From kellogge at msx.umsl.edu Mon Mar 1 15:32:57 2004 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 1 Mar 2004 15:32:57 -0500 Subject: progress and thought questions Message-ID: Hi folks - Felipe has posted or is about to post an updated version of the plant ontology to the CVS, with more bits of the hierarchy filled in and also definitions for everything so far. When you compare it to TAIR and GRAMENE, you'll see that we've omitted from the organ ontology any terms that refer to tissue types, and also have avoided including attributes of organs unless they seem absolutely necessary. (For example, we haven't included even-pinnate compound leaves and odd-pinnate compound leaves, since the parts of each are the same - leaflet, petiolule, stipel.) This lack of attributes also makes it much more "skeletal" than the Maize Ontology. You'll see in the notes that we keep running up against the question of detail and attributes of organs. If the ontology is a tool for binning genetic/genomic data, rather than for describing all aspects of all angiosperms in detail, then we want something with minimal elaboration. However, I'm still not really clear how an end user (as opposed to an annotator) will actually use this ontology, so I could be way off base here. A number of specific questions have come up, so I'll list them below for you to think about and discuss at some point in the future. 1. In this most recent version, parts of the embryo are egg cell, synergid cell, polar nucleus, and antipodal cell (just four terms), and central cell develops from polar nuclei. Alternatively, we could introduce another hierarchical level such that parts of the embryo are egg apparatus, central cell, and antipodal cells, with egg cell and synergid cell part of egg apparatus and polar nuclei part of central cell. Are things ever annotated to "egg apparatus" or is it always "egg plus synergid"? If the latter, then the former is superfluous. 2. Sporoderm is part of pollen, exine and intine are parts of sporoderm. There are then a whole bunch of terms for all the components of the pollen wall (endexine, ectexine, etc. etc. etc.). Do we really want all of those terms? It seems like overkill to me, but maybe they are necessary. 3. How are we going to define microgametophyte? e.g. does pollen = microgametophyte even though it contains some tissue (the pollen wall) that is of sporophytic origin? What about microspore? 4. Is it important to include endothelium as part of the inner integument? This is the same issue as #2 - how detailed do we want (need) to be? 5. In the version that Felipe has posted, we dispensed with apocarpous gynoecium and syncarpous gynoecium as instances of gynoecium, because it made it easier to handle the terms carpel, ovary, stigma and style. Also apocarpous and syncarpous are attributes of gynoecium, not really a separate structure. Is there any reason to re-instate them? (There are reasons *not* to, which Felipe or I can explain if anyone wants.) 6. Do we need to include leaf margin, leaf base, and leaf apex as parts of a leaf? They are obviously used for description of plants, but are they (or will they be) used for annotation of genes? 7. Is it worth including perigynium as an instance of a prophyll? The term is used only for species in the family Cyperaceae, specifically species of Carex. 8. Capsules are currently divided into circumscissile, poricidal, septifragal, septicidal, and lodulicidal, with silique being an instance of a septifragal capsule. Do we need all those types of capsules, or can we just use capsule (with silique as a instance)? (Same issue as #s 2 and 4.) 9. What are the relationships among epicotyl, plumule, coleoptile, and embryonic axis? Are all in common use? 10. Inflorescence can be defined with panicle, raceme, tassel, ear, and cob as synonyms. Alternatively, we can divide inflorescences into racemes (which do not terminate in a flower) and cymes (which do). Panicle, tassel, ear, and cob would thus be synonyms of raceme. Or we can keep dividing the inflorescence categories more and more finely depending on which axes end in flowers and which don't, and could end up with a plethora of terms. (Same issue as #s 2, 4, and 8.) How complex do we get? Cheers - Toby Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From pj37 at cornell.edu Mon Mar 1 17:16:59 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 1 Mar 2004 17:16:59 -0500 (EST) Subject: progress and thought questions In-Reply-To: References: Message-ID: <1563.128.253.246.53.1078179419.squirrel@webmail.cornell.edu> Hi Toby, Peter and Felipe, This version looks great. It is a great beginning. I will go through it in detail sometime this week. Following are my comments, though not many. Cheers Pankaj Toby Kellogg said: > Hi folks - > Felipe has posted or is about to post an updated version of the plant > ontology to the CVS, with more bits of the hierarchy filled in and also > definitions for everything so far. When you compare it to TAIR and > GRAMENE, you'll see that we've omitted from the organ ontology any terms > that refer to tissue types, and also have avoided including attributes of > organs unless they seem absolutely necessary. (For example, we haven't > included even-pinnate compound leaves and odd-pinnate compound leaves, > since the parts of each are the same - leaflet, petiolule, stipel.) This > lack of attributes also makes it much more "skeletal" than the Maize > Ontology. > You'll see in the notes that we keep running up against the question > of > detail and attributes of organs. If the ontology is a tool for binning > genetic/genomic data, rather than for describing all aspects of all > angiosperms in detail, then we want something with minimal elaboration. > However, I'm still not really clear how an end user (as opposed to an > annotator) will actually use this ontology, so I could be way off base > here. > A number of specific questions have come up, so I'll list them below > for > you to think about and discuss at some point in the future. > 1. In this most recent version, parts of the embryo are egg cell, > synergid > cell, polar nucleus, and antipodal cell (just four terms), and central > cell > develops from polar nuclei. Alternatively, we could introduce another > hierarchical level such that parts of the embryo are egg apparatus, > central > cell, and antipodal cells, with egg cell and synergid cell part of egg > apparatus and polar nuclei part of central cell. Are things ever > annotated > to "egg apparatus" or is it always "egg plus synergid"? If the latter, > then the former is superfluous. > 2. Sporoderm is part of pollen, exine and intine are parts of sporoderm. > There are then a whole bunch of terms for all the components of the pollen > wall (endexine, ectexine, etc. etc. etc.). Do we really want all of those > terms? It seems like overkill to me, but maybe they are necessary. I guess we need these terms. Sometimes the insitu hybridization experiments on gene expression identify such structures. > 3. How are we going to define microgametophyte? e.g. does pollen = > microgametophyte even though it contains some tissue (the pollen wall) > that > is of sporophytic origin? What about microspore? We agreed on the PART_OF relationship type that POC will not use it in a strict way. Our definition was that "a term could be a part of another term but is not necessarily always a part of it". > 4. Is it important to include endothelium as part of the inner > integument? > This is the same issue as #2 - how detailed do we want (need) to be? > 5. In the version that Felipe has posted, we dispensed with apocarpous > gynoecium and syncarpous gynoecium as instances of gynoecium, because it > made it easier to handle the terms carpel, ovary, stigma and style. Also > apocarpous and syncarpous are attributes of gynoecium, not really a > separate structure. Is there any reason to re-instate them? (There are > reasons *not* to, which Felipe or I can explain if anyone wants.) No problem as of now. > 6. Do we need to include leaf margin, leaf base, and leaf apex as parts > of > a leaf? They are obviously used for description of plants, but are they > (or will they be) used for annotation of genes? We want them. There are several reports on gene expression/mutant studies on these parts. > 7. Is it worth including perigynium as an instance of a prophyll? The > term is used only for species in the family Cyperaceae, specifically > species of Carex. My argument would be to include the terms on usage/requirement basis unless absolutely necessary to clarify some other node in the ontology. > 8. Capsules are currently divided into circumscissile, poricidal, > septifragal, septicidal, and lodulicidal, with silique being an instance > of > a septifragal capsule. Do we need all those types of capsules, or can we > just use capsule (with silique as a instance)? (Same issue as #s 2 and > 4.) These are all based on mode/type of dehiscence. We had this discussion when dehiscence term was introduced in the Gene ontology's biological process section. My suggestion is to go with you and if somebody realy identifies a gene associated with the process we can modify the structure. > 9. What are the relationships among epicotyl, plumule, coleoptile, and > embryonic axis? Are all in common use? I believe so. All are part of embryo or shoot of a seedling. > 10. Inflorescence can be defined with panicle, raceme, tassel, ear, and > cob as synonyms. Alternatively, we can divide inflorescences into racemes > (which do not terminate in a flower) and cymes (which do). Panicle, > tassel, ear, and cob would thus be synonyms of raceme. Or we can keep > dividing the inflorescence categories more and more finely depending on > which axes end in flowers and which don't, and could end up with a > plethora > of terms. (Same issue as #s 2, 4, and 8.) How complex do we get? I agree with you. My question here is how do we deal with terms like primary/secondary inflorescence branches? There are many mutants/genes responsible for the branching organization. > Cheers - > Toby > > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > -- Pankaj Jaiswal Gramene Database www.gramene.org From fzqhd at studentmail.umsl.edu Mon Mar 1 17:35:05 2004 From: fzqhd at studentmail.umsl.edu (Felipe Zapata) Date: Mon, 1 Mar 2004 16:35:05 -0600 Subject: Ontology & Definitions Message-ID: Hello, The latest versions of anatomy.onotology and anatomy.definition are in CVS. Please do an update. Thanks Pankaj for uploading the files. Most (if not all) the definitions have "APWeb:glossary" as Reference. This refers to the glossary Peter sent a couple of weeks ago that will be online pretty soon. Thanks Felipe ~~~~~~ Felipe Zapata University of Missouri St. Louis Department of Biology 8001 Natural Bridge Rd. St. Louis, MO 63121 314 516-6200 From kellogge at msx.umsl.edu Mon Mar 1 18:01:59 2004 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 1 Mar 2004 18:01:59 -0500 Subject: progress and thought questions In-Reply-To: <1563.128.253.246.53.1078179419.squirrel@webmail.cornell.edu> References: Message-ID: Thanks Pankaj - Just a couple of quick responses while I am thinking of it: > >> 7. Is it worth including perigynium as an instance of a prophyll? The >> term is used only for species in the family Cyperaceae, specifically >> species of Carex. > >My argument would be to include the terms on usage/requirement basis >unless absolutely necessary to clarify some other node in the ontology. this sounds like a good principle to me. > >> 10. Inflorescence can be defined with panicle, raceme, tassel, ear, and >> cob as synonyms. Alternatively, we can divide inflorescences into racemes >> (which do not terminate in a flower) and cymes (which do). Panicle, >> tassel, ear, and cob would thus be synonyms of raceme. Or we can keep >> dividing the inflorescence categories more and more finely depending on >> which axes end in flowers and which don't, and could end up with a >> plethora >> of terms. (Same issue as #s 2, 4, and 8.) How complex do we get? > >I agree with you. My question here is how do we deal with terms like >primary/secondary inflorescence branches? There are many mutants/genes >responsible for the branching organization. This gets back to the goal of the ontology. For the many mutants/genes that affect inflorescence branching, do we need to be able to describe each of them in detail (in which case we need lots of terms) or just to assign them to the bin "inflorescence" (in which case we only need a few terms)? I don't know the answer to this, but it will affect the structure I think. i.e., will we want to make queries such as "find all genes in any plant that, when mutated, affect phyllotaxis on third order inflorescence branches", or will it be sufficient to ask "what genes are expressed in inflorescences"? Food for thought anyway. Toby Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From katica at acoma.Stanford.EDU Mon Mar 1 21:55:52 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 1 Mar 2004 18:55:52 -0800 (PST) Subject: progress and thought questions Message-ID: Hi Toby, I've looked at updated anatomy.ontlogy, it looks great! What a nice job! I've gone through some of the issues you raised, and below are the minor comments. I may have some more later. 1. In this most recent version, parts of the embryo are egg cell, synergid cell, polar nucleus, and antipodal cell (just four terms), and central cell develops from polar nuclei. Alternatively, we could introduce another hierarchical level such that parts of the embryo are egg apparatus, central cell, and antipodal cells, with egg cell and synergid cell part of egg apparatus and polar nuclei part of central cell. Are things ever annotated to "egg apparatus" or is it always "egg plus synergid"? If the latter, then the former is superfluous. - I would go with the first. Although I am not aware of any annotation using term egg apparatus yet, I found a couple of abstracts coming from Thomas Dresselhaus' lab refering to genes expressed in the egg apparatus in maize and wheat (PMB meeting in Barcelona, 2003, see http://www.ispmb2003.com/abst/obtimpres.php?idAbst=422). So, we may need egg apparatus as a term, with childrens egg cell and synergids. 2. Sporoderm is part of pollen, exine and intine are parts of sporoderm. There are then a whole bunch of terms for all the components of the pollen wall (endexine, ectexine, etc. etc. etc.). Do we really want all of those terms? It seems like overkill to me, but maybe they are necessary. - I agree with you, they are overkill to me too, but then again, we may need these terms. I'll look to see what is in the published literature (if people actaully use these terms). 3. How are we going to define microgametophyte? e.g. does pollen = microgametophyte even though it contains some tissue (the pollen wall) that is of sporophytic origin? What about microspore? - I would go with synonym here (polen=microgametophyte), especially with the few options that we now have when it comes to synonyms. As for the microspores, I would include it in the micosporangium node, with microsporocyte as a_part_of, then microspore as its child (develops_from), and then pollen (which you already have there as a child of microsporangium). I could look into this in more details later. 9. What are the relationships among epicotyl, plumule, coleoptile, and embryonic axis? Are all in common use? - I agree with Pankaj, we need these terms since they are all in common use. At the end, very minor points, there is a typo in embryo sac node (symergids), and also, I would put sperm cell(s) instead sperm in the microgametophyte node (unless I am missing something here). Cheers, Katica From peter.stevens at mobot.org Tue Mar 2 08:03:06 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Tue, 2 Mar 2004 09:03:06 -0400 Subject: progress and thought questions In-Reply-To: References: Message-ID: >Hi Toby, > >I've looked at updated anatomy.ontlogy, it looks great! What a nice job! >I've gone through some of the issues you raised, and below are the minor >comments. I may have some more later. > >1. In this most recent version, parts of the embryo are egg cell, synergid >cell, polar nucleus, and antipodal cell (just four terms), and central cell >develops from polar nuclei. Alternatively, we could introduce another >hierarchical level such that parts of the embryo are egg apparatus, central >cell, and antipodal cells, with egg cell and synergid cell part of egg >apparatus and polar nuclei part of central cell. Are things ever annotated >to "egg apparatus" or is it always "egg plus synergid"? If the latter, >then the former is superfluous. > >- I would go with the first. Although I am not aware of any >annotation using term egg apparatus yet, I found a couple of abstracts coming >from Thomas Dresselhaus' lab refering to genes expressed in the egg >apparatus in maize and wheat (PMB meeting in Barcelona, 2003, see >http://www.ispmb2003.com/abst/obtimpres.php?idAbst=422). So, we may need >egg apparatus as a term, with childrens egg cell and synergids. > >2. Sporoderm is part of pollen, exine and intine are parts of sporoderm. >There are then a whole bunch of terms for all the components of the pollen >wall (endexine, ectexine, etc. etc. etc.). Do we really want all of those >terms? It seems like overkill to me, but maybe they are necessary. > >- I agree with you, they are overkill to me too, but then again, we may >need these terms. I'll look to see what is in the published literature >(if people actaully use these terms). I have made a little progress in disentangling pollen terms since the version of the glossary of about three weeks ago - which, incidentally, owing to a snafu lacked any introductory material at all. As far as I can work out the numerous terms in part represent two different ways of looking at pollen walls - morphology and staining properties. We will try and hash this out some more using in part a very good web glossary. P. > >3. How are we going to define microgametophyte? e.g. does pollen = >microgametophyte