From midori at ebi.ac.uk  Mon Jul  2 07:28:03 2007
From: midori at ebi.ac.uk (Midori Harris)
Date: Mon, 2 Jul 2007 15:28:03 +0100 (BST)
Subject: [gofriends] GoPubMed (fwd)
Message-ID: <Pine.LNX.4.64.0707021527590.315@pigeon.ebi.ac.uk>



---------- Forwarded message ----------
Date: Mon, 02 Jul 2007 16:24:30 +0200
From: Michael Schroeder <ms at biotec.tu-dresden.de>
To: "Harris, Midori" <midori at ebi.ac.uk>
Subject: GoPubMed

Hi Midori,

a new release of http://www.GoPubMed.org is out. We have integrated Mesh 
(besides GO) and links to Wikipedia articles and to Uniprot entries for 
proteins mentioned.

If you like it, please tell your friends and help spread the word.

Cheers, Michael


SOME QUESTIONS:

Question: Which techniques are frequently used to study zebrafish development?
Question: Which processes are osteoclasts involved in?
Question: What are common histone modifications?
Question: Which diseases are associated with wnt signalling?
Question: Who publishes most at the MPI-CBG?
Question: Which diseases are asociated with HIV?
Question: Which are leading centers and scientists for liver transplantation?
Question: Which anatomical structure is affected by the bacterium helicobacter 
pylori?
Question: Which biological process is the protein Rab5 involved in and where is 
located in the cell?
Question: In which organisms is toluene degradation studied?
Question: Which enzymes are inhibited by aspirin?
Question: Which enzymes are important for congenital muscular dystrophy?


ANSWERS:

Question: Which techniques are frequently used to study zebrafish development?

Answer: Search for "zebrafish development". Under "top five and more" open
"techniques and equipment". In situ hybridization is listed
first. Clicking the term retrieves relevant articles.


Question: Which process are osteoclasts involved in?

Answer: Search for "osteoclast". Under "top five and more" open "biological
process". The first entry is "bone resorption".


Question: What are common histone modifications?

Answer: Search for "histone modification". Under "top five and more" open 
"biological sciences" and find methylation and acetylation.


Question: Which diseases are associated with wnt signalling?

Answer: Search for "wnt signalling". Under "top five and more" open "disease" 
and find "carcinoma" and many other cancer terms.


Question: Who publishes most at the MPI-CBG?

Answer: Search for "dresden[ad] planck[ad] genetics[ad]" and click on "show
statistics for these 302 articles".  Shevchenko A comes out top with
42 articles. Looks like he/she is doing work for two...


Question: Which diseases are asociated with HIV?

Answer: Type "HIV" and wait for the tree on the left to appear. Go to "top five 
& more" and click on "disease". Among others hepatitis and tuberculosis are 
mentioned. Clicking on tuberculosis retrieves the relevant articles including 
statements such as "HIV and parasitic co-infections in tuberculosis patients".


Question: Which are leading centers and scientists for liver transplantation?

Answer: Type "liver transplantation" and click on statistics for term "liver 
transplantation" at the top of the results page. Among the top authors is "P 
Neuhaus" and among the cities is "Berlin". Prof. Peter Neuhaus works at the 
Charite Hospital in Berlin, Germany, is a leading specialist in the field.


Question: Which anatomical structure is affected by the bacterium helicobacter 
pylori?

Answer: Type "helicobacter pylori", go to "top five & more" and open "anatomy" 
Among other terms "gastric mucosa" is listed. Hovering the mouse over the term 
reveals an explanation, which mentions that gastric mucosa is the lining of the 
stomach.


Question: Which biological process is the protein Rab5 involved in and where is 
located in the cell?

Answer: Type "rab5" and wait for the tree on the left to appear. Go to "top 
five & more". Click on biological process shows "endcytosis" and clicking on 
"cellular component" shows "endosomes". Hovering over the terms displays brief 
explanations of what endocytosis and endosomes are.


Question: In which organisms is toluene degradation studied?

Answer: Type "toluene degradation" and wait for the tree on the left to appear.
Go to "top five & more" and open "organisms". The bacteria pseudomonas are 
listed first. A click retrieves the relevant articles


Question: Which enzymes are inhibited by aspirin?

