From pj37 at cornell.edu Thu Apr 1 16:46:34 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 01 Apr 2004 16:46:34 -0500 Subject: cell type node In-Reply-To: References: Message-ID: <406C8DBA.7030209@cornell.edu> Katica Ilic wrote: > A short question: Are epithem cell and epithelium cell children of > secretory cell? > > Katica > Definition by Fahn A suggests Epithem: Mesophyll of a hydathode concerned with the secretion of water Epithelium: A compact layer of cells often secretory in function, covering a free surface or lining a cavity. based on this Epithelium cells do qualify. I am not so sure about Epithem cells, because they are just part of the epithem tissue lying between the vein ending and the pore of the hydathode. From katica at acoma.Stanford.EDU Thu Apr 1 17:11:12 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 1 Apr 2004 14:11:12 -0800 (PST) Subject: cell type node In-Reply-To: <406C8DBA.7030209@cornell.edu> Message-ID: Thanks Pankaj, definitions in K Esau are identical. I'll change parentage for the epithelium cell. Katica On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: > > > Katica Ilic wrote: > > A short question: Are epithem cell and epithelium cell children of > > secretory cell? > > > > Katica > > > > Definition by Fahn A suggests > > Epithem: Mesophyll of a hydathode concerned with the secretion of water > > Epithelium: A compact layer of cells often secretory in function, > covering a free surface or lining a cavity. > > based on this Epithelium cells do qualify. I am not so sure about > Epithem cells, because they are just part of the epithem tissue lying > between the vein ending and the pore of the hydathode. > -------------------------------------------------------------------------- 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 katica at acoma.Stanford.EDU Thu Apr 1 20:17:19 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 1 Apr 2004 17:17:19 -0800 (PST) Subject: Synonym file In-Reply-To: <406C92F2.2040403@cornell.edu> Message-ID: Pankaj, Another question: I noticed that GO has a separate txt file with synonyms, describing exact type of the synonyms, IDs and relationships. This file is created manually, and now that GO has switched to OBO, it is no longer needed. How about us at POC, currently we are not using any other type of synonyms but the exact one (which has a lot of disadvantages). Should we stick to this till we move on to OBO, or do we need such a file very soon? Any thoughts on this? 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. -------------------------------------------------------------------------- From pj37 at cornell.edu Thu Apr 1 21:36:05 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 1 Apr 2004 21:36:05 -0500 (EST) Subject: Synonym file In-Reply-To: References: <406C92F2.2040403@cornell.edu> Message-ID: <4161.24.59.76.45.1080873365.squirrel@webmail.cornell.edu> GO did it at the time they were trying to switch over to the new synonym formats to become compatible with the UMLS system. This method is no more required because the new OBO format takes care of it in a very nice format. Managing a separate file is no more required. Pankaj Katica Ilic said: > Pankaj, > > Another question: I noticed that GO has a separate txt file with synonyms, > describing exact type of the synonyms, IDs and relationships. This file is > created manually, and now that GO has switched to OBO, it is no longer > needed. > > How about us at POC, currently we are not using any other type of synonyms > but the exact one (which has a lot of disadvantages). Should we stick to > this till we move on to OBO, or do we need such a file very soon? > > Any thoughts on this? > > 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. > -------------------------------------------------------------------------- > > > -- Pankaj Jaiswal Gramene Database www.gramene.org From katica at acoma.Stanford.EDU Thu Apr 1 21:51:42 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 1 Apr 2004 18:51:42 -0800 (PST) Subject: Synonym file In-Reply-To: <4161.24.59.76.45.1080873365.squirrel@webmail.cornell.edu> Message-ID: ...which means we should be swithcing to OBO sooner rather than later, right? Katica On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: > GO did it at the time they were trying to switch over to the new synonym > formats to become compatible with the UMLS system. This method is no more > required because the new OBO format takes care of it in a very nice > format. > > Managing a separate file is no more required. > > Pankaj > > Katica Ilic said: > > Pankaj, > > > > Another question: I noticed that GO has a separate txt file with synonyms, > > describing exact type of the synonyms, IDs and relationships. This file is > > created manually, and now that GO has switched to OBO, it is no longer > > needed. > > > > How about us at POC, currently we are not using any other type of synonyms > > but the exact one (which has a lot of disadvantages). Should we stick to > > this till we move on to OBO, or do we need such a file very soon? > > > > Any thoughts on this? > > > > 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. > > -------------------------------------------------------------------------- > > > > > > > > > -- > Pankaj Jaiswal > Gramene Database > 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 katica at acoma.Stanford.EDU Thu Apr 1 22:03:05 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 1 Apr 2004 19:03:05 -0800 (PST) Subject: Root node question In-Reply-To: Message-ID: Hello all, I have a question regarding the root node that I have been working on lately. There are few terms that I have hard time finding proper place within the node, since they are not exactly anatomy terms in a strict sense, which is why they are referred as developmental stages in Benfey's lab (see Science, 12 Dec 2003, vol. 203:1956). These terms are, meristematic zone, elongation zone, specialization zone, maturation zone, and additional transition zone (in root apices of maize and grasses, at least). In the paper above, for instance, stele node has all four zones, endodermis plus cortex have all four zones, and so the epidermis. This is of course very redundant, however, looking at TAIR and cereal anatomy ontology, I couldn't really come up with the good solution that would eliminate such redundancy. Since these terms refer to the regions of differentiation, I don't think that they necessarily belong to developmental stages ontology. I would appreciate if we could talk about this tomorrow morning. Best regards, 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. -------------------------------------------------------------------------- From pj37 at cornell.edu Thu Apr 1 22:15:47 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 1 Apr 2004 22:15:47 -0500 (EST) Subject: Synonym file In-Reply-To: References: <4161.24.59.76.45.1080873365.squirrel@webmail.cornell.edu> Message-ID: <4182.24.59.76.45.1080875747.squirrel@webmail.cornell.edu> I suggest sticking with the existing format until we start doing things differently. We can think about it at the time of making the first release. Pankaj Katica Ilic said: > > > ...which means we should be swithcing to OBO sooner rather than later, > right? > > Katica > > On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: > >> GO did it at the time they were trying to switch over to the new synonym >> formats to become compatible with the UMLS system. This method is no >> more >> required because the new OBO format takes care of it in a very nice >> format. >> >> Managing a separate file is no more required. >> >> Pankaj >> >> Katica Ilic said: >> > Pankaj, >> > >> > Another question: I noticed that GO has a separate txt file with >> synonyms, >> > describing exact type of the synonyms, IDs and relationships. This >> file is >> > created manually, and now that GO has switched to OBO, it is no longer >> > needed. >> > >> > How about us at POC, currently we are not using any other type of >> synonyms >> > but the exact one (which has a lot of disadvantages). Should we stick >> to >> > this till we move on to OBO, or do we need such a file very soon? >> > >> > Any thoughts on this? >> > >> > 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. >> > -------------------------------------------------------------------------- >> > >> > >> > >> >> >> -- >> Pankaj Jaiswal >> Gramene Database >> 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. > -------------------------------------------------------------------------- > > > -- Pankaj Jaiswal Gramene Database www.gramene.org From katica at acoma.Stanford.EDU Thu Apr 1 22:21:29 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 1 Apr 2004 19:21:29 -0800 (PST) Subject: cell type node definitions (fwd) Message-ID: Here is another topic for tomorrow, please see the thread bellow (since Pankaj and I started this discussion earlier). The question is whether epidermal cell is a child of parenchyma cell type, followed by a related one, whether chlorenchyma cell is a synonym of photosynthetic cell (with guard cell as an example). Now that I've been thinking more on this topic, here is another question: Is chlorenchyma cell really a cell type? 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: Wed, 31 Mar 2004 22:27:28 -0500 (EST) From: Pankaj Jaiswal To: Katica Ilic Subject: Re: cell type node definitions (fwd) Katica Ilic said: > > Pankaj, > Along the same line (looking at the cereal anatomy ontology), is epidermal > cell really a child of of parenchyma cell (instance_of)? > Yes. That is what I got from several sources pankaj > Katica > ---------- Forwarded message ---------- > Date: Wed, 31 Mar 2004 11:24:04 -0800 (PST) > From: Katica Ilic > To: Pankaj Jaiswal > Cc: Leszek at missouri.edu, fzqhd at studentmail.umsl.edu > Subject: Re: cell type node definitions (fwd) > > > Pankaj, > > About photosynthetic cell and chlorenchyma cell types, the first is a > broader (but not exact) synonym of latter, as all the chlorenchyma cells > are type of parenchyma cells (green parenchyma), while photosynthetic cell > is any cell that contains chloroplasts (not just parenchyma type). For > instance, guard cells have chloroplasts, therefore they can be considered > photosynthetic cells, but they are definitely not chlorenchyma type of > cells. > > For this reason I decide to keep them separately (for now, I didn't make > them synonyms). Later, when we start using other types of synonyms, I can > change this (another reson to switch to OBO format sooner than latter). > > Katica > > On Tue, 30 Mar 2004, Pankaj Jaiswal wrote: > >> Hi Katica, >> >> The first attempt is excellent. You may want to look at the gramene cell >> type section for more cell types. >> >> Also you may like to categorize/classify them into major classes, rather >> than just a simple list of all cell types. Means adding more Biology >> orientations. I have some in Gramene ! >> >> a quick comment >> >> isn't the photosynthetic cell a synonym of chlorenchymatous cell ? >> >> >> >> Katica Ilic wrote: >> >> > Hi Pankaj, Leszek and Felipe, >> > >> > Here are files fo my cell type node (once approved, it will get >> imported >> > to anatomy ontology with the po numbers asigned). Could you go through >> and >> > see if there is any term that need to be removed. There are some >> > subcellular structures (like filiform aparatus), but I decide to keep >> it >> > for now. This is perhaps a question for Friday's conf call. >> > >> > Thanks, >> > >> > Katica >> > >> > P.S. Pankaj, I'll go through your nodes this morning. >> > -------------------------------------------------------------------------- >> > 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: Tue, 23 Mar 2004 18:16:40 -0800 (PST) >> > From: Katica Ilic >> > To: Peter Stevens >> > Subject: cell type node definitions >> > >> > Hi Peter, >> > >> > I have finished the first draft of the cell type node. Attached is the >> > definition file, with definitions taken mostly from K Esau. >> > Would you have time to look at it and see if there is any definition >> that you >> > think need to be changed. >> > >> > IDs that have KI as a prefix are just temporary, they will all have PO >> IDs >> > once I import them into main the Plant anatomy.ontology. >> > >> > I will be adding few more terms, so any suggestions are appreciated. >> > After I hear from you , I'll go ahead and imoprt this node into >> anatomy.ontology, >> > and add these terms to the other nodes, first to Pankaj's tissue node, >> and eventually, when all other nodes >> > are done, I would need to add these terms to the other nodes, wherever >> needed. >> > >> > Thanks, >> > >> > Katica >> > P.S. I am not sending you flat file of the cell_type node ontology, >> since >> > it's rather 'flat', not much hierarchy at the present time, as I still >> > need to shufle some terms around. >> > >> > >> > >> > -------------------------------------------------------------------------- >> > 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. >> > -------------------------------------------------------------------------- >> > >> > >> > >> > ------------------------------------------------------------------------ >> > >> > !version: $Revision: 1.24 $ >> > !date: Tue Mar 23 17:53:40 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 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: 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: 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 constitute 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: 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 >> > >> > >> > >> > ------------------------------------------------------------------------ >> > >> > !autogenerated-by: DAG-Edit version 1.410 >> > !saved-by: Katica Ilic >> > !date: Tue Mar 23 17:53:40 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 >> > %apical cell ; KI:0004000 >> > %bulliform cell ; KI:0004001 >> > %cambial initial ; TAIR:0000295, TAIR:0000080 ; synonym:cambial cell >> > %fusiform initial ; TAIR:0000079 ; CL:0000009 >> > ~axial cell ; TAIR:0000081 ; CL:0000363 >> > %ray initial ; TAIR:0000082 ; CL:0000316 >> > ~ray cell ; TAIR:0000083 ; CL:0000364 >> > %central cell ; TAIR:0000194 >> > > > > > %collenchyma cell ; TAIR:0000075 >> > %contact cell ; KI:0004002 >> > %cork cell ; KI:0004003 >> > %egg cell ; TAIR:0000190 >> > %epithelium cell ; KI:0004004 >> > %epithem cell ; TAIR:0000066 ; CL:0000074 >> > %generative cell ; TAIR:0000168 >> > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ microspore ; >> TAIR:0000297 >> > %idioblast ; TAIR:0000283 >> > %laticiferous cell ; KI:0004005 >> > %megasporocyte ; TAIR:0000431 ; synonym:archesporial cell ; >> synonym:megaspore mother cell >> > ~megaspore ; TAIR:0000243 >> > %degenerate megaspore ; TAIR:0000245 >> > %functional megaspore ; TAIR:0000244 >> > %meristemoid ; TAIR:0000070 >> > %epidermal initial ; TAIR:0000349 >> > ~atrichoblast ; TAIR:0000263 ; synonym:non-hair cell >> > ~guard mother cell ; TAIR:0000351 >> > ~guard cell ; TAIR:0000293 >> > ~pavement cell ; TAIR:0000332 >> > ~socket cell ; TAIR:0000115 >> > ~trichoblast ; TAIR:0000262 ; synonym:hair cell >> > ~root hair ; TAIR:0000256 >> > %trichome ; TAIR:0000282 >> > %mesophyll cell ; KI:0004006 >> > %microsporocyte ; TAIR:0000160 ; synonym:pollen mother cell ; >> synonym:primary sporogenous cell >> > ~microspore ; TAIR:0000297 >> > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ generative >> cell ; TAIR:0000168 >> > %mucilage cell ; TAIR:0000373 >> > %myrosin cell ; TAIR:0000352 >> > %parenchyma cell ; TAIR:0000074 >> > %chlorenchyma cell ; TAIR:0000076 >> > %companion cell ; TAIR:0000071 >> > %transfer cell ; TAIR:0000078 >> > %passage cell ; TAIR:0000353 >> > %phelloid cell ; KI:0004007 >> > %phloem initial ; TAIR:0000400 >> > %photosynthetic cell ; KI:0004008 >> > %sclerenchyma cell ; TAIR:0000077 >> > %sieve element ; TAIR:0000286 >> > %sieve cell ; TAIR:0000285 >> > %sieve tube member ; TAIR:0000289 ; synonym:\ ; >> synonym:sieve tube element >> > %sillica cell ; KI:0004009 >> > %sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ >> microspore ; TAIR:0000297 >> > %starch sheath cell ; TAIR:0000020 >> > %subsidiary cell ; TAIR:0000284, TAIR:0000296 ; synonym:accessory >> cell >> > %synergid ; TAIR:0000191 >> > > > %tracheary element ; TAIR:0000290 >> > %fiber tracheid ; TAIR:0000355 >> > %tracheid ; TAIR:0000301 >> > %vegetative cell ; TAIR:0000169 >> > %xylem initial ; TAIR:0000275 ; synonym:xylem mother cell >> > ~xylem element ; TAIR:0000273 >> > ~xylem fiber cell ; TAIR:0000274 >> > %zygote ; TAIR:0000423 ; synonym:one cell stage % embryonic ; >> TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % >> embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; >> TAIR:0000374 >> >> -- >> ****************************** >> 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. > -------------------------------------------------------------------------- > > > > -- Pankaj Jaiswal Gramene Database www.gramene.org From rhee at acoma.Stanford.EDU Thu Apr 1 22:26:39 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Thu, 1 Apr 2004 19:26:39 -0800 (PST) Subject: Synonym file In-Reply-To: <4182.24.59.76.45.1080875747.squirrel@webmail.cornell.edu> Message-ID: I am not sure if I would agree with this. I think as soon as the OBO format and Dag-Edit is stablized (I would say another 2-4 weeks or so since GO recently went OBO), we should switch. Two reasons: 1. OBO supports the synonym type that we absolutely will depend on. 2. Dag-Edit enhancements will probably focus on the OBO format. Sue On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: > I suggest sticking with the existing format until we start doing things > differently. We can think about it at the time of making the first > release. > > Pankaj > > Katica Ilic said: > > > > > > ...which means we should be swithcing to OBO sooner rather than later, > > right? > > > > Katica > > > > On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: > > > >> GO did it at the time they were trying to switch over to the new synonym > >> formats to become compatible with the UMLS system. This method is no > >> more > >> required because the new OBO format takes care of it in a very nice > >> format. > >> > >> Managing a separate file is no more required. > >> > >> Pankaj > >> > >> Katica Ilic said: > >> > Pankaj, > >> > > >> > Another question: I noticed that GO has a separate txt file with > >> synonyms, > >> > describing exact type of the synonyms, IDs and relationships. This > >> file is > >> > created manually, and now that GO has switched to OBO, it is no longer > >> > needed. > >> > > >> > How about us at POC, currently we are not using any other type of > >> synonyms > >> > but the exact one (which has a lot of disadvantages). Should we stick > >> to > >> > this till we move on to OBO, or do we need such a file very soon? > >> > > >> > Any thoughts on this? > >> > > >> > 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. > >> > -------------------------------------------------------------------------- > >> > > >> > > >> > > >> > >> > >> -- > >> Pankaj Jaiswal > >> Gramene Database > >> 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. > > -------------------------------------------------------------------------- > > > > > > > > > -- > Pankaj Jaiswal > Gramene Database > www.gramene.org > ----------------------------------------------------------------------------- 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 Thu Apr 1 22:34:58 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 1 Apr 2004 19:34:58 -0800 (PST) Subject: Synonym file In-Reply-To: Message-ID: I aggree, synonym types are becoming really important, now that all of the nodes are nearly done, and the next step is mapping. That's why this is on the agenda for tomorrow as well. Katica On Thu, 1 Apr 2004, Sue Rhee wrote: > I am not sure if I would agree with this. I think as soon as the OBO > format and Dag-Edit is stablized (I would say another 2-4 weeks or so > since GO recently went OBO), we should switch. Two reasons: 1. OBO > supports the synonym type that we absolutely will depend on. 2. Dag-Edit > enhancements will probably focus on the OBO format. > > Sue > > On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: > > > I suggest sticking with the existing format until we start doing things > > differently. We can think about it at the time of making the first > > release. > > > > Pankaj > > > > Katica Ilic said: > > > > > > > > > ...which means we should be swithcing to OBO sooner rather than later, > > > right? > > > > > > Katica > > > > > > On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: > > > > > >> GO did it at the time they were trying to switch over to the new synonym > > >> formats to become compatible with the UMLS system. This method is no > > >> more > > >> required because the new OBO format takes care of it in a very nice > > >> format. > > >> > > >> Managing a separate file is no more required. > > >> > > >> Pankaj > > >> > > >> Katica Ilic said: > > >> > Pankaj, > > >> > > > >> > Another question: I noticed that GO has a separate txt file with > > >> synonyms, > > >> > describing exact type of the synonyms, IDs and relationships. This > > >> file is > > >> > created manually, and now that GO has switched to OBO, it is no longer > > >> > needed. > > >> > > > >> > How about us at POC, currently we are not using any other type of > > >> synonyms > > >> > but the exact one (which has a lot of disadvantages). Should we stick > > >> to > > >> > this till we move on to OBO, or do we need such a file very soon? > > >> > > > >> > Any thoughts on this? > > >> > > > >> > 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. > > >> > -------------------------------------------------------------------------- > > >> > > > >> > > > >> > > > >> > > >> > > >> -- > > >> Pankaj Jaiswal > > >> Gramene Database > > >> 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. > > > -------------------------------------------------------------------------- > > > > > > > > > > > > > > > -- > > Pankaj Jaiswal > > Gramene Database > > www.gramene.org > > > > ----------------------------------------------------------------------------- > 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. > ----------------------------------------------------------------------------- > -------------------------------------------------------------------------- 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 pj37 at cornell.edu Thu Apr 1 23:03:27 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 1 Apr 2004 23:03:27 -0500 (EST) Subject: Synonym file In-Reply-To: References: Message-ID: <4224.24.59.76.45.1080878607.squirrel@webmail.cornell.edu> We haven't gone upto that stage of defining synonyms by their class. I reiterate wait until the first release is ready to roll out. By that time OBO format and the DAG-Editor handling it should become stable. Pankaj Katica Ilic said: > > I aggree, synonym types are becoming really important, now that all > of the nodes are nearly done, and the next step is mapping. > > That's why this is on the agenda for tomorrow as well. > > Katica > > On Thu, 1 Apr 2004, Sue Rhee wrote: > >> I am not sure if I would agree with this. I think as soon as the OBO >> format and Dag-Edit is stablized (I would say another 2-4 weeks or so >> since GO recently went OBO), we should switch. Two reasons: 1. OBO >> supports the synonym type that we absolutely will depend on. 2. Dag-Edit >> enhancements will probably focus on the OBO format. >> >> Sue >> >> On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: >> >> > I suggest sticking with the existing format until we start doing >> things >> > differently. We can think about it at the time of making the first >> > release. >> > >> > Pankaj >> > >> > Katica Ilic said: >> > > >> > > >> > > ...which means we should be swithcing to OBO sooner rather than >> later, >> > > right? >> > > >> > > Katica >> > > >> > > On Thu, 1 Apr 2004, Pankaj Jaiswal wrote: >> > > >> > >> GO did it at the time they were trying to switch over to the new >> synonym >> > >> formats to become compatible with the UMLS system. This method is >> no >> > >> more >> > >> required because the new OBO format takes care of it in a very nice >> > >> format. >> > >> >> > >> Managing a separate file is no more required. >> > >> >> > >> Pankaj >> > >> >> > >> Katica Ilic said: >> > >> > Pankaj, >> > >> > >> > >> > Another question: I noticed that GO has a separate txt file with >> > >> synonyms, >> > >> > describing exact type of the synonyms, IDs and relationships. >> This >> > >> file is >> > >> > created manually, and now that GO has switched to OBO, it is no >> longer >> > >> > needed. >> > >> > >> > >> > How about us at POC, currently we are not using any other type of >> > >> synonyms >> > >> > but the exact one (which has a lot of disadvantages). Should we >> stick >> > >> to >> > >> > this till we move on to OBO, or do we need such a file very soon? >> > >> > >> > >> > Any thoughts on this? >> > >> > >> > >> > 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. >> > >> > -------------------------------------------------------------------------- >> > >> > >> > >> > >> > >> > >> > >> >> > >> >> > >> -- >> > >> Pankaj Jaiswal >> > >> Gramene Database >> > >> 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. >> > > -------------------------------------------------------------------------- >> > > >> > > >> > > >> > >> > >> > -- >> > Pankaj Jaiswal >> > Gramene Database >> > www.gramene.org >> > >> >> ----------------------------------------------------------------------------- >> 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. >> ----------------------------------------------------------------------------- >> > > -------------------------------------------------------------------------- > 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. > -------------------------------------------------------------------------- > > > -- Pankaj Jaiswal Gramene Database www.gramene.org From pj37 at cornell.edu Fri Apr 2 11:47:40 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 02 Apr 2004 11:47:40 -0500 Subject: cell type node In-Reply-To: References: Message-ID: <406D992C.6030001@cornell.edu> central cell < polar nucleus < primary endosperm nucleus Are we doing subcellular strutures too in the anatomy ? If not, I guess these children belong to the GO component ontology. Pankaj Katica Ilic wrote: > 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. > -------------------------------------------------------------------------- > > > > ------------------------------------------------------------------------ > > !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 > > > > ------------------------------------------------------------------------ > > !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 > %collenchyma cell ; TAIR:0000075 > %cork cell ; KI:0004003 > %egg cell ; TAIR:0000190 > %epidermal cell ; KI:0004013 > %bulliform cell ; KI:0004001 > %sillica cell ; KI:0004009 > %socket cell ; TAIR:0000115 ~ epidermal initial ; TAIR:0000349 > %subsidiary cell ; TAIR:0000284, TAIR:0000296 ; synonym:accessory cell > %epithelium cell ; KI:0004004 > %epithem cell ; TAIR:0000066 ; CL:0000074 > %generative cell ; TAIR:0000168 > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ microspore ; TAIR:0000297 > %idioblast ; TAIR:0000283 > %megasporocyte ; TAIR:0000431 ; synonym:archesporial cell ; synonym:megaspore mother cell > ~megaspore ; TAIR:0000243 > %degenerate megaspore ; TAIR:0000245 > %functional megaspore ; TAIR:0000244 > %meristematic cell ; KI:0004010 > %apical cell ; KI:0004000 > %meristemoid ; TAIR:0000070 > %initial cell ; KI:0004011 > %cambial initial ; TAIR:0000295, TAIR:0000080 ; synonym:cambial cell > %fusiform initial ; TAIR:0000079 ; CL:0000009 > ~axial cell ; TAIR:0000081 ; CL:0000363 > %phloem initial ; TAIR:0000400 > %ray initial ; TAIR:0000082 ; CL:0000316 > ~ray cell ; TAIR:0000083 ; CL:0000364 > %xylem initial ; TAIR:0000275 ; synonym:xylem mother cell > ~xylem element ; TAIR:0000273 > ~xylem fiber cell ; TAIR:0000274 > %epidermal initial ; TAIR:0000349 > ~atrichoblast ; TAIR:0000263 ; synonym:non-hair cell > ~guard mother cell ; TAIR:0000351 > ~guard cell ; TAIR:0000293 > ~pavement cell ; TAIR:0000332 > ~socket cell ; TAIR:0000115 % epidermal cell ; KI:0004013 > ~trichoblast ; TAIR:0000262 ; synonym:hair cell > ~root hair ; TAIR:0000256 > %microsporocyte ; TAIR:0000160 ; synonym:pollen mother cell ; synonym:primary sporogenous cell > ~microspore ; TAIR:0000297 > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ generative cell ; TAIR:0000168 > %parenchyma cell ; TAIR:0000074 > %chlorenchyma cell ; TAIR:0000076 % photosynthetic cell ; KI:0004008 > %mesophyll cell ; KI:0004006 > %companion cell ; TAIR:0000071 > %contact cell ; KI:0004002 > %transfer cell ; TAIR:0000078 > %passage cell ; TAIR:0000353 > %phelloid cell ; KI:0004007 > %photosynthetic cell ; KI:0004008 > %chlorenchyma cell ; TAIR:0000076 % parenchyma cell ; TAIR:0000074 > %mesophyll cell ; KI:0004006 > %sclerenchyma cell ; TAIR:0000077 > %secretory cell ; KI:0004012 > %laticiferous cell ; KI:0004005 > %mucilage cell ; TAIR:0000373 > %myrosin cell ; TAIR:0000352 > %sieve element ; TAIR:0000286 > %sieve cell ; TAIR:0000285 > %sieve tube member ; TAIR:0000289 ; synonym:\ ; synonym:sieve tube element > %sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ microspore ; TAIR:0000297 > %starch sheath cell ; TAIR:0000020 > %synergid ; TAIR:0000191 > %tracheary element ; TAIR:0000290 > %fiber tracheid ; TAIR:0000355 > %tracheid ; TAIR:0000301 > %trichome ; TAIR:0000282 > %vegetative cell ; TAIR:0000169 > %zygote ; TAIR:0000423 ; synonym:one cell stage % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 -- ****************************** 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 Fri Apr 2 11:53:12 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 2 Apr 2004 08:53:12 -0800 (PST) Subject: cell type node In-Reply-To: <406D992C.6030001@cornell.edu> Message-ID: This was one of my question for today. Katica On Fri, 2 Apr 2004, Pankaj Jaiswal wrote: > central cell > < polar nucleus > < primary endosperm nucleus > > Are we doing subcellular strutures too in the anatomy ? If not, I guess > these children belong to the GO component ontology. > > Pankaj > > > Katica Ilic wrote: > > > 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. > > -------------------------------------------------------------------------- > > > > > > > > ------------------------------------------------------------------------ > > > > !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 > > > > > > > > ------------------------------------------------------------------------ > > > > !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 > > > > %collenchyma cell ; TAIR:0000075 > > %cork cell ; KI:0004003 > > %egg cell ; TAIR:0000190 > > %epidermal cell ; KI:0004013 > > %bulliform cell ; KI:0004001 > > %sillica cell ; KI:0004009 > > %socket cell ; TAIR:0000115 ~ epidermal initial ; TAIR:0000349 > > %subsidiary cell ; TAIR:0000284, TAIR:0000296 ; synonym:accessory cell > > %epithelium cell ; KI:0004004 > > %epithem cell ; TAIR:0000066 ; CL:0000074 > > %generative cell ; TAIR:0000168 > > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ microspore ; TAIR:0000297 > > %idioblast ; TAIR:0000283 > > %megasporocyte ; TAIR:0000431 ; synonym:archesporial cell ; synonym:megaspore mother cell > > ~megaspore ; TAIR:0000243 > > %degenerate megaspore ; TAIR:0000245 > > %functional megaspore ; TAIR:0000244 > > %meristematic cell ; KI:0004010 > > %apical cell ; KI:0004000 > > %meristemoid ; TAIR:0000070 > > %initial cell ; KI:0004011 > > %cambial initial ; TAIR:0000295, TAIR:0000080 ; synonym:cambial cell > > %fusiform initial ; TAIR:0000079 ; CL:0000009 > > ~axial cell ; TAIR:0000081 ; CL:0000363 > > %phloem initial ; TAIR:0000400 > > %ray initial ; TAIR:0000082 ; CL:0000316 > > ~ray cell ; TAIR:0000083 ; CL:0000364 > > %xylem initial ; TAIR:0000275 ; synonym:xylem mother cell > > ~xylem element ; TAIR:0000273 > > ~xylem fiber cell ; TAIR:0000274 > > %epidermal initial ; TAIR:0000349 > > ~atrichoblast ; TAIR:0000263 ; synonym:non-hair cell > > ~guard mother cell ; TAIR:0000351 > > ~guard cell ; TAIR:0000293 > > ~pavement cell ; TAIR:0000332 > > ~socket cell ; TAIR:0000115 % epidermal cell ; KI:0004013 > > ~trichoblast ; TAIR:0000262 ; synonym:hair cell > > ~root hair ; TAIR:0000256 > > %microsporocyte ; TAIR:0000160 ; synonym:pollen mother cell ; synonym:primary sporogenous cell > > ~microspore ; TAIR:0000297 > > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ generative cell ; TAIR:0000168 > > %parenchyma cell ; TAIR:0000074 > > %chlorenchyma cell ; TAIR:0000076 % photosynthetic cell ; KI:0004008 > > %mesophyll cell ; KI:0004006 > > %companion cell ; TAIR:0000071 > > %contact cell ; KI:0004002 > > %transfer cell ; TAIR:0000078 > > %passage cell ; TAIR:0000353 > > %phelloid cell ; KI:0004007 > > %photosynthetic cell ; KI:0004008 > > %chlorenchyma cell ; TAIR:0000076 % parenchyma cell ; TAIR:0000074 > > %mesophyll cell ; KI:0004006 > > %sclerenchyma cell ; TAIR:0000077 > > %secretory cell ; KI:0004012 > > %laticiferous cell ; KI:0004005 > > %mucilage cell ; TAIR:0000373 > > %myrosin cell ; TAIR:0000352 > > %sieve element ; TAIR:0000286 > > %sieve cell ; TAIR:0000285 > > %sieve tube member ; TAIR:0000289 ; synonym:\ ; synonym:sieve tube element > > %sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ microspore ; TAIR:0000297 > > %starch sheath cell ; TAIR:0000020 > > %synergid ; TAIR:0000191 > > > %tracheary element ; TAIR:0000290 > > %fiber tracheid ; TAIR:0000355 > > %tracheid ; TAIR:0000301 > > %trichome ; TAIR:0000282 > > %vegetative cell ; TAIR:0000169 > > %zygote ; TAIR:0000423 ; synonym:one cell stage % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 > > -- > ****************************** > 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 rhee at acoma.Stanford.EDU Fri Apr 2 17:58:02 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Fri, 2 Apr 2004 14:58:02 -0800 (PST) Subject: cell type node In-Reply-To: Message-ID: I think we should ask GO to see if the two below should be appropriate terms in GO component. Other good examples are: pollen tube root hair Sue On Fri, 2 Apr 2004, Katica Ilic wrote: > > > This was one of my question for today. > > Katica > > On Fri, 2 Apr 2004, Pankaj Jaiswal > wrote: > > > central cell > > < polar nucleus > > < primary endosperm nucleus > > > > Are we doing subcellular strutures too in the anatomy ? If not, I guess > > these children belong to the GO component ontology. > > > > Pankaj > > > > > > Katica Ilic wrote: > > > > > 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. > > > -------------------------------------------------------------------------- > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > !