From r.bruskiewich at cgiar.org Mon May 3 04:43:31 2004 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Mon, 03 May 2004 01:43:31 -0700 Subject: friendly reminders Message-ID: <3EA5C75212CDD511B74100508BE0957607285C55@irriphx2.irri.cgiar.org> Hi Pankaj, I missed a chance to meet with an Agrovoc principal while in Rome in February. Not sure how that initiative is going. I guess my main point was to build some flexibility into our representations, to ensure linguistic universality. Like you say, many folks might help out with the actual translation, and yes... Keeping things synchronized is a problem. For our part here, we'll probably embed some flexibility in our management of ontology in Generation CP systems (at least, in our ICIS implementation thereof), to partly meet the challenge, then get our NARES to work on translations. Cheers Richard -----Original Message----- From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] Sent: Thursday, April 29, 2004 10:14 PM To: po-dev at plantontology.org Cc: po-dev at plantontology.org; Michael Ashburner; Hintum, Theo van Subject: RE: friendly reminders Hi Richard, There is an international effort going on with the help from FAO, AGVOC and UMLS if I am not wrong, on doing the translations as well as integrating the various vocabularies. These are called agricultural ontologies. http://www.fao.org/agrovoc/ A couple of years ago I met the project coordinator from FAO and he was very much interested in the PO and GO work. He even offerred that if we can provide the ontologies in some exchangeable format like OWL/RDF formats, it will help them in integrating our ontologies in their database. Not to mention an added advantage is getting the translations in 5-6 major languages other than English. The only problem Michael cited was on synchronizing translations with the GO & PO releases. If this works out then I think we don't have to worry about semantics of doing translations on our own. This will be an excellent example of working with a major international organization. Since it is FAO, I am pretty sure CGIAR will be more than willing to chip in with their help in coordinating the exchange. Pankaj Bruskiewich, Richard (IRRI) said: > One of Pankaj's points raises a issue here: translation of the POC/GO > into international languages... > > In principle, I don't see why we shouldn't be considering > "internationalization" of the POC (and GO) to accommodate ESL > researchers in other countries. I'm already considering such > generality in designing our next generation International Crop > Information System, that is, trying to split off the term "string" (in > unicode, of course) from the concept (indexed by accession identifier) > and the term definition (which could also be internationalized). > > I think that the CGIAR plant crop centers (and the ICIS project, and > the Generation CP) can probably help out in this regard given our > broad multi-national constituency, and extensive network of ESL > national research partners. If we collectively design the schemata to > accommodate such flexibility, then perhaps national partners from > major non-English speaking research constituencies will offer to do > the translation into their own languages(?). Big task, I know, but > doable... > > BTW, though English is one of the world's most widely spoken > languages, I wouldn't automatically assume that American English is > the dominant form... > Considering the size of some major ESL countries in the British > Empire, like India ;-))) > > Richard > > > > -----Original Message----- > From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] > Sent: Thursday, April 29, 2004 8:56 AM > To: POC-dev > Subject: friendly reminders > > Here are a few friendly reminders. > > -please do not use characters like ! # $ in the definitions. > -The main term should always have an American english spelling if > required. > -the synonyms can have British spellings. > -Same goes with definitions. Try using the American English spellings. > -do not use short forms of words like "str." for "structure" in the > definition. Always use full form. > -Always prefix /suffix the desired term mane if its a combination of > noun and an adjective. e.g. "indehiscent fruits". Having only > "indehiscent" as term name is insufficient. > > There are some more things, which I will post later on. I did some of > the changes but asombody has to go through them again. > > Cheers > > Pankaj > > ************************ > Pankaj Jaiswal, PhD > G15-Bradfiled Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > > -- Pankaj Jaiswal Gramene Database www.gramene.org From pj37 at cornell.edu Mon May 3 12:22:53 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 03 May 2004 12:22:53 -0400 Subject: friendly reminders In-Reply-To: <3EA5C75212CDD511B74100508BE0957607285C55@irriphx2.irri.cgiar.org> References: <3EA5C75212CDD511B74100508BE0957607285C55@irriphx2.irri.cgiar.org> Message-ID: <409671DD.9080605@cornell.edu> Hi Richard, I agree with you and hopefully POc will gain some useful hints from your IRIS experience. Bringing translations in our structure can be an objective for the future project. Infact inclusion of languages other than English was one such comment we received from the reviewers. Our suggestion was, we certainly plan to incorporate non-English terms into the core ontology whenever it is necessary to express a botanical concept that has no English equivalent. For example, the German term vorlauferspitze (the tip of a monocot leaf, obvious in early development, and hypothesized to be homologous to a dicot leaf blade) indeed has no counterpart in English, but is the term used in English botanical literature. (provided by Co-PIs, Toby Kellogg and Peter Stevens) On the other hand building a comprehensive plant ontology in multiple languages simultaneously would expand the project considerably, and would present multiple practical difficulties with updates. Changing a term in the English version of the ontology would require coordinated changes in the French and German versions as well. We think that it is a better use of our time to do the best job we can in English and then have the ontology translated into a series of synonyms in other languages. This would be best to do towards the end of the project, when the ontology has stabilized and could be accomplished either by seeking volunteers from the community, or by seeking supplementary funding for the task Cheers Pankaj Bruskiewich, Richard (IRRI) wrote: > Hi Pankaj, > > I missed a chance to meet with an Agrovoc principal while in Rome in > February. Not sure how that initiative is going. > > I guess my main point was to build some flexibility into our > representations, to ensure linguistic universality. Like you say, many folks > might help out with the actual translation, and yes... Keeping things > synchronized is a problem. > > For our part here, we'll probably embed some flexibility in our management > of ontology in Generation CP systems (at least, in our ICIS implementation > thereof), to partly meet the challenge, then get our NARES to work on > translations. > > Cheers > Richard > > -----Original Message----- > From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] > Sent: Thursday, April 29, 2004 10:14 PM > To: po-dev at plantontology.org > Cc: po-dev at plantontology.org; Michael Ashburner; Hintum, Theo van > Subject: RE: friendly reminders > > Hi Richard, > > There is an international effort going on with the help from FAO, AGVOC and > UMLS if I am not wrong, on doing the translations as well as integrating the > various vocabularies. These are called agricultural ontologies. > http://www.fao.org/agrovoc/ > > A couple of years ago I met the project coordinator from FAO and he was very > much interested in the PO and GO work. He even offerred that if we can > provide the ontologies in some exchangeable format like OWL/RDF formats, it > will help them in integrating our ontologies in their database. Not to > mention an added advantage is getting the translations in > 5-6 major languages other than English. The only problem Michael cited was > on synchronizing translations with the GO & PO releases. > > If this works out then I think we don't have to worry about semantics of > doing translations on our own. This will be an excellent example of working > with a major international organization. Since it is FAO, I am pretty sure > CGIAR will be more than willing to chip in with their help in coordinating > the exchange. > > > Pankaj > > > Bruskiewich, Richard (IRRI) said: > >>One of Pankaj's points raises a issue here: translation of the POC/GO >>into international languages... >> >>In principle, I don't see why we shouldn't be considering >>"internationalization" of the POC (and GO) to accommodate ESL >>researchers in other countries. I'm already considering such >>generality in designing our next generation International Crop >>Information System, that is, trying to split off the term "string" (in >>unicode, of course) from the concept (indexed by accession identifier) >>and the term definition (which could also be internationalized). >> >>I think that the CGIAR plant crop centers (and the ICIS project, and >>the Generation CP) can probably help out in this regard given our >>broad multi-national constituency, and extensive network of ESL >>national research partners. If we collectively design the schemata to >>accommodate such flexibility, then perhaps national partners from >>major non-English speaking research constituencies will offer to do >>the translation into their own languages(?). Big task, I know, but >>doable... >> >>BTW, though English is one of the world's most widely spoken >>languages, I wouldn't automatically assume that American English is >>the dominant form... >>Considering the size of some major ESL countries in the British >>Empire, like India ;-))) >> >>Richard >> >> >> >>-----Original Message----- >>From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] >>Sent: Thursday, April 29, 2004 8:56 AM >>To: POC-dev >>Subject: friendly reminders >> >>Here are a few friendly reminders. >> >>-please do not use characters like ! # $ in the definitions. >>-The main term should always have an American english spelling if >>required. >>-the synonyms can have British spellings. >>-Same goes with definitions. Try using the American English spellings. >>-do not use short forms of words like "str." for "structure" in the >>definition. Always use full form. >>-Always prefix /suffix the desired term mane if its a combination of >>noun and an adjective. e.g. "indehiscent fruits". Having only >>"indehiscent" as term name is insufficient. >> >>There are some more things, which I will post later on. I did some of >>the changes but asombody has to go through them again. >> >>Cheers >> >>Pankaj >> >>************************ >>Pankaj Jaiswal, PhD >>G15-Bradfiled Hall >>Dept. of