From feedback_submission at filetta.cshl.edu Fri Mar 3 18:19:22 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Fri, 3 Mar 2006 18:19:22 -0500 Subject: Feedback on POC Message-ID: <200603032319.k23NJMLM013345@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/amigo/go.cgi?action=replace_tree&search_constraint=terms&query=PO:00090 comments: I was browsing the annotations for inflorescence, some 955 records. After a few clicks to different sites and back to the AMIGO browser, the page stopped letting me advance to the 'next' page of annotations. BUG? Or ? name: Mary Schaeffer email: SchaefferM at missouri.edu organization: USDA ARS send_feedback: Send your feedback From katica at acoma.stanford.edu Fri Mar 3 18:48:48 2006 From: katica at acoma.stanford.edu (katica at acoma.stanford.edu) Date: Fri, 3 Mar 2006 15:48:48 -0800 (PST) Subject: Feedback on POC In-Reply-To: <200603032319.k23NJMLM013345@filetta.cshl.org> References: <200603032319.k23NJMLM013345@filetta.cshl.org> Message-ID: Mary, There are 25 pages on the term detail page for 'inflorescence'. I clicked on 10 or so, also clicking on the few links to the individual databases on each of those ten pages, and went back to PO term detail page with no problem ('next' link worked fine too). Which browser did you use? Katica On Fri, 3 Mar 2006 feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/amigo/go.cgi?action=replace_tree&search_constraint=terms&query=PO:00090 > > comments: I was browsing the annotations for inflorescence, some 955 records. > After a few clicks to different sites and back to the AMIGO browser, the page stopped letting me advance to the 'next' page of annotations. > BUG? Or ? > > name: Mary Schaeffer > > email: SchaefferM at missouri.edu > > organization: USDA ARS > > send_feedback: Send your feedback > -- -------------------------------------------------------------------------- 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 shuly at cshl.edu Fri Mar 3 19:51:08 2006 From: shuly at cshl.edu (Shuly Avraham) Date: Fri, 3 Mar 2006 19:51:08 -0500 Subject: Feedback on POC In-Reply-To: References: <200603032319.k23NJMLM013345@filetta.cshl.org> Message-ID: Mary, I played with the browser and didn't encounter this problem either. Do you think you can reproduce the error? Can you be more specific about the steps you took to reach the problem? Thanks, Shuly. On Mar 3, 2006, at 6:48 PM, katica at acoma.stanford.edu wrote: > > Mary, > > There are 25 pages on the term detail page for 'inflorescence'. I > clicked on 10 or so, also clicking on the few links to the > individual databases on each of those ten pages, and went back to > PO term detail page with no problem ('next' link worked fine too). > > Which browser did you use? > > Katica > > > On Fri, 3 Mar 2006 feedback_submission at filetta.cshl.edu wrote: > >> *** Feedback from Plant Ontology Live Site *** >> >> refer_to_url: http://www.plantontology.org/amigo/go.cgi? >> action=replace_tree&search_constraint=terms&query=PO:00090 >> >> comments: I was browsing the annotations for inflorescence, some >> 955 records. >> After a few clicks to different sites and back to the AMIGO >> browser, the page stopped letting me advance to the 'next' page >> of annotations. >> BUG? Or ? >> >> name: Mary Schaeffer >> >> email: SchaefferM at missouri.edu >> >> organization: USDA ARS >> >> send_feedback: Send your feedback >> > > -- > ---------------------------------------------------------------------- > ---- > 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 shuly at cshl.edu Mon Mar 6 12:17:42 2006 From: shuly at cshl.edu (Shuly Avraham) Date: Mon, 6 Mar 2006 12:17:42 -0500 Subject: Feedback on POC In-Reply-To: References: Message-ID: <12F97179-22D6-4110-8ED0-6B2138C5A4CC@cshl.edu> Mary, I can update the URL - this is actually the way to do it, if you provide me with the specific URL. Shuly. On Mar 6, 2006, at 11:23 AM, Mary (MaizeGDB) wrote: > Hi Shuly, > Not sure, but think the problem was my hyperactive 'clicking', and > that > there are multiple PO windows once once gets 'extra clicky'. In any > case, I > am unable to reproduce the problem, with careful note-taking (and less > hyperactivity). There is one small problem: in backing up from a > MaizeGDB > record, reached from a PO link, 2 back clicks (browser Explorer > back button) > are required. > > This seems to be the result of the MaizeGDB linking style which is > currently > to the look-up by id, and not id and entity; the first back up from > the > display goes to the intermediate 'call-forwarding' page (MaizeGDB) > which is > blank. Clicking the back button a second time takes me to the PO page > expected to get with a single back click. > One way to fix this would be for me to provide the specific URL > prefix for > each entity. I would be happy to work with updating those URLS, > unless you > can think of a different fix. > mary > > > >> From: Shuly Avraham >> Reply-To: po-dev at plantontology.org, Shuly Avraham >> Date: Fri, 3 Mar 2006 19:51:08 -0500 >> To: po-dev at plantontology.org >> Subject: Re: Feedback on POC >> >> Mary, >> >> I played with the browser and didn't encounter this problem either. >> Do you think you can reproduce the error? Can you be more specific >> about the steps you took to reach the problem? >> >> Thanks, >> Shuly. >> >> On Mar 3, 2006, at 6:48 PM, katica at acoma.stanford.edu wrote: >> >>> >>> Mary, >>> >>> There are 25 pages on the term detail page for 'inflorescence'. I >>> clicked on 10 or so, also clicking on the few links to the >>> individual databases on each of those ten pages, and went back to >>> PO term detail page with no problem ('next' link worked fine too). >>> >>> Which browser did you use? >>> >>> Katica >>> >>> >>> On Fri, 3 Mar 2006 feedback_submission at filetta.cshl.edu wrote: >>> >>>> *** Feedback from Plant Ontology Live Site *** >>>> >>>> refer_to_url: http://www.plantontology.org/amigo/go.cgi? >>>> action=replace_tree&search_constraint=terms&query=PO:00090 >>>> >>>> comments: I was browsing the annotations for inflorescence, some >>>> 955 records. >>>> After a few clicks to different sites and back to the AMIGO >>>> browser, the page stopped letting me advance to the 'next' page >>>> of annotations. >>>> BUG? Or ? >>>> >>>> name: Mary Schaeffer >>>> >>>> email: SchaefferM at missouri.edu >>>> >>>> organization: USDA ARS >>>> >>>> send_feedback: Send your feedback >>>> >>> >>> -- >>> -------------------------------------------------------------------- >>> -- >>> ---- >>> 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 cjm at fruitfly.org Fri Mar 17 20:04:10 2006 From: cjm at fruitfly.org (chris mungall) Date: Fri, 17 Mar 2006 17:04:10 -0800 Subject: Anatomy Workshop Invitation In-Reply-To: References: Message-ID: <1dbf7a79c82ee5b10bec399c04981a72@fruitfly.org> I had previously set up a mailing list for the discussion of anatomy ontologies within the context of OBO and the OBO Foundry; you can subscribe here: http://lists.sourceforge.net/lists/listinfo/obo-anatomy or send me an email and I will subscribe you. The list is an open list for the discussion of the issues Suzi mentions below, and anything else pertaining to anatomical ontologies; this list will be announced on obo-discuss too. See you in September! Chris On Mar 16, 2006, at 1:27 PM, Suzanna Lewis wrote: > Dear friends, > > We are organizing a Workshop for the Ontology of Anatomy on September > 8-9, 2006 in > Seattle, Washington. We have met before for a number of related > purposes, but never to explicitly address anatomical ontology itself. > Each of you are actively involved in the development and continued > improvements to a particular anatomy, for various organisms. > Regardless of organism differences, if we use common methodologies and > principles to build our ontologies then, ultimately, this will enable > us to tackle the big issue: to recognize homologous anatomical > structures of different species. > > The main focus of this workshop is to pave the way for > interoperability between the anatomical ontologies developed for > various organisms (including human) by agreeing on shared > methodologies for build our respecting ontology. Its objectives are to > develop: > > 1. a list of relations used within anatomical anatomies, their > definitions, and their consistent use within anatomy ontologies (esp > part_of); > > 2. a list of major organizational units of biological organisms at all > levels of granular partitions (e.g. biological macromolecule, cell, > organ); > > 3. a representation of developmental stages of organisms, that is, are > anatomy and development two separate, or one single integrated > ontology? If separate what are the relations between them and how > should they be applied; > > 4. a method that allows automated reasoners to recognize homologous > anatomical