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Source ontology files for the Gene Ontology
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new term requests from Incyte #927

Closed gocentral closed 9 years ago

gocentral commented 21 years ago

Hi All- Attached is a spreadsheet with a few more new term suggestions from our curation group. Thanks a lot, Renee

Reported by: reneewhite

Original Ticket: "geneontology/ontology-requests/930":https://sourceforge.net/p/geneontology/ontology-requests/930

gocentral commented 21 years ago

term suggestions from Incyte

Original comment by: reneewhite

gocentral commented 21 years ago

Original comment by: jenclark

gocentral commented 21 years ago

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Most of these look OK. Here's a text list of just the terms (parents, defs, etc are in the attachment), with comments on a few that need adjusting.

- pain response The proposed definition will not do; for GO, we need a definition of pain in a molecular biological sense. Also, we have 'perception of pain' (GO:0019233) with two children, so make sure they're connected up, analogous to other perception of/response to pairs.

- behavioral pain response as above

- rough endoplasmic reticulum lumen OK

- endoplasmic reticulum translocation See whether existing terms will do (see GO:0006616 and GO:0045319); if not, a new term could be made as a grouping term for the existing ones.

- sperm capacitation OK

- phytanoyl-CoA dioxygenase activity OK; use Enzyme Nomenclature site for reaction for definition

- Thiamine-triphosphatase activity The term is OK, but needs different parent because thiamine is not a nucleoside; use Enzyme Nomenclature site.

- adrenaline secretion This term is OK, but in general terms involving adrenaline/epinephrine and noradrenaline/norepinephrine aren't consistent wrt which is the term and which is the synonym.

- UDP-glucuronate 5'-epimerase activity OK; use Enzyme Nomenclature site

- eosinophil chemotaxis OK, I suppose, since there are already terms that mention specific cell types; good properties fodder

- CXCR3 chemokine receptor binding OK

- mRNA stabilization The term is OK; I would put it under mRNA metabolism rather than processing.

- 3' flap endonuclease activity GO:0017108 is defined as 5' flap endonuclease activity, so change its wording and add a new term for the generic activity (3' flap endonuclease activity will also be a child of the new term).

- 5' flap endonuclease activity as above

m

Original comment by: mah11

gocentral commented 21 years ago

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I've worked out thes bits so far: (My additions marked by **)

- phytanoyl-CoA dioxygenase activity OK; use Enzyme Nomenclature site for reaction for definition

*Definition: Catalysis of the reaction: phytanoyl-CoA + 2-oxoglutarate

- Thiamine-triphosphatase activity The term is OK, but needs different parent because thiamine is not a nucleoside; use Enzyme Nomenclature site.

Definition: Catalyses the reaction: thiamine triphosphate + H2O = thiamine diphosphate + phosphate parent = hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ; GO:0016818

- adrenaline secretion This term is OK, but in general terms involving adrenaline/epinephrine and noradrenaline/norepinephrine aren't consistent wrt which is the term and which is the synonym.

make SourceForge entry to come back and sort that out later

- UDP-glucuronate 5'-epimerase activity
reaction: Catalyses the reaction: UDP-glucuronate = UDP-L- iduronate EC 5.1.3.12

- 3' flap endonuclease activity GO:0017108 is defined as 5' flap endonuclease activity, so change its wording and add a new term for the generic activity (3' flap endonuclease activity will also be a child of the new term).

- 5' flap endonuclease activity as above

rightio, will do

These bits, I haven't worked out yet:

- pain response The proposed definition will not do; for GO, we need a definition of pain in a molecular biological sense. Also, we have 'perception of pain' (GO:0019233) with two children, so make sure they're connected up, analogous to other perception of/response to pairs.

- behavioral pain response as above

- endoplasmic reticulum translocation See whether existing terms will do (see GO:0006616 and GO:0045319); if not, a new term could be made as a grouping term for the existing ones.

- elastic-fiber assembly OK, but check whether it should be hyphenated

Original comment by: jenclark

gocentral commented 21 years ago

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enzyme activity defs start with 'Catalysis or the reaction' rather than 'Catalyses the reaction'

rest looks fine :)

Original comment by: mah11

gocentral commented 21 years ago

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These are the things I still need to develop a bit. Any help from incyte (as offered recently in e-mail) would be appreciated. I will go ahead and add the other terms as soon as possible.

