geneontology-gowebsite Mailing List for [DEPRECATED] Gene Ontology

GO website item #1937565, was opened at 2008-04-08 10:31
Message generated for change (Settings changed) made by girlwithglasses
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Category: request feature
Group: None
>Status: Closed
>Resolution: Accepted
Priority: 5
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: girlwithglasses (girlwithglasses)
Summary: New tool: FunNet

Initial Comment:
Subject:
GO tool submission: FunNet
From:
"Corneliu Henegar" <cor...@he...>
Date:
Sat, 5 Apr 2008 00:35:50 +0200
To:
go...@ge...
CC:
"Jean-Daniel Zucker" <jdz...@gm...>, "Clement Karine" <kar...@ps...>

Dear Sir or Madam,

Would you please consider for inclusion in the list of analytical tools based on Gene Ontology annotations a new tool, which I developed during my PhD, and whose purpose is to provide a biologically robust approach for exploring the modular architecture of transcriptional co-expression networks. Please find hereafter several details which I put together following the guidelines provided on the GO website in relation to the submission of new GO related tools.

Tool name: FunNet - Functional Analysis of Transcriptional Networks

URL of the tool: http://corneliu.henegar.info/FunNet.htm, http://www.funnet.info, http://www.funnet.ws

Organization: Institut National de la Santé et de la Recherche Medicale (INSERM), Centre de Recherche des Cordeliers, UMRS 872, Paris, FRANCE

URL of the organization: http://www.inserm.fr/en/home.html, http://www.crc.jussieu.fr/crc/index.php

Tool type: microarray-related

Brief description: "FunNet" was designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes.

Availability: FunNet is currently provided as a standalone R package (http://www.r-project.org/). A web-based implementation of the FunNet tool is currently in an advanced stage of preparation and is already available from the following URLs: http://www.funnet.info, http://www.funnet.ws). The standalone R implementation can be run on any operating system for which an R environment implementation is available: Windows, Mac OS, various flavors of Linux and Unix. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. The R implementation can be downloaded from a dedicated web page (http://corneliu.henegar.info/FunNet.htm) as well as from the worldwide mirrors of CRAN (http://cran.r-project.org/mirrors.html).

Associated publications:

1. Henegar C, Tordjman J, Achard V, Lacasa D, Cremer I, Guerre-Millo M, Poitou C, Basdevant A, Stich V, Viguerie N, Langin D, Bedossa P, Zucker J-D, Clement K. Adipose tissue transcriptomic signature highlights the pathologic relevance of extracellular matrix in human obesity. Genome Biology 2008, 9(1):R14. PMID: 18208606

2. Henegar C, Clément K, and Zucker JD (2006). Unsupervised multiple-instance learning for functional profiling of genomic data. Lecture Notes in Computer Science: ECML 2006. Springer Berlin / Heidelberg, 4212/2006 : 186-197. DOI: 10.1007/11871842. No PMID available.

Two other manuscripts, describing in detail the FunNet analytical approach, are currently in an advanced stage of preparation.

Technical details: the FunNet tool is using GO ontology files in the GO flat format, as provided on the GO web site, as well as the gene association files provided on the GO database web site (Stanford). Currently the FunNet analysis of transcriptional networks is available for three genomes: human, mouse and yeast. Annotation data will be updated automatically on a regular base (at least 6 times per year, possibly more frequently).

Please let me know if you need me to provide further details about this tool.
Thank you very much for considering this submission.

Best wishes,
Corneliu

--------------------------------------
Corneliu Henegar MD, PhD

INSERM UMRS 872 Eq. 7 Nutriomique
Hotel-Dieu Hospital
1 Place du Parvis Notre-Dame
75004, Paris, FRANCE
-------------------------------------




----------------------------------------------------------------------

>Comment By: girlwithglasses (girlwithglasses)
Date: 2008-04-14 11:48

Message:
Logged In: YES 
user_id=473796
Originator: NO

http://www.geneontology.org/GO.tools.microarray.shtml#funnet

----------------------------------------------------------------------

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GO website item #1933405, was opened at 2008-04-03 14:31
Message generated for change (Comment added) made by girlwithglasses
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1933405&group_id=36855

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: request feature
Group: None
>Status: Closed
>Resolution: Accepted
Priority: 5
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: girlwithglasses (girlwithglasses)
Summary: new tool - ProfCom

Initial Comment:
New tool for the tools page:

                     Tool name: ProfCom

·                     URL for the tool: http://webclu.bio.wzw.tum.de/profcom/

·                     Name and URL of the organization that produced the tool : The Institute of Bioinformatics and Systems Biology (IBIS) of the Helmholtz Zentrum München, http://mips.gsf.de/

·                     Tool type: microarray-related

·                     Brief description of tool :

 ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of “complex functions”. A “Complex function” is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes.

·                     Is the tool web-based or standalone? :web-based

·                     If the tool is standalone, which platforms can use it? (Windows / Mac / Unix / Linux / other)?
For web-based tools it is assumed that all platforms can use the tool unless otherwise stated.

·                     Is the tool free to academics? ProfCom is freely available at http://webclu.bio.wzw.tum.de/profcom/

 

·                     Any associated publications (please give PubMed ID if available)  PMID: 16959266

 

----------------------------------------------------------------------

>Comment By: girlwithglasses (girlwithglasses)
Date: 2008-04-14 11:46

Message:
Logged In: YES 
user_id=473796
Originator: NO

http://www.geneontology.org/GO.tools.microarray.shtml#profcom

----------------------------------------------------------------------

Comment By: Jane Lomax (jl242)
Date: 2008-04-03 14:34

Message:
Logged In: YES 
user_id=451873
Originator: YES

contact email: an...@gs...