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 > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > !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 > > > > > > > %collenchyma cell ; TAIR:0000075 > > > %cork cell ; KI:0004003 > > > %egg cell ; TAIR:0000190 > > > %epidermal cell ; KI:0004013 > > > %bulliform cell ; KI:0004001 > > > %sillica cell ; KI:0004009 > > > %socket cell ; TAIR:0000115 ~ epidermal initial ; TAIR:0000349 > > > %subsidiary cell ; TAIR:0000284, TAIR:0000296 ; synonym:accessory cell > > > %epithelium cell ; KI:0004004 > > > %epithem cell ; TAIR:0000066 ; CL:0000074 > > > %generative cell ; TAIR:0000168 > > > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ microspore ; TAIR:0000297 > > > %idioblast ; TAIR:0000283 > > > %megasporocyte ; TAIR:0000431 ; synonym:archesporial cell ; synonym:megaspore mother cell > > > ~megaspore ; TAIR:0000243 > > > %degenerate megaspore ; TAIR:0000245 > > > %functional megaspore ; TAIR:0000244 > > > %meristematic cell ; KI:0004010 > > > %apical cell ; KI:0004000 > > > %meristemoid ; TAIR:0000070 > > > %initial cell ; KI:0004011 > > > %cambial initial ; TAIR:0000295, TAIR:0000080 ; synonym:cambial cell > > > %fusiform initial ; TAIR:0000079 ; CL:0000009 > > > ~axial cell ; TAIR:0000081 ; CL:0000363 > > > %phloem initial ; TAIR:0000400 > > > %ray initial ; TAIR:0000082 ; CL:0000316 > > > ~ray cell ; TAIR:0000083 ; CL:0000364 > > > %xylem initial ; TAIR:0000275 ; synonym:xylem mother cell > > > ~xylem element ; TAIR:0000273 > > > ~xylem fiber cell ; TAIR:0000274 > > > %epidermal initial ; TAIR:0000349 > > > ~atrichoblast ; TAIR:0000263 ; synonym:non-hair cell > > > ~guard mother cell ; TAIR:0000351 > > > ~guard cell ; TAIR:0000293 > > > ~pavement cell ; TAIR:0000332 > > > ~socket cell ; TAIR:0000115 % epidermal cell ; KI:0004013 > > > ~trichoblast ; TAIR:0000262 ; synonym:hair cell > > > ~root hair ; TAIR:0000256 > > > %microsporocyte ; TAIR:0000160 ; synonym:pollen mother cell ; synonym:primary sporogenous cell > > > ~microspore ; TAIR:0000297 > > > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ generative cell ; TAIR:0000168 > > > %parenchyma cell ; TAIR:0000074 > > > %chlorenchyma cell ; TAIR:0000076 % photosynthetic cell ; KI:0004008 > > > %mesophyll cell ; KI:0004006 > > > %companion cell ; TAIR:0000071 > > > %contact cell ; KI:0004002 > > > %transfer cell ; TAIR:0000078 > > > %passage cell ; TAIR:0000353 > > > %phelloid cell ; KI:0004007 > > > %photosynthetic cell ; KI:0004008 > > > %chlorenchyma cell ; TAIR:0000076 % parenchyma cell ; TAIR:0000074 > > > %mesophyll cell ; KI:0004006 > > > %sclerenchyma cell ; TAIR:0000077 > > > %secretory cell ; KI:0004012 > > > %laticiferous cell ; KI:0004005 > > > %mucilage cell ; TAIR:0000373 > > > %myrosin cell ; TAIR:0000352 > > > %sieve element ; TAIR:0000286 > > > %sieve cell ; TAIR:0000285 > > > %sieve tube member ; TAIR:0000289 ; synonym:\ ; synonym:sieve tube element > > > %sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ microspore ; TAIR:0000297 > > > %starch sheath cell ; TAIR:0000020 > > > %synergid ; TAIR:0000191 > > > > > %tracheary element ; TAIR:0000290 > > > %fiber tracheid ; TAIR:0000355 > > > %tracheid ; TAIR:0000301 > > > %trichome ; TAIR:0000282 > > > %vegetative cell ; TAIR:0000169 > > > %zygote ; TAIR:0000423 ; synonym:one cell stage % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 > > > > -- > > ****************************** > > 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. > -------------------------------------------------------------------------- > > ----------------------------------------------------------------------------- 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 rhee at acoma.Stanford.EDU Fri Apr 2 18:05:18 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Fri, 2 Apr 2004 15:05:18 -0800 (PST) Subject: cell type node definitions (fwd) In-Reply-To: Message-ID: On Thu, 1 Apr 2004, Katica Ilic wrote: > > Here is another topic for tomorrow, please see the thread bellow (since > Pankaj and I started this discussion earlier). > > The question is whether epidermal cell is a child of parenchyma cell > type, followed by a related one, whether chlorenchyma cell is a synonym No. > of photosynthetic cell (with guard cell as an example). No. I think chlorenchyma cell is a type of photosynthetic cell. Pavement and guard cells are other examples of types of photosynthetic cell. > Now that I've been thinking more on this topic, here is another > question: Is chlorenchyma cell really a cell type? Why not? > > 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: Wed, 31 Mar 2004 22:27:28 -0500 (EST) > From: Pankaj Jaiswal > To: Katica Ilic > Subject: Re: cell type node definitions (fwd) > > > Katica Ilic said: > > > > Pankaj, > > Along the same line (looking at the cereal anatomy ontology), is epidermal > > cell really a child of of parenchyma cell (instance_of)? > > > Yes. That is what I got from several sources > > pankaj > > > > > > Katica > > ---------- Forwarded message ---------- > > Date: Wed, 31 Mar 2004 11:24:04 -0800 (PST) > > From: Katica Ilic > > To: Pankaj Jaiswal > > Cc: Leszek at missouri.edu, fzqhd at studentmail.umsl.edu > > Subject: Re: cell type node definitions (fwd) > > > > > > Pankaj, > > > > About photosynthetic cell and chlorenchyma cell types, the first is a > > broader (but not exact) synonym of latter, as all the chlorenchyma cells > > are type of parenchyma cells (green parenchyma), while photosynthetic cell > > is any cell that contains chloroplasts (not just parenchyma type). For > > instance, guard cells have chloroplasts, therefore they can be considered > > photosynthetic cells, but they are definitely not chlorenchyma type of > > cells. > > > > For this reason I decide to keep them separately (for now, I didn't make > > them synonyms). Later, when we start using other types of synonyms, I can > > change this (another reson to switch to OBO format sooner than latter). > > > > Katica > > > > On Tue, 30 Mar 2004, Pankaj Jaiswal wrote: > > > >> Hi Katica, > >> > >> The first attempt is excellent. You may want to look at the gramene cell > >> type section for more cell types. > >> > >> Also you may like to categorize/classify them into major classes, rather > >> than just a simple list of all cell types. Means adding more Biology > >> orientations. I have some in Gramene ! > >> > >> a quick comment > >> > >> isn't the photosynthetic cell a synonym of chlorenchymatous cell ? > >> > >> > >> > >> Katica Ilic wrote: > >> > >> > Hi Pankaj, Leszek and Felipe, > >> > > >> > Here are files fo my cell type node (once approved, it will get > >> imported > >> > to anatomy ontology with the po numbers asigned). Could you go through > >> and > >> > see if there is any term that need to be removed. There are some > >> > subcellular structures (like filiform aparatus), but I decide to keep > >> it > >> > for now. This is perhaps a question for Friday's conf call. > >> > > >> > Thanks, > >> > > >> > Katica > >> > > >> > P.S. Pankaj, I'll go through your nodes this morning. > >> > -------------------------------------------------------------------------- > >> > 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: Tue, 23 Mar 2004 18:16:40 -0800 (PST) > >> > From: Katica Ilic > >> > To: Peter Stevens > >> > Subject: cell type node definitions > >> > > >> > Hi Peter, > >> > > >> > I have finished the first draft of the cell type node. Attached is the > >> > definition file, with definitions taken mostly from K Esau. > >> > Would you have time to look at it and see if there is any definition > >> that you > >> > think need to be changed. > >> > > >> > IDs that have KI as a prefix are just temporary, they will all have PO > >> IDs > >> > once I import them into main the Plant anatomy.ontology. > >> > > >> > I will be adding few more terms, so any suggestions are appreciated. > >> > After I hear from you , I'll go ahead and imoprt this node into > >> anatomy.ontology, > >> > and add these terms to the other nodes, first to Pankaj's tissue node, > >> and eventually, when all other nodes > >> > are done, I would need to add these terms to the other nodes, wherever > >> needed. > >> > > >> > Thanks, > >> > > >> > Katica > >> > P.S. I am not sending you flat file of the cell_type node ontology, > >> since > >> > it's rather 'flat', not much hierarchy at the present time, as I still > >> > need to shufle some terms around. > >> > > >> > > >> > > >> > -------------------------------------------------------------------------- > >> > 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. > >> > -------------------------------------------------------------------------- > >> > > >> > > >> > > >> > ------------------------------------------------------------------------ > >> > > >> > !version: $Revision: 1.24 $ > >> > !date: Tue Mar 23 17:53:40 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 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: 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: 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 constitute 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: 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 > >> > > >> > > >> > > >> > ------------------------------------------------------------------------ > >> > > >> > !autogenerated-by: DAG-Edit version 1.410 > >> > !saved-by: Katica Ilic > >> > !date: Tue Mar 23 17:53:40 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 > >> > %apical cell ; KI:0004000 > >> > %bulliform cell ; KI:0004001 > >> > %cambial initial ; TAIR:0000295, TAIR:0000080 ; synonym:cambial cell > >> > %fusiform initial ; TAIR:0000079 ; CL:0000009 > >> > ~axial cell ; TAIR:0000081 ; CL:0000363 > >> > %ray initial ; TAIR:0000082 ; CL:0000316 > >> > ~ray cell ; TAIR:0000083 ; CL:0000364 > >> > %central cell ; TAIR:0000194 > >> > >> > >> > %collenchyma cell ; TAIR:0000075 > >> > %contact cell ; KI:0004002 > >> > %cork cell ; KI:0004003 > >> > %egg cell ; TAIR:0000190 > >> > %epithelium cell ; KI:0004004 > >> > %epithem cell ; TAIR:0000066 ; CL:0000074 > >> > %generative cell ; TAIR:0000168 > >> > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ microspore ; > >> TAIR:0000297 > >> > %idioblast ; TAIR:0000283 > >> > %laticiferous cell ; KI:0004005 > >> > %megasporocyte ; TAIR:0000431 ; synonym:archesporial cell ; > >> synonym:megaspore mother cell > >> > ~megaspore ; TAIR:0000243 > >> > %degenerate megaspore ; TAIR:0000245 > >> > %functional megaspore ; TAIR:0000244 > >> > %meristemoid ; TAIR:0000070 > >> > %epidermal initial ; TAIR:0000349 > >> > ~atrichoblast ; TAIR:0000263 ; synonym:non-hair cell > >> > ~guard mother cell ; TAIR:0000351 > >> > ~guard cell ; TAIR:0000293 > >> > ~pavement cell ; TAIR:0000332 > >> > ~socket cell ; TAIR:0000115 > >> > ~trichoblast ; TAIR:0000262 ; synonym:hair cell > >> > ~root hair ; TAIR:0000256 > >> > %trichome ; TAIR:0000282 > >> > %mesophyll cell ; KI:0004006 > >> > %microsporocyte ; TAIR:0000160 ; synonym:pollen mother cell ; > >> synonym:primary sporogenous cell > >> > ~microspore ; TAIR:0000297 > >> > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ generative > >> cell ; TAIR:0000168 > >> > %mucilage cell ; TAIR:0000373 > >> > %myrosin cell ; TAIR:0000352 > >> > %parenchyma cell ; TAIR:0000074 > >> > %chlorenchyma cell ; TAIR:0000076 > >> > %companion cell ; TAIR:0000071 > >> > %transfer cell ; TAIR:0000078 > >> > %passage cell ; TAIR:0000353 > >> > %phelloid cell ; KI:0004007 > >> > %phloem initial ; TAIR:0000400 > >> > %photosynthetic cell ; KI:0004008 > >> > %sclerenchyma cell ; TAIR:0000077 > >> > %sieve element ; TAIR:0000286 > >> > %sieve cell ; TAIR:0000285 > >> > %sieve tube member ; TAIR:0000289 ; synonym:\ ; > >> synonym:sieve tube element > >> > %sillica cell ; KI:0004009 > >> > %sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ > >> microspore ; TAIR:0000297 > >> > %starch sheath cell ; TAIR:0000020 > >> > %subsidiary cell ; TAIR:0000284, TAIR:0000296 ; synonym:accessory > >> cell > >> > %synergid ; TAIR:0000191 > >> > >> > %tracheary element ; TAIR:0000290 > >> > %fiber tracheid ; TAIR:0000355 > >> > %tracheid ; TAIR:0000301 > >> > %vegetative cell ; TAIR:0000169 > >> > %xylem initial ; TAIR:0000275 ; synonym:xylem mother cell > >> > ~xylem element ; TAIR:0000273 > >> > ~xylem fiber cell ; TAIR:0000274 > >> > %zygote ; TAIR:0000423 ; synonym:one cell stage % embryonic ; > >> TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % > >> embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; > >> TAIR:0000374 > >> > >> -- > >> ****************************** > >> 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. > > -------------------------------------------------------------------------- > > > > > > > > > > > -- > Pankaj Jaiswal > Gramene Database > www.gramene.org > ----------------------------------------------------------------------------- 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 Apr 2 19:29:56 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 2 Apr 2004 16:29:56 -0800 (PST) Subject: cell type node definitions (fwd) In-Reply-To: Message-ID: On Fri, 2 Apr 2004, Sue Rhee wrote: > On Thu, 1 Apr 2004, Katica Ilic wrote: > > > > > Here is another topic for tomorrow, please see the thread bellow (since > > Pankaj and I started this discussion earlier). > > > > The question is whether epidermal cell is a child of parenchyma cell > > type, followed by a related one, whether chlorenchyma cell is a synonym > > No. > > > of photosynthetic cell (with guard cell as an example). > > No. I think chlorenchyma cell is a type of photosynthetic cell. Pavement > and guard cells are other examples of types of photosynthetic cell. > > > Now that I've been thinking more on this topic, here is another > > question: Is chlorenchyma cell really a cell type? > Why not? Chlorenchyma tissue is parenchyma tissue containing chloroplasts (green parenchyma); chlorenchyma cell is esentially parenchyma cell with chloroplasts. With availability of different types of synonyms, parenchyma cell can be broader synonym of chlorenchyma cell. Just a thought, I already have chlorenchyma cell in the cell type node, but I like the idea taking advantage of diff types of synonyms too (otherwords, keeping it simple wherever we can). Katica > > 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: Wed, 31 Mar 2004 22:27:28 -0500 (EST) > > From: Pankaj Jaiswal > > To: Katica Ilic > > Subject: Re: cell type node definitions (fwd) > > > > > > Katica Ilic said: > > > > > > Pankaj, > > > Along the same line (looking at the cereal anatomy ontology), is epidermal > > > cell really a child of of parenchyma cell (instance_of)? > > > > > Yes. That is what I got from several sources > > > > pankaj > > > > > > > > > > > Katica > > > ---------- Forwarded message ---------- > > > Date: Wed, 31 Mar 2004 11:24:04 -0800 (PST) > > > From: Katica Ilic > > > To: Pankaj Jaiswal > > > Cc: Leszek at missouri.edu, fzqhd at studentmail.umsl.edu > > > Subject: Re: cell type node definitions (fwd) > > > > > > > > > Pankaj, > > > > > > About photosynthetic cell and chlorenchyma cell types, the first is a > > > broader (but not exact) synonym of latter, as all the chlorenchyma cells > > > are type of parenchyma cells (green parenchyma), while photosynthetic cell > > > is any cell that contains chloroplasts (not just parenchyma type). For > > > instance, guard cells have chloroplasts, therefore they can be considered > > > photosynthetic cells, but they are definitely not chlorenchyma type of > > > cells. > > > > > > For this reason I decide to keep them separately (for now, I didn't make > > > them synonyms). Later, when we start using other types of synonyms, I can > > > change this (another reson to switch to OBO format sooner than latter). > > > > > > Katica > > > > > > On Tue, 30 Mar 2004, Pankaj Jaiswal wrote: > > > > > >> Hi Katica, > > >> > > >> The first attempt is excellent. You may want to look at the gramene cell > > >> type section for more cell types. > > >> > > >> Also you may like to categorize/classify them into major classes, rather > > >> than just a simple list of all cell types. Means adding more Biology > > >> orientations. I have some in Gramene ! > > >> > > >> a quick comment > > >> > > >> isn't the photosynthetic cell a synonym of chlorenchymatous cell ? > > >> > > >> > > >> > > >> Katica Ilic wrote: > > >> > > >> > Hi Pankaj, Leszek and Felipe, > > >> > > > >> > Here are files fo my cell type node (once approved, it will get > > >> imported > > >> > to anatomy ontology with the po numbers asigned). Could