1) pain response def: An unpleasant sensory and/or emotional experience associated with actual or potential tissue damage or described in terms of such damage

behavioral pain response def: A change in the behavior of an organism as a result of an unpleasant sensory and/or emotional experience associated with actual or potential tissue damage

physiological pain response def: An acute physiological change resulting from an unpleasant sensory and/or emotional experience associated with actual or potential tissue damage

These proposed definitions will not do; for GO, we need a definition of pain in a molecular biological sense. Also, we have 'perception of pain' (GO:0019233) with two children, so make sure they're connected up, analogous to other perception of/response to pairs.

2) endoplasmic reticulum translocation def: the translocation of proteins across the endoplasmic reticulum (ER) membrane

Will existing terms do? (see GO:0006616 and GO:0045319); if not, a new term could be made as a grouping term for the existing ones.

3) elastic-fiber assembly def: Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching.

Should this term name be hyphenated?

4) 3' flap endonuclease activity 5' flap endonuclease activity see definition for term 17108 flap endonuclease activity

- 3' flap endonuclease activity GO:0017108 is defined as 5' flap endonuclease activity, so change its wording and add a new term for the generic activity (3' flap endonuclease activity will also be a child of the new term).

- 5' flap endonuclease activity as above

Original comment by: jenclark

gocentral commented 21 years ago

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Added new terms:

Term name: rough endoplasmic reticulum lumen ; GO:0048237 ontology - CC parent: endoplasmic reticulum lumen GO:0005788 parent: rough endoplasmic reticulum GO:0005791 def: The volume enclosed by the membranes of the rough endoplasmic reticulum.

Term name: smooth endoplasmic reticulum lumen ; GO:0048238 ontology - CC parent: endoplasmic reticulum lumen ; GO:0005788 parent: smooth endoplasmic reticulum ; GO:0005790 def: The volume enclosed by the membranes of the smooth endoplasmic reticulum.

Term name: supression of telomeric recombination at telomere ; GO:0048239 ontology - BP parent: telomerase-independent telomere maintenance ; GO:0000722 parent: negative regulation of DNA recombination ; GO:0045910 PMID:9635193 def: Any process that stops, prevents or reduces the rate of genetic recombination within the telomere.

Original comment by: jenclark

gocentral commented 21 years ago

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That's these ones done too:

New term:

Term name: sperm capacitation ; GO:0048240 parent: spermatid development ; GO:0007286 PMID:11820818 def: A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium.

New terms with the following parentage:

%neurotransmitter transport ; GO:0006836 -%norepinephrine transport ; GO:0015874 --%norepinephrine secretion ; GO:new GO:0048243 -%epinephrine transport ; GO:new GO:0048241 --%epinephrine secretion ; GO:new GO:0048242 %hormone transport ; GO:0009914 -%norepinephrine transport ; GO:0015874 --%norepinephrine secretion ; GO:new -%epinephrine transport ; GO:new GO:0048241 --%epinephrine secretion ; GO:new %secretion ; GO:0046903 -%neurotransmitter secretion ; GO:0007269 --%norepinephrine secretion ; GO:new --%epinephrine secretion ; GO:new
-%hormone secretion ; GO:0046879 --%norepinephrine secretion ; GO:new
--%epinephrine secretion ; GO:new

term name: epinephrine transport ; GO:new GO:0048241 def: The directed movement of epinephrine into, out of, within or between cells. synonym: adrenaline transport

Term name: epinephrine secretion ; GO:0048242 def: The regulated release of epinephrine from secretory granules into the blood. synonym: adrenaline secretion

Term name: norepinephrine secretion ; GO:0048243 def: The directed movement of norepinephrine out of cells. synonym: noradrenaline secretion

Did you mean the definitions for norepinephrine secretion and epinephrine secretion to be so different?

Thanks,

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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Hi Jennifer,

Here is most of the information you requested. I'm still working on the pain definitions and will get back to you later in the week. Thanks for working on these and for adding the ER lumen terms this week.

More later . . .

Karama

1) defs for pain related terms

behavioral pain response pain response physiological pain response

Incyte response to come later this week.

2) endoplasmic reticulum translocation def: the translocation of proteins across the endoplasmic reticulum (ER) membrane

Will existing terms do? (see GO:0006616 and GO:0045319); if not, a new term could be made as a grouping term for the existing ones.

