rearranging heavy metal terms with few additions

[gocentral]

Since all the heavy metals are not toxins(such as Zn, Fe in plant system), we need to rearrange heavy metal terms. Here is the proposal.

Reported by: smundodi

Original Ticket: "geneontology/ontology-requests/576":https://sourceforge.net/p/geneontology/ontology-requests/576

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Original comment by: smundodi

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Do we need to change the heavy metal response terms as 'ion' terms as well? eg mercuric ion, chromate ion, iron ion, copper ion, etc.

Original comment by: smundodi

[gocentral]

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I agree with Suparna. Just be consistent to use either the ionic name or the element name. Right now its a mix of both. eg. copper, zinc, mercuric, chromate etc.

You can have the element name on higher node and ionic forms as ISA

Check with the Chemical Ontology files

---

From Michael:

the CO file is now available by anonymous ftp from seeker.lbl.gov as

/pub/incoming/chemical.ontology.

-Pankaj

Original comment by: jaiswalp

[gocentral]

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Hi Suparna and Others,

Please check the discussion at

http://www.geneontology.org/email/go-arc/go-2002/2283.html

-Pankaj

Original comment by: jaiswalp

[gocentral]

Excel spreadsheet with ionic suggestions

Original comment by: girlwithglasses

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Hi Suparna,

I agree with you on adding "ion" to the term names. I had a look through all the metal terms I could find and have made a list (see the spreadsheet attached) of all the terms that could be changed. I removed all the terms already containing "ion" and then went through the remainder checking for EC/TC numbers - in these cases I thought it would be better not to add "ion" because the term name is a recognized transporter or enzyme name. There are also a couple of terms that I didn't think should be appended with "ion" because they refer to a compound rather than a metal ion (arsenate, chromate).

Have a look and see what you think. Happy reading!

Amelia.

Original comment by: girlwithglasses

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If there aren't any problems with the proposed term name changes (adding "ion" to metal term names), I will implement them on Tuesday, Feb 18 (unless you would like to do it Suparna!).

Original comment by: girlwithglasses

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Hi Amelia,

Please go ahead and make those changes. Thanx. I see the other metal ion terms are in today.

Suparna

Original comment by: smundodi

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I've made the following name changes:

Function ontology GO:0000287: magnesium binding --> magnesium ion binding GO:0005377: intracellular copper transporter --> intracellular copper ion transporter GO:0005381: iron transporter --> iron ion transporter GO:0005382: transmembrane iron permease --> transmembrane iron ion permease GO:0005506: iron binding --> iron ion binding GO:0005507: copper binding --> copper ion binding GO:0008270: zinc binding --> zinc ion binding GO:0015079: potassium transporter --> potassium ion transporter GO:0015080: silver transporter --> silver ion transporter GO:0015081: sodium transporter --> sodium ion transporter GO:0015089: high affinity copper transporter --> high affinity copper ion transporter GO:0015090: low affinity iron transporter --> low affinity iron ion transporter GO:0016151: nickel binding --> nickel ion binding GO:0030145: manganese binding --> manganese ion binding GO:0030151: molybdenum binding --> molybdenum ion binding GO:0045340: mercury binding --> mercury ion binding

Process ontology GO:0006852: mitochondrial sodium/calcium exchange --> mitochondrial sodium/calcium ion exchange GO:0006876: cadmium homeostasis --> cadmium ion homeostasis GO:0006877: cobalt homeostasis --> cobalt ion homeostasis GO:0006878: copper homeostasis --> copper ion homeostasis GO:0006879: iron homeostasis --> iron ion homeostasis GO:0006880: intracellular iron storage --> intracellular iron ion storage GO:0006881: extracellular iron storage --> extracellular iron ion storage GO:0006882: zinc homeostasis --> zinc ion homeostasis GO:0030026: manganese homeostasis --> manganese ion homeostasis GO:0046686: response to cadmium --> response to cadmium ion GO:0046688: response to copper --> response to copper ion GO:0046689: response to mercuric --> response to mercury ion GO:0046690: response to tellurium --> response to tellurium ion

You are now free to rearrange the heavy metals to your heart's content (within reason, obviously!). Set a date for doing it so people can check it and suggest any changes.

Original comment by: girlwithglasses

[gocentral]

Latest version as of april 9, 2003

Original comment by: smundodi

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I am attaching file with the new version of heavy metal rearrangement.

Original comment by: smundodi

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April 9, 2003 version in plain text

Original comment by: mah11

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plain text version of latest suggestions also attached

Original comment by: mah11

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This has all been done now. The new terms added were:

GO:0010033 SM response to organic substance GO:0010034 SM response to acetate GO:0010035 SM response to inorganic substance GO:0010036 SM response to boron GO:0010037 SM response to carbon dioxide GO:0010038 SM response to metal ion GO:0010039 SM response to iron ion GO:0010040 SM response to iron(II) ion GO:0010041 SM response to iron(III) ion GO:0010042 SM response to manganese ion GO:0010043 SM response to zinc ion GO:0010044 SM response to aluminum ion GO:0010045 SM response to nickel ion GO:0010046 SM response to mycotoxin

Original comment by: girlwithglasses

[gocentral]

• status: open --> closed-fixed

Original comment by: girlwithglasses