From jclark at ebi.ac.uk Thu Jun 3 05:32:07 2004 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 03 Jun 2004 10:32:07 +0100 Subject: plants in GO Message-ID: <40BEF017.8000603@ebi.ac.uk> Hi, I am a curator in the Gene Ontology Editorial Office, where we write the terms in the Gene Ontology. I am a plant scientist by training and so I have been working on lots of different plant terms in the ontologies. Recently I have been finding that I could often do with feedback from more plant scientists. Pankaj Jaiswal and I just agreed that it might be a good idea for me to write to the Plant Ontology e-mail list each time a new plant-related sourceforge item is opened. That way we can receive the widest possible feedback on all plant term changes in the ontology, and all the Plant Ontology people will be kept in touch with what is happening with plants in GO. So here's my first list of sourceforge items :-) [ 729414 ] Plant development terms, page 2 https://sourceforge.net/tracker/index.php?func=detail&aid=729414&group_id=36855&atid=440764 [ 877837 ] inflorescence development (+more) https://sourceforge.net/tracker/index.php?func=detail&aid=877837&group_id=36855&atid=440764 [ 899726 ] plant gametogenesis 2 https://sourceforge.net/tracker/index.php?func=detail&aid=899726&group_id=36855&atid=440764 [ 923627 ] GO:0010196 : nonphotochemical quenching https://sourceforge.net/tracker/index.php?func=detail&aid=923627&group_id=36855&atid=440764 [ 939385 ] GO:0009725 : response to hormone stimulus https://sourceforge.net/tracker/index.php?func=detail&aid=939385&group_id=36855&atid=440764 [ 944692 ] pollination https://sourceforge.net/tracker/index.php?func=detail&aid=944692&group_id=36855&atid=440764 [ 950151 ] merge trichome morphogenesis https://sourceforge.net/tracker/index.php?func=detail&aid=950151&group_id=36855&atid=440764 [ 951331 ] Dicot Flower development https://sourceforge.net/tracker/index.php?func=detail&aid=951331&group_id=36855&atid=440764 [ 953912 ] photosynthesis defs https://sourceforge.net/tracker/index.php?func=detail&aid=953912&group_id=36855&atid=440764 Thanks in advance for any feedback. :-) It is very much appreciated. Best wishes, Jennifer Clark -- EMBL - European Bioinformatics Institute, Gene Ontology Consortium, and Wolfson College, Cambridge. http://www.ebi.ac.uk/~jclark/ From jclark at ebi.ac.uk Thu Jun 3 08:20:09 2004 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 03 Jun 2004 13:20:09 +0100 Subject: plants in GO In-Reply-To: <40BEF017.8000603@ebi.ac.uk> References: <40BEF017.8000603@ebi.ac.uk> Message-ID: <40BF1779.4090103@ebi.ac.uk> Hi, A new plant-related GO sourceforge item has been opened: [ 965693 ] maintenance of 'x' identity https://sourceforge.net/tracker/index.php?func=detail&aid=965693&group_id=36855&atid=440764 Jen From katica at acoma.Stanford.EDU Thu Jun 3 16:34:22 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 3 Jun 2004 13:34:22 -0700 (PDT) Subject: plants in GO In-Reply-To: <40BEF017.8000603@ebi.ac.uk> Message-ID: Hi Jennifer, Thanks for sending us links for the plant-related sourceforge items. Yes, I think it's a great idea to forward the GO plant-related terms to the po-dev at plantontology.org, and I am confident that you'll get a lot of feedbacks from plant biology experts that are on our mailing list. Greetings, Katica Ilic On Thu, 3 Jun 2004, J Clark wrote: > Hi, > > I am a curator in the Gene Ontology Editorial Office, where > we write the > terms in the Gene Ontology. I am a plant scientist by > training and so I > have been working on lots of different plant terms in the > ontologies. > Recently I have been finding that I could often do with > feedback from > more plant scientists. Pankaj Jaiswal and I just agreed that > it might be > a good idea for me to write to the Plant Ontology e-mail > list each time > a new plant-related sourceforge item is