you go through > > >> and > > >> > see if there is any term that need to be removed. There are some > > >> > subcellular structures (like filiform aparatus), but I decide to keep > > >> it > > >> > for now. This is perhaps a question for Friday's conf call. > > >> > > > >> > Thanks, > > >> > > > >> > Katica > > >> > > > >> > P.S. Pankaj, I'll go through your nodes this morning. > > >> > -------------------------------------------------------------------------- > > >> > 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: Tue, 23 Mar 2004 18:16:40 -0800 (PST) > > >> > From: Katica Ilic > > >> > To: Peter Stevens > > >> > Subject: cell type node definitions > > >> > > > >> > Hi Peter, > > >> > > > >> > I have finished the first draft of the cell type node. Attached is the > > >> > definition file, with definitions taken mostly from K Esau. > > >> > Would you have time to look at it and see if there is any definition > > >> that you > > >> > think need to be changed. > > >> > > > >> > IDs that have KI as a prefix are just temporary, they will all have PO > > >> IDs > > >> > once I import them into main the Plant anatomy.ontology. > > >> > > > >> > I will be adding few more terms, so any suggestions are appreciated. > > >> > After I hear from you , I'll go ahead and imoprt this node into > > >> anatomy.ontology, > > >> > and add these terms to the other nodes, first to Pankaj's tissue node, > > >> and eventually, when all other nodes > > >> > are done, I would need to add these terms to the other nodes, wherever > > >> needed. > > >> > > > >> > Thanks, > > >> > > > >> > Katica > > >> > P.S. I am not sending you flat file of the cell_type node ontology, > > >> since > > >> > it's rather 'flat', not much hierarchy at the present time, as I still > > >> > need to shufle some terms around. > > >> > > > >> > > > >> > > > >> > -------------------------------------------------------------------------- > > >> > 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. > > >> > -------------------------------------------------------------------------- > > >> > > > >> > > > >> > > > >> > ------------------------------------------------------------------------ > > >> > > > >> > !version: $Revision: 1.24 $ > > >> > !date: Tue Mar 23 17:53:40 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 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: 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: 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 constitute 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: 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 > > >> > > > >> > > > >> > > > >> > ------------------------------------------------------------------------ > > >> > > > >> > !autogenerated-by: DAG-Edit version 1.410 > > >> > !saved-by: Katica Ilic > > >> > !date: Tue Mar 23 17:53:40 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 > > >> > %apical cell ; KI:0004000 > > >> > %bulliform cell ; KI:0004001 > > >> > %cambial initial ; TAIR:0000295, TAIR:0000080 ; synonym:cambial cell > > >> > %fusiform initial ; TAIR:0000079 ; CL:0000009 > > >> > ~axial cell ; TAIR:0000081 ; CL:0000363 > > >> > %ray initial ; TAIR:0000082 ; CL:0000316 > > >> > ~ray cell ; TAIR:0000083 ; CL:0000364 > > >> > %central cell ; TAIR:0000194 > > >> > > >> > > >> > %collenchyma cell ; TAIR:0000075 > > >> > %contact cell ; KI:0004002 > > >> > %cork cell ; KI:0004003 > > >> > %egg cell ; TAIR:0000190 > > >> > %epithelium cell ; KI:0004004 > > >> > %epithem cell ; TAIR:0000066 ; CL:0000074 > > >> > %generative cell ; TAIR:0000168 > > >> > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ microspore ; > > >> TAIR:0000297 > > >> > %idioblast ; TAIR:0000283 > > >> > %laticiferous cell ; KI:0004005 > > >> > %megasporocyte ; TAIR:0000431 ; synonym:archesporial cell ; > > >> synonym:megaspore mother cell > > >> > ~megaspore ; TAIR:0000243 > > >> > %degenerate megaspore ; TAIR:0000245 > > >> > %functional megaspore ; TAIR:0000244 > > >> > %meristemoid ; TAIR:0000070 > > >> > %epidermal initial ; TAIR:0000349 > > >> > ~atrichoblast ; TAIR:0000263 ; synonym:non-hair cell > > >> > ~guard mother cell ; TAIR:0000351 > > >> > ~guard cell ; TAIR:0000293 > > >> > ~pavement cell ; TAIR:0000332 > > >> > ~socket cell ; TAIR:0000115 > > >> > ~trichoblast ; TAIR:0000262 ; synonym:hair cell > > >> > ~root hair ; TAIR:0000256 > > >> > %trichome ; TAIR:0000282 > > >> > %mesophyll cell ; KI:0004006 > > >> > %microsporocyte ; TAIR:0000160 ; synonym:pollen mother cell ; > > >> synonym:primary sporogenous cell > > >> > ~microspore ; TAIR:0000297 > > >> > ~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ generative > > >> cell ; TAIR:0000168 > > >> > %mucilage cell ; TAIR:0000373 > > >> > %myrosin cell ; TAIR:0000352 > > >> > %parenchyma cell ; TAIR:0000074 > > >> > %chlorenchyma cell ; TAIR:0000076 > > >> > %companion cell ; TAIR:0000071 > > >> > %transfer cell ; TAIR:0000078 > > >> > %passage cell ; TAIR:0000353 > > >> > %phelloid cell ; KI:0004007 > > >> > %phloem initial ; TAIR:0000400 > > >> > %photosynthetic cell ; KI:0004008 > > >> > %sclerenchyma cell ; TAIR:0000077 > > >> > %sieve element ; TAIR:0000286 > > >> > %sieve cell ; TAIR:0000285 > > >> > %sieve tube member ; TAIR:0000289 ; synonym:\ ; > > >> synonym:sieve tube element > > >> > %sillica cell ; KI:0004009 > > >> > %sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ > > >> microspore ; TAIR:0000297 > > >> > %starch sheath cell ; TAIR:0000020 > > >> > %subsidiary cell ; TAIR:0000284, TAIR:0000296 ; synonym:accessory > > >> cell > > >> > %synergid ; TAIR:0000191 > > >> > > >> > %tracheary element ; TAIR:0000290 > > >> > %fiber tracheid ; TAIR:0000355 > > >> > %tracheid ; TAIR:0000301 > > >> > %vegetative cell ; TAIR:0000169 > > >> > %xylem initial ; TAIR:0000275 ; synonym:xylem mother cell > > >> > ~xylem element ; TAIR:0000273 > > >> > ~xylem fiber cell ; TAIR:0000274 > > >> > %zygote ; TAIR:0000423 ; synonym:one cell stage % embryonic ; > > >> TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % > > >> embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; > > >> TAIR:0000374 > > >> > > >> -- > > >> ****************************** > > >> 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. > > > -------------------------------------------------------------------------- > > > > > > > > > > > > > > > > > > -- > > Pankaj Jaiswal > > Gramene Database > > www.gramene.org > > > > ----------------------------------------------------------------------------- > 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. > ----------------------------------------------------------------------------- > -------------------------------------------------------------------------- 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 rhee at acoma.Stanford.EDU Tue Apr 6 15:54:07 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Tue, 6 Apr 2004 12:54:07 -0700 (PDT) Subject: PAPER: Morphology and Genetics in TiPS (fwd) Message-ID: ---------- Forwarded message ---------- Date: Mon, 5 Apr 2004 11:56:50 -0400 From: Matyas Buzgo To: rhee at acoma.Stanford.EDU Subject: PAPER: Morphology and Genetics in TiPS Dear Sue I am happy to inform you that today our paper was published. Buzgo, M., Soltis, D.E., Soltis, P.S., Ma, H. 2004. Towards a comprehensive integration of morphological and genetic studies of floral development. Trends Plant Sci. 9 (4): 164-173 Available under http://authors.elsevier.com/sd/article/S1360138504000494 I do not yet have the reprints, but the PDF and supplementary data are available online. I would like to thank you for your discussions and your interest. Sincerely Matyas Buzgo Department of Botany University of Florida, PO Box 111526, Gainesville, FL 32611 ph: 352-392-7924, fax: 352-392-3993 From rhee at acoma.Stanford.EDU Tue Apr 6 22:05:23 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Tue, 6 Apr 2004 19:05:23 -0700 (PDT) Subject: Root node question In-Reply-To: Message-ID: I agree that they are not really developmental stage terms. It seems to me they are pretty comparable to internodes and nodes in the shoot. Perhaps you could create a branch below the root that is analogous to the internodes in the shoot? Sue On Thu, 1 Apr 2004, Katica Ilic wrote: > Hello all, > > I have a question regarding the root node that I have been working on > lately. There are few terms that I have hard time finding proper place > within the node, since they are not exactly anatomy terms in a strict > sense, which is why they are referred as developmental stages in Benfey's > lab (see Science, 12 Dec 2003, vol. 203:1956). These terms are, > meristematic zone, elongation zone, specialization zone, maturation zone, > and additional transition zone (in root apices of maize and grasses, at > least). In the paper above, for instance, stele node has all four zones, > endodermis plus cortex have all four zones, and so the epidermis. This is > of course very redundant, however, looking at TAIR and cereal anatomy > ontology, I couldn't really come up with the good solution that would > eliminate such redundancy. Since these terms refer to the regions of > differentiation, I don't think that they necessarily belong to > developmental stages ontology. > > I would appreciate if we could talk about this tomorrow morning. > > Best regards, > > 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. > -------------------------------------------------------------------------- > > ----------------------------------------------------------------------------- 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 Wed Apr 7 17:41:28 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 7 Apr 2004 14:41:28 -0700 (PDT) Subject: annotation demo and ontology discussion Message-ID: Toby, Felipe, Leszek, Pankaj and Leonore, Thanks for attending our 'phone session' today. I hope it was helpful for the POC ontology developers and sorry that the presentation took much longer than I anticipated. Pankaj, thank you for providing us access to your local server. I am glad that connections and everything else worked well. The presentation will be posted on the po-dev internal site soon. Ontology discussion was very productive, all the conclusions and the consensus we came up with will be added to the minutes. Leszek, I'll send you the info on how to extract a node from the ontology ASAP. Again, let's stick to the DAG-edit version 1.140 for now. Best regards, 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. -------------------------------------------------------------------------- From Leszek at missouri.edu Thu Apr 15 12:30:57 2004 From: Leszek at missouri.edu (Vincent, Leszek) Date: Thu, 15 Apr 2004 11:30:57 -0500 Subject: Seed & embryo ontology Message-ID: Dear PO colleagues, Attached is my seed & embryo ontology for your perusal & evaluation. I look forward to your feedback. You will note that I included some cellular detail in places. This happened just because their inclusion helped me to work with concepts (from coarsely granular to finely granular). We can move/obsolete them as & when necessary. While some of the fine grained terms are probably appropriate for inclusion in GO they are NOT there yet. One way or another these terms need to be provided in the PO. These present gaps provided further motivation to 'paint' the 'full canvas' in this draft version. For the ID range I used 19000 - 20000. - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* 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 Ph/Fax (Home): (573) 441-1228 Email: Leszek at missouri.edu Yahoo! Messenger: leszekvincent Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 Associate Curator, Dunn-Palmer Herbarium (UMO) Research Associate, Missouri Botanical Garden (MO), USA CEO - PhytoSynergy, LLC *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* -------------- next part -------------- A non-text attachment was scrubbed... Name: seed_&_embryo.definitions Type: application/octet-stream Size: 25064 bytes Desc: seed_&_embryo.definitions URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: seed_&_embryo.ontology Type: application/octet-stream Size: 16444 bytes Desc: seed_&_embryo.ontology URL: From katica at acoma.Stanford.EDU Thu Apr 15 16:41:54 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 15 Apr 2004 13:41:54 -0700 (PDT) Subject: Seed & embryo ontology In-Reply-To: Message-ID: Hi Leszek, I've just looked at your seed node briefly. It looks good, good job, we are now getting very close to completing the first draft of anatomy ontology. I'll need more time to send you my detailed feedback on the actual structures and relationships. For now (since I am planning to commit my cell type node tomorrow), my comments are limited to some 'technical' issues. There are sevreal terms that I already have in my cell type node, and we should avoid duplications. Please see the cell type node (that I e-mailed sometime ago) and either try using the IDs from there. Or on the sec thought, wait for me, since I'll be adding all the cell type terms to the sec nodes as soon as we start merging nodes (see the April minutes for details). After the annotation demo session, we talked and aggreed on how to proceed with adding the terms to different nodes). At that time, you may remember, we also agreed that subcellular structures should not be in the anatomy ontology. I had a few (polar nucleus, filiform apparatus, etc) in my cell type node and I deleted them recently. Could you please do the same? Some definitions are in my opinion, too long (for instance, Aril PO:0009090 has 93 words and 437 characters in def). This may be a problem (I need to talk to Shuly), if it turns out that there is a space limit in the table structure. Even if it's not, it might be a good idea to keep the definitions short but still informative enough. And last comment is related to references. When you use a textbook and then add some of your own words into definition, please use ISBN:XXXXXXXXXX and then include the second ref as PO:LV. Don't put all in the same line (PO:LV:ISBN:XXXXXXXXXXX). These are two reference items, though there is only one reference. I think I already sent you an e-mail about adding proper dbxrefs sometimes last week. I'll get back to you later. Please see the minutes I sent out yesterday. I am also planning to put out the POC curator's style guide (similar to what GO has), where we can find out all the relevant issues and documentations related to creating ontologies, so that we don't need to go through our meeting documenation each time. All for now. If you want, we can talk over the phone on how to synchronize adding the cell type terms into your seed node. Cheers, Katica On Thu, 15 Apr 2004, Vincent, Leszek wrote: > Dear PO colleagues, > > Attached is my seed & embryo ontology for your perusal & evaluation. I > look forward to your feedback. You will note that I included some > cellular detail in places. This happened just because their inclusion > helped me to work with concepts (from coarsely granular to finely > granular). We can move/obsolete them as & when necessary. While some of > the fine grained terms are probably appropriate for inclusion in GO they > are NOT there yet. One way or another these terms need to be provided in > the PO. These present gaps provided further motivation to 'paint' the > 'full canvas' in this draft version. For the ID range I used 19000 - > 20000. > > - Leszek > > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > 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 > Ph/Fax (Home): (573) 441-1228 > Email: Leszek at missouri.edu > Yahoo! Messenger: leszekvincent > Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 > Associate Curator, Dunn-Palmer Herbarium (UMO) > Research Associate, Missouri Botanical Garden (MO), USA > CEO - PhytoSynergy, LLC > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > -------------------------------------------------------------------------- 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 katica at acoma.Stanford.EDU Thu Apr 15 16:55:03 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 15 Apr 2004 13:55:03 -0700 (PDT) Subject: Seed & embryo ontology In-Reply-To: Message-ID: Hi Leszek, I forgot to mention, about subcellular structures, polar nucleus is already in the GO (GO:0043078), primary endosperm nucleus will be on the Source forge soon, and filiform apapartus too will be there soon. Suparna will put them on the Source forge when she gets time. Katica On Thu, 15 Apr 2004, Vincent, Leszek wrote: > Dear PO colleagues, > > Attached is my seed & embryo ontology for your perusal & evaluation. I > look forward to your feedback. You will note that I included some > cellular detail in places. This happened just because their inclusion > helped me to work with concepts (from coarsely granular to finely > granular). We can move/obsolete them as & when necessary. While some of > the fine grained terms are probably appropriate for inclusion in GO they > are NOT there yet. One way or another these terms need to be provided in > the PO. These present gaps provided further motivation to 'paint' the > 'full canvas' in this draft version. For the ID range I used 19000 - > 