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1933405&group_id=36855

> just wondering where this email address leads to

This list was automagically created by SourceForge when we set up the
website tracker (every SF tracker has a list created, but I think not all
are active). I don't know who's on it (but I am, apparently ...).

> shouldn't the tracker be set up to email:
> web...@ge...
> ?

It can be ... any SF tracker can be set to send email only on new 
submissions, or on every change to an item, and a project admin can plug 
in any single address we want (SF's default address is that of the 
automagically created list, which is why the website tracker messages 
have come here). Want me to change it?

m

GO website item #1939761, was opened at 2008-04-10 15:10
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
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Please note that this message will contain a full copy of the comment thread,
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Chris Mungall (cmungall)
Assigned to: Nobody/Anonymous (nobody)
Summary: add pages for GO_REFs

Initial Comment:
There's no way to search these

I suggest a simple statically generated html page, with a single URL for each REF (we can then fill this in in xrf_abbs)

Also, is it just me that gets mixed up between bibliography, publications and references?
http://www.geneontology.org/cgi-bin/biblio.cgi

----------------------------------------------------------------------

You can respond by visiting: 
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just wondering where this email address leads to

shouldn't the tracker be set up to email:
web...@ge...
?

GO website item #1937565, was opened at 2008-04-08 10:31
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1937565&group_id=36855

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: girlwithglasses (girlwithglasses)
Summary: New tool: FunNet

Initial Comment:
Subject:
GO tool submission: FunNet
From:
"Corneliu Henegar" <cor...@he...>
Date:
Sat, 5 Apr 2008 00:35:50 +0200
To:
go...@ge...
CC:
"Jean-Daniel Zucker" <jdz...@gm...>, "Clement Karine" <kar...@ps...>

Dear Sir or Madam,

Would you please consider for inclusion in the list of analytical tools based on Gene Ontology annotations a new tool, which I developed during my PhD, and whose purpose is to provide a biologically robust approach for exploring the modular architecture of transcriptional co-expression networks. Please find hereafter several details which I put together following the guidelines provided on the GO website in relation to the submission of new GO related tools.

Tool name: FunNet - Functional Analysis of Transcriptional Networks

URL of the tool: http://corneliu.henegar.info/FunNet.htm, http://www.funnet.info, http://www.funnet.ws

Organization: Institut National de la Santé et de la Recherche Medicale (INSERM), Centre de Recherche des Cordeliers, UMRS 872, Paris, FRANCE

URL of the organization: http://www.inserm.fr/en/home.html, http://www.crc.jussieu.fr/crc/index.php

Tool type: microarray-related

Brief description: "FunNet" was designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes.

Availability: FunNet is currently provided as a standalone R package (http://www.r-project.org/). A web-based implementation of the FunNet tool is currently in an advanced stage of preparation and is already available from the following URLs: http://www.funnet.info, http://www.funnet.ws). The standalone R implementation can be run on any operating system for which an R environment implementation is available: Windows, Mac OS, various flavors of Linux and Unix. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. The R implementation can be downloaded from a dedicated web page (http://corneliu.henegar.info/FunNet.htm) as well as from the worldwide mirrors of CRAN (http://cran.r-project.org/mirrors.html).

Associated publications:

1. Henegar C, Tordjman J, Achard V, Lacasa D, Cremer I, Guerre-Millo M, Poitou C, Basdevant A, Stich V, Viguerie N, Langin D, Bedossa P, Zucker J-D, Clement K. Adipose tissue transcriptomic signature highlights the pathologic relevance of extracellular matrix in human obesity. Genome Biology 2008, 9(1):R14. PMID: 18208606

2. Henegar C, Clément K, and Zucker JD (2006). Unsupervised multiple-instance learning for functional profiling of genomic data. Lecture Notes in Computer Science: ECML 2006. Springer Berlin / Heidelberg, 4212/2006 : 186-197. DOI: 10.1007/11871842. No PMID available.

Two other manuscripts, describing in detail the FunNet analytical approach, are currently in an advanced stage of preparation.

Technical details: the FunNet tool is using GO ontology files in the GO flat format, as provided on the GO web site, as well as the gene association files provided on the GO database web site (Stanford). Currently the FunNet analysis of transcriptional networks is available for three genomes: human, mouse and yeast. Annotation data will be updated automatically on a regular base (at least 6 times per year, possibly more frequently).

Please let me know if you need me to provide further details about this tool.
Thank you very much for considering this submission.

Best wishes,
Corneliu

--------------------------------------
Corneliu Henegar MD, PhD

INSERM UMRS 872 Eq. 7 Nutriomique
Hotel-Dieu Hospital
1 Place du Parvis Notre-Dame
75004, Paris, FRANCE
-------------------------------------




----------------------------------------------------------------------

You can respond by visiting: 
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GO website item #1933405, was opened at 2008-04-03 14:31
Message generated for change (Comment added) made by jl242
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1933405&group_id=36855

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: girlwithglasses (girlwithglasses)
Summary: new tool - ProfCom

Initial Comment:
New tool for the tools page:

                     Tool name: ProfCom

·                     URL for the tool: http://webclu.bio.wzw.tum.de/profcom/

·                     Name and URL of the organization that produced the tool : The Institute of Bioinformatics and Systems Biology (IBIS) of the Helmholtz Zentrum München, http://mips.gsf.de/

·                     Tool type: microarray-related

·                     Brief description of tool :

 ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of “complex functions”. A “Complex function” is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes.