Plant Breeding >>Cornell University >>Ithaca, NY-14853, USA >> >>Tel: +1-607-255-3103 >> +1-607-255-4109 >>Fax: +1-607-255-6683 >>http://www.gramene.org >>************************ >> >> > > > > -- > Pankaj Jaiswal > Gramene Database > www.gramene.org > -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From lstein at cshl.edu Tue May 4 16:34:50 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Tue, 04 May 2004 16:34:50 -0400 Subject: % efforts Message-ID: <200405041634.50883.lstein@cshl.edu> Hi Folks, I'm preparing the progress report for NSF and I'd like to know your estimated percentage efforts on this project so that I can report accurate numbers. Thanks, Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From pj37 at cornell.edu Tue May 4 17:51:44 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 4 May 2004 17:51:44 -0400 (EDT) Subject: % efforts In-Reply-To: <200405041634.50883.lstein@cshl.edu> References: <200405041634.50883.lstein@cshl.edu> Message-ID: <3223.24.59.76.45.1083707504.squirrel@webmail.cornell.edu> It's 20% for me. -Pankaj Lincoln Stein said: > Hi Folks, > > I'm preparing the progress report for NSF and I'd like to know your > estimated percentage efforts on this project so that I can report > accurate numbers. > > Thanks, > > Lincoln > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > -- Pankaj Jaiswal Gramene Database www.gramene.org From shuly at cshl.edu Wed May 5 13:45:33 2004 From: shuly at cshl.edu (Shuly) Date: Wed, 05 May 2004 13:45:33 -0400 Subject: % efforts In-Reply-To: <200405041634.50883.lstein@cshl.edu> References: <200405041634.50883.lstein@cshl.edu> Message-ID: <4099283D.5030601@cshl.org> about %50 Lincoln Stein wrote: >Hi Folks, > >I'm preparing the progress report for NSF and I'd like to know your >estimated percentage efforts on this project so that I can report >accurate numbers. > >Thanks, > >Lincoln > > > From pj37 at cornell.edu Mon May 10 14:25:55 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 10 May 2004 14:25:55 -0400 Subject: fruit section Message-ID: <409FC933.5070703@cornell.edu> Hi, I have some comments on fruit section -term "legume" is currently a direct instance of fruit. Do you think it should be placed as an instance of term "seed as dispersal unit", which is an instance of dehiscent fruit. -do we need all the instances of (sort of attributes) of capsule, e.g. loculicidal, septicidal etc. I know the exclusion of "septifragal" will be difficult because of the following comment. Is there a way out? -people may like to see "slilique" as a primary term compared to a synonym for "septifragal" -a possible TPR violation.. generic term gynoecium appears under floret and this may cause TPR violation because not all the fruit types develop from "floret gynoecium" (newly coined term). It's only the "caryopsis" which develops from gynoecium in the floret. We need a resolution on this. may be we need to pull back the relationship fruit develops from gynoecium One such example is slilique appearing under floret.. http://brie.cshl.org:8080/amigo/go.cgi?action=replace_tree&search_constraint=terms&query=PO:0020072 References: <409FC933.5070703@cornell.edu> Message-ID: There are quite a few Leguminosae species that have indehiscent fruits; these are legumes in the sense that they are modified from species with typical legume fruits. Cronquist (1981, pp. 600-601) says the following: FRUIT commonly dry and dehiscent down both sutures (i.e., a typical legume) but sometimes follicular, or indehiscent and then sometimes winged or breaking transversely into 1-seeded joints (i.e., a loment), rarely bladdery-inflated or more or less drupaceous (Andira) or otherwise fleshy, or nut-like or achene-like; seldom (as in spp. of Astragalus) the dorsal suture of the fruit giving rise to a partial or even complete partition. A lot of variation to accommodate! --Jeff >Hi, > >I have some comments on fruit section > >-term "legume" is currently a direct instance of fruit. Do you >think it should be placed as an instance of term "seed as dispersal >unit", which is an instance of dehiscent fruit. >-do we need all the instances of (sort of attributes) of capsule, >e.g. loculicidal, septicidal etc. I know the exclusion of >"septifragal" will be difficult because of the following comment. Is >there a way out? >-people may like to see "slilique" as a primary term compared to a >synonym for "septifragal" >-a possible TPR violation.. > generic term gynoecium appears under floret and this may >cause TPR violation because not all the fruit types develop from >"floret gynoecium" (newly coined term). It's only the "caryopsis" >which develops from gynoecium in the floret. We need a resolution on >this. > >may be we need to pull back the relationship >fruit develops from gynoecium > >One such example is slilique appearing under floret.. > >http://brie.cshl.org:8080/amigo/go.cgi?action=replace_tree&search_constraint=terms&query=PO:0020072 > > %spikelet ; PO:0009051 > PO:0009046 % reproductive structures ; PO:0009083 > ~fruit ; PO:0009001 % mature dispersal unit ; PO:0009091 > %dehiscent fruit ; PO:0020064 > %seed as dispersal unit ; PO:0020081 > %capsule ; PO:0020067 > %septifragal ; PO:0020072 ; synonym:silicula ; >synonym:siliqua ; synonym:silique -- Jeff J. Doyle Professor, L. H. Bailey Hortorium, Department of Plant Biology, Cornell University office: 259 Plant Science Building tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407 http://www.plantbio.cornell.edu/faculty.php?PB=jjd5 mailing address: Department of Plant Biology 228 Plant Science Building Cornell University Ithaca, NY 14853-4301 From tkellogg at umsl.edu Mon May 10 14:54:56 2004 From: tkellogg at umsl.edu (Elizabeth Kellogg) Date: Mon, 10 May 2004 13:54:56 -0500 Subject: fruit section In-Reply-To: <409FC933.5070703@cornell.edu> References: <409FC933.5070703@cornell.edu> Message-ID: <87B84AFD-A2B3-11D8-803E-000393B121A8@umsl.edu> Hi Pankaj - The problem is that not all legumes dehisce, and the ones that do dehisce do not all do it in the same way - some dehisce along one suture, some along both, and some dehisce between the seeds. The term "legume" can only be defined strictly as "the fruit of a member of Leguminosae." That's why it ends up as an instance only of fruit and not of "seed as dispersal unit." The TPR violation comes from the attempt to include a time axis (development) in a structural ontology, along the lines that we were discussing last week. The relationships are not intrinsically hierarchical. We could create "floret gynoecium", but following the same logic we might also have to create a separate term for every sort of gynoecium that developed into a different kind of fruit. But I don't quite understand the example you've given below. Aren't there other instances of fruit, including indehiscent ones? I think the TPR violation in the example below comes from reading down the hierarchy. Presumably if you included indehiscent fruits then you could trace a true path from caryopsis up to floret. (I think....) Toby On May 10, 2004, at 1:25 PM, Pankaj Jaiswal wrote: > > Hi, > > I have some comments on fruit section > > -term "legume" is currently a direct instance of fruit. Do you think > it should be placed as an instance of term "seed as dispersal unit", > which is an instance of dehiscent fruit. > -do we need all the instances of (sort of attributes) of capsule, e.g. > loculicidal, septicidal etc. I know the exclusion of "septifragal" > will be difficult because of the following comment. Is there a way > out? > -people may like to see "slilique" as a primary term compared to a > synonym for "septifragal" > -a possible TPR violation.. > generic term gynoecium appears under floret and this may cause TPR > violation because not all the fruit types develop from "floret > gynoecium" (newly coined term). It's only the "caryopsis" which > develops from gynoecium in the floret. We need a resolution on this. > > may be we need to pull back the relationship > fruit develops from gynoecium > > One such example is slilique appearing under floret.. > > http://brie.cshl.org:8080/amigo/go.cgi? > action=replace_tree&search_constraint=terms&query=PO:0020072 > > %spikelet ; PO:0009051 > % reproductive structures ; PO:0009083 > ~fruit ; PO:0009001 % mature dispersal unit ; PO:0009091 > %dehiscent fruit ; PO:0020064 > %seed as dispersal unit ; PO:0020081 > %capsule ; PO:0020067 > %septifragal ; PO:0020072 ; synonym:silicula ; > synonym:siliqua ; synonym:silique > > 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/divisions/artscience/biology/Kellogg/Kellogg/ home.html From pj37 at cornell.edu Mon May 10 15:09:17 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 10 May 2004 15:09:17 -0400 Subject: fruit section In-Reply-To: <87B84AFD-A2B3-11D8-803E-000393B121A8@umsl.edu> References: <409FC933.5070703@cornell.edu> <87B84AFD-A2B3-11D8-803E-000393B121A8@umsl.edu> Message-ID: <409FD35D.3050708@cornell.edu> Elizabeth Kellogg wrote: > Hi Pankaj - > The problem is that not all legumes dehisce, and the ones that do > dehisce do not all do it in the same way - some dehisce along one > suture, some along both, and some dehisce between the seeds. The term > "legume" can only be defined strictly as "the fruit of a member of > Leguminosae." That's why it ends up as an instance only of fruit and > not of "seed as dispersal unit." This is fine. I did not know about the situation earlier. Can we revise the definition we have now: The fruit of Fabaceae, formed from one carpel and either dehiscent along both sides, explosively so or not, or indehiscent, winged or not, splitting transversely or not. > The TPR violation comes from the attempt to include a time axis > (development) in a structural ontology, along the lines that we were > discussing last week. The relationships are not intrinsically > hierarchical. We could create "floret gynoecium", but following the > same logic we might also have to create a separate term for every sort > of gynoecium that developed into a different kind of fruit. But I > don't quite understand the example you've given below. Aren't there > other instances of fruit, including indehiscent ones? I think the TPR > violation in the example below comes from reading down the hierarchy. > Presumably if you included indehiscent fruits then you could trace a > true path from caryopsis up to floret. (I think....) I guess in this case we may need to pull back the develops from relationship (fruit-gynoecium). Because reading down the hierarchy also matters when we start associating the terms to genes/phenotypes. The asssociations keep adding from bottom-up. e.g. genes expressed in anthers are also considered to be expressed in stamen as well as its parent terms flower and floret. All the associations of a child term are carried over to the parent term by default in addition to any direct associations that teh parent might have. So anything