Answer: Type "aspirin" and wait for the tree on the left to appear. Go to 
"hierarchy of content" and then "chemicals and drugs" and "enzymes and 
co-enzymes". From there always click the top child until you reach 
"cyclooxygenase 1" and "cyclooxygenase 2". Clicking reduces the articles to a 
few which mention that aspirin inhibits cyclooxygenases.


Question: Which enzymes are important for congenital muscular dystrophy?

Answer: Type "congenital muscular dystrophy" and wait for the tree on the left 
to appear. Go to "hierarchy of content" and then "chemicals and drugs", 
"enzymes and co-enzymes", "enzymes", "transferases". There are a number of 
articles with statements such as "glycosyltransferases has revealed a novel 
mechanism for congenital muscular dystrophy."

-- 
---
Michael Schroeder, Professor in Bioinformatics

Biotec/Dept. of Computing, TU Dresden
Tatzberg 47-51, 01307 Dresden, Germany

w: www.biotec.tu-dresden.de
t: +49 351 463 400 60
f: +49 351 463 400 61
e: ms at biotec.tu-dresden.de

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From jdeegan at ebi.ac.uk  Tue Jul  3 05:19:15 2007
From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark))
Date: Tue, 03 Jul 2007 13:19:15 +0100
Subject: [gofriends] transporter activity
Message-ID: <468A3EC3.5090603@ebi.ac.uk>

Dear GO-Friends,

The transporter activity working group has been working recently to 
overhaul the terms in the function ontology under transporter activity. 
We have been carrying out the work on a branch of the ontology file and 
we have now finished the high level changes. These changes have been 
committed back to the live repository today, and we will continue with 
the more detailed changes in the coming weeks.

In addition to a large number of changes to existing terms, we have also 
added a number of new terms, and these are listed below. If you see any 
problems with the file, or if you have any suggestions on how we can 
improve the terms, then please do get in touch. All feedback is very 
much appreciated.

Thanks, and best wishes,

Jennifer Deegan nee Clark
GO Curator

On behalf of the transporter activity working group:
Val Wood, Michelle Gwinn, Ian Paulsen, Jennifer Deegan.