·                     Is the tool web-based or standalone? :web-based

·                     If the tool is standalone, which platforms can use it? (Windows / Mac / Unix / Linux / other)?
For web-based tools it is assumed that all platforms can use the tool unless otherwise stated.

·                     Is the tool free to academics? ProfCom is freely available at http://webclu.bio.wzw.tum.de/profcom/

 

·                     Any associated publications (please give PubMed ID if available)  PMID: 16959266

 

----------------------------------------------------------------------

>Comment By: Jane Lomax (jl242)
Date: 2008-04-03 14:34

Message:
Logged In: YES 
user_id=451873
Originator: YES

contact email: an...@gs...

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1933405&group_id=36855

GO website item #1933405, was opened at 2008-04-03 14:31
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1933405&group_id=36855

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: girlwithglasses (girlwithglasses)
Summary: new tool - ProfCom

Initial Comment:
New tool for the tools page:

                     Tool name: ProfCom

·                     URL for the tool: http://webclu.bio.wzw.tum.de/profcom/

·                     Name and URL of the organization that produced the tool : The Institute of Bioinformatics and Systems Biology (IBIS) of the Helmholtz Zentrum München, http://mips.gsf.de/

·                     Tool type: microarray-related

·                     Brief description of tool :

 ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of “complex functions”. A “Complex function” is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes.

·                     Is the tool web-based or standalone? :web-based

·                     If the tool is standalone, which platforms can use it? (Windows / Mac / Unix / Linux / other)?
For web-based tools it is assumed that all platforms can use the tool unless otherwise stated.

·                     Is the tool free to academics? ProfCom is freely available at http://webclu.bio.wzw.tum.de/profcom/

 

·                     Any associated publications (please give PubMed ID if available)  PMID: 16959266

 

----------------------------------------------------------------------

You can respond by visiting: 
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GO website item #1899867, was opened at 2008-02-22 19:32
Message generated for change (Comment added) made by gomidori
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Tanya Berardini (tairtb)
Assigned to: Nobody/Anonymous (nobody)
Summary: Sensu in documentation

Initial Comment:
http://www.geneontology.org/GO.usage.shtml#sensu

This section needs to be removed from the documentation since we no longer support sensu terms. :)

----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2008-02-25 12:53

Message:
Logged In: YES 
user_id=436423
Originator: NO

Could just change the last sentence to ...

Where different terms are required to represent different types of process
or component observed in different taxa, the terms are named and definued
based on what features distinguish them from the parent(s) and sibling(s).
Narrow or related synonyms may be included that name the taxon/taxa to
which the term is known to apply.

... or some more elegant wording thereof.

possible example:

flocculation GO:0000128
[i] flocculation via cell wall protein-carbohydrate interaction GO:0000501
narrow synonym 'flocculation (sensu Saccharomyces)'
[i] flocculation via extracellular polymer

m

----------------------------------------------------------------------

Comment By: girlwithglasses (girlwithglasses)
Date: 2008-02-25 10:39

Message:
Logged In: YES 
user_id=473796
Originator: NO

I'll remove the section from that page. Any suggestions on a rewording for
this section:

Species-specific terms

The Gene Ontology aims to provide a controlled vocabulary that can be used
to describe any organism; nevertheless, many functions, processes and
components are not common to all life forms. The convention is to include
any term that can apply to more than one taxonomic class of organism. To
specify the class of organisms to which a term is applicable, GO uses the
designator sensu, 'in the sense of'; for example, trichome differentiation
(sensu Magnoliophyta) represents the differentiation of plant hair cells
(trichomes). 


It would be useful to have some kind of documentation about how we handle
species-specific stuff.

----------------------------------------------------------------------

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GO website item #1899867, was opened at 2008-02-22 19:32
Message generated for change (Comment added) made by girlwithglasses
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1899867&group_id=36855

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Tanya Berardini (tairtb)
Assigned to: Nobody/Anonymous (nobody)
Summary: Sensu in documentation

Initial Comment:
http://www.geneontology.org/GO.usage.shtml#sensu

This section needs to be removed from the documentation since we no longer support sensu terms. :)

----------------------------------------------------------------------

>Comment By: girlwithglasses (girlwithglasses)
Date: 2008-02-25 10:39

Message:
Logged In: YES 
user_id=473796
Originator: NO

I'll remove the section from that page. Any suggestions on a rewording for
this section:

Species-specific terms

The Gene Ontology aims to provide a controlled vocabulary that can be used
to describe any organism; nevertheless, many functions, processes and
components are not common to all life forms. The convention is to include
any term that can apply to more than one taxonomic class of organism. To
specify the class of organisms to which a term is applicable, GO uses the
designator sensu, 'in the sense of'; for example, trichome differentiation
(sensu Magnoliophyta) represents the differentiation of plant hair cells
(trichomes). 


It would be useful to have some kind of documentation about how we handle
species-specific stuff.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1899867&group_id=36855

GO website item #1899867, was opened at 2008-02-22 11:32
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1899867&group_id=36855

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Tanya Berardini (tairtb)
Assigned to: Nobody/Anonymous (nobody)
Summary: Sensu in documentation

Initial Comment:
http://www.geneontology.org/GO.usage.shtml#sensu

This section needs to be removed from the documentation since we no longer support sensu terms. :)

----------------------------------------------------------------------

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GO website item #1787118, was opened at 2007-09-03 07:11
Message generated for change (Comment added) made by cmungall
You can respond by visiting: 
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including the initial issue submission, for this request,
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Midori Harris (gomidori)
Assigned to: girlwithglasses (girlwithglasses)
Summary: format doc links awry

Initial Comment:
On the ontology downloads page (http://www.geneontology.org/GO.downloads.ontology.shtml) ...