associated with silique will also show up with floret and its parent spikelet, which should not happen. > Toby > > On May 10, 2004, at 1:25 PM, Pankaj Jaiswal wrote: > >> >> Hi, >> >> I have some comments on fruit section >> >> -term "legume" is currently a direct instance of fruit. Do you think >> it should be placed as an instance of term "seed as dispersal unit", >> which is an instance of dehiscent fruit. >> -do we need all the instances of (sort of attributes) of capsule, >> e.g. loculicidal, septicidal etc. I know the exclusion of >> "septifragal" will be difficult because of the following comment. Is >> there a way out? >> -people may like to see "slilique" as a primary term compared to a >> synonym for "septifragal" >> -a possible TPR violation.. >> generic term gynoecium appears under floret and this may cause >> TPR violation because not all the fruit types develop from "floret >> gynoecium" (newly coined term). It's only the "caryopsis" which >> develops from gynoecium in the floret. We need a resolution on this. >> >> may be we need to pull back the relationship >> fruit develops from gynoecium >> >> One such example is slilique appearing under floret.. >> >> http://brie.cshl.org:8080/amigo/go.cgi? >> action=replace_tree&search_constraint=terms&query=PO:0020072 >> >> > %spikelet ; PO:0009051 >> > > PO:0009046 % reproductive structures ; PO:0009083 >> ~fruit ; PO:0009001 % mature dispersal unit ; PO:0009091 >> %dehiscent fruit ; PO:0020064 >> %seed as dispersal unit ; PO:0020081 >> %capsule ; PO:0020067 >> %septifragal ; PO:0020072 ; synonym:silicula ; >> synonym:siliqua ; synonym:silique >> >> > 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/divisions/artscience/biology/Kellogg/Kellogg/ home.html > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From peter.stevens at mobot.org Mon May 10 14:15:45 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Mon, 10 May 2004 14:15:45 -0400 Subject: fruit section In-Reply-To: <409FD35D.3050708@cornell.edu> References: <409FC933.5070703@cornell.edu> <87B84AFD-A2B3-11D8-803E-000393B121A8@umsl.edu> <409FD35D.3050708@cornell.edu> Message-ID: >Looking to the future - all taxa in which there is only a single >carpel will now need to have fruits with distinct names - e.g. the >nutmeg family (Myristicaceae). No taxon that has several separate >carpels can have a legume fruit, even if the individual fruits are >indistinguishable from a legume as defined below. Findings aBout >legumes will not easily be generalisable, since nothing else has >them. Thus I would strongly recommend against using the term legume as defined below (i.e. the revised definition) - it simply means "fruit of Fabaceae". If there was a legume s. str. - e.g. "fruit of a single carpel dehiscing explosively down both sutures/sides" that might be OK. I have given up teaching "legume" (or silique/silicle/silicula for that matter). Peter S. >Elizabeth Kellogg wrote: > >>Hi Pankaj - >> The problem is that not all legumes dehisce, and the ones that >>do dehisce do not all do it in the same way - some dehisce along >>one suture, some along both, and some dehisce between the seeds. >>The term "legume" can only be defined strictly as "the fruit of a >>member of Leguminosae." That's why it ends up as an instance >>only of fruit and not of "seed as dispersal unit." > >This is fine. I did not know about the situation earlier. Can we >revise the definition we have now: >The fruit of Fabaceae, formed from one carpel and either dehiscent >along both sides, explosively so or not, or indehiscent, winged or >not, splitting transversely or not. > >> The TPR violation comes from the attempt to include a time axis >>(development) in a structural ontology, along the lines that we >>were discussing last week. The relationships are not >>intrinsically hierarchical. We could create "floret gynoecium", >>but following the same logic we might also have to create a >>separate term for every sort of gynoecium that developed into a >>different kind of fruit. But I don't quite understand the >>example you've given below. Aren't there other instances of >>fruit, including indehiscent ones? I think the TPR violation in >>the example below comes from reading down the hierarchy. >>Presumably if you included indehiscent fruits then you could trace >>a true path from caryopsis up to floret. (I think....) > >I guess in this case we may need to pull back the develops from >relationship (fruit-gynoecium). Because reading down the hierarchy >also matters when we start associating the terms to >genes/phenotypes. The asssociations keep adding from bottom-up. >e.g. genes expressed in anthers are also considered to be expressed >in stamen as well as its parent terms flower and floret. All the >associations of a child term are carried over to the parent term by >default in addition to any direct associations that teh parent might >have. So anything associated with silique will also show up with >floret and its parent spikelet, which should not happen. > >>Toby >> >>On May 10, 2004, at 1:25 PM, Pankaj Jaiswal wrote: >> >>> >>>Hi, >>> >>>I have some comments on fruit section >>> >>>-term "legume" is currently a direct instance of fruit. Do you >>>think it should be placed as an instance of term "seed as >>>dispersal unit", which is an instance of dehiscent fruit. >>>-do we need all the instances of (sort of attributes) of capsule, >>>e.g. loculicidal, septicidal etc. I know the exclusion of >>>"septifragal" will be difficult because of the following comment. >>>Is there a way out? >>>-people may like to see "slilique" as a primary term compared to a >>>synonym for "septifragal" >>>-a possible TPR violation.. >>> generic term gynoecium appears under floret and this may cause >>>TPR violation because not all the fruit types develop from >>>"floret gynoecium" (newly coined term). It's only the "caryopsis" >>>which develops from gynoecium in the floret. We need a resolution >>>on this. >>> >>>may be we need to pull back the relationship >>>fruit develops from gynoecium >>> >>>One such example is slilique appearing under floret.. >>> >>>http://brie.cshl.org:8080/amigo/go.cgi? >>>action=replace_tree&search_constraint=terms&query=PO:0020072 >>> >>> >> %spikelet ; PO:0009051 >>> >> >>PO:0009046 % reproductive structures ; PO:0009083 >>> ~fruit ; PO:0009001 % mature dispersal unit ; PO:0009091 >>> %dehiscent fruit ; PO:0020064 >>> %seed as dispersal unit ; PO:0020081 >>> %capsule ; PO:0020067 >>> %septifragal ; PO:0020072 ; synonym:silicula ; >>>synonym:siliqua ; synonym:silique >>> >>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/divisions/artscience/biology/Kellogg/Kellogg/ home.html >> > >-- >************************ >Pankaj Jaiswal, PhD >G15-Bradfiled Hall >Dept. of Plant Breeding >Cornell University >Ithaca, NY-14853, USA > >Tel: +1-607-255-3103 > +1-607-255-4109 >Fax: +1-607-255-6683 >http://www.gramene.org >************************ From Leszek at missouri.edu Mon May 10 16:00:30 2004 From: Leszek at missouri.edu (Vincent, Leszek) Date: Mon, 10 May 2004 15:00:30 -0500 Subject: fruit section Message-ID: Peter - That's a good & strong argument. But I'm wondering if we're not 'throwing the baby out with the bathwater' - this fruit area is very vexing! Another point for discussion at the May meeting. - Leszek > -----Original Message----- > From: owner-po-dev at brie4.cshl.org > [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Peter Stevens > Sent: Monday, May 10, 2004 1:16 PM > To: po-dev at plantontology.org > Subject: Re: fruit section > > > >Looking to the future - all taxa in which there is only a single > >carpel will now need to have fruits with distinct names - e.g. the > >nutmeg family (Myristicaceae). No taxon that has several separate > >carpels can have a legume fruit, even if the individual fruits are > >indistinguishable from a legume as defined below. Findings aBout > >legumes will not easily be generalisable, since nothing else has > >them. > > > Thus I would strongly recommend against using the term legume as > defined below (i.e. the revised definition) - it simply means "fruit > of Fabaceae". If there was a legume s. str. - e.g. "fruit of a > single carpel dehiscing explosively down both sutures/sides" that > might be OK. I have given up teaching "legume" (or > silique/silicle/silicula for that matter). > > Peter S. > > > > >Elizabeth Kellogg wrote: > > > >>Hi Pankaj - > >> The problem is that not all legumes dehisce, and the ones that > >>do dehisce do not all do it in the same way - some dehisce along > >>one suture, some along both, and some dehisce between the seeds. > >>The term "legume" can only be defined strictly as "the fruit of a > >>member of Leguminosae." That's why it ends up as an instance > >>only of fruit and not of "seed as dispersal unit." > > > >This is fine. I did not know about the situation earlier. Can we > >revise the definition we have now: > >The fruit of Fabaceae, formed from one carpel and either dehiscent > >along both sides, explosively so or not, or indehiscent, winged or > >not, splitting transversely or not. > > > >> The TPR violation comes from the attempt to include a time axis > >>(development) in a structural ontology, along the lines that we > >>were discussing last week. The relationships are not > >>intrinsically hierarchical. We could create "floret gynoecium", > >>but following the same logic we might also have to create a > >>separate term for every sort of gynoecium that developed into a > >>different kind of fruit. But I don't quite understand the > >>example you've given below. Aren't there other instances of > >>fruit, including indehiscent ones? I think the TPR violation in > >>the example below comes from reading down the hierarchy. > >>Presumably if you included indehiscent fruits then you could trace > >>a true path from caryopsis up to floret. (I think....) > > > >I guess in this case we may need to pull back the develops from > >relationship (fruit-gynoecium). Because reading down the hierarchy > >also matters when we start associating the terms to > >genes/phenotypes. The asssociations keep adding from bottom-up. > >e.g. genes expressed in anthers are also considered to be expressed > >in stamen as well as its parent terms flower and floret. All the > >associations of a child term are carried over to the parent term by > >default in addition to any direct associations that teh parent might > >have. So anything associated with silique will also show up with > >floret and its parent spikelet, which should not happen. > > > >>Toby > >> > >>On May 10, 2004, at 1:25 PM, Pankaj Jaiswal wrote: > >> > >>> > >>>Hi, > >>> > >>>I have some comments on fruit section > >>> > >>>-term "legume" is currently a direct instance of fruit. Do you > >>>think it should be placed as an instance of term "seed as > >>>dispersal unit", which is an instance of dehiscent fruit. > >>>-do we need all the instances of (sort