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#10725 new term request for zinc finger protein binding
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Hi Michael
We like to have a mapping to an InterPro domain or family for the protein binding terms as this will ultimately allow us to maintain this part of the hierarchy automatically.
Could you suggest which interpro domains/families this term would equate to? The union of multiple domains/families would probably be okay.
Jane
Jane,
The protein I requested the term for is SOX9, UniProt:O73668 which is a member of the High mobility group box domain (IPR009071), HMG-boxhttp://en.wikipedia.org/wiki/HMG-box class DNA-binding proteins, so it is a transcription factor. InterPro lists it's protein family membership as "none predicted" Do you need any further info? Thanks
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Monday, March 24, 2014 4:06 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] #10725 new term request for zinc finger protein binding
Hi Michael
We like to have a mapping to an InterPro domain or family for the protein binding terms as this will ultimately allow us to maintain this part of the hierarchy automatically.
Could you suggest which interpro domains/families this term would equate to? The union of multiple domains/families would probably be okay.
Jane
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: open
Group: None
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Wed Mar 19, 2014 10:06 PM UTC
Owner: nobody
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Related
Ontology requests:
#10725What paper are you annotating, Mike?
Jane,
The paper is PMID:23382206, I have attached it with my annotations; This is Adobe Acrobat Pro, so in case you can not view it, the particular excerpt is from p 2885:
Phosphorylation Is Required for Sox9 to Interact with Snail2. Previous
in vitro co-IP analysis revealed a physical interaction of
Sox9 and Snail2 proteins (6). To test whether this interaction was
promoted by phosphorylation and/or SUMOylation of Sox9, we
performed co-IP of protein extracts from chicken embryos
coexpressing Snail2 with WT-Sox9, nonphosphorylatable or non-
SUMOylatable Sox9 mutants. Consistent with previous in vitro
studies, IP of ectopic WT-Sox9 from embryos extracts showed an
association with the Snail2 protein (Fig. 4B). A similar association
was observed between Sox9S64D,S181D and Snail2 (Fig. 2G).
The interaction was abolished with Sox9S64A,S181A and somewhat
reduced with Sox9K61R,K254R,K376R (Fig. 4B). These data suggest
that phosphorylation is required for Sox9 to interact with Snail2.
I always try to annotate more specifically than "protein binding", so since SNAI2 is a zinc finger protein http://www.ncbi.nlm.nih.gov/gene/432368 I thought I could annotate SOX9 as binding to a zinc finger protein. If you could look this over and tell me if I am correct that would be great. Thanks for your help.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Tuesday, March 25, 2014 4:06 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] #10725 new term request for zinc finger protein binding
What paper are you annotating, Mike?
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: open
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Mon Mar 24, 2014 11:06 AM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Related
Ontology requests:
#10725Hi Mike
I see your motivation, but in this case because it's not clear whether or not SOX9 actually interacts with the zinc-finger domain of Snail2, and because Snail2 isn't predicted to be a member of any existing protein family I would not add a new term in this case.
I would just annotate to 'protein binding' and in the WITH column put the protein id for Snail2.
cheers
Jane
Jane,
Ok thanks, I was thinking the same so I am glad you looked it over.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Tuesday, March 25, 2014 9:29 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] #10725 new term request for zinc finger protein binding
Hi Mike
I see your motivation, but in this case because it's not clear whether or not SOX9 actually interacts with the zinc-finger domain of Snail2, and because Snail2 isn't predicted to be a member of any existing protein family I would not add a new term in this case.
I would just annotate to 'protein binding' and in the WITH column put the protein id for Snail2.
cheers
Jane
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: open
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 11:06 AM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Related
Ontology requests:
#10725Jane,
Could I trouble to ask you about new annotation extension terms? There is no single UniProt accession for interleukin 12, rather the protein is divided into alpha and beta subunits with each having it's own accession. In this paper the 2 subunits from sheep and human are assayed as a single protein. I understand that I could use the with column or in_the_presence_of, but it seems a term such as in_combination_with would be a better fit. The paper is PMID:11023671 figure 4. If you could tell me if this is the correct approach I would be grateful. Thank you for your time.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Michael E Rice [mikerice7@users.sf.net]
Sent: Tuesday, March 25, 2014 12:37 PM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] Re: #10725 new term request for zinc finger protein binding
Jane,
Ok thanks, I was thinking the same so I am glad you looked it over.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Tuesday, March 25, 2014 9:29 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] #10725 new term request for zinc finger protein binding
Hi Mike
I see your motivation, but in this case because it's not clear whether or not SOX9 actually interacts with the zinc-finger domain of Snail2, and because Snail2 isn't predicted to be a member of any existing protein family I would not add a new term in this case.