Yes. These terms

SRP-dependent cotranslational membrane targeting, translocation (term #6616) SRP-independent cotranslational membrane targeting, translocation (term

45319)

are fine. Thank you for finding them.

3) elastic-fiber assembly def: Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching.

Should this term name be hyphenated?

A case can be made for "elastic-fiber" being the adjective and "assembly" being the noun. That is grammatically correct, but it is not the popular choice:

* I did a Google search for "elastic-fiber assembly" (with quotes, with hyphen) and found that of the top ten hits only one used a hyphen in the phrase. No hyphen appears to be the popular choice.

* I did a PubMed search for "elastic-fiber assembly" (no quotes, with hyphen). I looked at the most recent twenty abstracts and only two of them used a hyphen in the phrase "elastic-fiber assembly" or "elastic-fiber formation". No hyphen seems to be the scientists' choice.

* Based on the way the Incyte search engines work, no hyphen would be a better choice. But either will be fine.

4) 3' flap endonuclease activity 5' flap endonuclease activity see definition for term 17108 flap endonuclease activity

- 3' flap endonuclease activity GO:0017108 is defined as 5' flap endonuclease activity, so change its wording and add a new term for the generic activity (3' flap endonuclease activity will also be a child of the new term).

- 5' flap endonuclease activity as above

No Incyte action required.

Original comment by: jenclark

gocentral commented 21 years ago

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This term was found to already exist:

Term name: UDP-glucuronate 5'-epimerase activity GO:0050379 ontology - MF parent: racemase and epimerase activity, acting on carbohydrates and derivatives ; GO:0016857 def: Catalysis of the reaction: UDP-glucuronate = UDP-L-iduronate EC 5.1.3.12

Original comment by: jenclark

gocentral commented 21 years ago

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new terms:

Term name: phytanoyl-CoA dioxygenase activity ; GO:0048244 ontology - MF parent: oxidoreductase activity ; GO:0016491 Definition: Catalysis of the reaction: phytanoyl-CoA + 2-oxoglutarate

Term name: CXCR3 chemokine receptor binding ; GO:0048248 ontology - MF parent: CXCR chemokine receptor binding ; GO:0045236 PMID:10556837 def: Interacting selectively with a the CXCR3 chemokine receptor.

Term name: high affinity phosphate transporter activity ; GO:0048249 ontology - MF parent: phosphate transporter activity ; GO:0015114 PMID:8709965 def: Transporter that catalyzes phosphate transport with a high affinity for phosphate.

Term name: mitochondrial iron ion transport ; GO:0048250 ontology - BP parent: mitochondrial transport ; GO:0006839 parent: iron ion transport ; GO:0006826 PMID:12006577 def: The directed movement of iron ions into, out of or within a mitochondrion.

Term name: eosinophil chemotaxis ; GO:0048245 ontology - BP parent: neutrophil chemotaxis ; GO:0030593 PMID:12391252 def: The movement of an eosinphil cell in response to an external stimulus.

Term name: macrophage chemotaxis ; GO:0048246 ontology - BP parent: immune cell chemotaxis ; GO:0030595 def: The movement of a macrophage cell in response to an external stimulus.

Term name: lymphocyte chemotaxis ; GO:0048247 ontology - BP parent: immune cell chemotaxis ; GO:0030595 PMID:12391252 def: The movement of a leukocyte cell in response to an external stimulus.

Original comment by: jenclark

gocentral commented 21 years ago

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More new terms added:

Term name: Thiamine-triphosphatase activity ; GO:0048253 ontology - MF parent: hydrolase activity, acting on acid carbon-phosphorus bonds ; GO:0016827 EC:3.6.1.- def: Catalysis of the reaction: thiamine triphosphate + H2O = thiamine diphosphate + phosphate EC:3.6.1.28

ontology - mf %endodeoxyribonuclease activity ; GO:0004520 -%flap endonuclease activity ; GO:new GO:0048256 --%5' flap endonuclease activity ; GO:0017108 --%3' flap endonuclease activity ; GO:new GO:0048257

flap endonuclease activity ; GO:new def: Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis.

5' flap endonuclease activity ; GO:0017108 def: Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.

3' flap endonuclease activity ; GO:new def: Catalysis of the cleavage of a 3' flap structure in DNA, but not other DNA structures; processes the 3' ends of Okazaki fragments in lagging strand DNA synthesis. PMID:10635319

Term name: mRNA stabilization ; GO:0048255 ontology - BP parent: mRNA metabolism ; GO:0016071 PMID:11733561 def: Prevention of degredation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degredation can result in an overall increase in the population of active mRNA molcules.