of attributes) of capsule, > >>>e.g. loculicidal, septicidal etc. I know the exclusion of > >>>"septifragal" will be difficult because of the following comment. > >>>Is there a way out? > >>>-people may like to see "slilique" as a primary term compared to a > >>>synonym for "septifragal" > >>>-a possible TPR violation.. > >>> generic term gynoecium appears under floret and this > may cause > >>>TPR violation because not all the fruit types develop from > >>>"floret gynoecium" (newly coined term). It's only the "caryopsis" > >>>which develops from gynoecium in the floret. We need a resolution > >>>on this. > >>> > >>>may be we need to pull back the relationship > >>>fruit develops from gynoecium > >>> > >>>One such example is slilique appearing under floret.. > >>> > >>>http://brie.cshl.org:8080/amigo/go.cgi? > >>>action=replace_tree&search_constraint=terms&query=PO:0020072 > >>> > >>> >>> %spikelet ; PO:0009051 > >>> >>> >>>PO:0009046 % reproductive structures ; PO:0009083 > >>> ~fruit ; PO:0009001 % mature dispersal unit ; PO:0009091 > >>> %dehiscent fruit ; PO:0020064 > >>> %seed as dispersal unit ; PO:0020081 > >>> %capsule ; PO:0020067 > >>> %septifragal ; PO:0020072 ; synonym:silicula ; > >>>synonym:siliqua ; synonym:silique > >>> > >>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/divisions/artscience/biology/Kellogg/Kel logg/ home.html >> > >-- >************************ >Pankaj Jaiswal, PhD >G15-Bradfiled Hall >Dept. of Plant Breeding >Cornell University >Ithaca, NY-14853, USA > >Tel: +1-607-255-3103 > +1-607-255-4109 >Fax: +1-607-255-6683 >http://www.gramene.org >************************ From djp4 at cornell.edu Tue May 11 11:08:17 2004 From: djp4 at cornell.edu (Dominick J. Paolillo, Jr.) Date: Tue, 11 May 2004 11:08:17 -0400 Subject: % efforts In-Reply-To: <200405041634.50883.lstein@cshl.edu> Message-ID: <5.2.1.1.2.20040511110709.009ef690@postoffice7.mail.cornell.edu> I am emeritus and do not have a timed line. I consult on an "as needed" basis. Regrads, Dominick J. Paolillo, Jr Professor Emeritus Plant Biology At 04:34 PM 5/4/2004 -0400, you wrote: >Hi Folks, > >I'm preparing the progress report for NSF and I'd like to know your >estimated percentage efforts on this project so that I can report >accurate numbers. > >Thanks, > >Lincoln > >-- >Lincoln D. Stein >Cold Spring Harbor Laboratory >1 Bungtown Road >Cold Spring Harbor, NY 11724 From lstein at cshl.edu Tue May 11 11:42:54 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Tue, 11 May 2004 11:42:54 -0400 Subject: % efforts In-Reply-To: <5.2.1.1.2.20040511110709.009ef690@postoffice7.mail.cornell.edu> References: <5.2.1.1.2.20040511110709.009ef690@postoffice7.mail.cornell.edu> Message-ID: <200405111142.54451.lstein@cshl.edu> Thanks! I appreciate the information. Lincoln On Tuesday 11 May 2004 11:08 am, Dominick J. Paolillo, Jr. wrote: > I am emeritus and do not have a timed line. > > I consult on an "as needed" basis. > > Regrads, > > Dominick J. Paolillo, Jr > Professor Emeritus > Plant Biology > > At 04:34 PM 5/4/2004 -0400, you wrote: > >Hi Folks, > > > >I'm preparing the progress report for NSF and I'd like to know > > your estimated percentage efforts on this project so that I can > > report accurate numbers. > > > >Thanks, > > > >Lincoln > > > >-- > >Lincoln D. Stein > >Cold Spring Harbor Laboratory > >1 Bungtown Road > >Cold Spring Harbor, NY 11724 -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From a.garcia at imb.uq.edu.au Tue May 11 09:39:06 2004 From: a.garcia at imb.uq.edu.au (a.garcia at imb.uq.edu.au) Date: Tue, 11 May 2004 23:39:06 +1000 Subject: inquiry/wheat Message-ID: I would like to know if there is an ontology for wheat; I would also like to know if someone has ported the plant ontology to protege. cheers From jitterbug at plantontology.org Wed May 12 15:18:05 2004 From: jitterbug at plantontology.org (Katica Ilic) Date: Wed, 12 May 2004 15:18:05 -0400 Subject: inquiry/wheat (fwd) (PR#7) Message-ID: <200405121918.i4CJI5jV016858@brie4.cshl.org> Dear Garcia, I am not aware of any ongoing effort in the public sector with respect to developing anatomy and developmental stages ontologies specifically for wheat. However, Gramene has a Cereal Plant Anatomy ontology (the controlled vocabulary of plant anatomy representing organs, tissues and cell types), and Cereal Plant Growth Stages ontology (the controlled vocabulary of growth and developmental stages; examples are germination, seedling, booting, flowering, etc.), available for rice, maize, sorghum, wheat, oat and barley. You can download and browse these two ontologies on our POC web site or at Gramene. Currently, we are in the process of integrating Arabidopsis and cereal ontologies into generic plant anatomy ontology. The first version of the ontology will be released in the summer. We hope to make it applicable to most of the flowering plants. Furthermore, over the next two years, POC project will expand its plant-ontology-development effort to include other crops such as wheat, barley, tomato legumes and cotton. At the end, the controlled vocabularies developed by the POC will be generic enough to encompass/cover all the plant model systems; this includes cereals/brassicas/solanaceae/gossypium/legumes. The short answer to your question about the ontology editing tool, Prot?g? is no, we don?t use it for our Plant anatomy ontology, and I am not sure how widely this tool is used for biological ontologies. Instead, we use the DAG-edit, which is also a standard editor for GO (http://www.geneontology.org). Arabidopsis, Gramene and maize ontologies that you have seen on the POC web site, are all edited using DAG editor. I have recently communicated with Shenghui Wang from UK (wangs at cs.man.ac.uk), who was telling me that he uses Prot?g? for building the ontology for Ranunculus, so my suggestion to you is to contact him. He might be able to give you some specific information about the Protege. Unfortunately, I don?t have any experience with this tool, but from what I understood, this ontology editor has only IS_A relationship type, which can be seen as a kind_of relationship type. The DAG edit has three relationship types describing the component/location (PART_OF), class (INSTANCE OF) and lineage (DERIVED_FROM). You can see example for each relationship type on our web site (http://www.plantontology.org/docs/otherdocs/poc_file.html). Thank you for your interest in POC and plant ontologies. For additional questions about our project, plant ontologies and editing tools, please feel free to contact me directly or send us an email at po at plantontology.org. Best regards, Katica Ilic, POC curator >Date: Tue, 11 May 2004 23:39:06 +1000 > From: a.garcia at imb.uq.edu.au > Reply-To: po-dev at plantontology.org > To: po at plantontology.org > Subject: inquiry/wheat > > I would like to know if there is an ontology for wheat; I > would also like to know if someone has ported the plant > ontology to protege. cheers > > Katica Ilic, TAIR Curator, E-mail: 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 r.bruskiewich at cgiar.org Thu May 13 01:05:49 2004 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Wed, 12 May 2004 22:05:49 -0700 Subject: inquiry/wheat (fwd) (PR#7) Message-ID: <5B37FD42AEA6C447B407B01116A40B6D13A972@IRRIMAIL> Diane Mather of McGill University, Canada is interested in this. A wheat ontology will also be relevant to the Generation Challenge Program. CIMMYT will probably guide that effort. Richard -----Original Message----- From: Katica Ilic [mailto:jitterbug at plantontology.org] Sent: Thursday, May 13, 2004 3:18 AM To: a.garcia at imb.uq.edu.au Cc: po-dev at plantontology.org Subject: Re: inquiry/wheat (fwd) (PR#7) Dear Garcia, I am not aware of any ongoing effort in the public sector with respect to developing anatomy and developmental stages ontologies specifically for wheat. However, Gramene has a Cereal Plant Anatomy ontology (the controlled vocabulary of plant anatomy representing organs, tissues and cell types), and Cereal Plant Growth Stages ontology (the controlled vocabulary of growth and developmental stages; examples are germination, seedling, booting, flowering, etc.), available for rice, maize, sorghum, wheat, oat and barley. You can download and browse these two ontologies on our POC web site or at Gramene. Currently, we are in the process of integrating Arabidopsis and cereal ontologies into generic plant anatomy ontology. The first version of the ontology will be released in the summer. We hope to make it applicable to most of the flowering plants. Furthermore, over the next two years, POC project will expand its plant-ontology-development effort to include other crops such as wheat, barley, tomato legumes and cotton. At the end, the controlled vocabularies developed by the POC will be generic enough to encompass/cover all the plant model systems; this includes cereals/brassicas/solanaceae/gossypium/legumes. The short answer to your question about the ontology editing tool, Prot?g? is no, we don't use it for our Plant anatomy ontology, and I am not sure how widely this tool is used for biological ontologies. Instead, we use the DAG-edit, which is also a standard editor for GO (http://www.geneontology.org). Arabidopsis, Gramene and maize ontologies that you have seen on the POC web site, are all edited using DAG editor. I have recently communicated with Shenghui Wang from UK (wangs at cs.man.ac.uk), who was telling me that he uses Prot?g? for building the ontology for Ranunculus, so my suggestion to you is to contact him. He might be able to give you some specific information about the Protege. Unfortunately, I don't have any experience with this tool, but from what I understood, this ontology editor has only IS_A relationship type, which can be seen as a kind_of relationship type. The DAG edit has three relationship types describing the component/location (PART_OF), class (INSTANCE OF) and lineage (DERIVED_FROM). You can see example for each relationship type on our web site (http://www.plantontology.org/docs/otherdocs/poc_file.html). Thank you for your interest in POC and plant ontologies. For additional questions about our project, plant ontologies and editing tools, please feel free to contact me directly or send us an email at po at plantontology.org. Best regards, Katica Ilic, POC curator >Date: Tue, 11 May 2004 23:39:06 +1000 > From: a.garcia at imb.uq.edu.au > Reply-To: po-dev at plantontology.org > To: po at plantontology.org > Subject: inquiry/wheat > > I would like to know if there is an ontology for wheat; I would also > like to know if someone has ported the plant ontology to protege. > cheers > > Katica Ilic, TAIR Curator, E-mail: 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 katica at acoma.Stanford.EDU Thu May 13 01:12:55 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 12 May 2004 22:12:55 -0700 (PDT) Subject: inquiry/wheat (fwd) (PR#7) In-Reply-To: <5B37FD42AEA6C447B407B01116A40B6D13A972@IRRIMAIL> Message-ID: Richard, Thanks for the info, I'll get in touch with Diane. See you next week. Katica On Wed, 12 May 2004, Bruskiewich, Richard (IRRI) wrote: > Diane Mather of McGill University, Canada is interested in this. A wheat > ontology will also be relevant to the Generation Challenge Program. CIMMYT > will probably guide that effort. > > Richard > > -----Original Message----- > From: Katica Ilic [mailto:jitterbug at plantontology.org] > Sent: Thursday, May 13, 2004 3:18 AM > To: a.garcia at imb.uq.edu.au > Cc: po-dev at plantontology.org > Subject: Re: inquiry/wheat (fwd) (PR#7) > > > Dear Garcia, > > I am not aware of any ongoing effort in the public sector with respect to > developing anatomy and developmental stages ontologies specifically for > wheat. > > However, Gramene has a Cereal Plant Anatomy ontology (the controlled > vocabulary of plant anatomy representing organs, tissues and cell types), > and Cereal Plant Growth Stages ontology (the controlled vocabulary of growth > and developmental stages; examples are germination, seedling, booting, > flowering, etc.), available for rice, maize, sorghum, wheat, oat and barley. > You can download and browse these two ontologies on our POC web site or at > Gramene. > > Currently, we are in the process of integrating Arabidopsis and cereal > ontologies into generic plant anatomy ontology. The first version of the > ontology will be released in the summer. We hope to make it applicable to > most of the flowering plants. Furthermore, over the next two years, POC > project will expand its plant-ontology-development effort to include other > crops such as wheat, barley, tomato legumes and cotton. At the end, the > controlled vocabularies developed by the POC will be generic enough to > encompass/cover all the plant model systems; this includes > cereals/brassicas/solanaceae/gossypium/legumes. > > The short answer to your question about the ontology editing tool, Prot?g? > is no, we don't use it for our Plant anatomy ontology, and I am not sure how > widely this tool is used for biological ontologies. Instead, we use the > DAG-edit, which is also a standard editor for GO > (http://www.geneontology.org). Arabidopsis, Gramene and maize ontologies > that you have seen on the POC web site, are all edited using DAG editor. > > I have recently communicated with Shenghui Wang from UK > (wangs at cs.man.ac.uk), who was telling me that he uses Prot?g? for building > the ontology for Ranunculus, so my suggestion to you is to contact him. He > might be able to give you some specific information about the Protege. > Unfortunately, I don't have any experience with this tool, but from what I > understood, this ontology editor has only IS_A relationship type, which can > be seen as a kind_of relationship type. > The DAG edit has three relationship types describing the component/location > (PART_OF), class (INSTANCE OF) and lineage (DERIVED_FROM). You can see > example for each relationship type on our web site > (http://www.plantontology.org/docs/otherdocs/poc_file.html). > > Thank you for your interest in POC and plant ontologies. For additional > questions about our project, plant ontologies and editing tools, please feel > free to contact me directly or send us an email at po at plantontology.org. > > Best regards, > > Katica Ilic, POC curator > > >Date: Tue, 11 May 2004 23:39:06 +1000 > > From: a.garcia at imb.uq.edu.au > > Reply-To: po-dev at plantontology.org > > To: po at plantontology.org > > Subject: inquiry/wheat > > > > I would like to know if there is an ontology for wheat; I would also > > like to know if someone has ported the plant ontology to protege. > > cheers > > > > > Katica Ilic, TAIR Curator, E-mail: 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. > -------------------------------------------------------------------------- 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 r.bruskiewich at cgiar.org Thu May 13 02:12:15 2004 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Wed, 12 May 2004 23:12:15 -0700 Subject: inquiry/wheat (fwd) (PR#7) Message-ID: <5B37FD42AEA6C447B407B01116A40B6D13A9D3@IRRIMAIL> One more week.. Yikes! Not ready yet... :-)) R -----Original Message----- From: Katica Ilic [mailto:katica at acoma.Stanford.EDU] Sent: Thursday, May 13, 2004 1:13 PM To: po-dev at plantontology.org Cc: a.garcia at imb.uq.edu.au Subject: RE: inquiry/wheat (fwd) (PR#7) Richard, Thanks for the info, I'll get in touch with Diane. See you next week. Katica On Wed, 12 May 2004, Bruskiewich, Richard (IRRI) wrote: > Diane Mather of McGill University, Canada is interested in this. A > wheat ontology will also be relevant to the Generation Challenge > Program. CIMMYT will probably guide that effort. > > Richard > > -----Original Message----- > From: Katica Ilic [mailto:jitterbug at plantontology.org] > Sent: Thursday, May 13, 2004 3:18 AM > To: a.garcia at imb.uq.edu.au > Cc: po-dev at plantontology.org > Subject: Re: inquiry/wheat (fwd) (PR#7) > > > Dear Garcia, > > I am not aware of any ongoing effort in the public sector with respect > to developing anatomy and developmental stages ontologies specifically > for wheat. > > However, Gramene has a Cereal Plant Anatomy ontology (the controlled > vocabulary of plant anatomy representing organs, tissues and cell > types), and Cereal Plant Growth Stages ontology (the controlled > vocabulary of growth and developmental stages; examples are > germination, seedling, booting, flowering, etc.), available for rice, maize, sorghum, wheat, oat and barley. > You can download and browse these two ontologies on our POC web site > or at Gramene. > > Currently, we are in the process of integrating Arabidopsis and cereal > ontologies into generic plant anatomy ontology. The first version of > the ontology will be released in the summer. We hope to make it > applicable to most of the flowering plants. Furthermore, over the next > two years, POC project will expand its plant-ontology-development > effort to include other crops such as wheat, barley, tomato legumes > and cotton. At the end, the controlled vocabularies developed by the > POC will be generic enough to encompass/cover all the plant model > systems; this includes cereals/brassicas/solanaceae/gossypium/legumes. > > The short answer to your question about the ontology editing tool, > Prot?g? is no, we don't use it for our Plant anatomy ontology, and I > am not sure how widely this tool is used for biological ontologies. > Instead, we use the DAG-edit, which is also a standard editor for GO > (http://www.geneontology.org). Arabidopsis, Gramene and maize > ontologies that you have seen on the POC web site, are all edited using DAG editor. > > I have recently communicated with Shenghui Wang from UK > (wangs at cs.man.ac.uk), who was telling me that he uses Prot?g? for > building the ontology for Ranunculus, so my suggestion to you is to > contact him. He might be able to give you some specific information about the Protege. > Unfortunately, I don't have any experience with this tool, but from > what I understood, this ontology editor has only IS_A relationship > type, which can be seen as a kind_of relationship type. > The DAG edit has three relationship types describing the > component/location (PART_OF), class (INSTANCE OF) and lineage > (DERIVED_FROM). You can see example for each relationship type on our > web site (http://www.plantontology.org/docs/otherdocs/poc_file.html). > > Thank you for your interest in POC and plant ontologies. For > additional questions about our project, plant ontologies and editing > tools, please feel free to contact me directly or send us an email at po at plantontology.org. > > Best regards, > > Katica Ilic, POC curator > > >Date: Tue, 11 May 2004 23:39:06 +1000 > > From: a.garcia at imb.uq.edu.au > > Reply-To: po-dev at plantontology.org > > To: po at plantontology.org > > Subject: inquiry/wheat > > > > I would like to know if there is an ontology for wheat; I would also > > like to know if someone has ported the plant ontology to protege. > > cheers > > > > > Katica Ilic, TAIR Curator, E-mail: 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. > -------------------------------------------------------------------------- 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 iot44 at whipmail.com Fri May 14 19:22:45 2004 From: iot44 at whipmail.com (INTERNATIONAL PROMOTIONS) Date: Fri, 14 May 2004 18:22:45 -0500 Subject: SWEEPSTAKE LOTTERY WINNER !!! 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Best regards, LOPEZFERNANDO (VICE PRESIDENT) From pj37 at cornell.edu Tue May 25 11:16:49 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 25 May 2004 11:16:49 -0400 Subject: question on monocot flower development Message-ID: <40B36361.5000402@cornell.edu> Hi Everyone, I have a question on flower development in Monocots. The reason I am asking this is because I am working with Gene Ontology group (www.geneontology.org) to introduce the biological process that represent a flower development. While doing this we need to instantiate whether, -It is possible to do most of the gene expression and phenotype annotation using a generic term or do we need a monocot and dicot specific term?. -Is there a conceptual difference between the development of a monocot and dicot flower and its parts? e.g. is there a difference between a monocot and dicot anther/carpel/petal/sepal/tepal development. Thanks Pankaj From jid1 at cornell.edu Tue May 25 13:23:21 2004 From: jid1 at cornell.edu (Jerrold I Davis) Date: Tue, 25 May 2004 13:23:21 -0400 Subject: question on monocot flower development In-Reply-To: <40B36361.5000402@cornell.edu> Message-ID: <5.2.0.9.2.20040525130509.02960430@postoffice8.mail.cornell.edu> Pankaj: Through the years, it has often been hypothesized that various floral parts of monocots and dicots (generally perianth parts, as opposed to stamen or pistil) have arisen independently. This view of things has been strengthened in recent years by the placement of various apetalous taxa as early-divering elements within the dicots. However, there are also many potential cases of parallel gains and gain/loss/gain events among dicots alone, so I would be wary of any attempt to distinguish monocots from dicots while failing to address equally or more compelling cases within the dicots. Jerry At 11:16 AM 5/25/2004 Tuesday -0400, you wrote: >Hi Everyone, > >I have a question on flower development in Monocots. The reason I am >asking this is because I am working with Gene Ontology group >(www.geneontology.org) to introduce the biological process that represent >a flower development. While doing this we need to instantiate whether, > >-It is possible to do most of the gene expression and phenotype annotation >using a generic term or do we need a monocot and dicot specific term?. >-Is there a conceptual difference