opened. That way we > can receive > the widest possible feedback on all plant term changes in > the ontology, > and all the Plant Ontology people will be kept in touch with > what is > happening with plants in GO. > > So here's my first list of sourceforge items :-) > > [ 729414 ] Plant development terms, page 2 > https://sourceforge.net/tracker/index.php?func=detail&aid=729414&group_id=36855&atid=440764 > > [ 877837 ] inflorescence development (+more) > https://sourceforge.net/tracker/index.php?func=detail&aid=877837&group_id=36855&atid=440764 > > [ 899726 ] plant gametogenesis 2 > https://sourceforge.net/tracker/index.php?func=detail&aid=899726&group_id=36855&atid=440764 > > [ 923627 ] GO:0010196 : nonphotochemical quenching > https://sourceforge.net/tracker/index.php?func=detail&aid=923627&group_id=36855&atid=440764 > > [ 939385 ] GO:0009725 : response to hormone stimulus > https://sourceforge.net/tracker/index.php?func=detail&aid=939385&group_id=36855&atid=440764 > > [ 944692 ] pollination > https://sourceforge.net/tracker/index.php?func=detail&aid=944692&group_id=36855&atid=440764 > > [ 950151 ] merge trichome morphogenesis > https://sourceforge.net/tracker/index.php?func=detail&aid=950151&group_id=36855&atid=440764 > > [ 951331 ] Dicot Flower development > https://sourceforge.net/tracker/index.php?func=detail&aid=951331&group_id=36855&atid=440764 > > [ 953912 ] photosynthesis defs > https://sourceforge.net/tracker/index.php?func=detail&aid=953912&group_id=36855&atid=440764 > > Thanks in advance for any feedback. :-) It is very much > appreciated. > > Best wishes, > > Jennifer Clark > > > > -- > EMBL - European Bioinformatics Institute, > Gene Ontology Consortium, > and Wolfson College, Cambridge. > http://www.ebi.ac.uk/~jclark/ > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From smundodi at acoma.Stanford.EDU Thu Jun 3 15:11:32 2004 From: smundodi at acoma.Stanford.EDU (Suparna Mundodi) Date: Thu, 3 Jun 2004 12:11:32 -0700 (PDT) Subject: plants in GO In-Reply-To: <40BF1779.4090103@ebi.ac.uk> Message-ID: I think it will be good if the plant group looks at the following sourceforge entry as well. https://sourceforge.net/tracker/?group_id=36855&atid=440764&func=detail&aid=965023 CHeers, Suparna On Thu, 3 Jun 2004, J Clark wrote: > Hi, > > A new plant-related GO sourceforge item has been opened: > > [ 965693 ] maintenance of 'x' identity > https://sourceforge.net/tracker/index.php?func=detail&aid=965693&group_id=36855&atid=440764 > > Jen > **************************************************************************** Suparna Mundodi, Ph.D. email:smundodi at acoma.stanford.edu The Arabidopsis Information Resources Fax:650-325-6857 Carnegie Institution of Washington URL:http://arabidopsis.org/ Department of Plant Biology phone:650-325-1521 x342 260 Panama St. Stanford, CA 94305 **************************************************************************** From lstein at cshl.edu Thu Jun 3 18:24:37 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 03 Jun 2004 18:24:37 -0400 Subject: plants in GO In-Reply-To: <40BEF017.8000603@ebi.ac.uk> References: <40BEF017.8000603@ebi.ac.uk> Message-ID: <200406031824.37655.lstein@cshl.edu> Excellent suggestion. I had no idea that so many plant-related sourceforge projects were running! Lincoln On Thursday 03 June 2004 05:32 am, J Clark wrote: > Hi, > > I am a curator in the Gene Ontology Editorial Office, where > we write the > terms in the Gene Ontology. I am a plant scientist by > training and so I > have been working on lots of different plant terms in the > ontologies. > Recently I have been finding that I could often do with > feedback from > more plant scientists. Pankaj Jaiswal and I just agreed that > it might be > a good idea for me to write to the Plant Ontology e-mail > list each time > a new plant-related sourceforge item is opened. That way we > can receive > the widest possible feedback on all plant term changes in > the ontology, > and all the Plant Ontology people will be kept in touch with > what is > happening with plants in GO. > > So here's my first list of sourceforge items :-) > > [ 729414 ] Plant development terms, page 2 > https://sourceforge.net/tracker/index.php?func=detail&aid=729414&group_id=3 >6855&atid=440764 > > [ 877837 ] inflorescence development (+more) > https://sourceforge.net/tracker/index.php?func=detail&aid=877837&group_id=3 >6855&atid=440764 > > [ 899726 ] plant gametogenesis 2 > https://sourceforge.net/tracker/index.php?func=detail&aid=899726&group_id=3 >6855&atid=440764 > > [ 923627 ] GO:0010196 : nonphotochemical quenching > https://sourceforge.net/tracker/index.php?func=detail&aid=923627&group_id=3 >6855&atid=440764 > > [ 939385 ] GO:0009725 : response to hormone stimulus > https://sourceforge.net/tracker/index.php?func=detail&aid=939385&group_id=3 >6855&atid=440764 > > [ 944692 ] pollination > https://sourceforge.net/tracker/index.php?func=detail&aid=944692&group_id=3 >6855&atid=440764 > > [ 950151 ] merge trichome morphogenesis > https://sourceforge.net/tracker/index.php?func=detail&aid=950151&group_id=3 >6855&atid=440764 > > [ 951331 ] Dicot Flower development > https://sourceforge.net/tracker/index.php?func=detail&aid=951331&group_id=3 >6855&atid=440764 > > [ 953912 ] photosynthesis defs > https://sourceforge.net/tracker/index.php?func=detail&aid=953912&group_id=3 >6855&atid=440764 > > Thanks in advance for any feedback. :-) It is very much > appreciated. > > Best wishes, > > Jennifer Clark -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From rhee at acoma.Stanford.EDU Thu Jun 3 23:03:43 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Thu, 3 Jun 2004 20:03:43 -0700 (PDT) Subject: plants in GO In-Reply-To: <40BEF017.8000603@ebi.ac.uk> Message-ID: Jen, > So here's my first list of sourceforge items :-) > > [ 729414 ] Plant development terms, page 2 > https://sourceforge.net/tracker/index.php?func=detail&aid=729414&group_id=36855&atid=440764 Shouldn't this be closed and a new one called 'monocot flower development' be opened? It's a bit wiedly to go through and it seems like you've already made a decision to split the item into two. > [ 877837 ] inflorescence development (+more) > https://sourceforge.net/tracker/index.php?func=detail&aid=877837&group_id=36855&atid=440764 > > [ 899726 ] plant gametogenesis 2 > https://sourceforge.net/tracker/index.php?func=detail&aid=899726&group_id=36855&atid=440764 > > [ 923627 ] GO:0010196 : nonphotochemical quenching > https://sourceforge.net/tracker/index.php?func=detail&aid=923627&group_id=36855&atid=440764 > > [ 939385 ] GO:0009725 : response to hormone stimulus > https://sourceforge.net/tracker/index.php?func=detail&aid=939385&group_id=36855&atid=440764 > > [ 944692 ] pollination > https://sourceforge.net/tracker/index.php?func=detail&aid=944692&group_id=36855&atid=440764 This is a closed item. Unless you want to reopen it, I think we should consider it 'resolved'. > [ 950151 ] merge trichome morphogenesis > https://sourceforge.net/tracker/index.php?func=detail&aid=950151&group_id=36855&atid=440764 > > [ 951331 ] Dicot Flower development > https://sourceforge.net/tracker/index.php?func=detail&aid=951331&group_id=36855&atid=440764 > > [ 953912 ] photosynthesis defs > https://sourceforge.net/tracker/index.php?func=detail&aid=953912&group_id=36855&atid=440764 > > Thanks in advance for any feedback. :-) It is very much > appreciated. > > Best wishes, > > Jennifer Clark > > > > -- > EMBL - European Bioinformatics Institute, > Gene Ontology Consortium, > and Wolfson College, Cambridge. > http://www.ebi.ac.uk/~jclark/ > ----------------------------------------------------------------------------- Sue Rhee rhee at acoma.stanford.edu The Arabidopsis Information Resource URL: www.arabidopsis.org