20000. > > - Leszek > > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > 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 > Ph/Fax (Home): (573) 441-1228 > Email: Leszek at missouri.edu > Yahoo! Messenger: leszekvincent > Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 > Associate Curator, Dunn-Palmer Herbarium (UMO) > Research Associate, Missouri Botanical Garden (MO), USA > CEO - PhytoSynergy, LLC > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > -------------------------------------------------------------------------- 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 pj37 at cornell.edu Thu Apr 15 23:00:04 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 15 Apr 2004 23:00:04 -0400 (EDT) Subject: Seed & embryo ontology In-Reply-To: References: Message-ID: <3770.24.59.76.45.1082084404.squirrel@webmail.cornell.edu> Hi Leszek, Thanks for the seed node, it looks great. This helped me a lot in refining the tissue node. I will send the tissue node structure by weekend. Here are some of my comments, though I agree with you that since many of the terms from tissue and cell nodes were not there you crested those to cover the big picture. I believe some of the terms will come from the ovule node. So they may be replaced in the final version. e.g. integument, micropyle etc. The same goes for cell and tissue types. However the structure presented by you will definitely help us filling those nodes. megaspore mother cell LV:0019032 this is not a part of seed ovule LV:0019045 is not an instance of seed. It's a part of ovary. I think you wanted to have a develops_from relationship here. Seed develops from ovule. I am not sure if we want to populate the POC with the phenotypes / attributes of ovule type instances. Do you think a generic term "ovule" will work right now. ovule primordium LV:0019045 again is not an instance of seed. correct structure is seed develops from ovule. Ovule develps from ovule primordium. cotyledon PO:0020030 by definition cotyledon is a part_of embryo atleast in dicots. I am not sure if it is true for monocots where scutellum is considered as an equivalent of dicot cotyledon. There are several other instances like obturator LV:0019021, transmitting tissue LV:0019027 etc. that seems to be part of ovule. Vincent, Leszek said: > Dear PO colleagues, > > Attached is my seed & embryo ontology for your perusal & evaluation. I > look forward to your feedback. You will note that I included some > cellular detail in places. This happened just because their inclusion > helped me to work with concepts (from coarsely granular to finely > granular). We can move/obsolete them as & when necessary. While some of > the fine grained terms are probably appropriate for inclusion in GO they > are NOT there yet. One way or another these terms need to be provided in > the PO. These present gaps provided further motivation to 'paint' the > 'full canvas' in this draft version. For the ID range I used 19000 - > 20000. > > - Leszek > > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > 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 > Ph/Fax (Home): (573) 441-1228 > Email: Leszek at missouri.edu > Yahoo! Messenger: leszekvincent > Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 > Associate Curator, Dunn-Palmer Herbarium (UMO) > Research Associate, Missouri Botanical Garden (MO), USA > CEO - PhytoSynergy, LLC > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > -- Pankaj Jaiswal Gramene Database www.gramene.org From Leszek at missouri.edu Thu Apr 15 23:12:10 2004 From: Leszek at missouri.edu (Vincent, Leszek) Date: Thu, 15 Apr 2004 22:12:10 -0500 Subject: Seed & embryo ontology Message-ID: Hi Katica, Thanks for the reply. I'll attend to the 'pruning' of terms as you suggest. I'll review definition lengths but let me know if there is a length/character limitation. Sometimes abbreviated defns are virtually useless to a reasonably informed reader let alone an inexperienced user. Regarding the Dbxrefs - from your explanation you gave me I understood that the PO:LV:ISBN..... format is what was required. The format that I used doesn't imply that I've merged my thoughts in with the published ref. def. My understanding was that the inclusion of the LV was to indicate the author or the definition. Where I did add to the defn I provided a separate Dbxref (PO:LV) to indicate that. So it seems like I should strip out all the "LV" characters just prior to the ISBN.... info. - corrrect? I'll check the recent minutes again & will get back to you if needed. Regards, - Leszek ________________________________ From: owner-po-dev at brie4.cshl.org on behalf of Katica Ilic Sent: Thu 4/15/2004 3:41 PM To: PO-Developers Cc: Shuly Avraham Subject: Re: Seed & embryo ontology Hi Leszek, I've just looked at your seed node briefly. It looks good, good job, we are now getting very close to completing the first draft of anatomy ontology. I'll need more time to send you my detailed feedback on the actual structures and relationships. For now (since I am planning to commit my cell type node tomorrow), my comments are limited to some 'technical' issues. There are sevreal terms that I already have in my cell type node, and we should avoid duplications. Please see the cell type node (that I e-mailed sometime ago) and either try using the IDs from there. Or on the sec thought, wait for me, since I'll be adding all the cell type terms to the sec nodes as soon as we start merging nodes (see the April minutes for details). After the annotation demo session, we talked and aggreed on how to proceed with adding the terms to different nodes). At that time, you may remember, we also agreed that subcellular structures should not be in the anatomy ontology. I had a few (polar nucleus, filiform apparatus, etc) in my cell type node and I deleted them recently. Could you please do the same? Some definitions are in my opinion, too long (for instance, Aril PO:0009090 has 93 words and 437 characters in def). This may be a problem (I need to talk to Shuly), if it turns out that there is a space limit in the table structure. Even if it's not, it might be a good idea to keep the definitions short but still informative enough. And last comment is related to references. When you use a textbook and then add some of your own words into definition, please use ISBN:XXXXXXXXXX and then include the second ref as PO:LV. Don't put all in the same line (PO:LV:ISBN:XXXXXXXXXXX). These are two reference items, though there is only one reference. I think I already sent you an e-mail about adding proper dbxrefs sometimes last week. I'll get back to you later. Please see the minutes I sent out yesterday. I am also planning to put out the POC curator's style guide (similar to what GO has), where we can find out all the relevant issues and documentations related to creating ontologies, so that we don't need to go through our meeting documenation each time. All for now. If you want, we can talk over the phone on how to synchronize adding the cell type terms into your seed node. Cheers, Katica On Thu, 15 Apr 2004, Vincent, Leszek wrote: > Dear PO colleagues, > > Attached is my seed & embryo ontology for your perusal & evaluation. I > look forward to your feedback. You will note that I included some > cellular detail in places. This happened just because their inclusion > helped me to work with concepts (from coarsely granular to finely > granular). We can move/obsolete them as & when necessary. While some of > the fine grained terms are probably appropriate for inclusion in GO they > are NOT there yet. One way or another these terms need to be provided in > the PO. These present gaps provided further motivation to 'paint' the > 'full canvas' in this draft version. For the ID range I used 19000 - > 20000. > > - Leszek > > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > 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 > Ph/Fax (Home): (573) 441-1228 > Email: Leszek at missouri.edu > Yahoo! Messenger: leszekvincent > Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 > Associate Curator, Dunn-Palmer Herbarium (UMO) > Research Associate, Missouri Botanical Garden (MO), USA > CEO - PhytoSynergy, LLC > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > -------------------------------------------------------------------------- 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 -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 8111 bytes Desc: not available URL: From pj37 at cornell.edu Fri Apr 16 11:12:31 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 16 Apr 2004 11:12:31 -0400 (EDT) Subject: DBXrefs In-Reply-To: References: Message-ID: <4359.24.59.76.45.1082128351.squirrel@webmail.cornell.edu> Hi Everyone, Here are the my suggestions for DBxrefs. Please use the consistent style by configuring the DBXrefs in your DAG-Edit DBXref library. Try to use lower case letters for your initials. Unless you have modified the definition available from another source do not add your id in addition to the source DBXref. If the definition is completely given by the developer based on his/her understanding, then the use of dveloper id DBXref is valid. I hope this will clear up some of the inconsistencies. Pankaj database name : TAIR database id: kl --->for Katica description: The Arabidopsis Information resource Similarly create ids for any other developer from TAIR database name : MaizeGDB database id: lv --->for Leszek description: maize Genetics and Genomics Database create ids for any other developer from MaizeGDB, e.g. mary (mp) database name : UMSL database id: fz --->for Felipe description: University of Missouri, St. Louis create ids for Toby (tk) and Peter (ps) database name : GR database id: pj --->for Pankaj description: Gramene Database database name : ISBN database id: 0080374913-->for Plant Anatomy by Fahn A description: International Standard Book Numbering similarly create any other ISBN ids for Essau's etc. database name : AP web Glosssary database id: http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html description: Angiosperm Phylogeny Website database name : Web database id: URL --->for any other web resource description: Website From katica at acoma.Stanford.EDU Fri Apr 16 12:20:47 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 16 Apr 2004 09:20:47 -0700 (PDT) Subject: DBXrefs In-Reply-To: <4359.24.59.76.45.1082128351.squirrel@webmail.cornell.edu> Message-ID: Hi Pankaj, I thought we agreed to use PO as the database name, so that every definition 'created' by POC ontology developers would have PO as database name. Term ID (which also has PO as prefix) would indicate where the term came from (by the number range). Is there any reason for doing it otherwise? By the way, I did not know about the lower case initials. I have it all in capital letters (and I also told Leszek to follow the same). Any particular reason for this? I ma just curious, of course we can always easily change it, but it seems that most of us have used capital letters so far (though I am not sure about Felipe). Katica On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > > > Hi Everyone, > > Here are the my suggestions for DBxrefs. Please use the consistent style > by configuring the DBXrefs in your DAG-Edit DBXref library. Try to use > lower case letters for your initials. Unless you have modified the > definition available from another source do not add your id in addition to > the source DBXref. If the definition is completely given by the developer > based on his/her understanding, then the use of dveloper id DBXref is > valid. > > I hope this will clear up some of the inconsistencies. > > Pankaj > > > database name : TAIR > database id: kl --->for Katica > description: The Arabidopsis Information resource > > Similarly create ids for any other developer from TAIR > > database name : MaizeGDB > database id: lv --->for Leszek > description: maize Genetics and Genomics Database > > create ids for any other developer from MaizeGDB, e.g. mary (mp) > > database name : UMSL > database id: fz --->for Felipe > description: University of Missouri, St. Louis > > create ids for Toby (tk) and Peter (ps) > > database name : GR > database id: pj --->for Pankaj > description: Gramene Database > > database name : ISBN > database id: 0080374913-->for Plant Anatomy by Fahn A > description: International Standard Book Numbering > > similarly create any other ISBN ids for Essau's etc. > > > database name : AP web Glosssary > database id: http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html > description: Angiosperm Phylogeny Website > > > > database name : Web > database id: URL --->for any other web resource > description: Website > > > -------------------------------------------------------------------------- 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 pj37 at cornell.edu Fri Apr 16 12:47:39 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 16 Apr 2004 12:47:39 -0400 Subject: DBXrefs In-Reply-To: References: Message-ID: <40800E2B.1050509@cornell.edu> Katica Ilic wrote: > Hi Pankaj, > > I thought we agreed to use PO as the database name, so that every > definition 'created' by POC ontology developers would have PO as > database name. Term ID (which also has PO as prefix) would indicate where > the term came from (by the number range). Is there any reason for doing it > otherwise? > Personally, I don't recall this conversation, though, there was a discussion on how are we going to put the DBXrefs for the definition, if they are coming from people in Monsanto for example. The reason was Monsanto do not want anyone to know if this term is tracing back to their ontologies. Therefore the agreement was that such cases where we do not want to disclose the identity, the database name will be "Poc" not "PO"and the database id will be "curators". In rest of the instances developers will use their own initials and the respective database id. Atleast this is also followed at GO. Every developer is not from GO for instance. You may want to cross check, following DBXrefs are already using the consistent style. definition_reference: Poc:curators definition_reference: TAIR:lr definition_reference: GR:pj definition_reference: MaizeDB:lv > By the way, I did not know about the lower case initials. I have it all in > capital letters (and I also told Leszek to follow the same). Any > particular reason for this? I ma just curious, of course we can always easily change > it, but it seems that most of us have used capital letters so far (though > I am not sure about Felipe). > My suggestion was based on precedence and following it with a consistent style. Infact it maintains the consistency when we are pulling out DBXrefs from species specific ontologies. Pankaj PS: I forgot to add the generic POC DBXref. Here it is database name : Poc database id: curators description: The Plant Ontology Consortium > Katica > > On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > > >> >>Hi Everyone, >> >>Here are the my suggestions for DBxrefs. Please use the consistent style >>by configuring the DBXrefs in your DAG-Edit DBXref library. Try to use >>lower case letters for your initials. Unless you have modified the >>definition available from another source do not add your id in addition to >>the source DBXref. If the definition is completely given by the developer >>based on his/her understanding, then the use of dveloper id DBXref is >>valid. >> >>I hope this will clear up some of the inconsistencies. >> >>Pankaj >> >> >>database name : TAIR >>database id: kl --->for Katica >>description: The Arabidopsis Information resource >> >>Similarly create ids for any other developer from TAIR >> >>database name : MaizeGDB >>database id: lv --->for Leszek >>description: maize Genetics and Genomics Database >> >>create ids for any other developer from MaizeGDB, e.g. mary (mp) >> >>database name : UMSL >>database id: fz --->for Felipe >>description: University of Missouri, St. Louis >> >>create ids for Toby (tk) and Peter (ps) >> >>database name : GR >>database id: pj --->for Pankaj >>description: Gramene Database >> >>database name : ISBN >>database id: 0080374913-->for Plant Anatomy by Fahn A >>description: International Standard Book Numbering >> >>similarly create any other ISBN ids for Essau's etc. >> >> >>database name : AP web Glosssary >>database id: http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html >>description: Angiosperm Phylogeny Website >> >> >> >>database name : Web >>database id: URL --->for any other web resource >>description: Website >> >> >> > > > -------------------------------------------------------------------------- > 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. > -------------------------------------------------------------------------- > > > -- ****************************** 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 fzqhd at studentmail.umsl.edu Fri Apr 16 13:53:24 2004 From: fzqhd at studentmail.umsl.edu (Felipe Zapata) Date: Fri, 16 Apr 2004 12:53:24 -0500 Subject: DBXrefs In-Reply-To: <40800E2B.1050509@cornell.edu> References: <40800E2B.1050509@cornell.edu> Message-ID: If I'm not wrong I think I have used little letters