between the development of a monocot and >dicot flower and its parts? e.g. is there a difference between a monocot >and dicot anther/carpel/petal/sepal/tepal development. > > >Thanks >Pankaj ______________________________ Jerrold I Davis Associate Professor Department of Plant Biology (office: 214 Plant Science Building) (mailing address: 228 Plant Science Building) Cornell University Ithaca, New York 14853 U.S.A. phone: 607-255-7980 fax: 607-255-5407 e-mail: JID1 at cornell.edu ______________________________ From jclark at ebi.ac.uk Wed May 26 04:31:26 2004 From: jclark at ebi.ac.uk (jennifer clark) Date: Wed, 26 May 2004 09:31:26 +0100 Subject: question on monocot flower development In-Reply-To: <5.2.0.9.2.20040525130509.02960430@postoffice8.mail.cornell.edu> References: <5.2.0.9.2.20040525130509.02960430@postoffice8.mail.cornell.edu> Message-ID: <40B455DE.3000408@ebi.ac.uk> Hi Jerrold, Thank you for your comments. I think it would be very interesting to consider subgroups within the dicots further down the line. However, right now we are just trying to cover the two groups: dicot and monocot. We've found in the past that if we try to make large sections of ontology covering lots of different species at once then things can get so complicated that we never reach the implementation stage. That's why we're sticking to solving one problem at a time. Pankaj has conveyed my question very well below. The motivation behind this question is that I need to make the terms: sepal development, petal development, stamen development, carpel development, for dicots. I would like to know whether the monocot annotators will need a sensu version of the same terms, or whether these flower parts would have different names in monocots anyway. Thanks, Jen Jerrold I Davis wrote: > Pankaj: > > Through the years, it has often been hypothesized that various floral > parts of monocots and dicots (generally perianth parts, as opposed to > stamen or pistil) have arisen independently. This view of things has > been strengthened in recent years by the placement of various > apetalous taxa as early-divering elements within the dicots. However, > there are also many potential cases of parallel gains and > gain/loss/gain events among dicots alone, so I would be wary of any > attempt to distinguish monocots from dicots while failing to address > equally or more compelling cases within the dicots. > > Jerry > > > At 11:16 AM 5/25/2004 Tuesday -0400, you wrote: > >> Hi Everyone, >> >> I have a question on flower development in Monocots. The reason I am >> asking this is because I am working with Gene Ontology group >> (www.geneontology.org) to introduce the biological process that >> represent a flower development. While doing this we need to >> instantiate whether, >> >> -It is possible to do most of the gene expression and phenotype >> annotation using a generic term or do we need a monocot and dicot >> specific term?. >> -Is there a conceptual difference between the development of a >> monocot and dicot flower and its parts? e.g. is there a difference >> between a monocot and dicot anther/carpel/petal/sepal/tepal development. >> >> >> Thanks >> Pankaj > > > > ______________________________ > > Jerrold I Davis > Associate Professor > > Department of Plant Biology > (office: 214 Plant Science Building) > (mailing address: 228 Plant Science Building) > Cornell University > Ithaca, New York 14853 > U.S.A. > > phone: 607-255-7980 > fax: 607-255-5407 > e-mail: JID1 at cornell.edu > ______________________________ > > From jid1 at cornell.edu Wed May 26 10:17:26 2004 From: jid1 at cornell.edu (Jerrold I Davis) Date: Wed, 26 May 2004 10:17:26 -0400 Subject: question on monocot flower development In-Reply-To: <40B455DE.3000408@ebi.ac.uk> References: <5.2.0.9.2.20040525130509.02960430@postoffice8.mail.cornell.edu> <5.2.0.9.2.20040525130509.02960430@postoffice8.mail.cornell.edu> Message-ID: <5.2.0.9.2.20040526100750.02d40948@postoffice8.mail.cornell.edu> Hi -- You know your needs best, but if my opinion were sought I would recommend that you NOT create a separate system for monocots and dicots. We do use the same general terms for floral parts in both groups, and arguments concerning separate origins are fairly speculative. On re-reading my earlier note, in which I suggested that the case for separate origins had been strengthened of late, I feel that I may have overstated the case. There really is no compelling case that I know of for treating the floral parts of monocots and dicots as different things. Another argument agains a dicot/monocot distinction lies in the fact that the monocots are phylogenetically nested within the dicots. Thus, some dicots are more closely related to monocots than they are to other dicots: _____ dicot 1 | -------------- _____ monocots | | |----- |____ dicot 2 So the old monocot/dicot distinction is misleading, and it might turn out that any peculiar floral attributes of monocots are shared with some dicots, but not with others. By setting up a dichotomy out the outset, one may tend to obscure this situation. Better to let the data accumulate, I would argue, and see how the chips fall. Best, Jerry Davis At 09:31 AM 5/26/2004 Wednesday +0100, you wrote: >Hi Jerrold, > >Thank you for your comments. I think it would be very interesting to >consider subgroups within the dicots further down the line. However, right >now we are just trying to cover the two groups: dicot and monocot. We've >found in the past that if we try to make large sections of ontology >covering lots of different species at once then things can get so >complicated that we never reach the implementation stage. That's why we're >sticking to solving one problem at a time. > >Pankaj has conveyed my question very well below. The motivation behind >this question is that I need to make the terms: sepal development, petal >development, stamen development, carpel development, for dicots. I would >like to know whether the monocot annotators will need a sensu version of >the same terms, or whether these flower parts would have different names >in monocots anyway. > >Thanks, > >Jen > > > > > > >Jerrold I Davis wrote: > >>Pankaj: >> >>Through the years, it has often been hypothesized that various floral >>parts of monocots and dicots (generally perianth parts, as opposed to >>stamen or pistil) have arisen independently. This view of things has >>been strengthened in recent years by the placement of various apetalous >>taxa as early-divering elements within the dicots. However, there are >>also many potential cases of parallel gains and gain/loss/gain events >>among dicots alone, so I would be wary of any attempt to distinguish >>monocots from dicots while failing to address equally or more compelling >>cases within the dicots. >> >>Jerry >> >> >>At 11:16 AM 5/25/2004 Tuesday -0400, you wrote: >> >>>Hi Everyone, >>> >>>I have a question on flower development in Monocots. The reason I am >>>asking this is because I am working with Gene Ontology group >>>(www.geneontology.org) to introduce the biological process that >>>represent a flower development. While doing this we need to instantiate >>>whether, >>> >>>-It is possible to do most of the gene expression and phenotype >>>annotation using a generic term or do we need a monocot and dicot >>>specific term?. >>>-Is there a conceptual difference between the development of a monocot >>>and dicot flower and its parts? e.g. is there a difference between a >>>monocot and dicot anther/carpel/petal/sepal/tepal development. >>> >>> >>>Thanks >>>Pankaj >> >> >> >>______________________________ >> >>Jerrold I Davis >>Associate Professor >> >>Department of Plant Biology >>(office: 214 Plant Science Building) >>(mailing address: 228 Plant Science Building) >>Cornell University >>Ithaca, New York 14853 >>U.S.A. >> >>phone: 607-255-7980 >>fax: 607-255-5407 >>e-mail: JID1 at cornell.edu >>______________________________ >> From pj37 at cornell.edu Wed May 26 10:27:20 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 26 May 2004 10:27:20 -0400 Subject: question on monocot flower development In-Reply-To: <5.2.0.9.2.20040526100750.02d40948@postoffice8.mail.cornell.edu> References: <5.2.0.9.2.20040525130509.02960430@postoffice8.mail.cornell.edu> <5.2.0.9.2.20040525130509.02960430@postoffice8.mail.cornell.edu> <5.2.0.9.2.20040526100750.02d40948@postoffice8.mail.cornell.edu> Message-ID: <40B4A948.1070109@cornell.edu> Dear Jerry, I agree with you and others. We should not make this distinction in the flower development area. We can keep it as generic as possible. Pankaj Jerrold I Davis wrote: > Hi -- > > You know your needs best, but if my opinion were sought I would > recommend that you NOT create a separate system for monocots and > dicots. We do use the same general terms for floral parts in both > groups, and arguments concerning separate origins are fairly > speculative. On re-reading my earlier note, in which I suggested that > the case for separate origins had been strengthened of late, I feel that > I may have overstated the case. There really is no compelling case > that I know of for treating the floral parts of monocots and dicots as > different things. > > Another argument agains a dicot/monocot distinction lies in the fact > that the monocots are phylogenetically nested within the dicots. Thus, > some dicots are more closely related to monocots than they are to other > dicots: > > _____ dicot 1 > | > -------------- _____ monocots > | | > |----- > |____ dicot 2 > > > So the old monocot/dicot distinction is misleading, and it might turn > out that any peculiar floral attributes of monocots are shared with some > dicots, but not with others. By setting up a dichotomy out the outset, > one may tend to obscure this situation. Better to let the data > accumulate, I would argue, and see how the chips fall. > > Best, > > Jerry Davis > > > > > > At 09:31 AM 5/26/2004 Wednesday +0100, you wrote: > >> Hi Jerrold, >> >> Thank you for your comments. I think it would be very interesting to >> consider subgroups within the dicots further down the line. However, >> right now we are just trying to cover the two groups: dicot and >> monocot. We've found in the past that if we try to make large sections >> of ontology covering lots of different species at once then things can >> get so complicated that we never reach the implementation stage. >> That's why we're sticking to solving one problem at a time. >> >> Pankaj has conveyed my question very well below. The motivation behind >> this question is that I need to make the terms: sepal development, >> petal development, stamen development, carpel development, for dicots. >> I would like to know whether the monocot annotators will need a sensu >> version of the same terms, or whether these flower parts would have >> different names in monocots anyway. >> >> Thanks, >> >> Jen >> >> >> >> >> >> >> Jerrold I Davis wrote: >> >>> Pankaj: >>> >>> Through the years, it has often been hypothesized that various floral >>> parts of monocots and dicots (generally perianth parts, as opposed to >>> stamen or pistil) have arisen independently. This view of things has >>> been strengthened in recent years by the placement of various >>> apetalous taxa as early-divering elements within the dicots. >>> However, there are also many potential cases of parallel gains and >>> gain/loss/gain events among dicots alone, so I would be wary of any >>> attempt to distinguish monocots from dicots while failing to address >>> equally or more compelling cases within the dicots. >>> >>> Jerry >>> >>> >>> At 11:16 AM 5/25/2004 Tuesday -0400, you wrote: >>> >>>> Hi Everyone, >>>> >>>> I have a question on flower development in Monocots. The reason I am >>>> asking this is because I am working with Gene Ontology group >>>> (www.geneontology.org) to introduce the biological process that >>>> represent a flower development. While doing this we need to >>>> instantiate whether, >>>> >>>> -It is possible to do most of the gene expression and phenotype >>>> annotation using a generic term or do we need a monocot and dicot >>>> specific term?. >>>> -Is there a conceptual difference between the development of a >>>> monocot and dicot flower and its parts? e.g. is there a difference >>>> between a monocot and dicot anther/carpel/petal/sepal/tepal >>>> development. >>>> >>>> >>>> Thanks >>>> Pankaj >>> >>> >>> >>> >>> ______________________________ >>> >>> Jerrold I Davis >>> Associate Professor >>> >>> Department of Plant Biology >>> (office: 214 Plant Science Building) >>> (mailing address: 228 Plant Science Building) >>> Cornell University >>> Ithaca, New York 14853 >>> U.S.A. >>> >>> phone: 607-255-7980 >>> fax: 607-255-5407 >>> e-mail: JID1 at cornell.edu >>> ______________________________ >>> > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From tkellogg at umsl.edu Wed May 26 11:08:12 2004 From: tkellogg at umsl.edu (Kellogg, Elizabeth A.) Date: Wed, 26 May 2004 10:08:12 -0500 Subject: question on monocot flower development Message-ID: <7953D8E2E57BF94393CA6B8D2599ADDFFA58DC@STL-MAIL2.umsl.edu> Just one slight amendment to the comments below: Grasses, which are very peculiar monocots, do not have sepals and petals as such, and I think there is still some disagreement about which organs, if any, correspond to the perianth in other monocots. Hence the terms lodicule (probably a petal or inner tepal), palea, and lemma will be needed. In other words, we will need terms for grass flowers even though we won't need special terms for most monocots. There's confusion In the literature about the relationship of grasses to other monocots. It is common to read a paper comparing gene expression or function in (for example) rice and Arabidopsis and find the authors saying that they are comparing monocots and dicots, by implication generalizing from the two models to the entire phylogenetic tree that Jerry sketched in his message. (Or perhaps implying that the authors think that the only monocots are grasses.) Presumably this is something that the annotators will have to be aware of. Cheers - Toby -----Original Message----- From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal Sent: Wed 5/26/2004 9:27 AM To: po-dev at plantontology.org Cc: Subject: Re: question on monocot flower development Dear Jerry, I agree with you and others. We should not make this distinction in the flower development area. We can keep it as generic as possible. Pankaj Jerrold I Davis wrote: > Hi -- > > You know your needs best, but if my opinion were sought I would > recommend that you NOT create a separate system for monocots and > dicots. We do use the same general terms for floral parts in both > groups, and arguments concerning separate origins are fairly > speculative. On re-reading my earlier note, in which I suggested that > the case for separate origins had been strengthened of late, I feel that > I may have overstated the case. There really is no compelling case > that I know of for treating the floral parts of monocots and dicots as > different things. > > Another argument agains a dicot/monocot distinction lies in the fact > that the monocots are phylogenetically nested within the dicots. Thus, > some dicots are more closely related to monocots than they are to other > dicots: > > _____ dicot 1 > | > -------------- _____ monocots > | | > |----- > |____ dicot 2 > > > So the old monocot/dicot distinction is misleading, and it might turn > out that any peculiar floral attributes of monocots are shared with some > dicots, but not with others. By setting up a dichotomy out the outset, > one may tend to obscure this situation. Better to let the data > accumulate, I would argue, and see how the chips fall. > > Best, > > Jerry Davis > > > > > > At 09:31 AM 5/26/2004 Wednesday +0100, you wrote: > >> Hi Jerrold, >> >> Thank you for your comments. I think it would be very interesting to >> consider subgroups within the dicots further down the line. However, >> right now we are just trying to cover the two groups: dicot and >> monocot. We've found in the past that if we try to make large sections >> of ontology covering lots of different species at once then things can >> get so complicated that we never reach the implementation stage. >> That's why we're sticking to solving one problem at a time. >> >> Pankaj has conveyed my question very well below. The motivation behind >> this question is that I need to make the terms: sepal development, >> petal development, stamen development, carpel development, for dicots. >> I would like to know whether the monocot annotators will need a sensu >> version of the same terms, or whether these flower parts would have >> different names in monocots anyway. >> >> Thanks, >> >> Jen >> >> >> >> >> >> >> Jerrold I Davis wrote: >> >>> Pankaj: >>> >>> Through the years, it has often been hypothesized that various floral >>> parts of monocots and dicots (generally perianth parts, as opposed to >>> stamen or pistil) have arisen independently. This view of things has >>> been strengthened in recent years by the placement of various >>> apetalous taxa as early-divering elements within the dicots. >>> However, there are also many potential cases of parallel gains and >>> gain/loss/gain events among dicots alone, so I would be wary of any >>> attempt to distinguish monocots from dicots while failing to address >>> equally or more compelling cases within the dicots. >>> >>> Jerry >>> >>> >>> At 11:16 AM 5/25/2004 Tuesday -0400, you wrote: >>> >>>> Hi Everyone, >>>> >>>> I have a question on flower development in Monocots. The reason I am >>>> asking this is because I am working with Gene Ontology group >>>> (www.geneontology.org) to introduce the biological process that >>>> represent a flower development. While doing this we need to >>>> instantiate whether, >>>> >>>> -It is possible to do most of the gene expression and phenotype >>>> annotation using a generic term or do we need a monocot and dicot >>>> specific term?. >>>> -Is there a conceptual difference between the development of a >>>> monocot and dicot flower and its parts? e.g. is there a difference >>>> between a monocot and dicot anther/carpel/petal/sepal/tepal >>>> development. >>>> >>>> >>>> Thanks >>>> Pankaj >>> >>> >>> >>> >>> ______________________________ >>> >>> Jerrold I Davis >>> Associate Professor >>> >>> Department of Plant Biology >>> (office: 214 Plant Science Building) >>> (mailing address: 228 Plant Science Building) >>> Cornell University >>> Ithaca, New York 14853 >>> U.S.A. >>> >>> phone: 607-255-7980 >>> fax: 607-255-5407 >>> e-mail: JID1 at cornell.edu >>> ______________________________ >>> > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 5591 bytes Desc: not available URL: From jclark at ebi.ac.uk Wed May 26 11:41:19 2004 From: jclark at ebi.ac.uk (JClark) Date: Wed, 26 May 2004 16:41:19 +0100 Subject: question on monocot flower development In-Reply-To: <7953D8E2E57BF94393CA6B8D2599ADDFFA58DC@STL-MAIL2.umsl.edu> References: <7953D8E2E57BF94393CA6B8D2599ADDFFA58DC@STL-MAIL2.umsl.edu> Message-ID: <40B4BA9F.4070805@ebi.ac.uk> Hi Elizabeth, Thanks, that's really helpful. These floral organs have names that will distinguish them from dicot floral organs so they will not be a problem at all. I will make sure they're on the list to be added. The only thing I really need to know about right now is if monocots (or any sub-taxon of monocots that is currently being annotated) have e.g. a petal that is significantly different from a dicot petal, or a stamen that is significantly different from a dicot stamen. Organs that have the same name but a significant difference with the dicot thing of the same name require a sensu term. If people know of any instance of this I'd really like to know: a) the name of the organ. b) The latin name of the taxon that has this organ. Jen Kellogg, Elizabeth A. wrote: > Just one slight amendment to the comments below: Grasses, which are very peculiar monocots, do not have sepals and petals as such, and I think there is still some disagreement about which organs, if any, correspond to the perianth in other monocots. Hence the terms lodicule (probably a petal or inner tepal), palea, and lemma will be needed. In other words, we will need terms for grass flowers even though we won't need special terms for most monocots. > There's confusion In the literature about the relationship of grasses to other monocots. It is common to read a paper comparing gene expression or function in (for example) rice and Arabidopsis and find the authors saying that they are comparing monocots and dicots, by implication generalizing from the two models to the entire phylogenetic tree that Jerry sketched in his message. (Or perhaps implying that the authors think that the only monocots are grasses.) Presumably this is something that the annotators will have to be aware of. > Cheers - > Toby > > -----Original Message----- > From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > Sent: Wed 5/26/2004 9:27 AM > To: po-dev at plantontology.org > Cc: > Subject: Re: question on monocot flower development > > Dear Jerry, > > I agree with you and others. We should not make this distinction in the > flower development area. We can keep it as generic as possible. > > Pankaj > > Jerrold I Davis wrote: > > >>Hi -- >> >>You know your needs best, but if my opinion were sought I would >>recommend that you NOT create a separate system for monocots and >>dicots. We do use the same general terms for floral parts in both >>groups, and arguments concerning separate origins are fairly >>speculative. On re-reading my earlier note, in which I suggested that >>the case for separate origins had been strengthened of late, I feel that >>I may have overstated the case. There really is no compelling case >>that I know of for treating the floral parts of