structures of different species. > > For the usual practical reasons we want to keep the number of people > attending small. We want to limit it to those who are in the trenches > building these ontologies, since it sharpens the mind to have a > tangible problem to be solved. If there is someone in your group who > might be more appropriate, or if there is a particular group or person > who has slipped our minds, please let us know, but we do want to limit > participants to those who have more than a passing interest. Your > applied ontology is your ticket in as it were. > > Suggestions for additional topics to cover are very welcome. We > (Fabian) have set up a URL for the work shop. Right now, there is > nothing on this page. But this is the place where people will be able > to find logistic details about the workshop as it forms. > > http://smi.stanford.edu/projects/cbio/mwiki-internal/index.php/ > Anatomy_Ontology_Workshop > > BTW, please let us introduce Fabian Neuhaus to you. He is a bright > young man who is now a post-doc with Barry Smith, and truly > understands the implications of what we put into our ontologies (and > is very good at pointing these out!). He will working with us to make > the meeting productive. > > Looking forward to seeing you in the fall, > > Suzi, Michael, Fabian, and Monte > From feedback_submission at filetta.cshl.edu Sat Mar 18 15:12:52 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Sat, 18 Mar 2006 15:12:52 -0500 Subject: Feedback on POC Message-ID: <200603182012.k2IKCqn0026416@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: a Content-Type: multipart/alternative; boundary=9244698f7fb78a34df0902f2d0c4b5b9 MIME-Version: 1.0 Subject: attempts so often passed off in society for bcc: frekiforbes at aol.com This is a multi-part message in MIME format. --9244698f7fb78a34df0902f2d0c4b5b9 Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit away. ust opposite to the entrance of the church may be seen, built into the wall, a stone, on which is a bas relief, and before --9244698f7fb78a34df0902f2d0c4b5b9-- . send_feedback: made3552 at plantontology.org Clear: made3552 at plantontology.org comments: made3552 at plantontology.org organization: made3552 at plantontology.org email: made3552 at plantontology.org name: made3552 at plantontology.org From feedback_submission at filetta.cshl.edu Sat Mar 18 15:12:51 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Sat, 18 Mar 2006 15:12:51 -0500 Subject: Feedback on POC Message-ID: <200603182012.k2IKCpWu026396@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: in6153 at plantontology.org send_feedback: in6153 at plantontology.org Clear: in6153 at plantontology.org comments: in6153 at plantontology.org organization: in6153 at plantontology.org email: in6153 at plantontology.org name: then Content-Type: multipart/alternative; boundary=0cc523c66f45fe710cc505fcc036c1fc MIME-Version: 1.0 Subject: will you now bring me out of my bcc: hollowiog1503 at aol.com This is a multi-part message in MIME format. --0cc523c66f45fe710cc505fcc036c1fc Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit from themselves boots and coats, sprang into the sea, and dived under the water. short and noiseless moment passed. ne of the --0cc523c66f45fe710cc505fcc036c1fc-- . From feedback_submission at filetta.cshl.edu Sat Mar 18 15:13:47 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Sat, 18 Mar 2006 15:13:47 -0500 Subject: Feedback on POC Message-ID: <200603182013.k2IKDlDr026454@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: ady956 at plantontology.org send_feedback: ady956 at plantontology.org Clear: ady956 at plantontology.org comments: ady956 at plantontology.org organization: think Content-Type: multipart/alternative; boundary=8d5fb686d3bd70f482509fcd7cce4f79 MIME-Version: 1.0 Subject: formed the horizon, drew he a bay so naturally it bcc: frekiforbes at aol.com This is a multi-part message in MIME format. --8d5fb686d3bd70f482509fcd7cce4f79 Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit if your mail bounces from archive.org, will still see it, if it bounces from prairienet.org, better resend later on. . . . rof. art will answer or forward your message. e would prefer to send you information by email. xample command line session ftp ftp.ibiblio.org --8d5fb686d3bd70f482509fcd7cce4f79-- . email: ady956 at plantontology.org name: ady956 at plantontology.org From