New Terms
==========

GO:0022803  passive transporter activity
GO:0022804 active transporter activity
GO:0022809 mobile ion carrier activity
GO:0022810 membrane potential driven uniporter activity
GO:0022814 facilitated diffusion
GO:0022815 large uncharged polar molecule transporter activity
GO:0022816 sodium ion transmembrane transporter activity
GO:0022817 potassium ion transmembrane transporter activity
GO:0022818 sodium ion uniporter activity
GO:0022819 potassium ion uniporter activity
GO:0022820 potassium ion symporter activity
GO:0022821 potassium ion antiporter activity
GO:0022824 transmitter-gated ion channel activity
GO:0022825 copper-exporting ATPase activity
GO:0022828 phosphorylation-gated channel activity
GO:0022829 wide pore channel activity
GO:0022831 narrow pore, gated channel activity
GO:0022832 voltage-gated channel activity
GO:0022833 mechanically gated channel activity
GO:0022834 ligand-gated channel activity
GO:0022835 transmitter-gated channel activity
GO:0022836 gated channel activity
GO:0022838 substrate specific channel activity
GO:0022839 ion gated channel activity
GO:0022840 leak channel activity
GO:0022841 potassium ion leak channel activity
GO:0022842 narrow pore channel activity
GO:0022843 voltage-gated cation channel activity
GO:0022844 voltage-gated anion channel activity
GO:0022848 acetylcholine-gated cation channel activity
GO:0022849 glutamate-gated calcium ion channel activity
GO:0022850 serotonin-gated cation channel activity
GO:0022851 GABA-gated chloride ion channel activity
GO:0022852 glycine-gated chloride ion channel activity
GO:0022853 active ion transmembrane transporter
GO:0022854 active large uncharged polar molecule transporter activity
GO:0022855 protein-N(PI)-phosphohistidine-glucose phosphotransferase 
system transporter activity
GO:0022856 protein-N(PI)-phosphohistidine-sorbitol phosphotransferase 
system transporter activity
GO:0022857 transmembrane transporter activity
GO:0022858 alanine transmembrane transporter activity
GO:0022859 dephosphorylation-gated channel activity
GO:0022865 transmembrane electron transfer carrier
GO:0022866 transmembrane 1-electron transfer carrier
GO:0022867 transmembrane 2-electron transfer carrier
GO:0022869 protein-N(PI)-phosphohistidine-lactose phosphotransferase 
system transporter activity
GO:0022870 protein-N(PI)-phosphohistidine-mannose phosphotransferase 
system transporter activity
GO:0022871 protein-N(PI)-phosphohistidine-sorbose phosphotransferase 
system transporter activity
GO:0022872 protein-N(PI)-phosphohistidine-mannitol phosphotransferase 
system transmembrane transporter activity
GO:0022873 protein-N(PI)-phosphohistidine-maltose phosphotransferase 
system transporter activity
GO:0022874 protein-N(PI)-phosphohistidine-cellobiose phosphotransferase 
system transporter activity
GO:0022875 protein-N(PI)-phosphohistidine-galactitol phosphotransferase 
system transmembrane transporter activity
GO:0022876 protein-N(PI)-phosphohistidine-galactosamine 
phosphotransferase system transporter activity
GO:0022877 protein-N(PI)-phosphohistidine-fructose phosphotransferase 
system transporter activity
GO:0022878 protein-N(PI)-phosphohistidine-sucrose phosphotransferase 
system transporter activity
GO:0022879 protein-N(PI)-phosphohistidine-trehalose phosphotransferase 
system transporter activity
GO:0022880 protein-N(PI)-phosphohistidine-N-acetylglucosamine 
phosphotransferase system transporter activity
GO:0022881 protein-N(PI)-phosphohistidine-N-acetylgalactosamine 
phosphotransferase system transporter activity
GO:0022882 protein-N(PI)-phosphohistidine-beta-glucoside 
phosphotransferase system transporter activity
GO:0022883 zinc efflux transmembrane transporter activity
GO:0022884 macromolecule transmembrane transporter activity
GO:0022885 bacteriocin transmembrane transporter activity
GO:0022886 channel-forming ionophore activity
GO:0022889 serine transmembrane transporter activity
GO:0022890 inorganic cation transporter activity
GO:0022891 substrate-specific transmembrane transporter activity
GO:0022892 substrate-specific transporter activity
GO:0022893 low-affinity tryptophan transmembrane transporter activity
GO:0022894 Intermediate conductance calcium-activated potassium channel 
activity
GO:0022897 proton-dependent peptide secondary active transmembrane 
transporter activity
GO:0022898 regulation of transmembrane transporter activity



-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium


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From dhowe at cs.uoregon.edu  Thu Jul 12 13:18:01 2007
From: dhowe at cs.uoregon.edu (Doug howe)
Date: Thu, 12 Jul 2007 13:18:01 -0700
Subject: [gofriends] 2007 Biocuration Meeting: registration extended to August 15th
Message-ID: <46968C79.3080108@cs.uoregon.edu>

*Second International Biocuration Meeting*
*October 25-28, 2007*
*San Jose, California*

The registration and abstract submission deadline for the Second 
International Biocuration Meeting
has been extended to August 15th.  This important meeting promises 
something for everyone, don't miss it!
 
Learn more about the on line tools you use from the people who produce them
See what new developments are on the horizon in formal training 
opportunities for biocurators
Hone your ontology development skills
Face to face interaction with colleagues and collaborators
Update the community on new developments in your group
Get feedback and new ideas to steer your own work
and more!

A detailed agenda can be viewed here:
http://tesuque.stanford.edu/biocurator.org/Mtg2007/index.html

Looking forward to seeing you there.