F On Apr 16, 2004, at 11:47 AM, Pankaj Jaiswal wrote: > > > Katica Ilic wrote: >> Hi Pankaj, >> I thought we agreed to use PO as the database name, so that every >> definition 'created' by POC ontology developers would have PO as >> database name. Term ID (which also has PO as prefix) would indicate >> where >> the term came from (by the number range). Is there any reason for >> doing it >> otherwise? > Personally, I don't recall this conversation, though, there was a > discussion on how are we going to put the DBXrefs for the definition, > if they are coming from people in Monsanto for example. The reason was > Monsanto do not want anyone to know if this term is tracing back to > their ontologies. > > Therefore the agreement was that such cases where we do not want to > disclose the identity, the database name will be "Poc" not "PO"and the > database id will be "curators". In rest of the instances developers > will use their own initials and the respective database id. Atleast > this is also followed at GO. Every developer is not from GO for > instance. > > You may want to cross check, following DBXrefs are already using the > consistent style. > definition_reference: Poc:curators > definition_reference: TAIR:lr > definition_reference: GR:pj > definition_reference: MaizeDB:lv > > >> By the way, I did not know about the lower case initials. I have it >> all in >> capital letters (and I also told Leszek to follow the same). Any >> particular reason for this? I ma just curious, of course we can >> always easily change >> it, but it seems that most of us have used capital letters so far >> (though >> I am not sure about Felipe). > My suggestion was based on precedence and following it with a > consistent style. Infact it maintains the consistency when we are > pulling out DBXrefs from species specific ontologies. > > Pankaj > > > PS: I forgot to add the generic POC DBXref. Here it is > > database name : Poc > database id: curators > description: The Plant Ontology Consortium > > >> Katica >> On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: >>> >>> Hi Everyone, >>> >>> Here are the my suggestions for DBxrefs. Please use the consistent >>> style >>> by configuring the DBXrefs in your DAG-Edit DBXref library. Try to >>> use >>> lower case letters for your initials. Unless you have modified the >>> definition available from another source do not add your id in >>> addition to >>> the source DBXref. If the definition is completely given by the >>> developer >>> based on his/her understanding, then the use of dveloper id DBXref is >>> valid. >>> >>> I hope this will clear up some of the inconsistencies. >>> >>> Pankaj >>> >>> >>> database name : TAIR >>> database id: kl --->for Katica >>> description: The Arabidopsis Information resource >>> >>> Similarly create ids for any other developer from TAIR >>> >>> database name : MaizeGDB >>> database id: lv --->for Leszek >>> description: maize Genetics and Genomics Database >>> >>> create ids for any other developer from MaizeGDB, e.g. mary (mp) >>> >>> database name : UMSL >>> database id: fz --->for Felipe >>> description: University of Missouri, St. Louis >>> >>> create ids for Toby (tk) and Peter (ps) >>> >>> database name : GR >>> database id: pj --->for Pankaj >>> description: Gramene Database >>> >>> database name : ISBN >>> database id: 0080374913-->for Plant Anatomy by Fahn A >>> description: International Standard Book Numbering >>> >>> similarly create any other ISBN ids for Essau's etc. >>> >>> >>> database name : AP web Glosssary >>> database id: >>> http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html >>> description: Angiosperm Phylogeny Website >>> >>> >>> >>> database name : Web >>> database id: URL --->for any other web resource >>> description: Website >>> >>> >>> >> ---------------------------------------------------------------------- >> ---- >> 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. >> ---------------------------------------------------------------------- >> ---- > > -- > ****************************** > 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 > ***************************** > > > ~~~~~~ Felipe Zapata University of Missouri St. Louis Department of Biology 8001 Natural Bridge Rd. St. Louis, MO 63121 314 516-6200 From lreiser at acoma.Stanford.EDU Fri Apr 16 14:04:12 2004 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Fri, 16 Apr 2004 11:04:12 -0700 (PDT) Subject: DBXrefs In-Reply-To: Message-ID: Im just curious about when these DBXrefs are being used and for what purpose. So when I included say TAIR:lr in a reference for a definition, I did to to mean 1) I wrote this definition myself from my own head OR 2) When used with another citation (eg. ISBN:XXXXXX) it means the definition has been paraphrased or modified from its original text. I never used it to say-- these terms came from TAIR or whereever. Thats why we all have numberspaces... like the GO... and we track who added the terms in CVS... Do I understand the usage of these dbxrefs correctly? Leonore On Fri, 16 Apr 2004, Felipe Zapata wrote: > If I'm not wrong I think I have used little letters > F > On Apr 16, 2004, at 11:47 AM, Pankaj Jaiswal wrote: > > > > > > > Katica Ilic wrote: > >> Hi Pankaj, > >> I thought we agreed to use PO as the database name, so that every > >> definition 'created' by POC ontology developers would have PO as > >> database name. Term ID (which also has PO as prefix) would indicate > >> where > >> the term came from (by the number range). Is there any reason for > >> doing it > >> otherwise? > > Personally, I don't recall this conversation, though, there was a > > discussion on how are we going to put the DBXrefs for the definition, > > if they are coming from people in Monsanto for example. The reason was > > Monsanto do not want anyone to know if this term is tracing back to > > their ontologies. > > > > Therefore the agreement was that such cases where we do not want to > > disclose the identity, the database name will be "Poc" not "PO"and the > > database id will be "curators". In rest of the instances developers > > will use their own initials and the respective database id. Atleast > > this is also followed at GO. Every developer is not from GO for > > instance. > > > > You may want to cross check, following DBXrefs are already using the > > consistent style. > > definition_reference: Poc:curators > > definition_reference: TAIR:lr > > definition_reference: GR:pj > > definition_reference: MaizeDB:lv > > > > > >> By the way, I did not know about the lower case initials. I have it > >> all in > >> capital letters (and I also told Leszek to follow the same). Any > >> particular reason for this? I ma just curious, of course we can > >> always easily change > >> it, but it seems that most of us have used capital letters so far > >> (though > >> I am not sure about Felipe). > > My suggestion was based on precedence and following it with a > > consistent style. Infact it maintains the consistency when we are > > pulling out DBXrefs from species specific ontologies. > > > > Pankaj > > > > > > PS: I forgot to add the generic POC DBXref. Here it is > > > > database name : Poc > > database id: curators > > description: The Plant Ontology Consortium > > > > > >> Katica > >> On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > >>> > >>> Hi Everyone, > >>> > >>> Here are the my suggestions for DBxrefs. Please use the consistent > >>> style > >>> by configuring the DBXrefs in your DAG-Edit DBXref library. Try to > >>> use > >>> lower case letters for your initials. Unless you have modified the > >>> definition available from another source do not add your id in > >>> addition to > >>> the source DBXref. If the definition is completely given by the > >>> developer > >>> based on his/her understanding, then the use of dveloper id DBXref is > >>> valid. > >>> > >>> I hope this will clear up some of the inconsistencies. > >>> > >>> Pankaj > >>> > >>> > >>> database name : TAIR > >>> database id: kl --->for Katica > >>> description: The Arabidopsis Information resource > >>> > >>> Similarly create ids for any other developer from TAIR > >>> > >>> database name : MaizeGDB > >>> database id: lv --->for Leszek > >>> description: maize Genetics and Genomics Database > >>> > >>> create ids for any other developer from MaizeGDB, e.g. mary (mp) > >>> > >>> database name : UMSL > >>> database id: fz --->for Felipe > >>> description: University of Missouri, St. Louis > >>> > >>> create ids for Toby (tk) and Peter (ps) > >>> > >>> database name : GR > >>> database id: pj --->for Pankaj > >>> description: Gramene Database > >>> > >>> database name : ISBN > >>> database id: 0080374913-->for Plant Anatomy by Fahn A > >>> description: International Standard Book Numbering > >>> > >>> similarly create any other ISBN ids for Essau's etc. > >>> > >>> > >>> database name : AP web Glosssary > >>> database id: > >>> http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html > >>> description: Angiosperm Phylogeny Website > >>> > >>> > >>> > >>> database name : Web > >>> database id: URL --->for any other web resource > >>> description: Website > >>> > >>> > >>> > >> ---------------------------------------------------------------------- > >> ---- > >> 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. > >> ---------------------------------------------------------------------- > >> ---- > > > > -- > > ****************************** > > 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 > > ***************************** > > > > > > > ~~~~~~ > Felipe Zapata > University of Missouri St. Louis > Department of Biology > 8001 Natural Bridge Rd. > St. Louis, MO 63121 > 314 516-6200 > ------------------------------------------------------------------------------- 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 Fri Apr 16 14:13:21 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 16 Apr 2004 14:13:21 -0400 Subject: DBXrefs In-Reply-To: References: Message-ID: <40802241.7020305@cornell.edu> Leonore Reiser wrote: > Im just curious about when these DBXrefs are being used and for what > purpose. > So when I included say TAIR:lr in a reference for a definition, I did to > to mean > 1) I wrote this definition myself from my own head OR > 2) When used with another citation (eg. ISBN:XXXXXX) it means the > definition has been paraphrased or modified from its original text. > > > I never used it to say-- these terms came from TAIR or whereever. Thats > why we all have numberspaces... like the GO... and we track who added the > terms in CVS... > > Do I understand the usage of these dbxrefs correctly? > Leonore > Yes you understood it correctly. Didn't I say the same thing. Pankaj >>>>On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: >>>> >>>>>Hi Everyone, >>>>> >>>>>Here are the my suggestions for DBxrefs. Please use the consistent >>>>>style >>>>>by configuring the DBXrefs in your DAG-Edit DBXref library. Try to >>>>>use >>>>>lower case letters for your initials. Unless you have modified the >>>>>definition available from another source do not add your id in >>>>>addition to >>>>>the source DBXref. If the definition is completely given by the >>>>>developer >>>>>based on his/her understanding, then the use of dveloper id DBXref is >>>>>valid. >>>>> >>>>>I hope this will clear up some of the inconsistencies. >>>>> >>>>>Pankaj From katica at acoma.Stanford.EDU Fri Apr 16 14:14:02 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 16 Apr 2004 11:14:02 -0700 (PDT) Subject: DBXrefs In-Reply-To: Message-ID: Pankaj, Yes, the particular conversation in San Diego I was reffering to, was inititated when we talked about Monsanto definitions and their requests not to disclose the source. Then I asked if it would be possible to trace the definitions in general, and I from what I recall the answer was no, and that it doesn't metter, all the definitions would have PO prefix (and I think we were not talking about Term IDs), and that only the term ID number would indicate who entered it. At the end, it doesn't really metter, as long as we are consistent. Speaking of GO, they have different reasons to keep the database name in dbxref, there are over 20 curators contributing to GO, with aprox. 15,000 terms so far, so it makes sense to keep track of who did what. Anyway, let's just agree on this and move on. I would like to hear breifly from other POC members regarding this issue. Thanks, Katica On Fri, 16 Apr 2004, Felipe Zapata wrote: > If I'm not wrong I think I have used little letters > F > On Apr 16, 2004, at 11:47 AM, Pankaj Jaiswal wrote: > > > > > > > Katica Ilic wrote: > >> Hi Pankaj, > >> I thought we agreed to use PO as the database name, so that every > >> definition 'created' by POC ontology developers would have PO as > >> database name. Term ID (which also has PO as prefix) would indicate > >> where > >> the term came from (by the number range). Is there any reason for > >> doing it > >> otherwise? > > Personally, I don't recall this conversation, though, there was a > > discussion on how are we going to put the DBXrefs for the definition, > > if they are coming from people in Monsanto for example. The reason was > > Monsanto do not want anyone to know if this term is tracing back to > > their ontologies. > > > > Therefore the agreement was that such cases where we do not want to > > disclose the identity, the database name will be "Poc" not "PO"and the > > database id will be "curators". In rest of the instances developers > > will use their own initials and the respective database id. Atleast > > this is also followed at GO. Every developer is not from GO for > > instance. > > > > You may want to cross check, following DBXrefs are already using the > > consistent style. > > definition_reference: Poc:curators > > definition_reference: TAIR:lr > > definition_reference: GR:pj > > definition_reference: MaizeDB:lv > > > > > >> By the way, I did not know about the lower case initials. I have it > >> all in > >> capital letters (and I also told Leszek to follow the same). Any > >> particular reason for this? I ma just curious, of course we can > >> always easily change > >> it, but it seems that most of us have used capital letters so far > >> (though > >> I am not sure about Felipe). > > My suggestion was based on precedence and following it with a > > consistent style. Infact it maintains the consistency when we are > > pulling out DBXrefs from species specific ontologies. > > > > Pankaj > > > > > > PS: I forgot to add the generic POC DBXref. Here it is > > > > database name : Poc > > database id: curators > > description: The Plant Ontology Consortium > > > > > >> Katica > >> On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > >>> > >>> Hi Everyone, > >>> > >>> Here are the my suggestions for DBxrefs. Please use the consistent > >>> style > >>> by configuring the DBXrefs in your DAG-Edit DBXref library. Try to > >>> use > >>> lower case letters for your initials. Unless you have modified the > >>> definition available from another source do not add your id in > >>> addition to > >>> the source DBXref. If the definition is completely given by the > >>> developer > >>> based on his/her understanding, then the use of dveloper id DBXref is > >>> valid. > >>> > >>> I hope this will clear up some of the inconsistencies. > >>> > >>> Pankaj > >>> > >>> > >>> database name : TAIR > >>> database id: kl --->for Katica > >>> description: The Arabidopsis Information resource > >>> > >>> Similarly create ids for any other developer from TAIR > >>> > >>> database name : MaizeGDB > >>> database id: lv --->for Leszek > >>> description: maize Genetics and Genomics Database > >>> > >>> create ids for any other developer from MaizeGDB, e.g. mary (mp) > >>> > >>> database name : UMSL > >>> database id: fz --->for Felipe > >>> description: University of Missouri, St. Louis > >>> > >>> create ids for Toby (tk) and Peter (ps) > >>> > >>> database name : GR > >>> database id: pj --->for Pankaj > >>> description: Gramene Database > >>> > >>> database name : ISBN > >>> database id: 0080374913-->for Plant Anatomy by Fahn A > >>> description: International Standard Book Numbering > >>> > >>> similarly create any other ISBN ids for Essau's etc. > >>> > >>> > >>> database name : AP web Glosssary > >>> database id: > >>> http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html > >>> description: Angiosperm Phylogeny Website > >>> > >>> > >>> > >>> database name : Web > >>> database id: URL --->for any other web resource > >>> description: Website > >>> > >>> > >>> > >> ---------------------------------------------------------------------- > >> ---- > >> 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. > >> ---------------------------------------------------------------------- > >> ---- > > > > -- > > ****************************** > > 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 > > ***************************** > > > > > > > ~~~~~~ > 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. -------------------------------------------------------------------------- From lreiser at acoma.Stanford.EDU Fri Apr 16 14:20:27 2004 