crystal growth

[gocentral]

Hi,

I need a GO term to describe 'crystal growth' and 'crystal growth inhibitor'

Specifically I'm looking for: 'calcium oxolate crystal growth'

but not sure whether you want to list all the crystal types.. I am annotating uropontin(osteopontin)P10451 1729712 PUBMED

http://www.copewithcytokines.de/cope.cgi?8398

Cheers Evelyn

Reported by: ecamon

Original Ticket: "geneontology/ontology-requests/608":https://sourceforge.net/p/geneontology/ontology-requests/608

[gocentral]

Logged In: YES user_id=473796

Calcium oxalate crystal growth (= urinary stone growth) is a pathological process so it can't be added to GO.

There isn't all that much information on uropontin (esp. in comparison with osteopontin - some sources say that uropontin is the urinary form of osteopontin) but both uropontin and osteopontin seem to be involved in crystal growth / mineralization in some way. Suggested solution:

mineralization ; GO:new ; synonym:crystal growth [I] otolith mineralization ; GO:0045299 [I] bone mineralization ; GO:0030282 [P] regulation of mineralization ; GO:new ---[I] negative regulation of mineralization ; GO:new ------[I] negative regulation of bone mineralization ; GO:0030502 ---[I] positive regulation of mineralization ; GO:new ------[I] positive regulation of bone mineralization ; GO:0030501 ---[I] regulation of bone mineralization ; GO:0030500 ------[I] negative regulation of bone mineralization ; GO:0030502 ------[I] positive regulation of bone mineralization ; GO:0030501

Mineralization would be a child of "physiological processes".

Suggested def for mineralization: The process of forming a mineral by combination of a metal with another element. A mineral is a class of naturally occurring inorganic substances of definite chemical composition and physical structure, often crystalline in structure.

You could annotate to 'negative regulation of mineralization'.

Original comment by: girlwithglasses

[gocentral]

• assigned_to: nobody --> girlwithglasses

Original comment by: girlwithglasses

[gocentral]

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Mineralisation isn't a biological process though - might be a bit misleading. Don't think we can glom together the two 'mineralization' processes here either - calcium oxalate crystal growth is something that occurs spontaneously while bone mineralization is a carefully controlled biological process.

Maybe we should have a function term - we already have things like 'anticoagulent' and 'antifreeze' - how about 'crystal growth inhibitor'? Or a process term under one of the 'response to xxx' parents?

Original comment by: jl242

[gocentral]

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After discussion with Jane, this is what we came up with:

function: calcium oxalate binding (the protein in question inhibits crystal formation by binding to the crystals)

process: response to mineralization (where mineralization is the spontaneous, non-physiological process)

However, the process isn't really a response, it's something that is happening all the time. Should we therefore have a term like 'negative regulation of crystal formation' somewhere to cover this?

Any suggestions gratefully received!

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

Added function term: calcium oxalate binding activity ; GO:0046904

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

How about we have 'negative regulation of crystal formation' under physiological processes? Crystal formation is the spontaneous, non- physiological process here. The mechanism in this case (and the protein in SF:667806) isn't clear so rather than having a function, the best thing might be to annotate to a general process term like this.

Go on. You know it's a good idea.

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

Added term 'negative regulation of crystal formation ; GO:0046908'.

Original comment by: girlwithglasses

[gocentral]

• status: open --> closed-works-for-me

Original comment by: girlwithglasses