The International Biocuration Meeting Organizing Committee

 

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From toyop at gsc.riken.go.jp  Wed Jul 18 15:23:01 2007
From: toyop at gsc.riken.go.jp (Tetsuro TOYODA)
Date: Thu, 19 Jul 2007 07:23:01 +0900
Subject: [gofriends] OmicBrowse open-source programs updated
Message-ID: <040801c7c98a$33dbef70$9b93ce50$@riken.go.jp>

Dear colleagues,

OmicBrowse source programs and installation package for LINUX are updated
and available from SourceForge,
http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html

Added new functions are
1) Access controls over secure datasets
2) Changing the browser's window size
3) human, mouse, rat, C.elegans, Arabidopsis and rice genome annotations
available

Please see a demonstration page:
http://omicspace.riken.jp/db/genome.html

OmicBrowse is a genome browser displaying an integrated view of multiple
omics annotations filtered with ontologies including GO. It consists of a
Flash client which retrieves XML data from a server composed of Java
servlets. Administrators can configure the server to subscribe to other
OmicBrowse servers and to return a response of merged data thereof, so the
user can search multiple datasets across every server simultaneously and
genome-widely.

Users can also integrate in-house private-data, along with various genomic
annotations from public internet servers. OmicBrowse also assists users to
share views by e-mail, to print out views, to register frequently-viewed
chromosomal intervals, and to define groups of often browsed datasets as
menu items.

This system has another unique feature in that it allows administrators to
have fine grained control over secure datasets. They can assign restrictions
to any datasets so that only authorized users can access them, which is very
useful for large-scale genome analysis projects that may consist of
collaborators from various laboratories.

OmicBrowse is developed by RIKEN in Japan and is released under the GPL.

For more details, please see

Tetsuro Toyoda, Yoshiki Mochizuki, Keith Player, Naohiko Heida, Norio
Kobayashi and Yoshiyuki Sakaki "OmicBrowse: a browser of multidimensional
omics annotations," Bioinformatics, 23, 524-526 (2007)

Tetsuro Toyoda, Ph.D.



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From jane at ebi.ac.uk  Thu Jul 26 09:47:43 2007
From: jane at ebi.ac.uk (Jane Lomax)
Date: Thu, 26 Jul 2007 17:47:43 +0100 (BST)
Subject: [gofriends] warning: new tags in gene_ontology_edit.obo file from 9th August
 2007
Message-ID: <Pine.LNX.4.62.0707261727380.11621@puffin.ebi.ac.uk>

Dear GO friends,

As of 9th August this year, the file gene_ontology_edit.obo, i.e.:

http://www.geneontology.org/ontology/gene_ontology_edit.obo
ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo
http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/ontology/gene_ontology_edit.obo

will contain an extra tag, disjoint_from. This tag will allow us to 
specify that certain pairs of terms within GO are disjoint, meaning that 
the two terms have no instances or subclasses in common. Initially this tag will only be 
applied to the terms 'cellular process', 'multicellular organismal 
process' and 'multi-organism process' in the process ontology, but it 
will be used more widely in the future. For more information about the disjoint_from
tag, see the OBO 1.2 file format specifications:

http://www.geneontology.org/GO.format.obo-1_2.shtml

Or email gohelp at genome.stanford.edu with any further questions.

* Note that the file gene_ontology.obo will remain unchanged.

many thanks,

The GO Consortium



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From dbarrell at ebi.ac.uk  Fri Jul 27 07:54:37 2007
From: dbarrell at ebi.ac.uk (Daniel Barrell)
Date: Fri, 27 Jul 2007 15:54:37 +0100
Subject: [gofriends] July 2007 GOA release
In-Reply-To: <42690FC8.8010409@ebi.ac.uk>
References: <42690FC8.8010409@ebi.ac.uk>
Message-ID: <46AA072D.5090800@ebi.ac.uk>

GOA releases: July 2007
=======================

GOA (GO Annotation at EBI) is a project run by the European Bioinformatics
Institute that aims to provide assignments of gene products to the Gene
Ontology (GO) resource.

The data can be obtained via:

            EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

            EBI SRS: http://srs.ebi.ac.uk. Search GOA data library

            GO FTP: 
ftp://ftp.geneontology.org/pub/go/gene-associations/ `	 
(updated over the weekend)

            GO CVS: http://www.geneontology.org/GO.CVS.help.html

For further information read: http://www.ebi.ac.uk/GOA or contact 
goa at ebi.ac.uk.

Regards

The UniProt GOA Team



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