PMID:35333350

[ValWood]

1. The annotation that were originally to meiotic chromosome alignment, but that we changed to telomere clustering, I reverted to alignment. I don't think telomere clustering is correct here, clustering is really about the attachment of the telomeres to the nuclear envelope, and this is clearly about alignment.

~2. NTR: abnormal chromatin loop formation during meiotic prophase I~ ~3. NTR: decreased number of chromatin loops during meiotic prophase I~ ~4. NTR: increased chromatin loop length during meiotic prophase I~ ~5. NTR: normal chromatin loop formation during meiotic prophase I~

6. NTR abnormal homologous chromosome pairing during meiosis I prophase
7. NTR decreased homologous chromosome pairing during meiosis I prophase

[ValWood]

most of these are already done/

Add synonyms ab/normal chromatin looping during meiotic prophase

[ValWood]

Added the remaining two terms but it would be useful to check which of the existing terms belong under abnormal/decreased homologous chromosome pairing during meiosis I prophase

also added missing synonyms

[manulera]

it would be useful to check which of the existing terms belong under abnormal/decreased homologous chromosome pairing during meiosis I prophase

I guess here the only thing to be done is to make 'decreased homologous chromosome pairing at cis-acting homologous chromosome pairing region' child of 'abnormal homologous chromosome pairing at cis-acting homologous chromosome pairing region'?

[ValWood]

So that relationship must be added by the reasoner because all [FYPO:0003054] are annotated to [FYPO:0003052] https://www.pombase.org/results/from/id/11c57a78-0930-4dd5-973e-08b64949a3b7

You could try running the reasoner within protege and see if you can see the inferred links.

[manulera]

I still don't know how to run the reasoner, and I don't know if it would mess up the edition of the ontology. However, I think moving the asserted relationship still makes sense. it's good that the reasoner picks it up, but for display purposes in protege, I guess it's good to have the asserted relationship as low in the tree as possible.

[ValWood]

I poked around and found https://oboacademy.github.io/obook/howto/installing-elk-in-protege/ I heard Pascale mention Elk, so I think this is the reasoner used by GO and uPHENO. Might be useful to try this between releases.

[ValWood]

I also asked on the Slack channel to see if this is sensible.

[ValWood]

I guess it's good to have the asserted relationship as low in the tree as possible

do you mean as close to the root node as possible ? I think the assertions are as close to root as possible so that they propagate to the descendants. I am a bit unclear on this.

[manulera]

I will check out the Elk after I make the release.

What I meant to say here:

I guess it's good to have the asserted relationship as low in the tree as possible

For the example there where we have

• Abnormal X
  • Abnormal X during phase Y
  • Decreased X during phase Y
  • others

It would make more sense to have the asserted relationships like this, I think:

• Abnormal X
  • Abnormal X during phase Y
  • Decreased X during phase Y
  • others

[ValWood]

That makes sense to me.

[manulera]

Rearranged the classes