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Fri, 16 Apr 2004 11:20:27 -0700 (PDT) Subject: DBXrefs In-Reply-To: <40802241.7020305@cornell.edu> Message-ID: cool-then does it really matter then if its TAIR:ki or PO:ki? since GO was an unfunded collaboration long before it was a funded consortium, perhaps thats why the id space was less generic. i dont think we need to be that complicated. leo On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > > > Leonore Reiser wrote: > > > Im just curious about when these DBXrefs are being used and for what > > purpose. > > So when I included say TAIR:lr in a reference for a definition, I did to > > to mean > > 1) I wrote this definition myself from my own head OR > > 2) When used with another citation (eg. ISBN:XXXXXX) it means the > > definition has been paraphrased or modified from its original text. > > > > > > I never used it to say-- these terms came from TAIR or whereever. Thats > > why we all have numberspaces... like the GO... and we track who added the > > terms in CVS... > > > > Do I understand the usage of these dbxrefs correctly? > > Leonore > > > > Yes you understood it correctly. Didn't I say the same thing. > > Pankaj > > >>>>On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > >>>> > >>>>>Hi Everyone, > >>>>> > >>>>>Here are the my suggestions for DBxrefs. Please use the consistent > >>>>>style > >>>>>by configuring the DBXrefs in your DAG-Edit DBXref library. Try to > >>>>>use > >>>>>lower case letters for your initials. Unless you have modified the > >>>>>definition available from another source do not add your id in > >>>>>addition to > >>>>>the source DBXref. If the definition is completely given by the > >>>>>developer > >>>>>based on his/her understanding, then the use of dveloper id DBXref is > >>>>>valid. > >>>>> > >>>>>I hope this will clear up some of the inconsistencies. > >>>>> > >>>>>Pankaj > > ------------------------------------------------------------------------------- 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 Fri Apr 16 14:26:04 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 16 Apr 2004 14:26:04 -0400 Subject: DBXrefs In-Reply-To: References: Message-ID: <4080253C.6090501@cornell.edu> My suggestion is to keep it informative. It's best to use the individual DB acronym instead of PO. It's less effort on POC to manage this. POC should assign only the number space. Pankaj Leonore Reiser wrote: > cool-then does it really matter then if its TAIR:ki or PO:ki? since GO was > an unfunded collaboration long before it was a funded consortium, perhaps > thats why the id space was less generic. i dont think we need to be that > complicated. > leo > > On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > > >> >>Leonore Reiser wrote: >> >> >>>Im just curious about when these DBXrefs are being used and for what >>>purpose. >>>So when I included say TAIR:lr in a reference for a definition, I did to >>>to mean >>>1) I wrote this definition myself from my own head OR >>>2) When used with another citation (eg. ISBN:XXXXXX) it means the >>>definition has been paraphrased or modified from its original text. >>> >>> >>>I never used it to say-- these terms came from TAIR or whereever. Thats >>>why we all have numberspaces... like the GO... and we track who added the >>>terms in CVS... >>> >>>Do I understand the usage of these dbxrefs correctly? >>>Leonore >>> >> >>Yes you understood it correctly. Didn't I say the same thing. >> >>Pankaj >> >> >>>>>>On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: >>>>>> >>>>>> >>>>>>>Hi Everyone, >>>>>>> >>>>>>>Here are the my suggestions for DBxrefs. Please use the consistent >>>>>>>style >>>>>>>by configuring the DBXrefs in your DAG-Edit DBXref library. Try to >>>>>>>use >>>>>>>lower case letters for your initials. Unless you have modified the >>>>>>>definition available from another source do not add your id in >>>>>>>addition to >>>>>>>the source DBXref. If the definition is completely given by the >>>>>>>developer >>>>>>>based on his/her understanding, then the use of dveloper id DBXref is >>>>>>>valid. >>>>>>> >>>>>>>I hope this will clear up some of the inconsistencies. >>>>>>> >>>>>>>Pankaj >> >> > > ------------------------------------------------------------------------------- > 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 katica at acoma.Stanford.EDU Fri Apr 16 14:42:14 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 16 Apr 2004 11:42:14 -0700 (PDT) Subject: DBXrefs In-Reply-To: Message-ID: OK, I'll use 'little' letters too from now on. Leszek, can you change yours too (you can simply search and replace all in emacs)? Sorry for the confusion. Katica On Fri, 16 Apr 2004, Felipe Zapata wrote: > If I'm not wrong I think I have used little letters > F > On Apr 16, 2004, at 11:47 AM, Pankaj Jaiswal wrote: > > > > > > > Katica Ilic wrote: > >> Hi Pankaj, > >> I thought we agreed to use PO as the database name, so that every > >> definition 'created' by POC ontology developers would have PO as > >> database name. Term ID (which also has PO as prefix) would indicate > >> where > >> the term came from (by the number range). Is there any reason for > >> doing it > >> otherwise? > > Personally, I don't recall this conversation, though, there was a > > discussion on how are we going to put the DBXrefs for the definition, > > if they are coming from people in Monsanto for example. The reason was > > Monsanto do not want anyone to know if this term is tracing back to > > their ontologies. > > > > Therefore the agreement was that such cases where we do not want to > > disclose the identity, the database name will be "Poc" not "PO"and the > > database id will be "curators". In rest of the instances developers > > will use their own initials and the respective database id. Atleast > > this is also followed at GO. Every developer is not from GO for > > instance. > > > > You may want to cross check, following DBXrefs are already using the > > consistent style. > > definition_reference: Poc:curators > > definition_reference: TAIR:lr > > definition_reference: GR:pj > > definition_reference: MaizeDB:lv > > > > > >> By the way, I did not know about the lower case initials. I have it > >> all in > >> capital letters (and I also told Leszek to follow the same). Any > >> particular reason for this? I ma just curious, of course we can > >> always easily change > >> it, but it seems that most of us have used capital letters so far > >> (though > >> I am not sure about Felipe). > > My suggestion was based on precedence and following it with a > > consistent style. Infact it maintains the consistency when we are > > pulling out DBXrefs from species specific ontologies. > > > > Pankaj > > > > > > PS: I forgot to add the generic POC DBXref. Here it is > > > > database name : Poc > > database id: curators > > description: The Plant Ontology Consortium > > > > > >> Katica > >> On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: > >>> > >>> Hi Everyone, > >>> > >>> Here are the my suggestions for DBxrefs. Please use the consistent > >>> style > >>> by configuring the DBXrefs in your DAG-Edit DBXref library. Try to > >>> use > >>> lower case letters for your initials. Unless you have modified the > >>> definition available from another source do not add your id in > >>> addition to > >>> the source DBXref. If the definition is completely given by the > >>> developer > >>> based on his/her understanding, then the use of dveloper id DBXref is > >>> valid. > >>> > >>> I hope this will clear up some of the inconsistencies. > >>> > >>> Pankaj > >>> > >>> > >>> database name : TAIR > >>> database id: kl --->for Katica > >>> description: The Arabidopsis Information resource > >>> > >>> Similarly create ids for any other developer from TAIR > >>> > >>> database name : MaizeGDB > >>> database id: lv --->for Leszek > >>> description: maize Genetics and Genomics Database > >>> > >>> create ids for any other developer from MaizeGDB, e.g. mary (mp) > >>> > >>> database name : UMSL > >>> database id: fz --->for Felipe > >>> description: University of Missouri, St. Louis > >>> > >>> create ids for Toby (tk) and Peter (ps) > >>> > >>> database name : GR > >>> database id: pj --->for Pankaj > >>> description: Gramene Database > >>> > >>> database name : ISBN > >>> database id: 0080374913-->for Plant Anatomy by Fahn A > >>> description: International Standard Book Numbering > >>> > >>> similarly create any other ISBN ids for Essau's etc. > >>> > >>> > >>> database name : AP web Glosssary > >>> database id: > >>> http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html > >>> description: Angiosperm Phylogeny Website > >>> > >>> > >>> > >>> database name : Web > >>> database id: URL --->for any other web resource > >>> description: Website > >>> > >>> > >>> > >> ---------------------------------------------------------------------- > >> ---- > >> 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. > >> ---------------------------------------------------------------------- > >> ---- > > > > -- > > ****************************** > > 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 > > ***************************** > > > > > > > ~~~~~~ > 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. -------------------------------------------------------------------------- From fzqhd at studentmail.umsl.edu Fri Apr 16 15:11:36 2004 From: fzqhd at studentmail.umsl.edu (Felipe Zapata) Date: Fri, 16 Apr 2004 14:11:36 -0500 Subject: DBXrefs In-Reply-To: References: Message-ID: Just to add: In our first ontology draft, most of the definitions were taken from APWeb glossary (that's OK). But when we used definitions that Gramene, TAIR or MayzeGDB had (either from ISBN XXXXX or not) we just used GR:pj, TAIR:lr and Mayze:lv and we did not make explicit reference to the ISBN used in those ontologies. F On Apr 16, 2004, at 1:04 PM, Leonore Reiser wrote: > > Im just curious about when these DBXrefs are being used and for what > purpose. > So when I included say TAIR:lr in a reference for a definition, I did > to > to mean > 1) I wrote this definition myself from my own head OR > 2) When used with another citation (eg. ISBN:XXXXXX) it means the > definition has been paraphrased or modified from its original text. > > > I never used it to say-- these terms came from TAIR or whereever. Thats > why we all have numberspaces... like the GO... and we track who added > the > terms in CVS... > > Do I understand the usage of these dbxrefs correctly? > Leonore > > On Fri, 16 Apr 2004, Felipe Zapata wrote: > >> If I'm not wrong I think I have used little letters >> F >> On Apr 16, 2004, at 11:47 AM, Pankaj Jaiswal wrote: >> >>> >>> >>> Katica Ilic wrote: >>>> Hi Pankaj, >>>> I thought we agreed to use PO as the database name, so that every >>>> definition 'created' by POC ontology developers would have PO as >>>> database name. Term ID (which also has PO as prefix) would indicate >>>> where >>>> the term came from (by the number range). Is there any reason for >>>> doing it >>>> otherwise? >>> Personally, I don't recall this conversation, though, there was a >>> discussion on how are we going to put the DBXrefs for the definition, >>> if they are coming from people in Monsanto for example. The reason >>> was >>> Monsanto do not want anyone to know if this term is tracing back to >>> their ontologies. >>> >>> Therefore the agreement was that such cases where we do not want to >>> disclose the identity, the database name will be "Poc" not "PO"and >>> the >>> database id will be "curators". In rest of the instances developers >>> will use their own initials and the respective database id. Atleast >>> this is also followed at GO. Every developer is not from GO for >>> instance. >>> >>> You may want to cross check, following DBXrefs are already using the >>> consistent style. >>> definition_reference: Poc:curators >>> definition_reference: TAIR:lr >>> definition_reference: GR:pj >>> definition_reference: MaizeDB:lv >>> >>> >>>> By the way, I did not know about the lower case initials. I have it >>>> all in >>>> capital letters (and I also told Leszek to follow the same). Any >>>> particular reason for this? I ma just curious, of course we can >>>> always easily change >>>> it, but it seems that most of us have used capital letters so far >>>> (though >>>> I am not sure about Felipe). >>> My suggestion was based on precedence and following it with a >>> consistent style. Infact it maintains the consistency when we are >>> pulling out DBXrefs from species specific ontologies. >>> >>> Pankaj >>> >>> >>> PS: I forgot to add the generic POC DBXref. Here it is >>> >>> database name : Poc >>> database id: curators >>> description: The Plant Ontology Consortium >>> >>> >>>> Katica >>>> On Fri, 16 Apr 2004, Pankaj Jaiswal wrote: >>>>> >>>>> Hi Everyone, >>>>> >>>>> Here are the my suggestions for DBxrefs. Please use the consistent >>>>> style >>>>> by configuring the DBXrefs in your DAG-Edit DBXref library. Try to >>>>> use >>>>> lower case letters for your initials. Unless you have modified the >>>>> definition available from another source do not add your id in >>>>> addition to >>>>> the source DBXref. If the definition is completely given by the >>>>> developer >>>>> based on his/her understanding, then the use of dveloper id DBXref >>>>> is >>>>> valid. >>>>> >>>>> I hope this will clear up some of the inconsistencies. >>>>> >>>>> Pankaj >>>>> >>>>> >>>>> database name : TAIR >>>>> database id: kl --->for Katica >>>>> description: The Arabidopsis Information resource >>>>> >>>>> Similarly create ids for any other developer from TAIR >>>>> >>>>> database name : MaizeGDB >>>>> database id: lv --->for Leszek >>>>> description: maize Genetics and Genomics Database >>>>> >>>>> create ids for any other developer from MaizeGDB, e.g. mary (mp) >>>>> >>>>> database name : UMSL >>>>> database id: fz --->for Felipe >>>>> description: University of Missouri, St. Louis >>>>> >>>>> create ids for Toby (tk) and Peter (ps) >>>>> >>>>> database name : GR >>>>> database id: pj --->for Pankaj >>>>> description: Gramene Database >>>>> >>>>> database name : ISBN >>>>> database id: 0080374913-->for Plant Anatomy by Fahn A >>>>> description: International Standard Book Numbering >>>>> >>>>> similarly create any other ISBN ids for Essau's etc. >>>>> >>>>> >>>>> database name : AP web Glosssary >>>>> database id: >>>>> http://www.mobot.org/MOBOT/Research/APweb/top/glossarya_h.html >>>>> description: Angiosperm Phylogeny Website >>>>> >>>>> >>>>> >>>>> database name : Web >>>>> database id: URL --->for any other web resource >>>>> description: Website >>>>> >>>>> >>>>> >>>> -------------------------------------------------------------------- >>>> -- >>>> ---- >>>> 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. >>>> -------------------------------------------------------------------- >>>> -- >>>> ---- >>> >>> -- >>> ****************************** >>> 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 >>> ***************************** >>> >>> >>> >> ~~~~~~ >> Felipe Zapata >> University of Missouri St. Louis >> Department of Biology >> 8001 Natural Bridge Rd. >> St. Louis, MO 63121 >> 314 516-6200 >> > > ----------------------------------------------------------------------- > -------- > 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 > ----------------------------------------------------------------------- > -------- > > ~~~~~~ Felipe Zapata University of Missouri St. Louis Department of Biology 8001 Natural Bridge Rd. St. Louis, MO 63121 314 516-6200 From katica at acoma.Stanford.EDU Mon Apr 19 14:07:11 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 19 Apr 2004 11:07:11 -0700 (PDT) Subject: Seed & embryo ontology In-Reply-To: Message-ID: Hi Leszek, Here are my two cents: 1. Embryo sac is not part of the embryo/seed node. This entire node (with all the children) belongs to the gynoecium node, child of the ovule (or develops from megaspore). Within this node, you have endosperm (with 4 children terms), which does not belong to the embryo sac node, but it does to seed node (and you already have it there). 2. Hypodermal nucellar cell should not be in the seed/embryo node either. Don't get me wrong, the whole node is OK, it just needs to be moved to the different node. Since none of the terms (please check this out again in the anatomy ontology) under this node exist in the main ontology, I'll suggest to Felipe t import the entire node to the megasporocite node (I would say, as a part of ovary). Similarly, megaspore mother cell should be deleted too from the seed node, as Pankaj already pointed out (and moved to the appropriate node in the main ontology). Also, ovule and ovule primordium are not instances of seed either (true path rule is violated in all of the cases above). 4. Cotyledon should be under the embryo node (part of). 5. (A minor point): Hypopcotyl-rood axis should have synonym embryo axis (or vice versa). 