I would just annotate to 'protein binding' and in the WITH column put the protein id for Snail2.
cheers
Jane
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: open
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 11:06 AM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Related
Ontology requests:
#10725Hi Mike
Which protein are you wanting to annotate, IL-12 itself?
Jane
On 26/03/2014 02:49, Michael E Rice wrote:
--
Dr Jane Lomax
Group co-ordinator
Gene Ontology Group - Samples Phenotypes and Ontologies Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
P: 01223 492516
skypename: janelomax
twitter: @jl242
Related
Ontology requests:
#10725Jane,
Right, IL12 for sheep and human as well as the chimeric sheep/human, human/sheep.
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Wednesday, March 26, 2014 7:26 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] Re: #10725 new term request for zinc finger protein binding
Hi Mike
Which protein are you wanting to annotate, IL-12 itself?
Jane
On 26/03/2014 02:49, Michael E Rice wrote:
Jane,
Could I trouble to ask you about new annotation extension terms? There
is no single UniProt accession for interleukin 12, rather the protein
is divided into alpha and beta subunits with each having it's own
accession. In this paper the 2 subunits from sheep and human are
assayed as a single protein. I understand that I could use the with
column or in_the_presence_of, but it seems a term such as
in_combination_with would be a better fit. The paper is PMID:11023671
figure 4. If you could tell me if this is the correct approach I would
be grateful. Thank you for your time.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Michael E Rice [mikerice7@users.sf.net]
Sent: Tuesday, March 25, 2014 12:37 PM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] Re: #10725 new term request
for zinc finger protein binding
Jane,
Ok thanks, I was thinking the same so I am glad you looked it over.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Tuesday, March 25, 2014 9:29 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] #10725 new term request for
zinc finger protein binding
Hi Mike
I see your motivation, but in this case because it's not clear whether
or not SOX9 actually interacts with the zinc-finger domain of Snail2,
and because Snail2 isn't predicted to be a member of any existing
protein family I would not add a new term in this case.
I would just annotate to 'protein binding' and in the WITH column put
the protein id for Snail2.
cheers
Jane
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
new term request for zinc finger protein binding
Status: open
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 11:06 AM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
new term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/ new
term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
--
Dr Jane Lomax
Group co-ordinator
Gene Ontology Group - Samples Phenotypes and Ontologies Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
P: 01223 492516
skypename: janelomax
twitter: @jl242
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Related
Ontology requests:
#10725cc-ing Rachael here but afaik the annotation extension only ever extends
the GO term, so no information about the entity being annotated should
go here.
I think each IL-12 subunit would be annotated to the appropriate GO term
for the process, and for the function you might also consider using the
contributes_to qualifier if it's unclear whether the subunit performs
the function on its own or if both subunits are required.
Is that what you were asking or have I misunderstood?
cheers
Jane
On 26/03/2014 15:11, Michael E Rice wrote:
--
Dr Jane Lomax
Group co-ordinator
Gene Ontology Group - Samples Phenotypes and Ontologies Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
P: 01223 492516
skypename: janelomax
twitter: @jl242
Related
Ontology requests:
#10725yes, so the process is GO:0032946 positive regulation of mononuclear cell proliferation, and I should annotate each subunit separately even though the experiment used the two together as a protein complex? The molecule together is biologically active and the action of each subunit alone is not clear. The function is simply binding, IPI, therefore I can use the with column, correct? Thanks for your help on this.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Wednesday, March 26, 2014 9:15 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] Re: #10725 new term request for zinc finger protein binding
cc-ing Rachael here but afaik the annotation extension only ever extends
the GO term, so no information about the entity being annotated should
go here.
I think each IL-12 subunit would be annotated to the appropriate GO term
for the process, and for the function you might also consider using the
contributes_to qualifier if it's unclear whether the subunit performs
the function on its own or if both subunits are required.
Is that what you were asking or have I misunderstood?
cheers
Jane
On 26/03/2014 15:11, Michael E Rice wrote:
Jane,
Right, IL12 for sheep and human as well as the chimeric sheep/human,
human/sheep.
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Wednesday, March 26, 2014 7:26 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] Re: #10725 new term request
for zinc finger protein binding
Hi Mike
Which protein are you wanting to annotate, IL-12 itself?