monocots and dicots as >>different things. >> >>Another argument agains a dicot/monocot distinction lies in the fact >>that the monocots are phylogenetically nested within the dicots. Thus, >>some dicots are more closely related to monocots than they are to other >>dicots: >> >> _____ dicot 1 >> | >>-------------- _____ monocots >> | | >> |----- >> |____ dicot 2 >> >> >>So the old monocot/dicot distinction is misleading, and it might turn >>out that any peculiar floral attributes of monocots are shared with some >>dicots, but not with others. By setting up a dichotomy out the outset, >>one may tend to obscure this situation. Better to let the data >>accumulate, I would argue, and see how the chips fall. >> >>Best, >> >>Jerry Davis >> >> >> >> >> >>At 09:31 AM 5/26/2004 Wednesday +0100, you wrote: >> >> >>>Hi Jerrold, >>> >>>Thank you for your comments. I think it would be very interesting to >>>consider subgroups within the dicots further down the line. However, >>>right now we are just trying to cover the two groups: dicot and >>>monocot. We've found in the past that if we try to make large sections >>>of ontology covering lots of different species at once then things can >>>get so complicated that we never reach the implementation stage. >>>That's why we're sticking to solving one problem at a time. >>> >>>Pankaj has conveyed my question very well below. The motivation behind >>>this question is that I need to make the terms: sepal development, >>>petal development, stamen development, carpel development, for dicots. >>>I would like to know whether the monocot annotators will need a sensu >>>version of the same terms, or whether these flower parts would have >>>different names in monocots anyway. >>> >>>Thanks, >>> >>>Jen >>> >>> >>> >>> >>> >>> >>>Jerrold I Davis wrote: >>> >>> >>>>Pankaj: >>>> >>>>Through the years, it has often been hypothesized that various floral >>>>parts of monocots and dicots (generally perianth parts, as opposed to >>>>stamen or pistil) have arisen independently. This view of things has >>>>been strengthened in recent years by the placement of various >>>>apetalous taxa as early-divering elements within the dicots. >>>>However, there are also many potential cases of parallel gains and >>>>gain/loss/gain events among dicots alone, so I would be wary of any >>>>attempt to distinguish monocots from dicots while failing to address >>>>equally or more compelling cases within the dicots. >>>> >>>>Jerry >>>> >>>> >>>>At 11:16 AM 5/25/2004 Tuesday -0400, you wrote: >>>> >>>> >>>>>Hi Everyone, >>>>> >>>>>I have a question on flower development in Monocots. The reason I am >>>>>asking this is because I am working with Gene Ontology group >>>>>(www.geneontology.org) to introduce the biological process that >>>>>represent a flower development. While doing this we need to >>>>>instantiate whether, >>>>> >>>>>-It is possible to do most of the gene expression and phenotype >>>>>annotation using a generic term or do we need a monocot and dicot >>>>>specific term?. >>>>>-Is there a conceptual difference between the development of a >>>>>monocot and dicot flower and its parts? e.g. is there a difference >>>>>between a monocot and dicot anther/carpel/petal/sepal/tepal >>>>>development. >>>>> >>>>> >>>>>Thanks >>>>>Pankaj >>>> >>>> >>>> >>>> >>>>______________________________ >>>> >>>>Jerrold I Davis >>>>Associate Professor >>>> >>>>Department of Plant Biology >>>>(office: 214 Plant Science Building) >>>>(mailing address: 228 Plant Science Building) >>>>Cornell University >>>>Ithaca, New York 14853 >>>>U.S.A. >>>> >>>>phone: 607-255-7980 >>>>fax: 607-255-5407 >>>>e-mail: JID1 at cornell.edu >>>>______________________________ >>>> >> >> > From pj37 at cornell.edu Thu May 27 09:23:02 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 27 May 2004 09:23:02 -0400 Subject: [Fwd: Call for Papers - PSB 2005 Session on Biomedical Ontologies] Message-ID: <40B5EBB6.5080405@cornell.edu> This is a forwarded message. -Pankaj -------- Original Message -------- Subject: Call for Papers - PSB 2005 Session on Biomedical Ontologies Date: Wed, 26 May 2004 17:31:11 -0400 From: Olivier Bodenreider Reply-To: olivier at nlm.nih.gov To: gofriends at genome.stanford.edu _______________________________________________________________________ This message is posted to several lists. We apologize if you receive multiple copies. Please forward it to everyone who might be interested. _______________________________________________________________________ Call for Papers and Posters Biomedical Ontologies at the Pacific Symposium on Biocomputing 2005 January 4-8, 2005 The Fairmont Orchid, Big Island of Hawaii _______________________________________________________________________ Biology is evolving from a science of organisms and molecules to a science of information. In modern biology, massive amounts of data are produced resulting, for example, from sequencing the genome of many organisms and studying gene expression under various conditions. In turn, there has been a shift from hypothesis-driven experiments to data-driven experiments. Ontologies provide a conceptualization of a domain that can be shared among diverse groups of researchers and health care professionals and used computationally for multiple purposes. Biologic knowledge is evolving so rapidly that it is difficult for most scientists to assimilate and integrate the new information with their existing knowledge. Promoting the creation and use of ontologies for the field and linking to other ontologies in related domains holds the promise of assisting those working in biomedical disciplines and thus making more rapid scientific progress. This session would welcome papers that discuss: * Biomedical ontology creation and use * Reasoning about the biomedical domain based on ontological knowledge * Use and development of ontologies to support natural language processing (NLP) * Ontologies in support of knowledge discovery * Intelligent agent technologies and associated ontologies * Scalability and versioning of biomedical ontologies * Linking and aligning multiple ontologies * Use of ontologies to bridge heterogeneous information resources (e.g., to connect genotype to gene expression and ultimately to clinical medicine, drug discoveries, etc.) * Advances in ontology languages and related technologies as applied to bioinformatics and biomedical problems * Other research associated with bioinformatics and biomedical ontologies _______________________________________________________________________ Session co-chairs * Olivier Bodenreider (contact person) National Library of Medicine olivier at nlm.nih.gov * Joyce A. Mitchell University of Missouri, Columbia MitchellJo at health.missouri.edu * Alexa T. McCray National Library of Medicine mccray at nlm.nih.gov _______________________________________________________________________ Submission information Papers and Posters The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings, and the best of these will be presented orally to the entire conference. Researchers wishing to present their research without official publication are encouraged to submit a one page abstract by November 1, 2004 to present their work in the poster sessions. Important dates * Paper submissions due: July 19, 2004 * Notification of paper acceptance: September 8, 2004 * Final paper deadline: September 22, 2004 * Abstract deadline: November 1, 2004 * Meeting: January 4-8, 2005 Paper format All papers must be submitted to russ.altman at stanford.edu in electronic format. The file formats we accept are: postscript (*.ps), Adobe Acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files should be named with the last name of the first author (e.g. altman.ps, altman.pdf, or altman.doc). Hardcopy submissions or unprocessed TEX or LATEX files will be rejected without review. Each paper must be accompanied by a cover letter. The cover letter must state the following: * The email address of the corresponding author * The specific PSB session that should review the paper or abstract * The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere. * All co-authors concur with the contents of the paper. Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit. Color pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission. Contact Russ Altman (russ.altman at stanford.edu) for additional information about paper submission requirements. -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From pj37 at cornell.edu Thu May 27 14:45:44 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 27 May 2004 14:45:44 -0400 Subject: [Fwd: Re: AmiGO 2.0] Message-ID: <40B63758.1040604@cornell.edu> -------- Original Message -------- Subject: Re: AmiGO 2.0 Date: Wed, 26 May 2004 14:09:14 -0400 From: Pankaj Jaiswal To: Chris Mungall CC: Bradley Marshall , go list References: Chris Mungall wrote: >>What is not possible is if the people try to search using MONOCOT/DICOT >>as text and not the species. >> >>#4 show me all the genes from MONOCOT (or DICOT) species expressed in >>plastids >> >>Monocots may include (rice/maize/onion/sorghum/wheat/oat etc) >>Dicot may include (Arabidopsis, Brassica, Medicago, Tomato etc.) >> >> >>So # 1-3 is fine, but #4 may need some discussion on DB, since we store >>only the species and not the phyla/classes. > > > Hi Pankaj > > It wouldn't be too hard to add the different phylogeny clades to the db, I > didn't plan to add them in the immediate future, but if people will find > this useful I'll start thinking about the most efficient way to do > this... > > At least Plant people would like to see it happening now. On a wider interest group, since we are using the GO database schema and the Amigo for POC project it would be useful to have this option. Thanks Pankaj -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From pj37 at cornell.edu Thu May 27 14:52:01 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 27 May 2004 14:52:01 -0400 Subject: [Fwd: Re: Announcing AmiGO and GOst 2.0] Message-ID: <40B638D1.9070103@cornell.edu> -------- Original Message -------- Subject: Re: Announcing AmiGO and GOst 2.0 Date: Thu, 20 May 2004 15:20:37 -0700 (PDT) From: Chris Mungall To: Pankaj Jaiswal CC: Bradley Marshall References: <1084552906.40a4f6ca8312f at imp.fruitfly.org> <40ACF935.8050108 at cornell.edu> yep, they should be pointing upwards - can you fix this brad? On Thu, 20 May 2004, Pankaj Jaiswal wrote: > > > Bradley Marshall wrote: > > > AmiGO 2.0 is now live at: > > > > http://www.godatabase.org/ > > http://www.godatabase.org/cgi-bin/amigo/go.cgi > > > > > Hi Brad > > I was just now looking at the graphical view at > http://www.godatabase.org/cgi-bin/amigo/go.cgi?action=dotty&search_constraint=terms&view=details&query=GO:0045735 > > Do you think that the arrows should be pointing upwards and NOT downwards. > > Pankaj > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************