-metadata.owl appears in both Direct and Indirect Imports in Protege.
4. Do we wanna add "id" annotation for NCRO terms? Especially, those terms in higher levels.

[harrisonstrachan]

The following ObjectProperties are still using the old prefix ncro-obo-WorkingVersion-######:
IAO_0000117
has_integral_part
homologous_to
integral_part_of
member_of
non_functional_homolog_of
part_of
similar_to

[Huang-OMIT]

Alan: Can u take care of bullets 2, 3, and 4 in my comment, and Harrison's comment as well?

[Huang-OMIT]

Alan: Some more issues identified.
Redundant relations: three "part_of" and two "has_part" - Need to remove redundant ones.
Relation imported from BFO 1.1: "occurs in" - Can it be replaced with some OBO_REL relation?
Relations "has output," "regulates," "negatively regulates," and "positively regulates" are imported from RO - Do they need to be replaced with some OBO_REL relation?

[alanruttenberg]

I will look at these. I noticed them as well an was planning to clean them
up. Happy to hear that you are too and seeing the same issues I do :)

On Tue, Dec 1, 2015 at 3:50 PM Jingshan Huang notifications@github.com
wrote:

Alan: Some more issues identified.
Redundant relations: three "part_of" and two "has_part" - Need to remove
redundant ones.
Relation imported from BFO 1.1: "occurs in" - Can it be replaced with some
OBO_REL relation?
Relations "has output," "regulates," "negatively regulates," and
"positively regulates" are imported from RO - Do they need to be replaced
with some OBO_REL relation?

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#2 (comment).

[Huang-OMIT]

Another issue identified: there are some relations with ID like "OBO_REL#_adjacent_to" - do we wanna change to some equivalent relation ID without "#" OR leave as is?

[alanruttenberg]

We want to fix them

[Huang-OMIT]

Ok.

[Huang-OMIT]

(1) If a similar/equivalent relation is found that does not have "#", we simply import that relation.
(2) Otherwise, are we able to change the ID of an imported relation?

[alanruttenberg]

Resolved in dea10b2