I've just noticed that two of the links that are supposed to go to format documentation don't do what they say on the tin: for both OBO-XML format and OWL format, there are amigo.geneontology.org URLs that are being redirected to the "GO Related Software Libraries" page -- which says nothing about the formats!

The OBO Download Matrix page at BBOP (http://www.berkeleybop.org/ontologies/) has the same problem ... can you chase Chris and get these links to point somewhere more enlightening?

thanx,
m

----------------------------------------------------------------------

>Comment By: Chris Mungall (cmungall)
Date: 2007-09-11 15:27

Message:
Logged In: YES 
user_id=254723
Originator: NO

fixed GO.formats.shtml

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GO website item #1787118, was opened at 2007-09-03 14:11
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1787118&group_id=36855

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Midori Harris (gomidori)
Assigned to: girlwithglasses (girlwithglasses)
Summary: format doc links awry

Initial Comment:
On the ontology downloads page (http://www.geneontology.org/GO.downloads.ontology.shtml) ...

I've just noticed that two of the links that are supposed to go to format documentation don't do what they say on the tin: for both OBO-XML format and OWL format, there are amigo.geneontology.org URLs that are being redirected to the "GO Related Software Libraries" page -- which says nothing about the formats!

The OBO Download Matrix page at BBOP (http://www.berkeleybop.org/ontologies/) has the same problem ... can you chase Chris and get these links to point somewhere more enlightening?

thanx,
m

----------------------------------------------------------------------

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GO website item #1778391, was opened at 2007-08-21 08:37
Message generated for change (Comment added) made by jenclark
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Category: request feature
Group: None
Status: Closed
Resolution: Fixed
Priority: 5
Private: No
Submitted By: Jennifer I Clark (jenclark)
Assigned to: girlwithglasses (girlwithglasses)
Summary: email archive

Initial Comment:
Hi,

The go email archives are now at http://genetics.stanford.edu/go-email/

Would it be possible to replace this info on ftp access with the new info on the html address? The ftp access is now gone. 

The text could say:

" There may be discussion of a given term in the GO e-mail archive and it can be useful to search the archive for pertinent e-mails. You can use the search facility on the website, or for a more sophisticated search you can download the e-mail archive and carry out a text search.

To download the e-mail archive visit:
http://www.geneontology.org/GO.curator.requests.shtml#history"

Thanks,

Jen

----------------------------------------------------------------------

>Comment By: Jennifer I Clark (jenclark)
Date: 2007-08-22 16:37

Message:
Logged In: YES 
user_id=735846
Originator: YES

Thanks. There was also an html archive to add but I've just put that in
myself to save time.

Jen

----------------------------------------------------------------------

Comment By: girlwithglasses (girlwithglasses)
Date: 2007-08-22 16:20

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removed the reference to getting the GO email archive by ftp.

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GO website item #1778391, was opened at 2007-08-21 08:37
Message generated for change (Settings changed) made by girlwithglasses
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Category: request feature
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Jennifer I Clark (jenclark)
>Assigned to: girlwithglasses (girlwithglasses)
Summary: email archive

Initial Comment:
Hi,

The go email archives are now at http://genetics.stanford.edu/go-email/

Would it be possible to replace this info on ftp access with the new info on the html address? The ftp access is now gone. 

The text could say:

" There may be discussion of a given term in the GO e-mail archive and it can be useful to search the archive for pertinent e-mails. You can use the search facility on the website, or for a more sophisticated search you can download the e-mail archive and carry out a text search.

To download the e-mail archive visit:
http://www.geneontology.org/GO.curator.requests.shtml#history"

Thanks,

Jen

----------------------------------------------------------------------

>Comment By: girlwithglasses (girlwithglasses)
Date: 2007-08-22 16:20

Message:
Logged In: YES 
user_id=473796
Originator: NO

removed the reference to getting the GO email archive by ftp.

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GO website item #1778391, was opened at 2007-08-21 08:37
Message generated for change (Tracker Item Submitted) made by Item Submitter
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Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jennifer I Clark (jenclark)
Assigned to: Nobody/Anonymous (nobody)
Summary: email archive

Initial Comment:
Hi,

The go email archives are now at http://genetics.stanford.edu/go-email/

Would it be possible to replace this info on ftp access with the new info on the html address? The ftp access is now gone. 

The text could say:

" There may be discussion of a given term in the GO e-mail archive and it can be useful to search the archive for pertinent e-mails. You can use the search facility on the website, or for a more sophisticated search you can download the e-mail archive and carry out a text search.

To download the e-mail archive visit:
http://www.geneontology.org/GO.curator.requests.shtml#history"

Thanks,

Jen

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GO website item #1111466, was opened at 2005-01-28 14:28
Message generated for change (Comment added) made by gomidori
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Category: request feature
Group: None
>Status: Closed
>Resolution: Out of Date
Priority: 5
Private: No
Submitted By: Jennifer I Clark (jenclark)
Assigned to: Nobody/Anonymous (nobody)
Summary: new obo docs

Initial Comment:
Chris has rewritten the OBO docs and he's not sure
whether to have them on the GO site or the GO database
site. I had a chat with Midori and we agreed it could
go on either as long as it's stable and we can link
directly to it. I've said that to Chris and also that
if he has any doubt about their ability to maintain it
that we're happy to host it. He hasn't got back to me yet.

His initial e-mail is below.

Jen



OK, the document is now checked in as
go-dev/doc/obo_format_spec.txt

(this was the original filename)

I've also cvs tagged it as 'obo_format_spec-1_2'

I've also checked in a Makefile for auto-generating the
html and pdf from
the txt file, and checked in the html and pdf themselves.