Carnegie Institution of Washington FAX: +1-650-325-6857 Department of Plant Biology Tel: +1-650-325-1521 ext. 251 260 Panama St. Stanford, CA 94305 U.S.A. ----------------------------------------------------------------------------- From jclark at ebi.ac.uk Fri Jun 4 11:35:03 2004 From: jclark at ebi.ac.uk (J Clark) Date: Fri, 04 Jun 2004 16:35:03 +0100 Subject: plants in GO In-Reply-To: References: Message-ID: <40C096A7.4070809@ebi.ac.uk> Sue Rhee wrote: >>[ 729414 ] Plant development terms, page 2 >>https://sourceforge.net/tracker/index.php?func=detail&aid=729414&group_id=36855&atid=440764 > > Shouldn't this be closed and a new one called 'monocot flower development' > be opened? It's a bit wiedly to go through and it seems like you've > already made a decision to split the item into two. > Yes that's a good point. I'm not sure that I've got all the threads from that page being carried on in other sourceforge items yet so I'll hang on to it for a bit longer until I can make sure everything is being carried on. However, the follow-on sourceforge item that has already been opened and is actually about monocot flower and inflorescence development was not named in an informative way so I have closed it and started two new pages called 966599 Monocot flower development terms https://sourceforge.net/tracker/index.php?func=detail&aid=966599&group_id=36855&atid=440764 966600 monocot inflorescence development https://sourceforge.net/tracker/index.php?func=detail&aid=966600&group_id=36855&atid=440764 Thank you for the suggestion. Best wishes, Jen From rhee at acoma.Stanford.EDU Thu Jun 10 09:41:41 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Thu, 10 Jun 2004 06:41:41 -0700 (PDT) Subject: AmiGO Security Alert (fwd) Message-ID: Shuly, It looks like you have to update AmiGO. Sue ---------- Forwarded message ---------- Date: Wed, 9 Jun 2004 17:14:09 -0700 From: Bradley Marshall To: Cc: Subject: AmiGO Security Alert The godatabase.org website AmiGO instantiation was hacked late Monday night. Someone figured out a way to pass a set of CGI parameters that allowed a nasty command to be run on the server. If you are running AmiGO 2.0, you should cvs update NOW. Once you've done that, everything should be fine. Sorry about any inconvenience. Brad ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From rhee at acoma.Stanford.EDU Thu Jun 10 09:44:16 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Thu, 10 Jun 2004 06:44:16 -0700 (PDT) Subject: Important go-dev Security Patch releases. (fwd) Message-ID: ---------- Forwarded message ---------- Date: Wed, 9 Jun 2004 19:49:30 -0700 From: Bradley Marshall To: Bradley Marshall Cc: , Subject: Important go-dev Security Patch releases. Thanks to a random internet hacker we have become aware of a major AmiGO security hole that was used to hose our server. If you have a local AmiGO installation, run, don't walk, to http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=33201 to grab one of the new software releases. AmiGO 1.x users should grab the go-dev-20040609-amigo1.5 release. AmiGO 2.0 users can either grab the go-dev-20040609-amigo2.0 release or just do a cvs update. For AmiGO 1.x users who want to touch their installation as little as possible, the files of interest are go-dev/perl-api/GO/CGI/Session.pm go-dev/perl-api/GO/CGI/Analysis.pm go-dev/perl-api/GO/CGI/HTML.pm go-dev/perl-api/GO/IO/HTML.pm You should be able to replace those 4 files with the versions in the new release and be OK. Brad ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From shuly at cshl.edu Thu Jun 10 12:35:26 2004 From: shuly at cshl.edu (Shuly) Date: Thu, 10 Jun 2004 12:35:26 -0400 Subject: AmiGO Security Alert (fwd) In-Reply-To: References: Message-ID: <40C88DCE.8070404@cshl.org> Already did! Thanks! Sue Rhee wrote: >Shuly, > >It looks like you have to update AmiGO. > >Sue > >---------- Forwarded