even though it contains some tissue (the pollen wall) that >is of sporophytic origin? What about microspore? > >- I would go with synonym here (polen=microgametophyte), especially with >the few options that we now have when it comes to synonyms. As for the >microspores, I would include it in the micosporangium node, with >microsporocyte as a_part_of, then microspore as its child (develops_from), >and then pollen (which you already have there as a child of >microsporangium). I could look into this in more details later. > >9. What are the relationships among epicotyl, plumule, coleoptile, and >embryonic axis? Are all in common use? > >- I agree with Pankaj, we need these terms since they are all in common >use. > >At the end, very minor points, there is a typo in embryo sac node >(symergids), and also, I would put sperm cell(s) instead sperm in the >microgametophyte node (unless I am missing something here). > >Cheers, > >Katica From kellogge at msx.umsl.edu Tue Mar 2 15:23:52 2004 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Tue, 2 Mar 2004 15:23:52 -0500 Subject: progress and thought questions In-Reply-To: Message-ID: >Hi Toby, > >I've looked at updated anatomy.ontlogy, it looks great! What a nice job! Thanks Katica - I'd love to take full credit, but most of the work really is Felipe's. Toby Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From katica at acoma.Stanford.EDU Thu Mar 4 10:28:32 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 4 Mar 2004 07:28:32 -0800 (PST) Subject: DAG-Edit 1.411 - warning to curators Message-ID: For the ontology developers, In addition to the bug reported by Amelia, this new version of Dag-edit has tendency to crash frequently, for instance, when multiple nodes are moved around. I don't know what wersion Felipe and Pankaj are currently using, but I would recomend the Dag-edit 1.410 till these bugs are fixed in the latest version. Greetings, Katica -------------------------------------------------------------------------- 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. -------------------------------------------------------------------------- ---------- Forwarded message ---------- Date: Thu, 4 Mar 2004 15:06:43 +0000 From: Amelia Ireland To: gene ontology Subject: DAG-Edit 1.411 - warning to curators Hi all, We have had a few problems with saving files in the new DAG-Edit so I would advise doing a cvs diff between the repository version and the version you are about to commit to ensure that only the changes you have made are being committed. Thanks! Amelia. -- ============================== Pretty Vacant Online http://www.pretty-vacant.net ====================== -@^@- = From pj37 at cornell.edu Thu Mar 4 10:40:48 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 04 Mar 2004 10:40:48 -0500 Subject: DAG-Edit 1.411 - warning to curators In-Reply-To: References: Message-ID: <40474E00.10906@cornell.edu> Hi Katica, Thanks for notifying everyone. I am a bit primitive in this aspect. My favorite one being v1.306 BTW, now most of the mails should go to po and not po-dev. Any suggestions Pankaj Katica Ilic wrote: > For the ontology developers, > > In addition to the bug reported by Amelia, this new version of Dag-edit > has tendency to crash frequently, for instance, when multiple nodes are > moved around. I don't know what wersion Felipe and Pankaj are currently using, > but I would recomend the Dag-edit 1.410 till these bugs are fixed in the > latest version. > > Greetings, > > Katica > > -------------------------------------------------------------------------- > 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. > -------------------------------------------------------------------------- > > ---------- Forwarded message ---------- > Date: Thu, 4 Mar 2004 15:06:43 +0000 > From: Amelia Ireland > To: gene ontology > Subject: DAG-Edit 1.411 - warning to curators > > Hi all, > > We have had a few problems with saving files in the new DAG-Edit so I > would advise doing a cvs diff between the repository version and the > version you are about to commit to ensure that only the changes you > have made are being committed. > > Thanks! > Amelia. > > -- > ============================== > Pretty Vacant Online > http://www.pretty-vacant.net > ====================== -@^@- = > > > From fzqhd at studentmail.umsl.edu Thu Mar 4 11:57:02 2004 From: fzqhd at studentmail.umsl.edu (Felipe Zapata) Date: Thu, 4 Mar 2004 10:57:02 -0600 Subject: DAG-Edit 1.411 - warning to curators In-Reply-To: References: Message-ID: <1078419422.40475fde3349e@studentmail.umsl.edu> I am using 1.410 F Quoting Katica Ilic : > > For the ontology developers, > > In addition to the bug reported by Amelia, this new version of Dag-edit > has tendency to crash frequently, for instance, when multiple nodes are > moved around. I don't know what wersion Felipe and Pankaj are currently > using, > but I would recomend the Dag-edit 1.410 till these bugs are fixed in the > latest version. > > Greetings, > > Katica > > -------------------------------------------------------------------------- > 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. > -------------------------------------------------------------------------- > > ---------- Forwarded message ---------- > Date: Thu, 4 Mar 2004 15:06:43 +0000 > From: Amelia Ireland > To: gene ontology > Subject: DAG-Edit 1.411 - warning to curators > > Hi all, > > We have had a few problems with saving files in the new DAG-Edit so I > would advise doing a cvs diff between the repository version and the > version you are about to commit to ensure that only the changes you > have made are being committed. > > Thanks! > Amelia. > > -- > ============================== > Pretty Vacant Online > http://www.pretty-vacant.net > ====================== -@^@- = > > > _____________ Felipe Zapata University of Missouri-St.Louis Department of Biology 8001 Natural Bridge Rd. St. Louis MO, 63121 Phone: (314) 516-6200 Fax: (314) 516-6233 From Leszek at missouri.edu Fri Mar 5 13:11:04 2004 From: Leszek at missouri.edu (Vincent, Leszek) Date: Fri, 5 Mar 2004 12:11:04 -0600 Subject: progress and thought questions Message-ID: Toby, Pankaj & colleagues, I offer some brief thoughts in response to the matters raised in the dialogue below. I've inserted these below, prefixed by XXX. - Leszek > -----Original Message----- > From: owner-po-dev at brie4.cshl.org > [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Toby Kellogg > Sent: Monday, March 01, 2004 5:02 PM > To: po-dev at plantontology.org > Subject: Re: progress and thought questions > > > Thanks Pankaj - > Just a couple of quick responses while I am thinking of it: > > > >> 7. Is it worth including perigynium as an instance of a > prophyll? > >> The term is used only for species in the family Cyperaceae, > >> specifically species of Carex. > > > >My argument would be to include the terms on usage/requirement basis > >unless absolutely necessary to clarify some other node in > the ontology. > > this sounds like a good principle to me. XXX While I appreciate the probable pragmatism associated with this principle I suggest that we need to be more proactive in these early days of our 'product'. I suspect that our potential users may be more sophisticated in their needs than we are perhaps currently anticipating. I offer further comment below.... > > > > >> 10. Inflorescence can be defined with panicle, raceme, > tassel, ear, > >> and cob as synonyms. Alternatively, we can divide inflorescences > >> into racemes (which do not terminate in a flower) and cymes (which > >> do). Panicle, tassel, ear, and cob would thus be synonyms > of raceme. > >> Or we can keep dividing the inflorescence categories more and more > >> finely depending on which axes end in flowers and which don't, and > >> could end up with a plethora of terms. (Same issue as #s > 2, 4, and > >> 8.) How complex do we get? > > > >I agree with you. My question here is how do we deal with terms like > >primary/secondary inflorescence branches? There are many > mutants/genes > >responsible for the branching organization. > > This gets back to the goal of the ontology. For the many > mutants/genes that affect inflorescence branching, do we need > to be able to describe each of them in detail (in which case > we need lots of terms) or just to assign them to the bin > "inflorescence" (in which case we only need a few terms)? I > don't know the answer to this, but it will affect the > structure I think. i.e., will we want to make queries such as > "find all genes in any plant that, when mutated, affect > phyllotaxis on third order inflorescence branches", or will > it be sufficient to ask "what genes are expressed in inflorescences"? > Food for thought anyway. > Toby > XXX To continue, the above example is seemingly very appropriate. Yes, I think we do need to provide the depth of information on all nodes so that detailed assigning can be done - so we do need to provide lots of terms. Providing the level of detail which just enables folk to assign info. to a very course bin (like 'inflorescence') is surely rather inadequate, considering the level of the science i.e. that many users are working at a much finer level of granularity. Furthermore, I think it is only when we 'sweat' at developing the finer structure now, will we encounter & overcome the 'structure difficulties' that are possibly lurking. This 'building' is going to be complex/multi-floored... -we need to ensure that we've built the foundation well so that the super-structure can be supported. While retrofitting should always be possible I urge us all to go deeper now rather than leaving that for later. To me this detailed approach is/should be the goal of the 'consensus ontology'. Perhaps, as a compromise, we could develop certain nodes with fine granularity, based on perceived needs of our potential consumers - here I'm assuming that some areas of anatomy are receiving much more research attention than other (perhaps a wrong assumption). Other nodes, perceived to be 'less needful' of fine granularity could be worked on 'later' - but we should advertise that users should voice their need for increased granularity wherever such needs are encountered. - Leszek > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biolo> gy/Kellogg/Kellogg/ > > > From rhee at acoma.Stanford.EDU Fri Mar 5 14:11:15 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Fri, 5 Mar 2004 11:11:15 -0800 (PST) Subject: progress and thought questions In-Reply-To: Message-ID: In general, I agree with your perspective. But we need to be a little more specific. I have a few questions for clarification. > XXX To continue, the above example is seemingly very appropriate. Yes, I > think we do need to provide the depth of information on all nodes so > that detailed assigning can be done - so we do need to provide lots of What do you mean by 'detailed assigning'? What data objects are you talking about and are they known to exist? > terms. Providing the level of detail which just enables folk to assign > info. to a very course bin (like 'inflorescence') is surely rather > inadequate, considering the level of the science i.e. that many users > are working at a much finer level of granularity. Furthermore, I think What do you mean by 'the science'? Surely we need to make some decisions on what subareas of science we are trying to faciliate. > it is only when we 'sweat' at developing the finer structure now, will > we encounter & overcome the 'structure difficulties' that are possibly > lurking. This 'building' is going to be complex/multi-floored... -we That is true to a certain extent but we need to do this incrementally with the understanding that the it is a dynamic process and has a very practical use case (i.e. annotate existing gene expression patterns and mutant phenotype). The best thing we can do now is to clearly define the organizing principles and stick to them for consistency. We don't need to solve all of the nuances in the beginning. Sue > need to ensure that we've built the foundation well so that the > super-structure can be supported. While retrofitting should always be > possible I urge us all to go deeper now rather than leaving that for > later. To me this detailed approach is/should be the goal of the > 'consensus ontology'. Perhaps, as a compromise, we could develop certain > nodes with fine granularity, based on perceived needs of our potential > consumers - here I'm assuming that some areas of anatomy are receiving > much more research attention than other (perhaps a wrong assumption). > Other nodes, perceived to be 'less needful' of fine granularity could be > worked on 'later' - but we should advertise that users should voice > their need for increased granularity wherever such needs are > encountered. > > - Leszek > > > > Elizabeth A. Kellogg > > Department of Biology > > University of Missouri-St. Louis > > 8001 Natural Bridge Road > > St. Louis, MO 63121 > > phone: 314-516-6217 > > fax: 314-516-6233 > > http://www.umsl.edu/divisions/artscience/biolo> gy/Kellogg/Kellogg/ > > > > > > > ----------------------------------------------------------------------------- Sue Rhee rhee at acoma.stanford.edu The Arabidopsis Information Resource URL: www.arabidopsis.org Carnegie Institution of Washington FAX: +1-650-325-6857 Department of Plant Biology Tel: +1-650-325-1521 ext. 251 260 Panama St. Stanford, CA 94305 U.S.A. ----------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Fri Mar 5 16:20:22 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 5 Mar 2004 13:20:22 -0800 (PST) Subject: DAG-Edit Meeting: Save the Date! (fwd) Message-ID: To Felipe, Leszek and the other ontology developers, Here is John's e-amil about Dag-edit workshop I mentioned during the meeting. The final date is May 26-28, location Walnut Creek, CA, (not far from Stanford). Let me know if you are interested to attend, and I'll keep you updated regarding programs and other details. Katica -------------------------------------------------------------------------- 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. -------------------------------------------------------------------------- ---------- Forwarded message ---------- Date: Fri, 5 Mar 2004 12:07:25 -0800 (PST) From: John Richter To: go at genome.stanford.edu Cc: Suzanna Lewis , Karen Eilbeck Subject: DAG-Edit Meeting: Save the Date! Hello, good consortium members. After much gnashing of teeth, and rearranging, we have come up with tentative dates/locations for the DAG-Edit meeting... The fine people at the Joint Genome Institute in Walnut Creek, CA have offered us the use of their facilities for the dates of May 26-May 28th (I'm thinking 10am - 5:00 pm running time). Breakfast, lunch and afternoon snack will be provided (and I'll make damned sure that the caterers pull out a decent offering for vegetarians this time around). At the moment, we are still working out a budget, so it's not clear whether we'll need to ask attendees for a contribution. My main concern right now is for dates. I'm hoping that May 26-28th will accomodate Stanford's remote curators, and any curators who might be coming to the Bay Area for the curatorial meeting this summer. If anyone can think of serious problems with these dates, please let me know immediately. Failure to hear loud complaints within the next week will be taken to mean consent (this is the same system I use when communicating with God, and He has yet to object). The DAG-Edit meeting format will be similar to the last time. There will be new software releases and bug fixes each day, mini-talks on a variety of topics in the morning and afternoon, with most of the day devoted to developing one's own ontology. Since there's the potential for many GO curators to be in the room at once, I'd like to make this an opportunity for curators from entirely different sites to get a chance to actually work side-by-side, and see how other curators do things. To this end, I'd like to encourage curators who plan to attend to start thinking about things they'd like to work on with curators from other sites. Also, if anyone is interested in giving a mini-talk, please let me know. Potential topics might be: * This piece of software that really helps me develop the ontologies * DAG-Edit tips * This thing about DAG-Edit sucks; here's how my group would rather have it * A tricky logical issue that showed up while developing our ontology; how we dealt with it And so on. Anyway, the point is: * If you have a problem with May 26-28, let me know right away * If you want to give a talk, let me know right away Once we're sure about dates and prices, I'll be putting up a web page for signups. Thanks for reading to the end, John From pj37 at cornell.edu Mon Mar 22 10:14:44 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 22 Mar 2004 10:14:44 -0500 Subject: spatial terms Message-ID: <405F02E4.7030303@cornell.edu> Hi Everyone, I just now started working on the leaf section and encountered the problem on how do we represent the spatial organization. Since PATO/phenotype attribute ontology is way off from implementation what are our rules on this. here are a few spatial attribute examples which I think are necessary to describe a gene's transcript/protein expression profile or a phenotype. first second third fourth fifth e.g. first leaf second leaf first / second internode first / second node basal uppermost ; synonym:topmost lower upper e.g. basal / uppermost internodes topmost leaves lower floret upper floret primary secondary e.g. primary / secondary panicle branches spikelets of the primary branches From pj37 at cornell.edu Mon Mar 22 10:24:48 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 22 Mar 2004 10:24:48 -0500 Subject: synonym problem Message-ID: <405F0540.2060302@cornell.edu> After having a quick look at the last release here in one potential problem which the curators might face. example term name: rachis. The term appears twice in the ontology. Once as a term itself Rachis:PO:0020055: The main axis of a pinnate or more highly compound leaf. and second time as a