Jane
On 26/03/2014 02:49, Michael E Rice wrote:
Jane,
Could I trouble to ask you about new annotation extension terms? There
is no single UniProt accession for interleukin 12, rather the protein
is divided into alpha and beta subunits with each having it's own
accession. In this paper the 2 subunits from sheep and human are
assayed as a single protein. I understand that I could use the with
column or in_the_presence_of, but it seems a term such as
in_combination_with would be a better fit. The paper is PMID:11023671
figure 4. If you could tell me if this is the correct approach I would
be grateful. Thank you for your time.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Michael E Rice [mikerice7@users.sf.net]
Sent: Tuesday, March 25, 2014 12:37 PM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] Re: #10725 new term request
for zinc finger protein binding
Jane,
Ok thanks, I was thinking the same so I am glad you looked it over.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: Jane Lomax [jl242@users.sf.net]
Sent: Tuesday, March 25, 2014 9:29 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] #10725 new term request for
zinc finger protein binding
Hi Mike
I see your motivation, but in this case because it's not clear whether
or not SOX9 actually interacts with the zinc-finger domain of Snail2,
and because Snail2 isn't predicted to be a member of any existing
protein family I would not add a new term in this case.
I would just annotate to 'protein binding' and in the WITH column put
the protein id for Snail2.
cheers
Jane
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
new term request for zinc finger protein binding
Status: open
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 11:06 AM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
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[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
new term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10725/
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[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/ new
term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit
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--
Dr Jane Lomax
Group co-ordinator
Gene Ontology Group - Samples Phenotypes and Ontologies Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
P: 01223 492516
skypename: janelomax
twitter: @jl242
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/http://sourceforge.net/p/geneontology/ontology-requests/10725/
new term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/
http://sourceforge.net/p/geneontology/ontology-requests/10725/ new
term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein
containing a Zinc finger domain. Zinc finger domains are relatively
small protein motifs that contain multiple finger-like protrusions
that make tandem contacts with their target molecule which can be DNA,
RNA, protein, and/or lipid substrates. Their binding properties depend
on the amino acid sequence of the finger domains and of the linker
between fingers, as well as on the higher-order structures and the
number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
--
Dr Jane Lomax
Group co-ordinator
Gene Ontology Group - Samples Phenotypes and Ontologies Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
P: 01223 492516
skypename: janelomax
twitter: @jl242
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Related
Ontology requests:
#10725Hi Mike,
Ideally in these situations we would be annotating the complex ID, we are working on allowing Protein2GO to do this, but we're not there yet. So for now, you should annotate the individual subunits with the process term. If there is evidence, you can also add the complex term GO:0043514 interleukin-12 complex to both subunits.
Rachael.
Thanks Rachael, that will be fine; it can be changed in the future. appreciate your help.
Mike
Michael E. Rice AgBase biocurator
School of Animal and Comparative Biomedical Science
1117 E. Lowell st. Rm 101A
PO Box 210090-0090
Tucson, AZ 85721-0038
The College of Agriculture and Life Sciences
The University of Arizona
520 955-2745
mrice@email.arizona.eduhttp://mrice@email.arizona.edu
From: rach_huntley [huntley@users.sf.net]
Sent: Thursday, March 27, 2014 2:47 AM
To: [geneontology:ontology-requests]
Subject: [geneontology:ontology-requests] #10725 new term request for zinc finger protein binding
Hi Mike,
Ideally in these situations we would be annotating the complex ID, we are working on allowing Protein2GO to do this, but we're not there yet. So for now, you should annotate the individual subunits with the process term. If there is evidence, you can also add the complex term GO:0043514 interleukin-12 complex to both subunits.
Rachael.
[ontology-requests:#10725]http://sourceforge.net/p/geneontology/ontology-requests/10725/ new term request for zinc finger protein binding
Status: closed-rejected
Group: None
Labels: binding
Created: Wed Mar 19, 2014 10:06 PM UTC by Michael E Rice
Last Updated: Tue Mar 25, 2014 04:30 PM UTC
Owner: Jane Lomax
Zinc-finger protein binding
Definition: Interacting selectively and non-covalently with a protein containing a Zinc finger domain. Zinc finger domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule which can be DNA, RNA, protein, and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers.
Source: GOC:go_curators
is_a protein domain specific binding GO:0019904
PMID: 17210253, PMID: 9478126
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10725/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Related
Ontology requests:
#10725