feedback_submission at filetta.cshl.edu Sat Mar 18 15:12:51 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Sat, 18 Mar 2006 15:12:51 -0500 Subject: Feedback on POC Message-ID: <200603182012.k2IKCpTQ026406@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: one6088 at plantontology.org name: one6088 at plantontology.org Clear: one6088 at plantontology.org comments: gradations Content-Type: multipart/alternative; boundary=0d95efe638b2e52cc55d011b97c1daa1 MIME-Version: 1.0 Subject: unsteady. he olonel s son is a bcc: Voiettag at aol.com This is a multi-part message in MIME format. --0d95efe638b2e52cc55d011b97c1daa1 Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit endowed with this sentiment of pride, which drives me on to active exertion. y fate wavered whether should become one such as these or whether should rise into that circle which the world calls the higher. he mist form did not sink down into the mire, but rose above --0d95efe638b2e52cc55d011b97c1daa1-- . organization: one6088 at plantontology.org email: one6088 at plantontology.org send_feedback: one6088 at plantontology.org From pj37 at cornell.edu Sat Mar 18 16:33:40 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Sat, 18 Mar 2006 16:33:40 -0500 Subject: [Fwd: Re: [Fwd: [ geneontology-AmiGO Requests-1413431 ] displaying obsotele nodes/terms]] Message-ID: <441C7CB4.7000803@cornell.edu> I hope the GO group will appreciate this feedback. Pankaj -------- Original Message -------- Subject: Re: [Fwd: [ geneontology-AmiGO Requests-1413431 ] displaying obsotele nodes/terms] Date: Sat, 18 Mar 2006 14:52:00 -0400 From: Peter Stevens Reply-To: po-internal at plantontology.org To: References: <67bf5c58a1d1d6f3b9357be916290448 at msx.umsl.edu> I agree about obsolete - "archived" may be best. "Terms not in current use" may be linked with "names not in current use" and so acquire guilt through mistaken association. P. >I'd like to second Pankaj's request that the obsolete nodes be place >after the active ones. I would also like to request that the term >"obsolete" be replaced with something like "archived terms" or >"terms not in current use". The word "obsolete" has caused >considerable misunderstanding in the botanical community, and has >cost the PO a great deal of good will. People are interpreting the >word "obsolete" to mean "worthless" or "hopelessly old-fashioned". > >Toby > > >On Mar 17, 2006, at 8:54 PM, Pankaj Jaiswal wrote: > > > > >-------- Original Message -------- > >Subject: [ geneontology-AmiGO Requests-1413431 ] displaying obsotele >nodes/terms > >Date: Fri, 17 Mar 2006 17:34:57 -0800 > >From: SourceForge.net > >To: noreply at sourceforge.net > > >AmiGO Requests item #1413431, was opened at 2006-01-23 20:17 > >Message generated for change (Comment added) made by sshu > >You can respond by visiting: > >https://sourceforge.net/tracker/?func=detail&atid=494390&aid=1413431&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: AmiGO 1.5 > >Group: None > >Status: Closed > >Resolution: None > >Priority: 5 > >Submitted By: Pankaj Jaiswal (pj37) > >Assigned to: Nobody/Anonymous (nobody) > >Summary: displaying obsotele nodes/terms > > >Initial Comment: > > > >Compared to GO > >http://www.godatabase.org/cgi-bin/amigo/go.cgi?search_constraint=terms&action=replace_tree > > >if you look at the PO which uses the same AMIGO browser > >(http://www.plantontology.org/amigo/go.cgi) > > >is it possible to display the "obsolete" nodes by > >default at the last in the list. > > >I presume the list is displayed alphabetically and it > >is not a problem because 'G' precedes 'O'. However this > >is a problem in PO db. > > >Users have objected to looking at 'obsolete' at the > >very top. > > >-Pankaj > > >---------------------------------------------------------------------- > > >Comment By: Shengqiang Shu (sshu) > >Date: 2006-03-17 17:34 > > >Message: > >Logged In: YES > >user_id=255734 > > >they are show last. will be in next release. > > > >Shu > > >---------------------------------------------------------------------- > > >You can respond by visiting: > >https://sourceforge.net/tracker/?func=detail&atid=494390&aid=1413431&group_id=36855 > > > > > >Elizabeth A. Kellogg > >E. Desmond Lee and Family Professor of Botanical Studies > >Department of Biology > >University of Missouri-St. Louis > >St. Louis, MO 63121 > >Tel: 314-516-6217 > >FAX: 314-516-6233 > >http://www.umsl.edu/services/kellogg/