synonym of Peduncle:PO:0009053, The stalk of an inflorescence. Can we adopt a rule here to always prefix the second anatomy term like leaf/inflorescence thus making it distinguishable. In this example it will be leaf rachis PO:0020055 and Peduncle:PO:0009053 synonym; inflorescence rachis Pankaj From peter.stevens at mobot.org Mon Mar 22 09:33:01 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Mon, 22 Mar 2004 10:33:01 -0400 Subject: synonym problem In-Reply-To: <405F0540.2060302@cornell.edu> References: <405F0540.2060302@cornell.edu> Message-ID: >This kind of problem may well crop up quite frequently and a >solution like this seems essential. P. >After having a quick look at the last release here in one potential >problem which the curators might face. > >example > >term name: rachis. >The term appears twice in the ontology. Once as a term itself > >Rachis:PO:0020055: The main axis of a pinnate or more highly compound leaf. > > >and second time as a synonym of >Peduncle:PO:0009053, The stalk of an inflorescence. > >Can we adopt a rule here to always prefix the second anatomy term >like leaf/inflorescence thus making it distinguishable. In this >example it will be >leaf rachis PO:0020055 >and >Peduncle:PO:0009053 synonym; inflorescence rachis > >Pankaj From peter.stevens at mobot.org Mon Mar 22 09:57:25 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Mon, 22 Mar 2004 10:57:25 -0400 Subject: spatial terms In-Reply-To: <405F02E4.7030303@cornell.edu> References: <405F02E4.7030303@cornell.edu> Message-ID: >Hi Everyone, > >I just now started working on the leaf section and encountered the >problem on how do we represent the spatial organization. Since >PATO/phenotype attribute ontology is way off from implementation >what are our rules on this. > >here are a few spatial attribute examples which I think are >necessary to describe a gene's transcript/protein expression profile >or a phenotype. > > >first >second >third >fourth >fifth > e.g. > first leaf > second leaf > first / second internode > first / second node >basal >uppermost ; synonym:topmost >lower >upper > e.g. > basal / uppermost internodes > topmost leaves > lower floret upper floret >primary >secondary > e.g. > primary / secondary panicle branches > spikelets of the primary branches By analogy with leaf venation, first-order (i.e. midrib/main axis), second order, etc., branches may well be best here - used in inflorescence descriptions as well. And you may need the general adaxial/abaxial to describe surfaces of the leaf, and then there is ad/abmedial... P. From lreiser at acoma.Stanford.EDU Mon Mar 22 12:40:35 2004 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 22 Mar 2004 09:40:35 -0800 (PST) Subject: spatial terms In-Reply-To: <405F02E4.7030303@cornell.edu> Message-ID: Depends on how you are defining the first leaf- doesnt it. Counting from first leaf after the cotyledon (which may or may not be formed in the embryo prior to dessication)... Leonore On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > > Hi Everyone, > > I just now started working on the leaf section and encountered the > problem on how do we represent the spatial organization. Since > PATO/phenotype attribute ontology is way off from implementation what > are our rules on this. > > here are a few spatial attribute examples which I think are necessary to > describe a gene's transcript/protein expression profile or a phenotype. > > > first > second > third > fourth > fifth > e.g. > first leaf > second leaf > first / second internode > first / second node > basal > uppermost ; synonym:topmost > lower > upper > e.g. > basal / uppermost internodes > topmost leaves > lower floret > upper floret > primary > secondary > e.g. > primary / secondary panicle branches > spikelets of the primary branches > > > ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- From kellogge at msx.umsl.edu Mon Mar 22 13:17:17 2004 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 22 Mar 2004 13:17:17 -0500 Subject: synonym problem In-Reply-To: References: <405F0540.2060302@cornell.edu> <405F0540.2060302@cornell.edu> Message-ID: Makes sense to me too. I might argue that inflorescence rachis and peduncle are not actually the same thing, but that's a separate issue. toby >>This kind of problem may well crop up quite frequently and a >>solution like this seems essential. > > >P. > > > >>After having a quick look at the last release here in one potential >>problem which the curators might face. >> >>example >> >>term name: rachis. >>The term appears twice in the ontology. Once as a term itself >> >>Rachis:PO:0020055: The main axis of a pinnate or more highly compound leaf. >> >> >>and second time as a synonym of >>Peduncle:PO:0009053, The stalk of an inflorescence. >> >>Can we adopt a rule here to always prefix the second anatomy term >>like leaf/inflorescence thus making it distinguishable. In this >>example it will be >>leaf rachis PO:0020055 >>and >>Peduncle:PO:0009053 synonym; inflorescence rachis >> >>Pankaj Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From kellogge at msx.umsl.edu Mon Mar 22 13:22:48 2004 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 22 Mar 2004 13:22:48 -0500 Subject: spatial terms In-Reply-To: References: <405F02E4.7030303@cornell.edu> Message-ID: I think we need to think hard about what will be gained or lost by including terms like first second third leaf. The conventions on counting are different in different plants (e.g top down vs. bottom up), and leaves with the same number may or may not be comparable. Even among maize inbreds there is variation in the number of leaves before the juvenile/adult transition and before flowering. I'd suggest that such numbering schemes fall into species-specific ontologies and therefore should be excluded from the general plant ontology. Perhaps this is something we should discuss at our May meeting. Toby >Depends on how you are defining the first leaf- doesnt it. >Counting from first leaf after the cotyledon (which may or may not be >formed in the embryo prior to dessication)... >Leonore > >On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > >> >> Hi Everyone, >> >> I just now started working on the leaf section and encountered the >> problem on how do we represent the spatial organization. Since >> PATO/phenotype attribute ontology is way off from implementation what >> are our rules on this. >> >> here are a few spatial attribute examples which I think are necessary to >> describe a gene's transcript/protein expression profile or a phenotype. >> >> >> first >> second >> third >> fourth >> fifth >> e.g. >> first leaf >> second leaf >> first / second internode >> first / second node >> basal >> uppermost ; synonym:topmost >> lower >> upper >> e.g. >> basal / uppermost internodes >> topmost leaves >> lower floret >> upper floret >> primary >> secondary >> e.g. >> primary / secondary panicle branches >> spikelets of the primary branches >> >> >> > >------------------------------------------------------------------------------- >Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu >The Arabidopsis Information Resource FAX: (650) 325-6857 >Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 >Department of Plant Biology URL: http://arabidopsis.org/ >260 Panama St. >Stanford, CA 94305 >------------------------------------------------------------------------------- Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From lreiser at acoma.Stanford.EDU Mon Mar 22 13:21:50 2004 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 22 Mar 2004 10:21:50 -0800 (PST) Subject: spatial terms In-Reply-To: Message-ID: I agree. For maize, there are well defined plastochron idicies, but from what I have seen, not so well defined for arabidopsis. And like maize , can be quite variable in the number of leaves produced prior to flowering- especially when the light regime is altered. Maybe the thing to is look at what sorts of annotations Pankaj is referring to and see how they can be accomodated. Always helps to have the data at hand. On Mon, 22 Mar 2004, Toby Kellogg wrote: > I think we need to think hard about what will be gained or lost by > including terms like first second third leaf. The conventions on counting > are different in different plants (e.g top down vs. bottom up), and leaves > with the same number may or may not be comparable. Even among maize > inbreds there is variation in the number of leaves before the > juvenile/adult transition and before flowering. I'd suggest that such > numbering schemes fall into species-specific ontologies and therefore > should be excluded from the general plant ontology. Perhaps this is > something we should discuss at our May meeting. > Toby > > >Depends on how you are defining the first leaf- doesnt it. > >Counting from first leaf after the cotyledon (which may or may not be > >formed in the embryo prior to dessication)... > >Leonore > > > >On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > > > >> > >> Hi Everyone, > >> > >> I just now started working on the leaf section and encountered the > >> problem on how do we represent the spatial organization. Since > >> PATO/phenotype attribute ontology is way off from implementation what > >> are our rules on this. > >> > >> here are a few spatial attribute examples which I think are necessary to > >> describe a gene's transcript/protein expression profile or a phenotype. > >> > >> > >> first > >> second > >> third > >> fourth > >> fifth > >> e.g. > >> first leaf > >> second leaf > >> first / second internode > >> first / second node > >> basal > >> uppermost ; synonym:topmost > >> lower > >> upper > >> e.g. > >> basal / uppermost internodes > >> topmost leaves > >> lower floret > >> upper floret > >> primary > >> secondary > >> e.g. > >> primary / secondary panicle branches > >> spikelets of the primary branches > >> > >> > >> > > > >------------------------------------------------------------------------------- > >Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu > >The Arabidopsis Information Resource FAX: (650) 325-6857 > >Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 > >Department of Plant Biology URL: http://arabidopsis.org/ > >260 Panama St. > >Stanford, CA 94305 > >------------------------------------------------------------------------------- > > > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- From pj37 at cornell.edu Mon Mar 22 13:37:20 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 22 Mar 2004 13:37:20 -0500 Subject: spatial terms In-Reply-To: References: <405F02E4.7030303@cornell.edu> Message-ID: <405F3260.5060708@cornell.edu> Toby Kellogg wrote: > I think we need to think hard about what will be gained or lost by > including terms like first second third leaf. The conventions on counting > are different in different plants (e.g top down vs. bottom up), and leaves > with the same number may or may not be comparable. Even among maize > inbreds there is variation in the number of leaves before the > juvenile/adult transition and before flowering. I'd suggest that such > numbering schemes fall into species-specific ontologies and therefore > should be excluded from the general plant ontology. Perhaps this is > something we should discuss at our May meeting. > Toby > I agree with Leonore and Toby on how you count the numbers and how many numbers, based on the germplasm/variety/population type and the species. Looks like we need to comeup with a solution soon. I know in majority of the rice reports the counts are from the top, because often researchers do not see the 1st and 2nd internode/node. To make things simple we can always say that gene-x is expressed in internode. But then we loose the granularity we want to suggest to our user that look the gene is expressed in Second internode ONLY. This is different than assigning it to the generic term internode. I think this issue will keep coming up every now and then, because at Gramene we do not want to maintain two different ontology sets. I guess the same goes with TAIR and MaizeGDB. A generic one from POC and species specific from our own databases. This is too much of work and was also the main reason why we wanted to have this project. Pankaj > >>Depends on how you are defining the first leaf- doesnt it. >>Counting from first leaf after the cotyledon (which may or may not be >>formed in the embryo prior to dessication)... >>Leonore >> >>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >> >> >>>Hi Everyone, >>> >>>I just now started working on the leaf section and encountered the >>>problem on how do we represent the spatial organization. Since >>>PATO/phenotype attribute ontology is way off from implementation what >>>are our rules on this. >>> >>>here are a few spatial attribute examples which I think are necessary to >>>describe a gene's transcript/protein expression profile or a phenotype. >>> >>> >>>first >>>second >>>third >>>fourth >>>fifth >>> e.g. >>> first leaf >>> second leaf >>> first / second internode >>> first / second node >>>basal >>>uppermost ; synonym:topmost >>>lower >>>upper >>> e.g. >>> basal / uppermost internodes >>> topmost leaves >>> lower floret >>> upper floret >>>primary >>>secondary >>> e.g. >>> primary / secondary panicle branches >>> spikelets of the primary branches >>> >>> From pj37 at cornell.edu Mon Mar 22 13:48:04 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 22 Mar 2004 13:48:04 -0500 Subject: synonym problem In-Reply-To: References: <405F0540.2060302@cornell.edu> <405F0540.2060302@cornell.edu> Message-ID: <405F34E4.7070907@cornell.edu> That's fine as long as we do not go farther by creating a parent term rachis and both leaf and inflorescence rachis as its instances. If that's an agreed resolution please say YES After hearing from everyone may be Katica should include it in our development SOPs. Pankaj Toby Kellogg wrote: > Makes sense to me too. I might argue that inflorescence rachis and > peduncle are not actually the same thing, but that's a separate issue. > toby > > >>>This kind of problem may well crop up quite frequently and a >>>solution like this seems essential. >> >> >>P. >> >> >> >> >>>After having a quick look at the last release here in one potential >>>problem which the curators might face. >>> >>>example >>> >>>term name: rachis. >>>The term appears twice in the ontology. Once as a term itself >>> >>>Rachis:PO:0020055: The main axis of a pinnate or more highly compound leaf. >>> >>> >>>and second time as a synonym of >>>Peduncle:PO:0009053, The stalk of an inflorescence. >>> >>>Can we adopt a rule here to always prefix the second anatomy term >>>like leaf/inflorescence thus making it distinguishable. In this >>>example it will be >>>leaf rachis PO:0020055 >>>and >>>Peduncle:PO:0009053 synonym; inflorescence rachis >>> >>>Pankaj > > > > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > -- ****************************** Pankaj Jaiswal, PhD Gramene Database Department of Plant Breeding G-15 Bradfield Hall Cornell University Ithaca, NY-14853 tel: +1-607-255-3103 fax: +1-607-255-6683 web: http://www.gramene.org ***************************** From kellogge at msx.umsl.edu Mon Mar 22 14:05:18 2004 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 22 Mar 2004 14:05:18 -0500 Subject: spatial terms In-Reply-To: <405F3260.5060708@cornell.edu> References: <405F02E4.7030303@cornell.edu> Message-ID: I think maize counts from the bottom. so at a minimu we'd have to say "internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty cumbersome to me. Leonore's question is probably the most relevant - how many genes are currently annotated to a specific internode? Toby >Toby Kellogg wrote: >> I think we need to think hard about what will be gained or lost by >> including terms like first second third leaf. The conventions on counting >> are different in different plants (e.g top down vs. bottom up), and leaves >> with the same number may or may not be comparable. Even among maize >> inbreds there is variation in the number of leaves before the >> juvenile/adult transition and before flowering. I'd suggest that such >> numbering schemes fall into species-specific ontologies and therefore >> should be excluded from the general plant ontology. Perhaps this is >> something we should discuss at our May meeting. >> Toby >> > >I agree with Leonore and Toby on how you count the numbers and how many >numbers, based on the germplasm/variety/population type and the species. >Looks like we need to comeup with a solution soon. I know in majority of >the rice reports the counts are from the top, because often researchers >do not see the 1st and 2nd internode/node. > >To make things simple we can always say that gene-x is expressed in >internode. But then we loose the granularity we want to suggest to our >user that look the gene is expressed in Second internode ONLY. This is >different than assigning it to the generic term internode. > >I think this issue will keep coming up every now and then, because at >Gramene we do not want to maintain two different ontology sets. I guess >the same goes with TAIR and MaizeGDB. A generic one from POC and >species specific from our own databases. This is too much of work and >was also the main reason why we wanted to have this project. > >Pankaj > > >> >>>Depends on how you are defining the first leaf- doesnt it. >>>Counting from first leaf after the cotyledon (which may or may not be >>>formed in the embryo prior to dessication)... >>>Leonore >>> >>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >>> >>> >>>>Hi Everyone, >>>> >>>>I just now started working on the leaf section and encountered the >>>>problem on how do we represent the spatial organization. Since >>>>PATO/phenotype attribute ontology is way off from implementation what >>>>are our rules on this. >>>> >>>>here are a few spatial attribute examples which I think are necessary to >>>>describe a gene's transcript/protein expression profile or a phenotype. >>>> >>>> >>>>first >>>>second >>>>third >>>>fourth >>>>fifth >>>> e.g. >>>> first leaf >>>> second leaf >>>> first / second internode >>>> first / second node >>>>basal >>>>uppermost ; synonym:topmost >>>>lower >>>>upper >>>> e.g. >>>> basal / uppermost internodes >>>> topmost leaves >>>> lower floret >>>> upper floret >>>>primary >>>>secondary >>>> e.g. >>>> primary / secondary panicle branches >>>> spikelets of the primary branches >>>> >>>> Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From pj37 at cornell.edu Mon Mar 22 14:07:45 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 22 Mar 2004 14:07:45 -0500 Subject: spatial terms In-Reply-To: References: <405F02E4.7030303@cornell.edu> Message-ID: <405F3981.4040807@cornell.edu> Toby Kellogg wrote: > I think maize counts from the bottom. so at a minimu we'd have to say > "internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty > cumbersome to me. Leonore's question is probably the most relevant - how > many genes are currently annotated to a specific internode? > Toby > About 5-6 sequenced genes and 40 classical genes identified by phenotype. Rice does not have may sequenced genes with expression profile. This trend has just picked up and is much more focussed on the parts with agronomic value (stem, seed, panicle). Pankaj > >>Toby Kellogg wrote: >> >>>I think we need to think hard about what will be gained or lost by >>>including terms like first second third leaf. The conventions on counting >>>are different in different plants (e.g top down vs. bottom up), and leaves >>>with the same number may or may not be comparable. Even among maize >>>inbreds there is variation in the number of leaves before the >>>juvenile/adult transition and before flowering. I'd suggest that such >>>numbering schemes fall into species-specific ontologies and therefore >>>should be excluded from the general plant ontology. Perhaps this is >>>something we should discuss at our May meeting. >>>Toby >>> >> >>I agree with Leonore and Toby on how you count the numbers and how many >>numbers, based on the germplasm/variety/population type and the species. >>Looks like we need to comeup with a solution soon. I know in majority of >>the rice reports the counts are from the top, because often researchers >>do not see the 1st and 2nd internode/node. >> >>To make things simple we can always say that gene-x is expressed in >>internode. But then we loose the granularity we want to suggest to our >>user that look the gene is expressed in Second internode ONLY. This is >>different than assigning it to the generic term internode. >> >>I think this issue will keep coming up every now and then, because at >>Gramene we do not want to maintain two different ontology sets. I guess >>the same goes with TAIR and MaizeGDB. A generic one from POC and >>species specific from our own databases. This is too much of work and >>was also the main reason why we wanted to have this project. >> >>Pankaj >> >> >> >>>>Depends on how you are defining the first leaf- doesnt it. >>>>Counting from first leaf after the cotyledon (which may or may not be >>>>formed in the embryo prior to dessication)... >>>>Leonore >>>> >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >>>> >>>> >>>> >>>>>Hi Everyone, >>>>> >>>>>I just now started working on the leaf section and encountered the >>>>>problem on how do we represent the spatial organization. Since >>>>>PATO/phenotype attribute ontology is way off from implementation what >>>>>are our rules on this. >>>>> >>>>>here are a few spatial attribute examples which I think are necessary to >>>>>describe a gene's transcript/protein expression profile or a phenotype. >>>>> >>>>> >>>>>first >>>>>second >>>>>third >>>>>fourth >>>>>fifth >>>>> e.g. >>>>> first leaf >>>>> second leaf >>>>> first / second internode >>>>> first / second node >>>>>basal >>>>>uppermost ; synonym:topmost >>>>>lower >>>>>upper >>>>> e.g. >>>>> basal / uppermost internodes >>>>> topmost leaves >>>>> lower floret >>>>> upper floret >>>>>primary >>>>>secondary >>>>> e.g. >>>>> primary / secondary panicle branches >>>>> spikelets of the primary branches >>>>> >>>>> > > > > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > -- ****************************** Pankaj Jaiswal, PhD Gramene Database Department of Plant Breeding G-15 Bradfield Hall Cornell University Ithaca, NY-14853 tel: +1-607-255-3103 fax: +1-607-255-6683 web: http://www.gramene.org ***************************** From katica at acoma.Stanford.EDU Mon Mar 22 14:11:52 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 22 Mar 2004 11:11:52 -0800 (PST) Subject: synonym problem In-Reply-To: <405F34E4.7070907@cornell.edu> Message-ID: I too agree with you Pankaj. Let's make it a rule. What the other POC members think? Katica On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > That's fine as long as we do not go farther by creating a parent term > rachis and both leaf and inflorescence rachis as its instances. > > If that's an agreed resolution please say YES > After hearing from everyone may be Katica should include it in our > development SOPs. > > Pankaj > > Toby Kellogg wrote: > > > Makes sense to me too. I might argue that inflorescence rachis and > > peduncle are not actually the same thing, but that's a separate issue. > > toby > > > > > >>>This kind of problem may well crop up quite frequently and a > >>>solution like this seems essential. > >> > >> > >>P. > >> > >> > >> > >> > >>>After having a quick look at the last release here in one potential > >>>problem which the curators might face. > >>> > >>>example > >>> > >>>term name: rachis. > >>>The term appears twice in the ontology. Once as a term itself > >>> > >>>Rachis:PO:0020055: The main axis of a pinnate or more highly compound leaf. > >>> > >>> > >>>and second time as a synonym of > >>>Peduncle:PO:0009053, The stalk of an inflorescence. > >>> > >>>Can we adopt a rule here to always prefix the second anatomy term > >>>like leaf/inflorescence thus making it distinguishable. In this > >>>example it will be > >>>leaf rachis PO:0020055 > >>>and > >>>Peduncle:PO:0009053 synonym; inflorescence rachis > >>> > >>>Pankaj > > > > > > > > Elizabeth A. Kellogg > > Department of Biology > > University of Missouri-St. Louis > > 8001 Natural Bridge Road > > St. Louis, MO 63121 > > phone: 314-516-6217 > > fax: 314-516-6233 > > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > > > > > > -- > ****************************** > Pankaj Jaiswal, PhD > Gramene Database > Department of Plant Breeding > G-15 Bradfield Hall > Cornell University > Ithaca, NY-14853 > > tel: +1-607-255-3103 > fax: +1-607-255-6683 > web: http://www.gramene.org > ***************************** > > -------------------------------------------------------------------------- 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 lreiser at acoma.Stanford.EDU Mon Mar 22 14:15:13 2004 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 22 Mar 2004 11:15:13 -0800 (PST) Subject: spatial terms In-Reply-To: <405F3981.4040807@cornell.edu> Message-ID: Maybe it would help to have a description or two to look at? Do they say things like ONLY EXPRESSED IN THE FOURTH INTERNODE? On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > > > Toby Kellogg wrote: > > > I think maize counts from the bottom. so at a minimu we'd have to say > > "internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty > > cumbersome to me. Leonore's question is probably the most relevant - how > > many genes are currently annotated to a specific internode? > > Toby > > > About 5-6 sequenced genes and 40 classical genes identified by > phenotype. Rice does not have may sequenced genes with expression > profile. This trend has just picked up and is much more focussed on the > parts with agronomic value (stem, seed, panicle). > > Pankaj > > > > > >>Toby Kellogg wrote: > >> > >>>I think we need to think hard about what will be gained or lost by > >>>including terms like first second third leaf. The conventions on counting > >>>are different in different plants (e.g top down vs. bottom up), and leaves > >>>with the same number may or may not be comparable. Even among maize > >>>inbreds there is variation in the number of leaves before the > >>>juvenile/adult transition and before flowering. I'd suggest that such > >>>numbering schemes fall into species-specific ontologies and therefore > >>>should be excluded from the general plant ontology. Perhaps this is > >>>something we should discuss at our May meeting. > >>>Toby > >>> > >> > >>I agree with Leonore and Toby on how you count the numbers and how many > >>numbers, based on the germplasm/variety/population type and the species. > >>Looks like we need to comeup with a solution soon. I know in majority of > >>the rice reports the counts are from the top, because often researchers > >>do not see the 1st and 2nd internode/node. > >> > >>To make things simple we can always say that gene-x is expressed in > >>internode. But then we loose the granularity we want to suggest to our > >>user that look the gene is expressed in Second internode ONLY. This is > >>different than assigning it to the generic term internode. > >> > >>I think this issue will keep coming up every now and then, because at > >>Gramene we do not want to maintain two different ontology sets. I guess > >>the same goes with TAIR and MaizeGDB. A generic one from POC and > >>species specific from our own databases. This is too much of work and > >>was also the main reason why we wanted to have this project. > >> > >>Pankaj > >> > >> > >> > >>>>Depends on how you are defining the first leaf- doesnt it. > >>>>Counting from first leaf after the cotyledon (which may or may not be > >>>>formed in the embryo prior to dessication)... > >>>>Leonore > >>>> > >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > >>>> > >>>> > >>>> > >>>>>Hi Everyone, > >>>>> > >>>>>I just now started working on the leaf section and encountered the > >>>>>problem on how do we represent the spatial organization. Since > >>>>>PATO/phenotype attribute ontology is way off from implementation what > >>>>>are our rules on this. > >>>>> > >>>>>here are a few spatial attribute examples which I think are necessary to > >>>>>describe a gene's transcript/protein expression profile or a phenotype. > >>>>> > >>>>> > >>>>>first > >>>>>second > >>>>>third > >>>>>fourth > >>>>>fifth > >>>>> e.g. > >>>>> first leaf > >>>>> second leaf > >>>>> first / second internode > >>>>> first / second node > >>>>>basal > >>>>>uppermost ; synonym:topmost > >>>>>lower > >>>>>upper > >>>>> e.g. > >>>>> basal / uppermost internodes > >>>>> topmost leaves > >>>>> lower floret > >>>>> upper floret > >>>>>primary > >>>>>secondary > >>>>> e.g. > >>>>> primary / secondary panicle branches > >>>>> spikelets of the primary branches > >>>>> > >>>>> > > > > > > > > Elizabeth A. Kellogg > > Department of Biology > > University of Missouri-St. Louis > > 8001 Natural Bridge Road > > St. Louis, MO 63121 > > phone: 314-516-6217 > > fax: 314-516-6233 > > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > > > > > > -- > ****************************** > Pankaj Jaiswal, PhD > Gramene Database > Department of Plant Breeding > G-15 Bradfield Hall > Cornell University > Ithaca, NY-14853 > > tel: +1-607-255-3103 > fax: +1-607-255-6683 > web: http://www.gramene.org > ***************************** > > ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- From lreiser at acoma.Stanford.EDU Mon Mar 22 14:16:58 2004 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 22 Mar 2004 11:16:58 -0800 (PST) Subject: synonym problem In-Reply-To: Message-ID: Seems like it would have to be, since by definition, a synonym- well, has the same definition. Since a leaf rachis and inflorescence rachis are NOT defined asthe same thing, they shouldnt share a synonym... Leonore On Mon, 22 Mar 2004, Katica Ilic wrote: > > I too agree with you Pankaj. Let's make it a rule. What the other POC > members think? > > Katica > > On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > > > That's fine as long as we do not go farther by creating a parent term > > rachis and both leaf and inflorescence rachis as its instances. > > > > If that's an agreed resolution please say YES > > After hearing from everyone may be Katica should include it in our > > development SOPs. > > > > Pankaj > > > > Toby Kellogg wrote: > > > > > Makes sense to me too. I might argue that inflorescence rachis and > > > peduncle are not actually the same thing, but that's a separate issue. > > > toby > > > > > > > > >>>This kind of problem may well crop up quite frequently and a > > >>>solution like this seems essential. > > >> > > >> > > >>P. > > >> > > >> > > >> > > >> > > >>>After having a quick look at the last release here in one potential > > >>>problem which the curators might face. > > >>> > > >>>example > > >>> > > >>>term name: rachis. > > >>>The term appears twice in the ontology. Once as a term itself > > >>> > > >>>Rachis:PO:0020055: The main axis of a pinnate or more highly compound leaf. > > >>> > > >>> > > >>>and second time as a synonym of > > >>>Peduncle:PO:0009053, The stalk of an inflorescence. > > >>> > > >>>Can we adopt a rule here to always prefix the second anatomy term > > >>>like leaf/inflorescence thus making it distinguishable. In this > > >>>example it will be > > >>>leaf rachis PO:0020055 > > >>>and > > >>>Peduncle:PO:0009053 synonym; inflorescence rachis > > >>> > > >>>Pankaj > > > > > > > > > > > > Elizabeth A. Kellogg > > > Department of Biology > > > University of Missouri-St. Louis > > > 8001 Natural Bridge Road > > > St. Louis, MO 63121 > > > phone: 314-516-6217 > > > fax: 314-516-6233 > > > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > > > > > > > > > > > -- > > ****************************** > > Pankaj Jaiswal, PhD > > Gramene Database > > Department of Plant Breeding > > G-15 Bradfield Hall > > Cornell University > > Ithaca, NY-14853 > > > > tel: +1-607-255-3103 > > fax: +1-607-255-6683 > > web: http://www.gramene.org > > ***************************** > > > > > > -------------------------------------------------------------------------- > 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. > -------------------------------------------------------------------------- > > ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- From pj37 at cornell.edu Mon Mar 22 14:29:31 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 22 Mar 2004 14:29:31 -0500 Subject: spatial terms In-Reply-To: References: Message-ID: <405F3E9B.6090003@cornell.edu> Here is an example. The example I gave you is somewhat similar. http://www.pnas.org/cgi/content/full/97/21/11638/F4 pankaj Leonore Reiser wrote: > Maybe it would help to have a description or two to look at? Do they say > things like ONLY EXPRESSED IN THE FOURTH INTERNODE? > > > On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > > >> >>Toby Kellogg wrote: >> >> >>>I think maize counts from the bottom. so at a minimu we'd have to say >>>"internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty >>>cumbersome to me. Leonore's question is probably the most relevant - how >>>many genes are currently annotated to a specific internode? >>>Toby >>> >> >>About 5-6 sequenced genes and 40 classical genes identified by >>phenotype. Rice does not have may sequenced genes with expression >>profile. This trend has just picked up and is much more focussed on the >>parts with agronomic value (stem, seed, panicle). >> >>Pankaj >> >> >> >>>>Toby Kellogg wrote: >>>> >>>> >>>>>I think we need to think hard about what will be gained or lost by >>>>>including terms like first second third leaf. The conventions on counting >>>>>are different in different plants (e.g top down vs. bottom up), and leaves >>>>>with the same number may or may not be comparable. Even among maize >>>>>inbreds there is variation in the number of leaves before the >>>>>juvenile/adult transition and before flowering. I'd suggest that such >>>>>numbering schemes fall into species-specific ontologies and therefore >>>>>should be excluded from the general plant ontology. Perhaps this is >>>>>something we should discuss at our May meeting. >>>>>Toby >>>>> >>>> >>>>I agree with Leonore and Toby on how you count the numbers and how many >>>>numbers, based on the germplasm/variety/population type and the species. >>>>Looks like we need to comeup with a solution soon. I know in majority of >>>>the rice reports the counts are from the top, because often researchers >>>>do not see the 1st and 2nd internode/node. >>>> >>>>To make things simple we can always say that gene-x is expressed in >>>>internode. But then we loose the granularity we want to suggest to our >>>>user that look the gene is expressed in Second internode ONLY. This is >>>>different than assigning it to the generic term internode. >>>> >>>>I think this issue will keep coming up every now and then, because at >>>>Gramene we do not want to maintain two different ontology sets. I guess >>>>the same goes with TAIR and MaizeGDB. A generic one from POC and >>>>species specific from our own databases. This is too much of work and >>>>was also the main reason why we wanted to have this project. >>>> >>>>Pankaj >>>> >>>> >>>> >>>> >>>>>>Depends on how you are defining the first leaf- doesnt it. >>>>>>Counting from first leaf after the cotyledon (which may or may not be >>>>>>formed in the embryo prior to dessication)... >>>>>>Leonore >>>>>> >>>>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Hi Everyone, >>>>>>> >>>>>>>I just now started working on the leaf section and encountered the >>>>>>>problem on how do we represent the spatial organization. Since >>>>>>>PATO/phenotype attribute ontology is way off from implementation what >>>>>>>are our rules on this. >>>>>>> >>>>>>>here are a few spatial attribute examples which I think are necessary to >>>>>>>describe a gene's transcript/protein expression profile or a phenotype. >>>>>>> >>>>>>> >>>>>>>first >>>>>>>second >>>>>>>third >>>>>>>fourth >>>>>>>fifth >>>>>>> e.g. >>>>>>> first leaf >>>>>>> second leaf >>>>>>> first / second internode >>>>>>> first / second node >>>>>>>basal >>>>>>>uppermost ; synonym:topmost >>>>>>>lower >>>>>>>upper >>>>>>> e.g. >>>>>>> basal / uppermost