You can see the results here:

http://www.godatabase.org/dev/doc/obo_format_spec.txt
http://www.godatabase.org/dev/doc/obo_format_spec.html
http://www.godatabase.org/dev/doc/obo_format_spec.pdf

I haven't created any links to this yet

Jen: I don't know whether it makes sense to replicate
this documentation
across go-dev and go, or whether it makes sense to just
have it at one
place. If you want to keep it at go, the parameters for
asciidoc can be
changed so stylesheets aren't used, or you can just fix
it to use to go
stylesheet. I think it may be problematic to embed the
autogenerated html
inside the single page we have now for all the formats.
However, I think
this page needs changed anyway - we should tuck away
the old docs on the
old format, and the docs on the rdf-xml seem to make
more sense on the
go-dev site...

----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2007-06-19 12:55

Message:
Logged In: YES 
user_id=436423
Originator: NO

all righty then!

----------------------------------------------------------------------

Comment By: Jennifer I Clark (jenclark)
Date: 2007-06-19 12:53

Message:
Logged In: YES 
user_id=735846
Originator: YES

Good idea. Practically prehistoric in GO terms.

Jen

----------------------------------------------------------------------

Comment By: Midori Harris (gomidori)
Date: 2007-06-19 12:49

Message:
Logged In: YES 
user_id=436423
Originator: NO

this seems rather out of date. shall we close it?

m

----------------------------------------------------------------------

Comment By: Jennifer I Clark (jenclark)
Date: 2005-02-01 11:07

Message:
Logged In: YES 
user_id=735846

Chris suggests that I install asciidoc here and have a go of
generating the page from the obo doc they've written. I'm
going to have a try of that since it looks like it could be
useful for other things too. He also has this suggestion for
how to integrate it with the format guide:


"keep GO.formats.html, since there's a zillion hrefs
pointing to it

make this page contain just a *summary* of each format
(someone has to write this - bagsy not me!). then there will
be a link to a detailed
description of the format, which a programmer can use to
write a parser. that page can live at either godb or go.
this page is the autogenerated output of asciidoc.py on the
obo_format.txt file in go-dev/doc cvs.

the summary will help people who want to just get a feel for
the format, maybe inspect it by eye and look for whatever
(tho they should of course use dag edit ot amigo for this).
the detailed format page is for hardcore programmers.

this is in addition to the changes and notification that has
to be sent to
gofriends"

Would you all be happy with this plan? 

Jen

----------------------------------------------------------------------

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https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1111466&group_id=36855

GO website item #1111466, was opened at 2005-01-28 14:28
Message generated for change (Comment added) made by jenclark
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Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jennifer I Clark (jenclark)
Assigned to: Nobody/Anonymous (nobody)
Summary: new obo docs

Initial Comment:
Chris has rewritten the OBO docs and he's not sure
whether to have them on the GO site or the GO database
site. I had a chat with Midori and we agreed it could
go on either as long as it's stable and we can link
directly to it. I've said that to Chris and also that
if he has any doubt about their ability to maintain it
that we're happy to host it. He hasn't got back to me yet.

His initial e-mail is below.

Jen



OK, the document is now checked in as
go-dev/doc/obo_format_spec.txt

(this was the original filename)

I've also cvs tagged it as 'obo_format_spec-1_2'

I've also checked in a Makefile for auto-generating the
html and pdf from
the txt file, and checked in the html and pdf themselves.

You can see the results here:

http://www.godatabase.org/dev/doc/obo_format_spec.txt
http://www.godatabase.org/dev/doc/obo_format_spec.html
http://www.godatabase.org/dev/doc/obo_format_spec.pdf

I haven't created any links to this yet

Jen: I don't know whether it makes sense to replicate
this documentation
across go-dev and go, or whether it makes sense to just
have it at one
place. If you want to keep it at go, the parameters for
asciidoc can be
changed so stylesheets aren't used, or you can just fix
it to use to go
stylesheet. I think it may be problematic to embed the
autogenerated html
inside the single page we have now for all the formats.
However, I think
this page needs changed anyway - we should tuck away
the old docs on the
old format, and the docs on the rdf-xml seem to make
more sense on the
go-dev site...

----------------------------------------------------------------------

>Comment By: Jennifer I Clark (jenclark)
Date: 2007-06-19 12:53

Message:
Logged In: YES 
user_id=735846
Originator: YES

Good idea. Practically prehistoric in GO terms.

Jen

----------------------------------------------------------------------

Comment By: Midori Harris (gomidori)
Date: 2007-06-19 12:49

Message:
Logged In: YES 
user_id=436423
Originator: NO

this seems rather out of date. shall we close it?

m

----------------------------------------------------------------------

Comment By: Jennifer I Clark (jenclark)
Date: 2005-02-01 11:07

Message:
Logged In: YES 
user_id=735846

Chris suggests that I install asciidoc here and have a go of
generating the page from the obo doc they've written. I'm
going to have a try of that since it looks like it could be
useful for other things too. He also has this suggestion for
how to integrate it with the format guide:


"keep GO.formats.html, since there's a zillion hrefs
pointing to it

make this page contain just a *summary* of each format
(someone has to write this - bagsy not me!). then there will
be a link to a detailed
description of the format, which a programmer can use to
write a parser. that page can live at either godb or go.
this page is the autogenerated output of asciidoc.py on the
obo_format.txt file in go-dev/doc cvs.

the summary will help people who want to just get a feel for
the format, maybe inspect it by eye and look for whatever
(tho they should of course use dag edit ot amigo for this).
the detailed format page is for hardcore programmers.

this is in addition to the changes and notification that has
to be sent to
gofriends"

Would you all be happy with this plan? 