message ---------- >Date: Wed, 9 Jun 2004 17:14:09 -0700 >From: Bradley Marshall >To: >Cc: >Subject: AmiGO Security Alert > > >The godatabase.org website AmiGO instantiation was hacked late Monday night. >Someone figured out a way to pass a set of CGI parameters that allowed a nasty >command to be run on the server. > >If you are running AmiGO 2.0, you should cvs update NOW. Once you've done that, >everything should be fine. Sorry about any inconvenience. > >Brad > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > > From lstein at cshl.edu Fri Jun 11 12:05:19 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 11 Jun 2004 12:05:19 -0400 Subject: Important go-dev Security Patch releases. (fwd) In-Reply-To: References: Message-ID: <200406111205.19649.lstein@cshl.edu> Hi Shuly, Please take down AmiGO until the upgrade is effected. Lincoln On Thursday 10 June 2004 09:44 am, Sue Rhee wrote: > ---------- Forwarded message ---------- > Date: Wed, 9 Jun 2004 19:49:30 -0700 > From: Bradley Marshall > To: Bradley Marshall > Cc: , > Subject: Important go-dev Security Patch releases. > > > Thanks to a random internet hacker we have become aware of a major > AmiGO security hole that was used to hose our server. > > If you have a local AmiGO installation, run, don't walk, to > http://sourceforge.net/project/showfiles.php?group_id=36855&package >_id=33201 to grab one of the new software releases. > > AmiGO 1.x users should grab the go-dev-20040609-amigo1.5 release. > AmiGO 2.0 users can either grab the go-dev-20040609-amigo2.0 > release or just do a cvs update. > > For AmiGO 1.x users who want to touch their installation as little > as possible, the files of interest are > > go-dev/perl-api/GO/CGI/Session.pm > go-dev/perl-api/GO/CGI/Analysis.pm > go-dev/perl-api/GO/CGI/HTML.pm > go-dev/perl-api/GO/IO/HTML.pm > > You should be able to replace those 4 files with the versions in > the new release and be OK. > > Brad > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From shuly at cshl.edu Fri Jun 11 12:32:35 2004 From: shuly at cshl.edu (Shuly) Date: Fri, 11 Jun 2004 12:32:35 -0400 Subject: Important go-dev Security Patch releases. (fwd) In-Reply-To: <200406111205.19649.lstein@cshl.edu> References: <200406111205.19649.lstein@cshl.edu> Message-ID: <40C9DEA3.2080309@cshl.org> Thanks everybody for all the warnings. I have already updated go-dev, and amigo. Shuly. Lincoln Stein wrote: >Hi Shuly, > >Please take down AmiGO until the upgrade is effected. > >Lincoln > >On Thursday 10 June 2004 09:44 am, Sue Rhee wrote: > > >>---------- Forwarded message ---------- >>Date: Wed, 9 Jun 2004 19:49:30 -0700 >>From: Bradley Marshall >>To: Bradley Marshall >>Cc: , >>Subject: Important go-dev Security Patch releases. >> >> >>Thanks to a random internet hacker we have become aware of a major >>AmiGO security hole that was used to hose our server. >> >>If you have a local AmiGO installation, run, don't walk, to >>http://sourceforge.net/project/showfiles.php?group_id=36855&package >>_id=33201 to grab one of the new software releases. >> >>AmiGO 1.x users should grab the go-dev-20040609-amigo1.5 release. >>AmiGO 2.0 users can either grab the go-dev-20040609-amigo2.0 >>release or just do a cvs update. >> >>For AmiGO 1.x users who want to touch their installation as little >>as possible, the files of interest are >> >>go-dev/perl-api/GO/CGI/Session.pm >>go-dev/perl-api/GO/CGI/Analysis.pm >>go-dev/perl-api/GO/CGI/HTML.pm >>go-dev/perl-api/GO/IO/HTML.pm >> >>You should be able to replace those 4 files with the versions in >>the new release and be OK. >> >>Brad >> >>---------------------------------------------------------------- >>This message was sent using IMP, the Internet Messaging Program. >> >> > > > -------------- next part -------------- An HTML attachment was scrubbed... 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