internodes >>>>>>> topmost leaves >>>>>>> lower floret >>>>>>> upper floret >>>>>>>primary >>>>>>>secondary >>>>>>> e.g. >>>>>>> primary / secondary panicle branches >>>>>>> spikelets of the primary branches >>>>>>> >>>>>>> >>> >>> >>> >>>Elizabeth A. Kellogg >>>Department of Biology >>>University of Missouri-St. Louis >>>8001 Natural Bridge Road >>>St. Louis, MO 63121 >>>phone: 314-516-6217 >>>fax: 314-516-6233 >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ >>> >>> >>> >> >>-- >>****************************** >>Pankaj Jaiswal, PhD >>Gramene Database >>Department of Plant Breeding >>G-15 Bradfield Hall >>Cornell University >>Ithaca, NY-14853 >> >>tel: +1-607-255-3103 >>fax: +1-607-255-6683 >>web: http://www.gramene.org >>***************************** >> >> > > > ------------------------------------------------------------------------------- > Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu > The Arabidopsis Information Resource FAX: (650) 325-6857 > Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > ------------------------------------------------------------------------------- > > -- ****************************** Pankaj Jaiswal, PhD Gramene Database Department of Plant Breeding G-15 Bradfield Hall Cornell University Ithaca, NY-14853 tel: +1-607-255-3103 fax: +1-607-255-6683 web: http://www.gramene.org ***************************** From pj37 at cornell.edu Mon Mar 22 14:37:46 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 22 Mar 2004 14:37:46 -0500 Subject: spatial terms In-Reply-To: <405F3E9B.6090003@cornell.edu> References: <405F3E9B.6090003@cornell.edu> Message-ID: <405F408A.4020909@cornell.edu> Some more http://www.plantcell.org/cgi/content/full/12/9/1591 Pankaj Pankaj Jaiswal wrote: > Here is an example. The example I gave you is somewhat similar. > > http://www.pnas.org/cgi/content/full/97/21/11638/F4 > > pankaj > > Leonore Reiser wrote: > >> Maybe it would help to have a description or two to look at? Do they say >> things like ONLY EXPRESSED IN THE FOURTH INTERNODE? >> >> >> On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >> >> >>> >>> Toby Kellogg wrote: >>> >>> >>>> I think maize counts from the bottom. so at a minimu we'd have to say >>>> "internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty >>>> cumbersome to me. Leonore's question is probably the most relevant >>>> - how >>>> many genes are currently annotated to a specific internode? >>>> Toby >>>> >>> >>> About 5-6 sequenced genes and 40 classical genes identified by >>> phenotype. Rice does not have may sequenced genes with expression >>> profile. This trend has just picked up and is much more focussed on the >>> parts with agronomic value (stem, seed, panicle). >>> >>> Pankaj >>> >>> >>> >>>>> Toby Kellogg wrote: >>>>> >>>>> >>>>>> I think we need to think hard about what will be gained or lost by >>>>>> including terms like first second third leaf. The conventions on >>>>>> counting >>>>>> are different in different plants (e.g top down vs. bottom up), >>>>>> and leaves >>>>>> with the same number may or may not be comparable. Even among maize >>>>>> inbreds there is variation in the number of leaves before the >>>>>> juvenile/adult transition and before flowering. I'd suggest that >>>>>> such >>>>>> numbering schemes fall into species-specific ontologies and therefore >>>>>> should be excluded from the general plant ontology. Perhaps this is >>>>>> something we should discuss at our May meeting. >>>>>> Toby >>>>>> >>>>> >>>>> I agree with Leonore and Toby on how you count the numbers and how >>>>> many >>>>> numbers, based on the germplasm/variety/population type and the >>>>> species. >>>>> Looks like we need to comeup with a solution soon. I know in >>>>> majority of >>>>> the rice reports the counts are from the top, because often >>>>> researchers >>>>> do not see the 1st and 2nd internode/node. >>>>> >>>>> To make things simple we can always say that gene-x is expressed in >>>>> internode. But then we loose the granularity we want to suggest to our >>>>> user that look the gene is expressed in Second internode ONLY. This is >>>>> different than assigning it to the generic term internode. >>>>> >>>>> I think this issue will keep coming up every now and then, because at >>>>> Gramene we do not want to maintain two different ontology sets. I >>>>> guess >>>>> the same goes with TAIR and MaizeGDB. A generic one from POC and >>>>> species specific from our own databases. This is too much of work and >>>>> was also the main reason why we wanted to have this project. >>>>> >>>>> Pankaj >>>>> >>>>> >>>>> >>>>> >>>>>>> Depends on how you are defining the first leaf- doesnt it. >>>>>>> Counting from first leaf after the cotyledon (which may or may >>>>>>> not be >>>>>>> formed in the embryo prior to dessication)... >>>>>>> Leonore >>>>>>> >>>>>>> On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Hi Everyone, >>>>>>>> >>>>>>>> I just now started working on the leaf section and encountered the >>>>>>>> problem on how do we represent the spatial organization. Since >>>>>>>> PATO/phenotype attribute ontology is way off from implementation >>>>>>>> what >>>>>>>> are our rules on this. >>>>>>>> >>>>>>>> here are a few spatial attribute examples which I think are >>>>>>>> necessary to >>>>>>>> describe a gene's transcript/protein expression profile or a >>>>>>>> phenotype. >>>>>>>> >>>>>>>> >>>>>>>> first >>>>>>>> second >>>>>>>> third >>>>>>>> fourth >>>>>>>> fifth >>>>>>>> e.g. >>>>>>>> first leaf >>>>>>>> second leaf >>>>>>>> first / second internode >>>>>>>> first / second node >>>>>>>> basal >>>>>>>> uppermost ; synonym:topmost >>>>>>>> lower >>>>>>>> upper >>>>>>>> e.g. >>>>>>>> basal / uppermost internodes >>>>>>>> topmost leaves >>>>>>>> lower floret >>>>>>>> upper floret >>>>>>>> primary >>>>>>>> secondary >>>>>>>> e.g. >>>>>>>> primary / secondary panicle branches >>>>>>>> spikelets of the primary branches >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> Elizabeth A. Kellogg >>>> Department of Biology >>>> University of Missouri-St. Louis >>>> 8001 Natural Bridge Road >>>> St. Louis, MO 63121 >>>> phone: 314-516-6217 >>>> fax: 314-516-6233 >>>> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ >>>> >>>> >>>> >>> >>> -- >>> ****************************** >>> Pankaj Jaiswal, PhD >>> Gramene Database >>> Department of Plant Breeding >>> G-15 Bradfield Hall >>> Cornell University >>> Ithaca, NY-14853 >>> >>> tel: +1-607-255-3103 >>> fax: +1-607-255-6683 >>> web: http://www.gramene.org >>> ***************************** >>> >>> >> >> >> ------------------------------------------------------------------------------- >> >> Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu >> The Arabidopsis Information Resource FAX: (650) 325-6857 >> Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 >> Department of Plant Biology URL: http://arabidopsis.org/ >> 260 Panama St. >> Stanford, CA 94305 >> ------------------------------------------------------------------------------- >> >> >> > -- ****************************** Pankaj Jaiswal, PhD Gramene Database Department of Plant Breeding G-15 Bradfield Hall Cornell University Ithaca, NY-14853 tel: +1-607-255-3103 fax: +1-607-255-6683 web: http://www.gramene.org ***************************** From rpwise at iastate.edu Mon Mar 22 16:26:31 2004 From: rpwise at iastate.edu (Roger Wise) Date: Mon, 22 Mar 2004 15:26:31 -0600 Subject: spatial terms In-Reply-To: References: <405F02E4.7030303@cornell.edu> Message-ID: It seems to make sense to me to count from the bottom, because in many global expression studies, tissue is harvested, or dissected, before maturity. It is also important to have these stages well-defined, possibly species specific, because, again, in global expression studies, hundreds of genes are differentially expressed between specific stages or tissues (including anthers from upper and lower florets). At least for this particular application, and in the foreseeable future (eg. laser capture) more detail is better. As for cultivar differences, this should be defined by stating the cultivar along with the definition. Roger At 2:05 PM -0500 3/22/04, Toby Kellogg wrote: >I think maize counts from the bottom. so at a minimu we'd have to say >"internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty >cumbersome to me. Leonore's question is probably the most relevant - how >many genes are currently annotated to a specific internode? >Toby > >>Toby Kellogg wrote: >>> I think we need to think hard about what will be gained or lost by >>> including terms like first second third leaf. The conventions on counting >>> are different in different plants (e.g top down vs. bottom up), and leaves >>> with the same number may or may not be comparable. Even among maize >>> inbreds there is variation in the number of leaves before the >>> juvenile/adult transition and before flowering. I'd suggest that such >>> numbering schemes fall into species-specific ontologies and therefore >>> should be excluded from the general plant ontology. Perhaps this is >>> something we should discuss at our May meeting. >>> Toby >>> >> >>I agree with Leonore and Toby on how you count the numbers and how many >>numbers, based on the germplasm/variety/population type and the species. >>Looks like we need to comeup with a solution soon. I know in majority of >>the rice reports the counts are from the top, because often researchers >>do not see the 1st and 2nd internode/node. >> >>To make things simple we can always say that gene-x is expressed in >>internode. But then we loose the granularity we want to suggest to our >>user that look the gene is expressed in Second internode ONLY. This is >>different than assigning it to the generic term internode. >> >>I think this issue will keep coming up every now and then, because at >>Gramene we do not want to maintain two different ontology sets. I guess >>the same goes with TAIR and MaizeGDB. A generic one from POC and >>species specific from our own databases. This is too much of work and >>was also the main reason why we wanted to have this project. >> >>Pankaj >> >> >>> >>>>Depends on how you are defining the first leaf- doesnt it. >>>>Counting from first leaf after the cotyledon (which may or may not be >>>>formed in the embryo prior to dessication)... >>>>Leonore >>>> >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >>>> >>>> >>>>>Hi Everyone, >>>>> >>>>>I just now started working on the leaf section and encountered the >>>>>problem on how do we represent the spatial organization. Since >>>>>PATO/phenotype attribute ontology is way off from implementation what >>>>>are our rules on this. >>>>> >>>>>here are a few spatial attribute examples which I think are necessary to >>>>>describe a gene's transcript/protein expression profile or a phenotype. >>>>> >>>>> >>>>>first >>>>>second >>>>>third >>>>>fourth >>>>>fifth >>>>> e.g. >>>>> first leaf >>>>> second leaf >>>>> first / second internode >>>>> first / second node >>>>>basal >>>>>uppermost ; synonym:topmost >>>>>lower >>>>>upper >>>>> e.g. >>>>> basal / uppermost internodes >>>>> topmost leaves >>>>> lower floret >>>>> upper floret >>>>>primary >>>>>secondary >>>>> e.g. >>>>> primary / secondary panicle branches >>>>> spikelets of the primary branches >>>>> >>>>> > > >Elizabeth A. Kellogg >Department of Biology >University of Missouri-St. Louis >8001 Natural Bridge Road >St. Louis, MO 63121 >phone: 314-516-6217 >fax: 314-516-6233 >http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ -- _____________________________ Roger Wise, USDA-ARS Department of Plant Pathology 411 Bessey Hall Iowa State University, Ames, IA 50011-1020 USA Phone: 515-294-9756 Fax: 515-294-9420 E-mail: rpwise at iastate.edu _____________________________ http://wiselab.org/ http://barleybase.org/ http://www.plantstress.iastate.edu/ From r.bruskiewich at cgiar.org Tue Mar 23 01:22:48 2004 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Mon, 22 Mar 2004 22:22:48 -0800 Subject: spatial terms Message-ID: <3EA5C75212CDD511B74100508BE0957606DE1E8E@irriphx2.irri.cgiar.org> Why is PATO so far away from implementation? -----Original Message----- From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] Sent: Monday, March 22, 2004 11:15 PM To: POC-dev Subject: spatial terms Hi Everyone, I just now started working on the leaf section and encountered the problem on how do we represent the spatial organization. Since PATO/phenotype attribute ontology is way off from implementation what are our rules on this. here are a few spatial attribute examples which I think are necessary to describe a gene's transcript/protein expression profile or a phenotype. first second third fourth fifth e.g. first leaf second leaf first / second internode first / second node basal uppermost ; synonym:topmost lower upper e.g. basal / uppermost internodes topmost leaves lower floret upper floret primary secondary e.g. primary / secondary panicle branches spikelets of the primary branches From paulien.adamse at wur.nl Tue Mar 23 05:32:16 2004 From: paulien.adamse at wur.nl (Adamse, Paulien) Date: Tue, 23 Mar 2004 11:32:16 +0100 Subject: spatial terms Message-ID: I have been reading this list quietly, but now it is probably appropriate to say something. I checked some of the (Arabidopsis) databases that are related to PlaNet for similar terms in phenotype descriptions of mutants (also going to be annotated with PO terms in the near future). I did not find anything with numbered leaves, internodes, etc. but did find: (expression in) true leaf, cauline leaf, first leaf Paulien Adamse Wageningen www.watdb.nl -----Original Message----- From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org]On Behalf Of Leonore Reiser Sent: Monday, March 22, 2004 20:15 To: po-dev at plantontology.org Subject: Re: spatial terms Maybe it would help to have a description or two to look at? Do they say things like ONLY EXPRESSED IN THE FOURTH INTERNODE? On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > > > Toby Kellogg wrote: > > > I think maize counts from the bottom. so at a minimu we'd have to say > > "internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty > > cumbersome to me. Leonore's question is probably the most relevant - how > > many genes are currently annotated to a specific internode? > > Toby > > > About 5-6 sequenced genes and 40 classical genes identified by > phenotype. Rice does not have may sequenced genes with expression > profile. This trend has just picked up and is much more focussed on the > parts with agronomic value (stem, seed, panicle). > > Pankaj > > > > > >>Toby Kellogg wrote: > >> > >>>I think we need to think hard about what will be gained or lost by > >>>including terms like first second third leaf. The conventions on counting > >>>are different in different plants (e.g top down vs. bottom up), and leaves > >>>with the same number may or may not be comparable. Even among maize > >>>inbreds there is variation in the number of leaves before the > >>>juvenile/adult transition and before flowering. I'd suggest that such > >>>numbering schemes fall into species-specific ontologies and therefore > >>>should be excluded from the general plant ontology. Perhaps this is > >>>something we should discuss at our May meeting. > >>>Toby > >>> > >> > >>I agree with Leonore and Toby on how you count the numbers and how many > >>numbers, based on the germplasm/variety/population type and the species. > >>Looks like we need to comeup with a solution soon. I know in majority of > >>the rice reports the counts are from the top, because often researchers > >>do not see the 1st and 2nd internode/node. > >> > >>To make things simple we can always say that gene-x is expressed in > >>internode. But then we loose the granularity we want to suggest to our > >>user that look the gene is expressed in Second internode ONLY. This is > >>different than assigning it to the generic term internode. > >> > >>I think this issue will keep coming up every now and then, because at > >>Gramene we do not want to maintain two different ontology sets. I guess > >>the same goes with TAIR and MaizeGDB. A generic one from POC and > >>species specific from our own databases. This is too much of work and > >>was also the main reason why we wanted to have this project. > >> > >>Pankaj > >> > >> > >> > >>>>Depends on how you are defining the first leaf- doesnt it. > >>>>Counting from first leaf after the cotyledon (which may or may not be > >>>>formed in the embryo prior to dessication)... > >>>>Leonore > >>>> > >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > >>>> > >>>> > >>>> > >>>>>Hi Everyone, > >>>>> > >>>>>I just now started working on the leaf section and encountered the > >>>>>problem on how do we represent the spatial organization. Since > >>>>>PATO/phenotype attribute ontology is way off from implementation what > >>>>>are our rules on this. > >>>>> > >>>>>here are a few spatial attribute examples which I think are necessary to > >>>>>describe a gene's transcript/protein expression profile or a phenotype. > >>>>> > >>>>> > >>>>>first > >>>>>second > >>>>>third > >>>>>fourth > >>>>>fifth > >>>>> e.g. > >>>>> first leaf > >>>>> second leaf > >>>>> first / second internode > >>>>> first / second node > >>>>>basal > >>>>>uppermost ; synonym:topmost > >>>>>lower > >>>>>upper > >>>>> e.g. > >>>>> basal / uppermost internodes > >>>>> topmost leaves > >>>>> lower floret > >>>>> upper floret > >>>>>primary > >>>>>secondary > >>>>> e.g. > >>>>> primary / secondary panicle branches > >>>>> spikelets of the primary branches > >>>>> > >>>>> > > > > > > > > Elizabeth A. Kellogg > > Department of Biology > > University of Missouri-St. Louis > > 8001 Natural Bridge Road > > St. Louis, MO 63121 > > phone: 314-516-6217 > > fax: 314-516-6233 > > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > > > > > > -- > ****************************** > Pankaj Jaiswal, PhD > Gramene Database > Department of Plant Breeding > G-15 Bradfield Hall > Cornell University > Ithaca, NY-14853 > > tel: +1-607-255-3103 > fax: +1-607-255-6683 > web: http://www.gramene.org > ***************************** > > ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- From pj37 at cornell.edu Tue Mar 23 10:30:45 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 23 Mar 2004 10:30:45 -0500 Subject: spatial terms In-Reply-To: <3EA5C75212CDD511B74100508BE0957606DE1E8E@irriphx2.irri.cgiar.org> References: <3EA5C75212CDD511B74100508BE0957606DE1E8E@irriphx2.irri.cgiar.org> Message-ID: <40605825.9010001@cornell.edu> Hi Richard, We have just started this exploration exercise and would like to wait on committing something that requires more of our efforts. Best Pankaj Bruskiewich, Richard (IRRI) wrote: > Why is PATO so far away from implementation? > > -----Original Message----- > From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] > Sent: Monday, March 22, 2004 11:15 PM > To: POC-dev > Subject: spatial terms > > > Hi Everyone, > > I just now started working on the leaf section and encountered the problem > on how do we represent the spatial organization. Since PATO/phenotype > attribute ontology is way off from implementation what are our rules on > this. > > here are a few spatial attribute examples which I think are necessary to > describe a gene's transcript/protein expression profile or a phenotype. > > > first > second > third > fourth > fifth > e.g. > first leaf > second leaf > first / second internode > first / second node > basal > uppermost ; synonym:topmost > lower > upper > e.g. > basal / uppermost internodes > topmost leaves > lower floret > upper floret > primary > secondary > e.g. > primary / secondary panicle branches > spikelets of the primary branches > > > -- ****************************** Pankaj Jaiswal, PhD Gramene Database Department of Plant Breeding G-15 Bradfield Hall Cornell University Ithaca, NY-14853 tel: +1-607-255-3103 fax: +1-607-255-6683 web: http://www.gramene.org ***************************** From Leszek at missouri.edu Tue Mar 23 14:15:12 2004 From: Leszek at missouri.edu (Vincent, Leszek) Date: Tue, 23 Mar 2004 13:15:12 -0600 Subject: spatial terms Message-ID: Colleagues, Leonore's question is very relevant ('how many genes are currently annotated to a specific internode?') for it cites the need to annotate genes to 'body parts' e.g. internodes. Pankaj's comments about rice leaf position (top down counting) & Toby's comments about 'sensu...' being cumbersome & the suggestion that "such numbering schemes fall into species-specific ontologies and therefore should be excluded from the general plant ontology." - and Sue's counter to the latter point. And Pankaj's comments: "I think this issue will keep coming up every now and then, because at Gramene we do not want to maintain two different ontology sets. I guess the same goes with TAIR and MaizeGDB. A generic one from POC and species specific from our own databases. This is too much of work and was also the main reason why we wanted to have this project." All these perspectives point to our wrestling with how to incorporate the complex diversity of plant structure into a general/composite plant ontology. OK - nothing new here - but please consider the following contribution. This is an important discussion because it again points to the sophistication of the foundation upon which we are building the PO which in turn will probably determine the acceptance (or otherwise) of the PO controlled vocabulary by the plant science community. Having a single plant ontology which accommodates the needed diversity of plant structure for many taxa vs a simplified (consensus) ontology & separate species specific ontologies are two rather different paradigms. My understanding of the mandate of the POC is that it was focusing on the former & not the latter. Am I wrong? Why does it seem to be a stumbling block to include taxon-specific plant structure vocabulary (where needed) in our PO product? I look forward to discussing this matter further (at the May meeting - hopefully before then). - Leszek ------- Optional reading: A little detail on the complexity of leaf position nomenclature for Zea mays: In maize (Zea mays a member of the grass family, Poaceae) there appear to be 2 'nomenclatures' that are used: 1. Juvenile leaves vs adult leaves 2. Leaf Number (L), counting the non-leaf coleoptile as zero and Plastochron Number (P), counting the established but predivision meristematic founder cells as zero (complex? rather!). Toby mentioned the first system in her earlier email. The second system may seem more tricky than the first BUT there's some counter-intuition in the first system. How? Well, the term "Juvenile leaves" has a distinct developmental tag in that juvenile leaves arise earlier and in a more basal position than the younger, more adult leaves (quoting from Freeling & Lane, Ch3 in The Maize Handbook). In MaizeGDB there are 10,708 ESTs associated with 'juvenile leaf' & 8,789 ESTs associated with adult tissue (incl. adult leaves). At present MaizeGDB is not using explicitly using a leaf number system, counting from the bottom up, but this is implicit in the use of juvenile & adult leaves. Using the L & P convention, L10, P3 would be referring to the tenth leaf above the coleoptile when the leaf is the third leaf from the meristem (a leaf at approx. 4 mm primordial devel. stage). There are a few publications using the L & P nomenclature but no use of it (YET) in MaizeGDB. *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Plant Science Unit Dept. of Agronomy 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850 Email: Leszek at missouri.edu Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 Associate Curator, Dunn-Palmer Herbarium (UMO) Research Associate, Missouri Botanical Garden (MO), USA *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > -----Original Message----- > From: owner-po-dev at brie4.cshl.org > [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Roger Wise > Sent: Monday, March 22, 2004 3:27 PM > To: po-dev at plantontology.org > Subject: Re: spatial terms > > > It seems to make sense to me to count from the bottom, because in > many global expression studies, tissue is harvested, or dissected, > before maturity. It is also important to have these stages > well-defined, possibly species specific, because, again, in global > expression studies, hundreds of genes are differentially expressed > between specific stages or tissues (including anthers from upper and > lower florets). At least for this particular application, and in the > foreseeable future (eg. laser capture) more detail is better. As for > cultivar differences, this should be defined by stating the cultivar > along with the definition. > > Roger > > At 2:05 PM -0500 3/22/04, Toby Kellogg wrote: > >I think maize counts from the bottom. so at a minimu we'd > have to say > >"internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty > >cumbersome to me. Leonore's question is probably the most > relevant - > >how many genes are currently annotated to a specific internode? Toby > > > >>Toby Kellogg wrote: > >>> I think we need to think hard about what will be gained > or lost by > >>> including terms like first second third leaf. The > conventions on counting > >>> are different in different plants (e.g top down vs. > bottom up), and > >>> leaves with the same number may or may not be comparable. Even > >>> among maize inbreds there is variation in the number of leaves > >>> before the juvenile/adult transition and before flowering. I'd > >>> suggest that such numbering schemes fall into species-specific > >>> ontologies and therefore should be excluded from the > general plant > >>> ontology. Perhaps this is something we should discuss > at our May > >>> meeting. Toby > >>> > >> > >>I agree with Leonore and Toby on how you count the numbers and how > >>many numbers, based on the germplasm/variety/population > type and the > >>species. Looks like we need to comeup with a solution soon. > I know in > >>majority of the rice reports the counts are from the top, because > >>often researchers do not see the 1st and 2nd internode/node. > >> > >>To make things simple we can always say that gene-x is expressed in > >>internode. But then we loose the granularity we want to > suggest to our > >>user that look the gene is expressed in Second internode > ONLY. This is > >>different than assigning it to the generic term internode. > >> > >>I think this issue will keep coming up every now and then, > because at > >>Gramene we do not want to maintain two different ontology sets. I > >>guess the same goes with TAIR and MaizeGDB. A generic one from POC > >>and species specific from our own databases. This is too > much of work > >>and was also the main reason why we wanted to have this project. > >> > >>Pankaj > >> > >> > >>> > >>>>Depends on how you are defining the first leaf- doesnt > it. Counting > >>>>from first leaf after the cotyledon (which may or may not > be formed > >>>>in the embryo prior to dessication)... Leonore > >>>> > >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: > >>>> > >>>> > >>>>>Hi Everyone, > >>>>> > >>>>>I just now started working on the leaf section and > encountered the > >>>>>problem on how do we represent the spatial organization. Since > >>>>>PATO/phenotype attribute ontology is way off from implementation > >>>>>what are our rules on this. > >>>>> > >>>>>here are a few spatial attribute examples which I think are > >>>>>necessary to describe a gene's transcript/protein expression > >>>>>profile or a phenotype. > >>>>> > >>>>> > >>>>>first > >>>>>second > >>>>>third > >>>>>fourth > >>>>>fifth > >>>>> e.g. > >>>>> first leaf > >>>>> second leaf > >>>>> first / second internode > >>>>> first / second node > >>>>>basal > >>>>>uppermost ; synonym:topmost > >>>>>lower > >>>>>upper > >>>>> e.g. > >>>>> basal / uppermost internodes > >>>>> topmost leaves > >>>>> lower floret > >>>>> upper floret > >>>>>primary > >>>>>secondary > >>>>> e.g. > >>>>> primary / secondary panicle branches > >>>>> spikelets of the primary branches > >>>>> > >>>>> > > > > > >Elizabeth A. Kellogg > >Department of Biology > >University of Missouri-St. Louis > >8001 Natural Bridge Road > >St. Louis, MO 63121 > >phone: 314-516-6217 > >fax: 314-516-6233 > >http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > -- > _____________________________ > Roger Wise, USDA-ARS > Department of Plant Pathology > 411 Bessey Hall > Iowa State University, Ames, IA > 50011-1020 USA > Phone: 515-294-9756 > Fax: 515-294-9420 > E-mail: rpwise at iastate.edu > _____________________________ > http://wiselab.org/ > http://barleybase.org/ > http://www.plantstress.iastate.edu/ > From peter.stevens at mobot.org Tue Mar 23 15:09:41 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Tue, 23 Mar 2004 16:09:41 -0400 Subject: spatial terms In-Reply-To: References: Message-ID: >I thought the general point of this whole operation was to have a >general onotology so that indeed different people can talk to one >another without needing a translator. Our chaotic terminology is >one of the major taxonomic impediments, to say nothing of other >problems it causes.. Peter S. >Colleagues, > >Leonore's question is very relevant ('how many genes are currently >annotated to a specific internode?') for it cites the need to annotate >genes to 'body parts' e.g. internodes. Pankaj's comments about rice leaf >position (top down counting) & Toby's comments about 'sensu...' being >cumbersome & the suggestion that "such numbering schemes fall into >species-specific ontologies and therefore should be excluded from the >general plant ontology." - and Sue's counter to the latter point. And >Pankaj's comments: "I think this issue will keep coming up every now and >then, because at Gramene we do not want to maintain two different >ontology sets. I guess >the same goes with TAIR and MaizeGDB. A generic one from POC and >species specific from our own databases. This is too much of work and >was also the main reason why we wanted to have this project." All these >perspectives point to our wrestling with how to incorporate the complex >diversity of plant structure into a general/composite plant ontology. OK >- nothing new here - but please consider the following contribution. > >This is an important discussion because it again points to the >sophistication of the foundation upon which we are building the PO which >in turn will probably determine the acceptance (or otherwise) of the PO >controlled vocabulary by the plant science community. Having a single >plant ontology which accommodates the needed diversity of plant >structure for many taxa vs a simplified (consensus) ontology & separate >species specific ontologies are two rather different paradigms. My >understanding of the mandate of the POC is that it was focusing on the >former & not the latter. Am I wrong? Why does it seem to be a stumbling >block to include taxon-specific plant structure vocabulary (where >needed) in our PO product? I look forward to discussing this matter >further (at the May meeting - hopefully before then). > >- Leszek >------- >Optional reading: A little detail on the complexity of leaf position >nomenclature for Zea mays: > >In maize (Zea mays a member of the grass family, Poaceae) there appear >to be 2 'nomenclatures' that are used: 1. Juvenile leaves vs adult >leaves 2. Leaf Number (L), counting the non-leaf coleoptile as zero and >Plastochron Number (P), counting the established but predivision >meristematic founder cells as zero (complex? rather!). Toby mentioned >the first system in her earlier email. > >The second system may seem more tricky than the first BUT there's some >counter-intuition in the first system. How? Well, the term "Juvenile >leaves" has a distinct developmental tag in that juvenile leaves arise >earlier and in a more basal position than the younger, more adult leaves >(quoting from Freeling & Lane, Ch3 in The Maize Handbook). In MaizeGDB >there are 10,708 ESTs associated with 'juvenile leaf' & 8,789 ESTs >associated with adult tissue (incl. adult leaves). At present MaizeGDB >is not using explicitly using a leaf number system, counting from the >bottom up, but this is implicit in the use of juvenile & adult leaves. > >Using the L & P convention, L10, P3 would be referring to the tenth leaf >above the coleoptile when the leaf is the third leaf from the meristem >(a leaf at approx. 4 mm primordial devel. stage). There are a few >publications using the L & P nomenclature but no use of it (YET) in >MaizeGDB. > >*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* >P. Leszek D. Vincent Ph.D., FLS >Plant Science Unit >Dept. of Agronomy >215 Curtis Hall >University of Missouri-Columbia >Columbia >MO 65211-7020 >USA >Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850 >Email: Leszek at missouri.edu >Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 >Associate Curator, Dunn-Palmer Herbarium (UMO) >Research Associate, Missouri Botanical Garden (MO), USA >*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > >> -----Original Message----- >> From: owner-po-dev at brie4.cshl.org >> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Roger Wise >> Sent: Monday, March 22, 2004 3:27 PM >> To: po-dev at plantontology.org >> Subject: Re: spatial terms >> >> >> It seems to make sense to me to count from the bottom, because in >> many global expression studies, tissue is harvested, or dissected, >> before maturity. It is also important to have these stages >> well-defined, possibly species specific, because, again, in global >> expression studies, hundreds of genes are differentially expressed >> between specific stages or tissues (including anthers from upper and >> lower florets). At least for this particular application, and in the >> foreseeable future (eg. laser capture) more detail is better. As for >> cultivar differences, this should be defined by stating the cultivar >> along with the definition. >> >> Roger >> >> At 2:05 PM -0500 3/22/04, Toby Kellogg wrote: >> >I think maize counts from the bottom. so at a minimu we'd >> have to say >> >"internode 3 sensu maize" or "internode 3 sensu rice". Seems pretty >> >cumbersome to me. Leonore's question is probably the most >> relevant - >> >how many genes are currently annotated to a specific internode? Toby >> > >> >>Toby Kellogg wrote: >> >>> I think we need to think hard about what will be gained >> or lost by >> >>> including terms like first second third leaf. The >> conventions on counting >> >>> are different in different plants (e.g top down vs. >> bottom up), and >> >>> leaves with the same number may or may not be comparable. Even >> >>> among maize inbreds there is variation in the number of leaves >> >>> before the juvenile/adult transition and before flowering. I'd >> >>> suggest that such numbering schemes fall into species-specific >> >>> ontologies and therefore should be excluded from the >> general plant >> >>> ontology. Perhaps this is something we should discuss >> at our May >> >>> meeting. Toby >> >>> >> >> >> >>I agree with Leonore and Toby on how you count the numbers and how >> >>many numbers, based on the germplasm/variety/population >> type and the >> >>species. Looks like we need to comeup with a solution soon. >> I know in >> >>majority of the rice reports the counts are from the top, because >> >>often researchers do not see the 1st and 2nd internode/node. >> >> >> >>To make things simple we can always say that gene-x is expressed in >> >>internode. But then we loose the granularity we want to >> suggest to our >> >>user that look the gene is expressed in Second internode >> ONLY. This is >> >>different than assigning it to the generic term internode. >> >> >> >>I think this issue will keep coming up every now and then, >> because at >> >>Gramene we do not want to maintain two different ontology sets. I >> >>guess the same goes with TAIR and MaizeGDB. A generic one from POC >> >>and species specific from our own databases. This is too >> much of work >> >>and was also the main reason why we wanted to have this project. >> >> >> >>Pankaj >> >> >> >> >> >>> >> >>>>Depends on how you are defining the first leaf- doesnt >> it. Counting >> >>>>from first leaf after the cotyledon (which may or may not >> be formed >> >>>>in the embryo prior to dessication)... Leonore >> >>>> >> >>>>On Mon, 22 Mar 2004, Pankaj Jaiswal wrote: >> >>>> >> >>>> >> >>>>>Hi Everyone, >> >>>>> >> >>>>>I just now started working on the leaf section and >> encountered the >> >>>>>problem on how do we represent the spatial organization. Since >> >>>>>PATO/phenotype attribute ontology is way off from implementation >> >>>>>what are our rules on this. >> >>>>> >> >>>>>here are a few spatial attribute examples which I think are >> >>>>>necessary to describe a gene's transcript/protein expression >> >>>>>profile or a phenotype. >> >>>>> >> >>>>> >> >>>>>first >> >>>>>second >> >>>>>third >> >>>>>fourth >> >>>>>fifth >> >>>>> e.g. >> >>>>> first leaf >> >>>>> second leaf >> >>>>> first / second internode >> >>>>> first / second node >> >>>>>basal >> >>>>>uppermost ; synonym:topmost >> >>>>>lower > > >>>>>upper >> >>>>> e.g. >> >>>>> basal / uppermost internodes >> >>>>> topmost leaves >> >>>>> lower floret >> >>>>> upper floret >> >>>>>primary >> >>>>>secondary >> >>>>> e.g. >> >>>>> primary / secondary panicle branches >> >>>>> spikelets of the primary branches >> >>>>> >> >>>>> >> > >> > >> >Elizabeth A. Kellogg >> >Department of Biology >> >University of Missouri-St. Louis >> >8001 Natural Bridge Road >> >St. Louis, MO 63121 >> >phone: 314-516-6217 >> >fax: 314-516-6233 >> >http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ >> >> >> -- >> _____________________________ >> Roger Wise, USDA-ARS >> Department of Plant Pathology >> 411 Bessey Hall >> Iowa State University, Ames, IA >> 50011-1020 USA >> Phone: 515-294-9756 >> Fax: 515-294-9420 >> E-mail: rpwise at iastate.edu >> _____________________________ >> http://wiselab.org/ >> http://barleybase.org/ >> http://www.plantstress.iastate.edu/ >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.bruskiewich at cgiar.org Tue Mar 23 21:26:14 2004 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Tue, 23 Mar 2004 18:26:14 -0800 Subject: spatial terms Message-ID: <3EA5C75212CDD511B74100508BE0957606EDCCB6@irriphx2.irri.cgiar.org> Hi Pankaj, I'd be willing at our end to explore the PATO framework a bit further, both in software/database terms and in terms of curation, to better cataloging rice mutant phenotypes (starting with IRRI's IR64 mutants) :-)) Cheers Richard -----Original Message----- From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] Sent: Tuesday, March 23, 2004 11:31 PM To: po-dev at plantontology.org Subject: Re: spatial terms Hi Richard, We have just started this exploration exercise and would like to wait on committing something that requires more of our efforts. Best Pankaj Bruskiewich, Richard (IRRI) wrote: > Why is PATO so far away from implementation? > > -----Original Message----- > From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] > Sent: Monday, March 22, 2004 11:15 PM > To: POC-dev > Subject: spatial terms > > > Hi Everyone, > > I just now started working on the leaf section and encountered the > problem on how do we represent the spatial organization. Since > PATO/phenotype attribute ontology is way off from implementation what > are our rules on this. > > here are a few spatial attribute examples which I think are necessary > to describe a gene's transcript/protein expression profile or a phenotype. > > > first > second > third > fourth > fifth > e.g. > first leaf > second leaf > first / second internode > first / second node > basal > uppermost ; synonym:topmost > lower > upper > e.g. > basal / uppermost internodes > topmost leaves > lower floret > upper floret > primary > secondary > e.g. > primary / secondary panicle branches > spikelets of the primary branches > > > -- ****************************** Pankaj Jaiswal, PhD Gramene Database Department of Plant Breeding G-15 Bradfield Hall Cornell University Ithaca, NY-14853 tel: +1-607-255-3103 fax: +1-607-255-6683 web: http://www.gramene.org ***************************** From pj37 at cornell.edu Wed Mar 24 14:41:21 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 24 Mar 2004 14:41:21 -0500 (EST) Subject: spatial terms In-Reply-To: <3EA5C75212CDD511B74100508BE0957606EDCCB6@irriphx2.irri.cgiar.org> References: <3EA5C75212CDD511B74100508BE0957606EDCCB6@irriphx2.irri.cgiar.org> Message-ID: <3654.24.59.74.148.1080157281.squirrel@webmail.cornell.edu> Hi Richard, This is great. May be we can learn something from your experience. Cheers Pankaj Bruskiewich, Richard (IRRI) said: > Hi Pankaj, > > I'd be willing at our end to explore the PATO framework a bit further, > both > in software/database terms and in terms of curation, to better cataloging > rice mutant phenotypes (starting with IRRI's IR64 mutants) :-)) > > Cheers > Richard > > -----Original Message----- > From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] > Sent: Tuesday, March 23, 2004 11:31 PM > To: po-dev at plantontology.org > Subject: Re: spatial terms > > Hi Richard, > > We have just started this exploration exercise and would like to wait on > committing something that requires more of our efforts. > > Best > Pankaj > > Bruskiewich, Richard (IRRI) wrote: > >> Why is PATO so far away from implementation? >> > > > > > >> -----Original Message----- >> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] >> Sent: Monday, March 22, 2004 11:15 PM >> To: POC-dev >> Subject: spatial terms >> >> >> Hi Everyone, >> >> I just now started working on the leaf section and encountered the >> problem on how do we represent the spatial organization. Since >> PATO/phenotype attribute ontology is way off from implementation what >> are our rules on this. >> >> here are a few spatial attribute examples which I think are necessary >> to describe a gene's transcript/protein expression profile or a >> phenotype. >> >> >> first >> second >> third >> fourth >> fifth >> e.g. >> first leaf >> second leaf >> first / second internode >> first / second node >> basal >> uppermost ; synonym:topmost >> lower >> upper >> e.g. >> basal / uppermost internodes >> topmost leaves >> lower floret >> upper floret >> primary >> secondary >> e.g. >> primary / secondary panicle branches >> spikelets of the primary branches >> >> >> > > -- > ****************************** > Pankaj Jaiswal, PhD > Gramene Database > Department of Plant Breeding > G-15 Bradfield Hall > Cornell University > Ithaca, NY-14853 > > tel: +1-607-255-3103 > fax: +1-607-255-6683 > web: http://www.gramene.org > ***************************** > > -- Pankaj Jaiswal Gramene Database www.gramene.org From fzqhd at studentmail.umsl.edu Mon Mar 29 17:26:54 2004 From: fzqhd at studentmail.umsl.edu (Felipe Zapata) Date: Mon, 29 Mar 2004 16:26:54 -0600 Subject: Botany meeting: Abstracts Message-ID: <2EB4E588-81D0-11D8-8458-000A95AF2466@studentmail.umsl.edu> Hello, I am sending the abstracts for the 2 presentations we (Peter, Toby and I) are planning to give at Botany 2004 (Botanical Society of America/American Society of Plant Taxonomists/American Fern Society/American Bryological and Lichenological Society). Toby or Peter would give the first talk and I would give the second one. Please send us your comments. Thanks, Felipe Overview of the Plant Ontology Consortium: goals and general structure. Kellogg etc. As genomic data accumulate, databases have been established to coordinate and disseminate information about specific plant species, primarily Arabidopsis (The Arabidopsis Information Resource, TAIR), rice (OryzaBase and Gramene), and maize (Maize Genome Database, MaizeGDGB), although others exist for other species as well.? One goal of these databases is to provide an index of genes, such that a user could, for example, find all genes known to affect fruit morphology, or all genes known to be expressed in young roots.? However, the databases have developed largely independently of each other, so that descriptions of phenotypes are not uniform. Searching TAIR with the word "fruit" will produce no results, because all fruit-related genes are connected to the word "silique," and in Gramene a similar search would have to be conducted using the word "caryopsis."? The Plant Ontology Consortium (POC) is a collaborative effort that will provide a standard vocabulary to be applied across multiple plant databases, such that one could search each one using the same descriptor. The POC (www.plantontology.org) currently involves several plant databases and workers in plant systematics, development and genomics.? Our first efforts are to unite terminology for Arabidopsis and the cereals; in subsequent years we will expand the descriptors as necessary to include tomato and legumes, and we will develop ontologies for describing plant growth and developmental stages.? The goal is to provide a set of "bins" into which genes and associated phenotypes can be placed.? The Plant Ontology is not designed to recapitulate or replace the entire rich vocabulary of plant taxonomy. It will also not provide a full set of morphological descriptors, although those it uses will be familiar.? Rather it will provide a framework for connecting genotypic data with phenotypes in a way that permits comparisons across databases and among plants. The project is supported by National Science Foundation grant No. 0321666 to the Plant Ontology Consortium. Developing the Plant Ontology: examples and computational tools F. Zapata, et al. The Plant Ontology follows an existing structure and set of rules already developed for the Gene Ontology. It includes a set of terms related according to a Directed Acyclic Graph (DAG), in which parent terms can have multiple children (like a conventional hierarchy), but child terms can also have multiple parents (unlike a strict hierarchy or classification). For example, the gynoecium (a parent term) is composed of carpel, ovary, style and stigma (all of them child terms). A carpel is also a particular kind of modified leaf, a megasporophyll. Hence, carpel, a child term, has multiple parents: gynoecium and megasporophyll. The resulting structure is quite flexible and can accommodate plant morphological data that are not strictly hierarchical in nature. For instance, some wholes cannot be defined exhaustively by their parts; not all embryos have cotyledons, and the only thing common to all embryos would be a mass of four cells. We use the computer program DAG Edit, an application that creates and maintains the files in a standard format for describing and modifying DAGs (DAG-edit format). Individual members of the consortium are assigned particular sets of terms (nodes) in the hierarchy. The hierarchy is not intended to be exhaustive even for the organisms currently under focus, but care is taken not to label nodes in such a way that subsequent inclusion of plants with very different morphologies will necessitate a restructuring of the hierachy. As portions of the ontology are drafted they are submitted to the CVS (control version system) repository, where all versions of the working files and documents are stored. There they can be viewed, compared with older versions, discussed and edited simultaneously by all members of the group. The project is supported by National Science Foundation grant No. 0321666 to the Plant Ontology Consortium. ~~~~~~ Felipe Zapata University of Missouri St. Louis Department of Biology 8001 Natural Bridge Rd. St. Louis, MO 63121 314 516-6200 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 4681 bytes Desc: not available URL: From katica at acoma.Stanford.EDU Mon Mar 29 19:32:18 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 29 Mar 2004 16:32:18 -0800 (PST) Subject: Botany meeting: Abstracts In-Reply-To: <2EB4E588-81D0-11D8-8458-000A95AF2466@studentmail.umsl.edu> Message-ID: Hi Felipe, I tried sending you the world document of my comments on abstracts thorugh the Explorer, but it failed for (to me) unknown reasons, so here is the txt attachement (unfortunately you can't see the red lines of what I added), and instead of the PDF of Sue's review in NRG (that I thought might be helpful to you), here is the URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Search&DB=PubMed. I hope this helps. As for my suggestions, take what you like and leave out what you don't. Italicized were (those are now in brackets), just my comments, they don't belong to the body of the abstract. I'll try to send you the proper doc file with my comments again later. Cheers, Katica P.S. I am going to take a look at your updated anatomy ontology right now. On Mon, 29 Mar 2004, Felipe Zapata wrote: > Hello, > > I am sending the abstracts for the 2 presentations we (Peter, Toby and > I) are planning to give at Botany 2004 (Botanical Society of > America/American Society of Plant Taxonomists/American Fern > Society/American Bryological and Lichenological Society). Toby or Peter > would give the first talk and I would give the second one. > > Please send us your comments. > > Thanks, > > Felipe > > Overview of the Plant Ontology Consortium: goals and general structure. > Kellogg etc. > > As genomic data accumulate, databases have been established to > coordinate and disseminate information about specific plant species, > primarily Arabidopsis (The Arabidopsis Information Resource, TAIR), > rice (OryzaBase and Gramene), and maize (Maize Genome Database, > MaizeGDGB), although others exist for other species as well.? One goal > of these databases is to provide an index of genes, such that a user > could, for example, find all genes known to affect fruit morphology, or > all genes known to be expressed in young roots.? However, the databases > have developed largely independently of each other, so that > descriptions of phenotypes are not uniform. Searching TAIR with the > word "fruit" will produce no results, because all fruit-related genes > are connected to the word "silique," and in Gramene a similar search > would have to be conducted using the word "caryopsis."? The Plant > Ontology Consortium (POC) is a collaborative effort that will provide a > standard vocabulary to be applied across multiple plant databases, such > that one could search each one using the same descriptor. The POC > (www.plantontology.org) currently involves several plant databases and > workers in plant systematics, development and genomics.? Our first > efforts are to unite terminology for Arabidopsis and the cereals; in > subsequent years we will expand the descriptors as necessary to include > tomato and legumes, and we will develop ontologies for describing plant > growth and developmental stages.? The goal is to provide a set of > "bins" into which genes and associated phenotypes can be placed.? The > Plant Ontology is not designed to recapitulate or replace the entire > rich vocabulary of plant taxonomy. It will also not provide a full set > of morphological descriptors, although those it uses will be familiar.? > Rather it will provide a framework for connecting genotypic data with > phenotypes in a way that permits comparisons across databases and among > plants. > The project is supported by National Science Foundation grant No. > 0321666 to the Plant Ontology Consortium. > > Developing the Plant Ontology: examples and computational tools > F. Zapata, et al. > > The Plant Ontology follows an existing structure and set of rules > already developed for the Gene Ontology. It includes a set of terms > related according to a Directed Acyclic Graph (DAG), in which parent > terms can have multiple children (like a conventional hierarchy), but > child terms can also have multiple parents (unlike a strict hierarchy > or classification). For example, the gynoecium (a parent term) is > composed of carpel, ovary, style and stigma (all of them child terms). > A carpel is also a particular kind of modified leaf, a megasporophyll. > Hence, carpel, a child term, has multiple parents: gynoecium and > megasporophyll. The resulting structure is quite flexible and can > accommodate plant morphological data that are not strictly hierarchical > in nature. For instance, some wholes cannot be defined exhaustively by > their parts; not all embryos have cotyledons, and the only thing common > to all embryos would be a mass of four cells. We use the computer > program DAG Edit, an application that creates and maintains the files > in a standard format for describing and modifying DAGs (DAG-edit > format). Individual members of the consortium are assigned particular > sets of terms (nodes) in the hierarchy. The hierarchy is not intended > to be exhaustive even for the organisms currently under focus, but care > is taken not to label nodes in such a way that subsequent inclusion of > plants with very different morphologies will necessitate a > restructuring of the hierachy. As portions of the ontology are drafted > they are submitted to the CVS (control version system) repository, > where all versions of the working files and documents are stored. There > they can be viewed, compared with older versions, discussed and edited > simultaneously by all members of the group. > The project is supported by National Science Foundation grant No. > 0321666 to the Plant Ontology Consortium. > > > > ~~~~~~ > Felipe Zapata > University of Missouri St. Louis > Department of Biology > 8001 Natural Bridge Rd. > St. Louis, MO 63121 > 314 516-6200 -------------------------------------------------------------------------- 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. -------------------------------------------------------------------------- -------------- next part -------------- (Note: I don't have any suggestion in this one) I. Abstract: Overview of the Plant Ontology Consortium: goals and general structure. Kellogg etc. As genomic data accumulate, databases have been established to coordinate and disseminate information about specific plant species, primarily Arabidopsis (The Arabidopsis Information Resource, TAIR), rice (OryzaBase and Gramene), and maize (Maize Genome Database, MaizeGDGB), although others exist for other species as well. One goal of these databases is to provide