Jen

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1111466&group_id=36855

GO website item #1111466, was opened at 2005-01-28 14:28
Message generated for change (Comment added) made by gomidori
You can respond by visiting: 
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including the initial issue submission, for this request,
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Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jennifer I Clark (jenclark)
Assigned to: Nobody/Anonymous (nobody)
Summary: new obo docs

Initial Comment:
Chris has rewritten the OBO docs and he's not sure
whether to have them on the GO site or the GO database
site. I had a chat with Midori and we agreed it could
go on either as long as it's stable and we can link
directly to it. I've said that to Chris and also that
if he has any doubt about their ability to maintain it
that we're happy to host it. He hasn't got back to me yet.

His initial e-mail is below.

Jen



OK, the document is now checked in as
go-dev/doc/obo_format_spec.txt

(this was the original filename)

I've also cvs tagged it as 'obo_format_spec-1_2'

I've also checked in a Makefile for auto-generating the
html and pdf from
the txt file, and checked in the html and pdf themselves.

You can see the results here:

http://www.godatabase.org/dev/doc/obo_format_spec.txt
http://www.godatabase.org/dev/doc/obo_format_spec.html
http://www.godatabase.org/dev/doc/obo_format_spec.pdf

I haven't created any links to this yet

Jen: I don't know whether it makes sense to replicate
this documentation
across go-dev and go, or whether it makes sense to just
have it at one
place. If you want to keep it at go, the parameters for
asciidoc can be
changed so stylesheets aren't used, or you can just fix
it to use to go
stylesheet. I think it may be problematic to embed the
autogenerated html
inside the single page we have now for all the formats.
However, I think
this page needs changed anyway - we should tuck away
the old docs on the
old format, and the docs on the rdf-xml seem to make
more sense on the
go-dev site...

----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2007-06-19 12:49

Message:
Logged In: YES 
user_id=436423
Originator: NO

this seems rather out of date. shall we close it?

m

----------------------------------------------------------------------

Comment By: Jennifer I Clark (jenclark)
Date: 2005-02-01 11:07

Message:
Logged In: YES 
user_id=735846

Chris suggests that I install asciidoc here and have a go of
generating the page from the obo doc they've written. I'm
going to have a try of that since it looks like it could be
useful for other things too. He also has this suggestion for
how to integrate it with the format guide:


"keep GO.formats.html, since there's a zillion hrefs
pointing to it

make this page contain just a *summary* of each format
(someone has to write this - bagsy not me!). then there will
be a link to a detailed
description of the format, which a programmer can use to
write a parser. that page can live at either godb or go.
this page is the autogenerated output of asciidoc.py on the
obo_format.txt file in go-dev/doc cvs.

the summary will help people who want to just get a feel for
the format, maybe inspect it by eye and look for whatever
(tho they should of course use dag edit ot amigo for this).
the detailed format page is for hardcore programmers.

this is in addition to the changes and notification that has
to be sent to
gofriends"

Would you all be happy with this plan? 

Jen

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=600519&aid=1111466&group_id=36855

GO website item #1618963, was opened at 2006-12-19 18:47
Message generated for change (Comment added) made by gomidori
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Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: fcouto (fcouto)
>Assigned to: girlwithglasses (girlwithglasses)
Summary: web tools update

Initial Comment:
1. Could you change the name of the institution for the 
FuSSiMeG tool to:
"XLDB Group, Faculdade de Ciências da Universidade de Lisboa" 
to be cohenrent with the GOAnnotator and ProteInOn tools.

2. Could you add the following associated publications to FuSSiMeG:
- F. Couto, M. Silva and P. Coutinho, Measuring Semantic Similarity between Gene Ontology Terms, DKE - Data & Knowledge Engineering, Elsevier Science.
- F. Couto and M. Silva and P. Coutinho, Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors, ACM CIKM - Conference in Information and Knowledge Management, October, 2005
- F. Couto, M. Silva and P. Coutinho, Implementation of a Functional Semantic Similarity Measure between Gene-Products, Department of Informatics, University of Lisbon, DI/FCUL TR 03--29, November, 2003 

3. and to GOAnnotator:
- F. Couto, M. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, D. Rebholz-Schuhmann,
GOAnnotator: linking electronic protein GO annotation to evidence text. Journal of Biomedical Discovery and Collaboration 
- F. Couto and M. Silva,
Chapter XV: Mining the BioLiterature: towards automatic annotation of genes and proteins.
Advanced Data Mining Technologies in Bioinformatics, 2006, ISBN: 1-59140-863-6

----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2007-06-19 12:45

Message:
Logged In: YES 
user_id=436423
Originator: NO

this has been overlooked! can it be done soon?

ta,
m

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GO website item #1669876, was opened at 2007-02-27 11:23
Message generated for change (Comment added) made by gomidori
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: girlwithglasses (girlwithglasses)
Summary: Move editor guides to wiki

Initial Comment:
Hi - I think we should move the editor guide and the cvs guide to the internal wiki at some point:

http://www.geneontology.org/GO.CVS.help.shtml
http://www.geneontology.org/GO.contents.curator.guides.shtml

these are internal docs and there's no reason to keep them on the public website when there's somewhere else for them to go.

thanks!

