Review annotations to GO:0110148 biomineralization & regulation children

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0110148 biomineralization & regulation children, see geneontology/go-ontology#24213

There are 80 EXP annotations:

Group	Number of annotations
MGI	66
UniProt	9
ZFIN	5

Annotation review spreadsheet with suggestions for corrections is here: https://docs.google.com/spreadsheets/d/1ygIejQOrONTyuEk4UZyvHF5f3M6jqUnSVje973wPQPw/edit#gid=0

[pgaudet]

One possible replacement for some of these annotation could be a new term “inhibition of ectopic tissue mineralization", to annotate genes that increase levels of inorganic pyrophosphate, a mineralization inhibitor that prevents ossification/mineralization of non-bone tissue. This term would not be using the ‘negative regulation’, label, because it does not negatively regulate a normal process, but it would be a process that prevents an aberrant process.

@hdrabkin @sramachand would that be helpful?

Thanks, Pascale

[hdrabkin]

We (MGI) plan to discuss this at group meeting tomorrow. Most likely YES, the new term might be helpful to rehouse those annotations.

[sramachand]

Thanks, Pascale. The new term would be helpful.

[hdrabkin]

Doesn't 'ectopic' imply an 'abnormal' process?

[hdrabkin]

This needs to be discussed on ontology call

[pgaudet]

Doesn't 'ectopic' imply an 'abnormal' process?

Yes, the idea of the term is to say that they is a pathway that counteracts the abnormal process.

[deustp01]

Yes, the idea of the term is to say that they is a pathway that counteracts the abnormal process

But the original term encompasses all of normal mineralization, if I read the definition correctly, and the proposed term is confined to inhibition of a specific kind of biomineralization. Is that intended? What new parentage will be available for all the grandchildren that describe various tissue-specific (bone, shell, ...) mineralization processes?

[pgaudet]

@deustp01
The definition is " A homeostatic process involved in the maintenance of non-mineral tissue, by preventing ectopic mineralization of non-bone tissue. " (see geneontology/go-ontology#24228) - I can wider this if you have a better suggestion for wording this. As far as I can tell, this applies to the papers under review here, but maybe there are other cases that should also be covered.

[deustp01]

@ukemi @hdrabkin our concern is parentage. Consider GO:0030282 bone mineralization
bone mineralization is_a biomineral tissue development (GO:0031214) is_a (GO:0110148) biomineralization.
Maybe I'm missing something here, but if GO:0031214 is edited (or replaced by a new term) to cover only prevention of ectopic mineralization, what becomes of the correct mineralization of tissues that are supposed to become bone?

[pgaudet]

We are not changing GO:0031214

The proposal is to obsolete the parent, GO:0110148 biomineralization, to distinguish between cellular biomineralization (of which so far there is a single example, magnetosome assembly), and the biomineralization that occur in multicellular organisms.

The review is about genes directly annotated to GO:0110148 biomineralization, GO:0110150 negative regulation of biomineralization, GO:0110151 positive regulation of biomineralization, to annotate them to something more specific.

[pgaudet]

@AndreaAuchincloss replaced the bacterial annotations

[sramachand]

ZFIN done

[hdrabkin]

mgi done