Update rRNA_gene hierarchy to mirror rRNA hierarchy

[sjm41]

Current rRNA hierarchy looks like this:

rRNA
    |_large_subunit_rRNA
        |_rRNA_21S
        |_rRNA_23S
        |_rRNA_25S
        |_rRNA_28S
        |_rRNA_5S
        |_rRNA_5_8S
    |_mt_rRNA
    |_small_subunit_rRNA
        |_rRNA_16S
        |_rRNA_18S

(though see request for improvements in #493)

In contrast, the rRNA_gene hierarchy is flatter and lacks any mt_rRNA_gene specification:

rRNA_gene
    |_rRNA_16S_gene
    |_rRNA_18S_gene
    |_rRNA_21S_gene
    |_rRNA_23S_gene
    |_rRNA_25S_gene
    |_rRNA_28S_gene
    |_rRNA_5S_gene
    |_rRNA_5_8S_gene

Once the rRNA tree has been improved as per #493, can you make the rRNA_gene tree match it?

[sjm41]

Hi @davidwsant

So, if we want to mirror the revised rRNA tree structure exactly, I think we need:

rRNA_gene
    |_cytosolic_rRNA_gene (NEW)
        |_cytosolic_LSU_rRNA_gene (NEW)
            |_cytosolic_2S_rRNA_gene (RENAME)
            |_cytosolic_23S_rRNA_gene (RENAME)
            |_cytosolic_25S_rRNA_gene (RENAME)
            |_cytosolic_28S_rRNA_gene (RENAME)
            |_cytosolic_5S_rRNA_gene (RENAME)
            |_cytosolic_5_8S_rRNA_gene (RENAME)
        |_cytosolic_SSU_rRNA_gene (NEW)
            |_cytosolic_16S_rRNA_gene (RENAME)
            |_cytosolic_18S_rRNA_gene (RENAME)
    |_mt_rRNA_gene (NEW)
        |_mt_LSU_rRNA_gene (NEW)
        |_mt_SSU_rRNA_gene (NEW)
    |_plastid_rRNA_gene (NEW)
        |_plastid_LSU_rRNA_gene (NEW)
        |_plastid_SSU_rRNA_gene (NEW)

(And then delete the existing rRNA_21S_gene term referring specifically to a yeast mt_LSU_rRNA gene)

If that looks good to you, I could check/supply definitions based on what we did for the rRNAs. In that regard, it best practice to say something like: "A gene that codes for cytosolic 5S_rRNA (SO:0000652)." and leave the definition on the related SO term or repeat the definition in full, like: "A gene that codes for cytosolic 5S_rRNA (SO:0000652), an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes."

[egchristensen]

@sjm41 Is there anything left to do on this issue, or did @davidwsant take care of this with his last update?

[sjm41]

@egchr There's been no work at all on this ticket AFAIK. Compare the the tree in my previous comment to that at http://sequenceontology.org/browser/current_svn/term/SO:0001637 Would be very happy if you could implement the new tree (so that the rRNA_gene and rRNA trees then match)!

[sjm41]

Hi @egchr Thanks for addressing my other ncRNA tickets! Would be great if this one could also be addressed ahead of the RNAcentral meeting next week.

[egchristensen]

@sjm I believe I have taken care of the hierarchy as you intended, but could I ask you to double check?

@keilbeck Just double checking that I’m ok to obsolete the term “rRNA_21S_gene” or do we need to discuss this more? The comments for that term currently read, “Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472) Removed relationship derives_from SO:0001171 on 10 June 2021 when SO:0001171 rRNA_21S was obsoleted into SO:0002345 mt_LSU_rRNA. See GitHub Issue #493.”

[sjm41]

Thanks @egchr !

SO:0002241 (rRNA_21S_gene) could be made a secondary ID of the new 'mt_LSU_rRNA_gene' term, to at least preserve the ID for searching etc. (I think that's what happened for the SO:0001171 rRNA_21S term.)

[sjm41]

@egchr New rRNA_gene hierarchy looks good, thanks.

I think these parents need adding though:

• mt_rRNA_gene: add 'mt_gene' (SO:0000088) as parent
• plastid_rRNA_gene: add plastid_gene (SO:0000090) as parent

[sjm41]

One other thing - all of the 'old' rRNA_gene terms have a 'derives from' relationship to the corresponding rRNA. E.g.: id: SO:0002236 name: cytosolic_rRNA_18S_gene is_a: SO:0002362 (cytosolic_SSU_rRNA_gene) relationship: derives_from SO:0000407 (cytosolic_18S_rRNA)

I think this must be a mistake - if anything, the relationship should be the other way round - the rRNA derives from the corresponding rRNA_gene.

Terms affected: cytosolic_rRNA_23S_gene cytosolic_rRNA_25S_gene cytosolic_rRNA_28S_gene cytosolic_rRNA_2S_gene cytosolic_rRNA_5S_gene cytosolic_rRNA_5_8S_gene cytosolic_rRNA_16S_gene cytosolic_rRNA_18S_gene

[sjm]

Just a heads-up; I've been getting some of the alerts which I think should be heading towards @sjm41 - looks like they picked up on the thread, anyway.

Just thought I'd let you know!

[sjm41]

Aha, thanks @sjm ! Yes, @egchr please use @sjm41 !

[egchristensen]

@sjm @sjm41 Sorry about that! My mistake.

[sjm]

No problem- easily done. I should clearly have chosen a longer username ;-)

[sjm41]

Hi @egchr Did you see my comments of 22nd Nov?

[egchristensen]

@egchr New rRNA_gene hierarchy looks good, thanks.

I think these parents need adding though:

* mt_rRNA_gene: add 'mt_gene' (SO:0000088) as parent

* plastid_rRNA_gene: add plastid_gene (SO:0000090) as parent

@sjm41 Added these in commit 13f2da99bc2f28dda7d1e8006fd1a5b95d37872a.

[egchristensen]

Thanks @egchr !

SO:0002241 (rRNA_21S_gene) could be made a secondary ID of the new 'mt_LSU_rRNA_gene' term, to at least preserve the ID for searching etc. (I think that's what happened for the SO:0001171 rRNA_21S term.)

@davidwsant am I ok to obsolete this term?

[egchristensen]

One other thing - all of the 'old' rRNA_gene terms have a 'derives from' relationship to the corresponding rRNA. E.g.: id: SO:0002236 name: cytosolic_rRNA_18S_gene is_a: SO:0002362 (cytosolic_SSU_rRNA_gene) relationship: derives_from SO:0000407 (cytosolic_18S_rRNA)

I think this must be a mistake - if anything, the relationship should be the other way round - the rRNA derives from the corresponding rRNA_gene.

Terms affected: cytosolic_rRNA_23S_gene cytosolic_rRNA_25S_gene cytosolic_rRNA_28S_gene cytosolic_rRNA_2S_gene cytosolic_rRNA_5S_gene cytosolic_rRNA_5_8S_gene cytosolic_rRNA_16S_gene cytosolic_rRNA_18S_gene

@sjm41 Corrected the derives_from relationship for the cited terms in commit 60704ed7b0a107356c9daa8b58989bd86feead84.

[egchristensen]

OBSOLETED rRNA_21S_gene SO:0002241 and added as a synonym of mt_LSU_rRNA_gene SO:0002364 see GitHub Issue #513. See commit d9afc5372a07fb16815c20c0523fdeb0b385f714.