Jane

----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2007-06-19 11:43

Message:
Logged In: YES 
user_id=436423
Originator: NO

Agreed about GO.contents.curator.guides.shtml, but GO.CVS.help.shtml is
for users so should stay on the web page.

m

----------------------------------------------------------------------

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GO website item #1658103, was opened at 2007-02-12 15:00
Message generated for change (Comment added) made by gomidori
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Category: report error
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: girlwithglasses (girlwithglasses)
Summary: go tools - remove GOODIES

Initial Comment:
Looks like GOODIES in microarray tools no longer active. I've mailed the developers (12 Feb) and if we don't hear anything back in a week or so, lets take them off.

Jane 

----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2007-06-19 11:41

Message:
Logged In: YES 
user_id=436423
Originator: NO

seems this got done ...

----------------------------------------------------------------------

Comment By: Jane Lomax (jl242)
Date: 2007-02-12 15:02

Message:
Logged In: YES 
user_id=451873
Originator: YES

Well, those email addresses no longer work either, so just remove it
whenever...

Jane

----------------------------------------------------------------------

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GO website item #1642078, was opened at 2007-01-23 01:12
Message generated for change (Comment added) made by gomidori
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>Category: request feature
Group: None
>Status: Closed
>Resolution: Accepted
Priority: 5
Private: No
Submitted By: Eurie Hong (eurie)
>Assigned to: girlwithglasses (girlwithglasses)
Summary: Links to unfiltered UniProt files on downloads page

Initial Comment:
>From the GOC meeting, an action item was for the AmiGO working group to come up with a proposal for how to link to the unfiltered UniProt files on the downloads page:

http://www.geneontology.org/GO.current.annotations.shtml

Because there would be two UniProt files on that page, the distinction between the files needs to be clearly stated.


----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2007-06-19 11:39

Message:
Logged In: YES 
user_id=436423
Originator: NO

this got done a little while back

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GO website item #1338308, was opened at 2005-10-26 10:18
Message generated for change (Comment added) made by gomidori
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Category: None
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Valerie Wood (val_wood)
Assigned to: Nobody/Anonymous (nobody)
Summary: query evidence code hierarchy documentation

Initial Comment:
Added 2000-11-08: Heather has seen cases where a paper
presents several lines of evidence supporting a
conclusion, of which each line of evidence alone is
sufficient to annotate to a higher-level (more generic)
node, but combining the lines of evidence gives the
author (or curator) enough data to support annotating
to a lower-level (more specific) node. We've decided to
annotate each line of evidence singly, with the
appropriate evidence code, for the higher node (e.g.
have a line for IMP, another line for IPI, for one GO
ID). The annotation to the lower node can then be
included with 'TAS' as the evidence; cite the paper if
the author draws the conclusion. If the curator draws
the conclusion, keep some record of what went into the
decision.


"If the curator draws the conclusion, keep some record
of what went into the decision."

Perhaps thsi needs to be updated; this is a valid type
of IC annotation where the GO IDS of all of the higher
level terms used to make the more granular association
are included in the with column (pipe separated).

I don't think this type of curator inference is
documented under IC.....perhaps it should be

----------------------------------------------------------------------

>Comment By: Midori Harris (gomidori)
Date: 2007-06-19 11:32

Message:
Logged In: YES 
user_id=436423
Originator: NO

the offending 'hierarchy' blurb is now gone, and, with more changes to the
documentation, including IC, in the works, it seems it's time to close
this.

----------------------------------------------------------------------

Comment By: Midori Harris (gomidori)
Date: 2005-11-09 16:14

Message:
Logged In: YES 
user_id=436423

I'm quite willing to lose the hierachy blurb ... it's mainly inertia that
has kept in 
on the page for the past couple years anyway.

m

----------------------------------------------------------------------

Comment By: Valerie Wood (val_wood)
Date: 2005-11-02 09:53

Message:
Logged In: YES 
user_id=516865

Hi Karen,

I agree with your comments about ditching  statements
refering to an 'evidence code heirarchy'. They are
misleading and open to misinterpretation.

It has always worried me that an IDA from a high throughput
screen is given more credability than a high quality ISS (or
any other code). As you say the reliability of the
annotation depends on the experiment/author/curator
interpretation/graularity of inference. The statement  
about ranking evidence types is not only misleading but
untrue.

----------------------------------------------------------------------

Comment By: Karen Christie (kchris)
Date: 2005-11-01 23:28

Message:
Logged In: YES 
user_id=473890


good suggestion about using IC now. I agree.


... speaking of the "evidence code hierarchy", quoting
from the documentation:

"The evidence fields can be thought of in a loose hierarchy of
reliability:


...TAS/IDA
......IMP/IGI/IPI
......ISS/IEP
......NAS
.........IEA

This hierarchy should not be interpreted as a rigid
ranking of evidence types; users can and should form
their own conclusions as to the reliability of each
type of evidence and each individual annotation. It is
a loose hierarchy also partly because the strength of
the evidence will also depend on to what resolution you
are annotating, and because there is a range of
reliability within each evidence category (e.g. 90%
versus 20% identity for "sequence similarity" or a
two-hybrid result versus co- purification over several
columns for "physical interaction")."



Ever since the second annotation camp, I've been
thinking that maybe we should ditch this
altogether. Every time the group has discussed the
relative reliability/confidence of the evidence codes,
it is apparent that one's confidence depends on which
type of IMP/IGI/IDA/ISS/etc and on which author. We
have come to the conclusion multiple times that the
evidence code does not correlate with one's confidence
in the annotation. Thus, I think that this "loose
hierarchy of reliability" is a holdover from the early
days of GO before we had come to the conclusion that
one cannot make statements of reliability based on the
evidence code.