Term name: snoRNA localization ; GO:0048254 ontology - BP parent: RNA localization ; GO:0006403 parent: snoRNA metabolism ; GO:0016074 def: The processes that lead to the specific localization of small nucleolus-restricted RNA species. synonym: small nucleolar RNA localisation ISBN 07167313631986

Term name: elastic fiber assembly ; GO:0048251 ontology - BP parent: extracellular matrix organization and biogenesis ; GO:0030198 "PMID:10841810, PMID:12615674" def: Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching.

Term name: lauric acid metabolism ; GO:0048252 ontology - BP parent: fatty acid metabolism ; GO:0006631 parent: carboxylic acid metabolism ; GO:0019752 def: The chemical reactions and physical changes involving lauric acid, a fatty acid with the formula CH3(CH2)10COOH. Derived from vegetable sources. exact synonym: n-dodecanoic acid metabolism

Original comment by: jenclark

gocentral commented 21 years ago

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Pain definition suggestions from incyte, sent by e-mail:

* pain response

A change in state or activity of an organism (in terms of movement, secretion, gene expression, enzyme production, etc.) in response to activation of nociceptors, or nociception.

Nociceptors, which are peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. Nociception is the perception of pain.

http://www.wikipedia.org/wiki/Nociception PMIDs: 12723742, 12843304, 10203867

* behavioral pain response

A change in the behavior of an organism as a result of nociceptor activation, or nociception.

http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptive http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptor

* physiological pain response

An acute physiological change resulting from activation of nociceptors, or nociception.

http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptive http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptor

Original comment by: jenclark

gocentral commented 20 years ago

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Thoughts from Amelia on the pain defintions:

These defs look good - the only thing I would change would be to make sure that each def explains clearly what nociceptors/nociception are (I didn't know they were pain receptors/reception). Also, the first def says that nociceptors are peripheral pain receptors - are there such things as non-peripheral pain receptors? They might need to be in the def if so.

I have also Written to David Hill to ask his advice on how to deal with these terms.

Original comment by: jenclark

gocentral commented 20 years ago

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Hi Renee,

It seems to me that clathrin cage should be added as a synonym of clathrin coat. Would you be happy with that?

Thanks,

Jen

Original comment by: jenclark

gocentral commented 20 years ago

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Hi Jen- That sounds fine to us. Thanks a lot, Renee

Original comment by: reneewhite

gocentral commented 20 years ago

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new terms:

%response to stress ; GO:0006950 -%response to pain ; GO:0048265 --%behavioral response to pain ; GO:0048266 --%physiological response to pain ; GO:0048267

additional parents: -%behavior ; GO:0007610 --%behavioral response to pain ; GO:0048266

response to pain ; GO:0048265 def: A change in state or activity of an organism (in terms of movement, secretion, gene expression, enzyme production, etc.) in response to activation of nociceptors, or nociception. Nociceptors, which are peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. Nociception is the perception of pain. http://www.wikipedia.org/wiki/Nociception PMIDs: 12723742, 12843304, 10203867

%behavioral response to pain ; GO:0048266 def: A change in the behavior of an organism as a result of nociceptor activation, or nociception. Nociceptors, which are peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. Nociception is the perception of pain. http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptive http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptor

--%physiological response to pain ; GO:0048267 def: An acute physiological change resulting from activation of nociceptors, or nociception. Nociceptors, which are peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. Nociception is the perception of pain. http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptive http://cancerweb.ncl.ac.uk/cgi-bin/omd?nociceptor

Other terms:

clathrin coat ; GO:0030118 new synonym: clathrin cage PMID:9531549

New Term: clathrin cage assembly ; GO:0048268 parent: cell organization and biogenesis ; GO:0016043 "PMID:9531549, PMID:11977118, PMID:11460887" def: Assembly of clathrin triskelia into clathrin cage

Additional child: %clathrin cage assembly ; GO:0048268 -%clathrin coating of Golgi vesicle ; GO:0048202

All of the requested terms have been added now. Thank you for your request.

Best wishes,

Jen

Original comment by: jenclark

gocentral commented 20 years ago

Original comment by: jenclark

gocentral commented 20 years ago

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Please see the new physiology file in Sourceforge.

Original comment by: ukemi