an index of genes, such that a user could, for example, find all genes known to affect fruit morphology, or all genes known to be expressed in young roots. However, the databases have developed largely independently of each other, so that descriptions of phenotypes are not uniform. Searching TAIR with the word "fruit" will produce no results, because all fruit-related genes are connected to the word "silique," and in Gramene a similar search would have to be conducted using the word "caryopsis." The Plant Ontology Consortium (POC) is a collaborative effort that will provide a standard vocabulary to be applied across multiple plant databases, such that one could search each one using the same descriptor. The POC (www.plantontology.org) currently involves several plant databases and workers in plant systematics, development and genomics. Our first efforts are to unite terminology for Arabidopsis and the cereals; in subsequent years we will expand the descriptors as necessary to include tomato and legumes, and we will develop ontologies for describing plant growth and developmental stages. The goal is to provide a set of "bins" into which genes and associated phenotypes can be placed. The Plant Ontology is not designed to recapitulate or replace the entire rich vocabulary of plant taxonomy. It will also not provide a full set of morphological descriptors, although those it uses will be familiar. Rather it will provide a framework for connecting genotypic data with phenotypes in a way that permits comparisons across databases and among plants. The project is supported by National Science Foundation grant No. 0321666 to the Plant Ontology Consortium. II Abstract: Developing the Plant Ontologies: examples and computational tools F. Zapata, et al. (Note: Perhaps you may want to add an introductory sentence here on POC.) The Plant Ontology follows an existing structure and set of rules already developed by the Gene Ontology Consortium (http://www.geneontology.org/). It includes a set of terms arranged in a structure called Directed Acyclic Graph (DAG), in which parent terms can have multiple children (like a conventional hierarchy), but child terms can also have multiple parents (unlike a simple hierarchy or classification). Also, children are not allowed to be their own ancestors; hence cycles are forbidden. For example, the gynoecium (a parent term) is composed of carpel, ovary, style and stigma (all of them child terms). A carpel is also a particular kind of modified leaf, a megasporophyll. Hence, carpel, a child term, has multiple parents: gynoecium and megasporophyll. The resulting structure is quite flexible and can accommodate plant morphological data that are not strictly hierarchical in nature. For instance, some wholes cannot be defined exhaustively by their parts; not all embryos have cotyledons, and the only thing common to all embryos would be a mass of four cells. We use the ontology editing tool, DAG Edit (available from SourceForge.net), for creating and editing plant ontology files in a standard flat file format. Individual members of the POC consortium are assigned particular sets of terms (nodes) in the hierarchy. The hierarchy is not intended to be exhaustive even for the organisms currently under focus, but care is taken not to label nodes in such a way that subsequent inclusion of plants with very different morphologies will necessitate a restructuring of the hierarchy. As portions of the ontology are drafted they are submitted to the CVS (control version system) repository, where all versions of the working files and documents are stored. There they can be viewed, compared with older versions, discussed and edited simultaneously by all members of the group. (This last part is a bit too technical, to me at least, considering the audience. It would be just fine if it's shorter. I would rather like to see an info on where to find and download the plant ontologies, i.e., availability of PO.) The project is supported by National Science Foundation grant No. 0321666 to the Plant Ontology Consortium. (Note: You may also want to mention different relationship types, instance_of, a, part_of and develops_from, and perhaps synonyms too.) From katica at acoma.Stanford.EDU Wed Mar 31 22:00:25 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 31 Mar 2004 19:00:25 -0800 (PST) Subject: cell type node Message-ID: Hello all, Here is my cell type node (anatomy and definition file). So far, 70 terms, with definitions mostly from K Esau. Please take a look, if it's good (as I believe so), I'll import it to the anatomy ontology. IDs are temporary, all the terms will have proper PO ID numbers once I import this node to PO file. Pankaj and Felipe, thanks for the earlier comments. Please, delete the old version, this one has more hierarchy. A short question: Are epithem cell and epithelium cell children of secretory cell? Katica -------------------------------------------------------------------------- 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. -------------------------------------------------------------------------- -------------- next part -------------- !version: $Revision: 1.24 $ !date: Wed Mar 31 18:15:51 PST 2004 !saved-by: Katica Ilic !autogenerated-by: DAG-Edit version 1.410 ! !Gene Ontology definitions ! term: antipodal cell goid: TAIR:0000192 definition: cells located at the chalazal end of the mature embryo sac in angiosperms definition_reference: ISBN:047125208 term: apical cell goid: KI:0004000 definition: The single cell that occupies the distal position in an apical meristem of root or shoot and is usually interpreted as the initial cell in the apical meristem. definition_reference: ISBN:0471245208 term: atrichoblast goid: TAIR:0000263 definition: A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair definition_reference: ISBN:0387987819 term: axial cell goid: TAIR:0000081 definition: A secondary vascular cell derived from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system. definition_reference: ISBN:0471245208 term: bulliform cell goid: KI:0004001 definition: An enlarged epidermal cell present, with other similar cells, in longitudinal rows in leaves of grasses. Also called motor cell because of its presumed participation in the mechanism of rolling and unrolling of leaves. definition_reference: ISBN:0471245208 term: cambial initial goid: TAIR:0000295 definition: Cells so localized in the vascular cambium or phellogen that their periclinal divisions can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells). definition_reference: ISBN:0471245208 term: central cell goid: TAIR:0000194 definition: cell type containing the two polar nuclei which, after double fertilization, will develop into the endosperm. definition_reference: TAIR:lr term: chlorenchyma cell goid: TAIR:0000076 definition: Parenchyma cells containng chloroplasts; a component of leaf mesophyll and other green parenchyma tissue. definition_reference: ISBN:0471245208 term: collenchyma cell goid: TAIR:0000075 definition: Elongated living cells with unevenly thickened nonlignified primary walls. definition_reference: ISBN:0471245208 term: companion cell goid: TAIR:0000071 definition: A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member. definition_reference: ISBN:0879015322 term: contact cell goid: KI:0004002 definition: An axial parenchyma or a ray cell physiologically associated with a tracheary element. Also a cell next to a stoma. definition_reference: ISBN:0471245208 term: cork cell goid: KI:0004003 definition: A phellem cell derived from the phellogen, nonliving at maturity, and having suberized walls; protective in function because the walls are highly impervious to water. definition_reference: ISBN:0471245208 term: degenerate megaspore goid: TAIR:0000245 definition: in monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis. definition_reference: TAIR:lr term: egg cell goid: TAIR:0000190 definition: the female gamete definition_reference: TAIR:lr term: epidermal cell goid: KI:0004013 definition: Cell that constitutes dermal tissue. definition_reference: TAIR:KI term: epidermal initial goid: TAIR:0000349 definition: a relatively unspecialized cell that will give rise to specialized cell types of the epidermis. definition_reference: TAIR:lr term: epithelium cell goid: KI:0004004 definition: A compact layer of cells, often secretory in function, covering a free surface or lining a cavity. definition_reference: ISBN:0471245208 term: epithem cell goid: TAIR:0000066 definition: Cells that constitute the mesophyll of a hydathode and are located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap. definition_reference: PMID:12662305 definition_reference: ISBN:0471245208 term: fiber tracheid goid: TAIR:0000355 definition: A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures. definition_reference: ISBN:0471245208 term: filliform apparatus goid: TAIR:0000193 definition: A complex of cell wall invaginations in a synergid cell similar to those in transfer cells. definition_reference: ISBN:0471245208 term: functional megaspore goid: TAIR:0000244 definition: in monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis. definition_reference: TAIR:lr term: fusiform initial goid: TAIR:0000079 definition: An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues. definition_reference: ISBN:0471245208 term: generative cell goid: TAIR:0000168 definition: The cell that will give rise to two sperm cells which will participate in double fertilization. definition_reference: TAIR:KI term: guard cell goid: TAIR:0000293 definition: one of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor. definition_reference: ISBN:0471245208 term: guard mother cell goid: TAIR:0000351 definition: epidermal cell that that divides to produce the guard cells. definition_reference: ISBN:0471245208 term: idioblast goid: TAIR:0000283 definition: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue. definition_reference: ISBN:0471245208 term: initial cell goid: KI:0004011 definition: Cell in a meristem that by division gives rise to two cells one of which remains in the meristem, the other is added to the plant body definition_reference: ISBN:0471245208 term: laticiferous cell goid: KI:0004005 definition: A specialized cells or ducts resembling vessels; they form branched networks of latex-secreting cells in the phloem and other parts of plants. definition_reference: :http://academic.kellogg.edu/herbrandsonc/bio111/glossary/glossary.htm term: megaspore goid: TAIR:0000243 definition: A haploid (1n) spore developing into a female gametophyte in heterosporous plants. definition_reference: ISBN:0471245208 term: megasporocyte goid: TAIR:0000431 definition: A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell. definition_reference: ISBN:0471245208 term: meristematic cell goid: KI:0004010 definition: A cell synthesizing protoplasm and producing new cells by division; varies in form, size, wall thickness, and degree of vacuolation, but has only a primary cell wall. definition_reference: ISBN:0471245208 term: meristemoid goid: TAIR:0000070 definition: A cell or a group of cells constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells. definition_reference: TAIR:syr definition_reference: ISBN:0471245208 term: mesophyll cell goid: KI:0004006 definition: Cell that constitutes leaf mesophyll. definition_reference: TAIR:KI term: microspore goid: TAIR:0000297 definition: A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants. definition_reference: ISBN:0471245208 term: microsporocyte goid: TAIR:0000160 definition: A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell. definition_reference: ISBN:0471245208 term: mucilage cell goid: TAIR:0000373 definition: Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water. definition_reference: ISBN:0471245208 term: myrosin cell goid: TAIR:0000352 definition: Cell containing glucosinolates ("mustard oil glucosides") and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae. definition_reference: ISBN:0471245208 term: parenchyma cell goid: TAIR:0000074 definition: Typically this is a not distinctly specialized cell with a nucleate protoplast concerned with one or more of the various physiological and biochemical activities in plants. Varies in size, form, and wall structure. definition_reference: ISBN:0471245208 term: passage cell goid: TAIR:0000353 definition: Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis. definition_reference: ISBN:0471245208 term: pavement cell goid: TAIR:0000332 definition: epidermal cells with a characteristic convoluted anticlinal cell walls that give a jigsaw like appearance to the lamina. definition_reference: ISBN:087694289 term: phelloid cell goid: KI:0004007 definition: A cell within the phellem (cork) but distinct from the cork cell in having no suberin in its walls. definition_reference: ISBN:0471245208 term: phloem initial goid: TAIR:0000400 definition: A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes. Sometimes called phloem mother cell. definition_reference: ISBN:0471245208 term: photosynthetic cell goid: KI:0004008 definition: A chloroplast-containing cell engaged in photosynthesis. definition_reference: ISBN:0471245208 term: polar nucleus goid: TAIR:0000196 definition: One of two nuclei in the central cell of a mature embryo sac. The two nuclei are derived from groups of nuclei at the two opposite poles of the eight-nucleate embryo sac. definition_reference: ISBN:047125208 term: primary endosperm nucleus goid: TAIR:0000195 definition: Nucleus resulting from the fusion of the male gamete and two polar nuclei in the central cell of the embryo sac. definition_reference: ISBN:0471245208 term: ray cell goid: TAIR:0000083 definition: A cell derived from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues. definition_reference: ISBN:0471245208 term: ray initial goid: TAIR:0000082 definition: A meristematic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem. definition_reference: ISBN:0471245208 term: root hair goid: TAIR:0000256 definition: A type of trichome on root epidermis that is a simple extension of an epidermal cell and is concerned with absorption of soil solution. definition_reference: ISBN:0471245208 term: sclerenchyma cell goid: TAIR:0000077 definition: Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity. definition_reference: ISBN:0471245208 term: secretory cell goid: KI:0004012 definition: Cell that produces secreted substances. definition_reference: TAIR:KI term: sieve cell goid: TAIR:0000285 definition: A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants. definition_reference: ISBN:0471245208 term: sieve element goid: TAIR:0000286 definition: The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member. definition_reference: ISBN:0471245208 term: sieve tube member goid: TAIR:0000289 definition: One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment. definition_reference: ISBN:0471245208 term: sillica cell goid: KI:0004009 definition: One of two types of short cells in the epidermis of grasses, silica cells have deposits of silica in them. definition_reference: ISBN:0471245208 term: socket cell goid: TAIR:0000115 definition: Cell that surround a trichome and provides support for the trichome. definition_reference: ISBN:0471245208 term: sperm cell goid: TAIR:0000084 definition: Male gamete, part of male germ unit. definition_reference: TAIR:KI term: starch sheath cell goid: TAIR:0000020 definition: Cells characterized by conspicuous and rather stable accumulation of starch. definition_reference: ISBN:044174520 term: subsidiary cell goid: TAIR:0000284 definition: An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue. definition_reference: ISBN:047124520 term: synergid goid: TAIR:0000191 definition: cells in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Play a vital role in fertilization. definition_reference: ISBN:047125208 term: tracheary element goid: TAIR:0000290 definition: general term for a water conducting cell, tracheid or vessel member. definition_reference: ISBN:0471245208 term: tracheid goid: TAIR:0000301 definition: A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements. definition_reference: ISBN:0471245208 term: transfer cell goid: TAIR:0000078 definition: Parenchyma cell with the wall ingrowth (or ivaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes. definition_reference: ISBN:0471245208 term: trichoblast goid: TAIR:0000262 definition: Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair. definition_reference: ISBN:0471245208 term: trichome goid: TAIR:0000282 definition: An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata. definition_reference: ISBN:0471245208 term: vegetative cell goid: TAIR:0000169 definition: Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus. definition_reference: TAIR:lr definition_reference: ISBN:0140514031 term: xylem element goid: TAIR:0000273 definition: Cells composing the xylem definition_reference: ISBN:0471245208 term: xylem fiber cell goid: TAIR:0000274 definition: A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers. definition_reference: ISBN:0471245208 term: xylem initial goid: TAIR:0000275 definition: A cambial cell on the xylem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into xylem elements either with or without additional divisions in various planes. Sometimes called xylem mother cell. definition_reference: ISBN:047125208 term: zygote goid: TAIR:0000423 definition: Diploid cell produced by the fusion of sperm cell nucleus and egg cell in the process of double fertilization. definition_reference: TAIR:KI -------------- next part -------------- !autogenerated-by: DAG-Edit version 1.410 !saved-by: Katica Ilic !date: Wed Mar 31 18:15:51 PST 2004 !version: $Revision: 1.24 $ !type: % is_a is a !type: < part_of Part of !type: ~ develops_from develops from $cell type ; TAIR:0000298 %antipodal cell ; TAIR:0000192 %central cell ; TAIR:0000194 ; synonym:sieve tube element %sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ microspore ; TAIR:0000297 %starch sheath cell ; TAIR:0000020 %synergid ; TAIR:0000191