Further, I think that keeping this "loose hierarchy of
reliability" in our documentation encourages people to
do/say things like "Well, this is a good annotation, so
I don't want to give it NAS, I'd rather give it TAS."
The evidence codes should be applied purely on the
basis of what type of statement or experiment is made,
with respect to whether it is a "better" code or not.
If we get rid of the loose hierarchy, we can eliminate
the "better" code idea.

I think it might be more accurate to say something like
there are two classes of codes: those assigned by
curators and those assigned without any input from a
human curator, and then we can divide the codes
assigned by curators into another couple classes:
experimental codes and author statement codes

Curator Assigned Evidence codes:

	Experimental codes:

		IDA/IMP/IGI/IPI/ISS/IEP

	Author Statement codes:

		TAS/NAS


Evidence code assigned withoug curator input:

	IEA


and we'd need to figure out where to put the new code
RCA, it might need it's own class under "curator
assigned codes"

-Karen Christie

----------------------------------------------------------------------

Comment By: kpilcher (kpilcher)
Date: 2005-10-27 15:53

Message:
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That would be great, thanks!

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Comment By: Valerie Wood (val_wood)
Date: 2005-10-27 15:35

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I agree there should be a best practice.

Now I am thinking about this more I will document new cases.
At the moment I am reading thourough the documentation and
the curation camp minutes (hence this SF deluge). 

There seem to be lots of 'unresolved' areas, maybe they will
be discussed furhter at the next consortium meeting?

When I have my draft SOP I'll sent it to you and Pascale and
you can see if it sounds sensible





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Comment By: kpilcher (kpilcher)
Date: 2005-10-27 15:28

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Hmm...this is tricky.  I agree that the IC annotation is
more informative than the NAS annotation, however, as a
curator I try to give credit to the published authors as
much as possible.  Perhaps you could keep both?

This is definitely confusing and needs to be documented. 
I've been looking through the minutes from the last
annotation camp and the distinction between IC and TAS (and
sometimes NAS) is a recurring theme.

Karen

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Comment By: Valerie Wood (val_wood)
Date: 2005-10-27 15:18

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hmm it all gets a bit murky though. For many of these, I
make an inference, then the inference gets published. Do I
then change the IC to NAS and the paper because it is now
published. It is still at this point only an inference based
on other annotations, except now it is cited in a
publication. I have noticed this for a few things
recently....at least IC with the GO terms allows the user to
see which pieces of information the inference was derived
from. Perhaps with (GO:0005816|GO:0003674)  should be
allowed with NAS?



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Comment By: kpilcher (kpilcher)
Date: 2005-10-27 15:06

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It seems to me that NAS is the right one to use.  It is an
author statement but it's not traceable to anything except
that statement.  IC with a published reference seems a
little strange since it's inferred by an author, not a curator.

Karen

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Comment By: Valerie Wood (val_wood)
Date: 2005-10-27 13:37

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I see why I used NAS for this rather than IC.

The authors seem pretty convinced this is a membrane bound,
they even mention it in the title:

Two-hybrid search for proteins that interact with Sad1 and
Kms1, two membrane-bound components of the spindle
pole body in fission yeast.

I used NAS as there is no direct experimental evidence (but
I should of added the Pubmed ID. I only recently reilised I
could use Pubmed IDs with NAS!

I still don't know which evidence code would be best to
capture this......



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Comment By: Valerie Wood (val_wood)
Date: 2005-10-27 13:32

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I have been thinking more recently about the NAS/TAS
distinction. I think you are right that "If an author states
a more granular function/process in a conclusion" and it
seems reilistic enough to be captured it should get NAS. I
think it is useful to annotate things which have no
experimental verification in this way as they are
annotations which a researcher would want to test
experimentally. 

I use NAS for anything which I don't have experimental data
for :
conference abstracts (rarely)
pers comm (more frequently), usually when publication is
pendng
Things I can see which are obvious/highly likely  but I
don't have a more suitable evidence code (see below). 

statments made by authors in papers which appear to be
reasonable but don't have any direct experimental evidence.

here is an example

spindle pole body IDA (PMID:14655046)
membrane  ISS (GOC:unpublished) with CBS:TMHMM
nuclear membrane NAS (GOC:unpublished)

In this case I think I should change this to clarify where
the inference came from and change to

nuclear membrane IC (GO:0005816|GO:0003674) 

which is more informative.  

I think we discussed these more granular IC inferences from
2 existing GO terms on the annotation tracker at some point
and agreed that this was OK (although i obviously haven't
implemented it !)

 

                                                   




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Comment By: kpilcher (kpilcher)
Date: 2005-10-26 19:03

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Hi Val,

I've been having a hard time with TAS lately, re-evaluating
how it's used.  If an author states a more granular
function/process in a conclusion, it's not traceable back to
anything, and therefore this should not be TAS, but perhaps
NAS instead?

"...discussion sections should usually be regarded with
greater skepticism."

"With a few exceptions, TAS should be used only if
references to the original work are available."

Also, how do people feel about having a higher level term
and a lower level term with the SAME evidence code and the
SAME reference?  I tend to think only the more granular term
should be included when using the same ev code/same ref (but
not for diff ev code/diff ref).

Thanks for working on this,

Karen

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GO website item #1732735, was opened at 2007-06-07 12:25
Message generated for change (Tracker Item Submitted) made by Item Submitter
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Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: request feature
Group: None
Status: Open
Resolution: None
Priority: 3
Private: No
Submitted By: Jane Lomax (jl242)
Assigned to: Nobody/Anonymous (nobody)
Summary: RSS feed?

Initial Comment:
(suggestion from Suzi from managers meeting)

Can we have a GO RSS feed for new terms etc, that scrolls across the front page of the website somewhere? Will show people what a dynamic project we are!



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