6. Please, delete completely following 4 terms: polar nucleus, primary polar nucleus, sec endosperm nucleus and filiform apparatus (all subcellular structures). Also, make sure that no term in your node already exists in the main anatomy ontology (which will have cell type node in with today's update). We should avoid duplication. If a term do exist in the mani ont and deleting it is not an option, my suggestion is to copy and paste exact definition for that term from the anatomy ont, and then manually change the term ID to the one from the anatomy ontology. This way, when you import your node (without choosing the ID stripping option), the two terms will 'merge' into one. I myself have had a problems when importing a node due to term duplications. After trimming all these terms, your seed node will get much shorter (and it may look to you as incomplete), but don't worry, the other tissue and cell type terms will be placed in and the final version will be more comprehensive. Also, do we need the term parietal cell? I am asking because it should be in the cell type node too, and so far I did not find any gene annotated or any publication referring to gene expression in this cell type. This is all for now. Cheers, Katica On Thu, 15 Apr 2004, Vincent, Leszek wrote: > Dear PO colleagues, > > Attached is my seed & embryo ontology for your perusal & evaluation. I > look forward to your feedback. You will note that I included some > cellular detail in places. This happened just because their inclusion > helped me to work with concepts (from coarsely granular to finely > granular). We can move/obsolete them as & when necessary. While some of > the fine grained terms are probably appropriate for inclusion in GO they > are NOT there yet. One way or another these terms need to be provided in > the PO. These present gaps provided further motivation to 'paint' the > 'full canvas' in this draft version. For the ID range I used 19000 - > 20000. > > - Leszek > > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > 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 > Ph/Fax (Home): (573) 441-1228 > Email: Leszek at missouri.edu > Yahoo! Messenger: leszekvincent > Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 > Associate Curator, Dunn-Palmer Herbarium (UMO) > Research Associate, Missouri Botanical Garden (MO), USA > CEO - PhytoSynergy, LLC > *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > -------------------------------------------------------------------------- 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 pj37 at cornell.edu Mon Apr 19 16:49:16 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 19 Apr 2004 16:49:16 -0400 Subject: tissue node Message-ID: <40843B4C.5060401@cornell.edu> Hi Everyone, Attached are the ontology and definition files for tissue node. While working on this node, I came up with some of the terms that need attention. - I did not create a separate term for meristem zones. All the valid zone terms are part of the localized meristem in this ontology. - tunica and corpus terms were dropped as part of Shoot apical meristem - only L1, L2 and L3 went in - To which node the organ primordium belong ? - the term Vascular bundle did not go in. because it is a kind or organized region where vascular tissue are found. I look forward to your feedback. ****************************** 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 ***************************** -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: tissue-combo1.definition URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: tissue-combo1.ontology URL: From katica at acoma.Stanford.EDU Mon Apr 19 21:04:17 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 19 Apr 2004 18:04:17 -0700 (PDT) Subject: Cell type node committed In-Reply-To: <40843B4C.5060401@cornell.edu> Message-ID: Hi everyone, My cell type node has been merged to the main anatomy ontology (as of last Friday). However, I need to correct some nodes, since the cell node ended up with the structures that don't belong there, because they were childrens of the terms that already existed in the anatomy file. For instance, pollen and embryo sac ended up in the cell node, just because they were childrens of the terms microspore and megaspore, both already existing terms in the main anatomy ontology. So please, don't use the latest version (April 16), I am committing new, corrected version of anatomy ontology tonight. Thanks, 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. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Tue Apr 20 15:41:03 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 20 Apr 2004 12:41:03 -0700 (PDT) Subject: Changes on the POC e-mail lists Message-ID: To the POC e-mail list subscribers, Please notice that the Plant Ontology Consortium has implemented the following changes to the POC e-mail lists: 1. Subscribers of the po at plantontology.org e-mail list are now assigned to the po-dev at plantontology.org list, which has become a discussion e-mail list for Plant Ontology Consortium members, collaborators, ontology developers and curators. Archives of these messages will soon be available from the POC e-mail archive (please see URL:www.plantontology.org/mailarch/). 2. The po at plantontology.org e-mail list no longer exists as a discussion list. Instead, this e-mail address will remain the main contact address on the POC web site, and all incoming e-mails to po at plantology.org will be forwarded to the po-dev at plant ontology.org. 3. No changes have been made to the po-announce at plantontology.org e-mail list. Public announcements related to the POC Project are distributed to this e-mail list and are available from the POC email archive (please see URL: http://www.plantontology.org/mailarch-announce/). These changes are effective April 20, 2004. Sincerely, Katica Ilic, POC Project Coordinator -------------------------------------------------------------------------- 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 katica at acoma.Stanford.EDU Tue Apr 20 20:31:55 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 20 Apr 2004 17:31:55 -0700 (PDT) Subject: New changes to plant anatomy ontology In-Reply-To: Message-ID: Hello, Here is the list of changes that I made to the plant anatomy ontology yesterday. I have not committed it yet, and if everyone agrees, I would like to commit the new files to the cvs as soon as possible. I've corrected all the mistakes in my cell type node that ocurred after this node got imported to the main ontology (due to the parantage of the terms that already existed in the anatomy ontology). 1. Merged the existing PO term sperm nuclei (PO:0020098) to the cell type term sperm cell (PO:0000084). This seems better idea than deleting the term sperm nuclei (when I did this, it didn't show up in the obsolete node). First, sperm cells are indeed whole cells, not just nuclei, and second, we agreed not to have subcellular structures in the anatomy ontology. 2. Changed Felipe's term antipodals to antipodal cell (to avoid plurals). 3.Deleted embryo sac from the cell type node; this term is still present in the gametophyte node. 4. Couldn't do the same with pollen under the microspore term, that ended up there as I explained in the earlier message (when I did, all the instances of pollen were gone with all the childrens). So I had to make term pollen a synonym of the male gametophyte. This way, pollen was gone from my cell type node, and male gametophyte is still present as a child of the gametophyte. (I should do the same with embryo sac and female gametophyte at later times). Please let me know if you have objections to any of the changes described above. 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. -------------------------------------------------------------------------- From jitterbug at plantontology.org Wed Apr 21 18:36:54 2004 From: jitterbug at plantontology.org (Katica Ilic) Date: Wed, 21 Apr 2004 18:36:54 -0400 Subject: Feedback Submission from Plant Ontology Live Site (fwd) (PR#1) Message-ID: <200404212236.i3LMasnE024322@brie4.cshl.org> Dear Thomas, I am not aware of any ongoing effort in the public sector with respect to developing anatomy and developmental stages ontologies for soybean. Currently, we are in the process of integrating Arabidopsis and cereal ontologies into generic plant anatomy ontology. The first version of the ontology will be released in the summer. We hope to make it applicable to most of the flowering plants including legumes such as Medicago and soybean. As soon as we release the generic version, we would like to hear from you and other interested legume experts for the feedback, in order to improve/incorporate any new terminology to better represent legumes. Furthermore, over the next two years, POC project will expand its plant-ontology-development effort to include other crops such as barley, tomato legumes and cotton. At the end, the controlled vocabularies developed by the POC will be generic enough to encompass/cover all the plant model systems; this includes cereals/brassicas/solanaceae/gossypium/legumes. Thank you for your interest in POC and plant ontologies. For any other question about our project and plant ontologies, please feel free to contact me directly or send us an email at po at plantontology.org. Best regards, Katica Ilic From katica at acoma.Stanford.EDU Fri Apr 23 14:43:18 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 23 Apr 2004 11:43:18 -0700 (PDT) Subject: Anatomy ontology - Root node Message-ID: Hello, Here is a draft of the root node, it has only 28 terms, due to the fact that many of the tissue and cell terms are absent, and will be added in the next round (once the tissue node is imported to the main anatomy ontology). There are some discrepancies in the structures due to the propagation of the children terms under the specific parentage (for instance, see meristematic zone under the lateral root node). I'll deal with this soon. Please send me your comments/suggestions. Thanks, Katica P.S. Pankaj, do you have time to take a quick look at this node before we talk today? -------------------------------------------------------------------------- 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 -------------- !autogenerated-by: DAG-Edit version 1.410 !saved-by: Katica Ilic !date: Fri Apr 23 11:17:51 PDT 2004 !version: $Revision: 1.24 $ !type: % is_a is a !type: < part_of part of !type: ~ develops_from develops from $root ; PO:0009005 %adventitious root ; PO:0020129 %aerial root ; PO:0003006 %crown root ; PO:0003008 Hi Everyone, The tissue node (ontology and definitions) is now committed to the POC anatomy.ontology and anatomy.definition file in the CVS as of April 28, 8.40pm EST. Please update your working directories to see the new changes. I hope this will work and look forward to your feedback. Katica, thanks for your patience. You can go ahead and work on populating the tissue node with cell types. Cheers Pankaj ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From pj37 at cornell.edu Wed Apr 28 20:55:47 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 28 Apr 2004 20:55:47 -0400 Subject: friendly reminders Message-ID: <40905293.9000009@cornell.edu> Here are a few friendly reminders. -please do not use characters like ! # $ in the definitions. -The main term should always have an American english spelling if required. -the synonyms can have British spellings. -Same goes with definitions. Try using the American English spellings. -do not use short forms of words like "str." for "structure" in the definition. Always use full form. -Always prefix /suffix the desired term mane if its a combination of noun and an adjective. e.g. "indehiscent fruits". Having only "indehiscent" as term name is insufficient. There are some more things, which I will post later on. I did some of the changes but asombody has to go through them again. Cheers Pankaj ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From katica at acoma.Stanford.EDU Wed Apr 28 21:11:28 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 28 Apr 2004 18:11:28 -0700 (PDT) Subject: Tissue node In-Reply-To: <40905212.8070307@cornell.edu> Message-ID: Great! Thanks Pankaj, I'll have a look right now. I'll get back to you tomorrow. Hopefully, it'll be ready for you by the end of the day. Cheers, Katica On Wed, 28 Apr 2004, Pankaj Jaiswal wrote: > > Hi Everyone, > > The tissue node (ontology and definitions) is now committed to the POC > anatomy.ontology and anatomy.definition file in the CVS as of April 28, > 8.40pm EST. > > Please update your working directories to see the new changes. > > I hope this will work and look forward to your feedback. > > Katica, thanks for your patience. You can go ahead and work on > populating the tissue node with cell types. > > > Cheers > > Pankaj > > > > > > > ************************ > Pankaj Jaiswal, PhD > G15-Bradfiled Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From r.bruskiewich at cgiar.org Wed Apr 28 22:13:37 2004 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Wed, 28 Apr 2004 19:13:37 -0700 Subject: friendly reminders Message-ID: <3EA5C75212CDD511B74100508BE09576071C12FC@irriphx2.irri.cgiar.org> One of Pankaj's points raises a issue here: translation of the POC/GO into international languages... In principle, I don't see why we shouldn't be considering "internationalization" of the POC (and GO) to accommodate ESL researchers in other countries. I'm already considering such generality in designing our next generation International Crop Information System, that is, trying to split off the term "string" (in unicode, of course) from the concept (indexed by accession identifier) and the term definition (which could also be internationalized). I think that the CGIAR plant crop centers (and the ICIS project, and the Generation CP) can probably help out in this regard given our broad multi-national constituency, and extensive network of ESL national research partners. If we collectively design the schemata to accommodate such flexibility, then perhaps national partners from major non-English speaking research constituencies will offer to do the translation into their own languages(?). Big task, I know, but doable... BTW, though English is one of the world's most widely spoken languages, I wouldn't automatically assume that American English is the dominant form... Considering the size of some major ESL countries in the British Empire, like India ;-))) Richard -----Original Message----- From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] Sent: Thursday, April 29, 2004 8:56 AM To: POC-dev Subject: friendly reminders Here are a few friendly reminders. -please do not use characters like ! # $ in the definitions. -The main term should always have an American english spelling if required. -the synonyms can have British spellings. -Same goes with definitions. Try using the American English spellings. -do not use short forms of words like "str." for "structure" in the definition. Always use full form. -Always prefix /suffix the desired term mane if its a combination of noun and an adjective. e.g. "indehiscent fruits". Having only "indehiscent" as term name is insufficient. There are some more things, which I will post later on. I did some of the changes but asombody has to go through them again. Cheers Pankaj ************************ Pankaj Jaiswal, PhD G15-Bradfiled Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From pj37 at cornell.edu Thu Apr 29 10:13:57 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 29 Apr 2004 10:13:57 -0400 (EDT) Subject: friendly reminders In-Reply-To: <3EA5C75212CDD511B74100508BE09576071C12FC@irriphx2.irri.cgiar.org> References: <3EA5C75212CDD511B74100508BE09576071C12FC@irriphx2.irri.cgiar.org> Message-ID: <3385.24.59.76.45.1083248037.squirrel@webmail.cornell.edu> Hi Richard, There is an international effort going on with the help from FAO, AGVOC and UMLS if I am not wrong, on doing the translations as well as integrating the various vocabularies. These are called agricultural ontologies. http://www.fao.org/agrovoc/ A couple of years ago I met the project coordinator from FAO and he was very much interested in the PO and GO work. He even offerred that if we can provide the ontologies in some exchangeable format like OWL/RDF formats, it will help them in integrating our ontologies in their database. Not to mention an added advantage is getting the translations in 5-6 major languages other than English. The only problem Michael cited was on synchronizing translations with the GO & PO releases. If this works out then I think we don't have to worry about semantics of doing translations on our own. This will be an excellent example of working with a major international organization. Since it is FAO, I am pretty sure CGIAR will be more than willing to chip in with their help in coordinating the exchange. Pankaj Bruskiewich, Richard (IRRI) said: > One of Pankaj's points raises a issue here: translation of the POC/GO into > international languages... > > In principle, I don't see why we shouldn't be considering > "internationalization" of the POC (and GO) to accommodate ESL researchers > in > other countries. I'm already considering such generality in designing our > next generation International Crop Information System, that is, trying to > split off the term "string" (in unicode, of course) from the concept > (indexed by accession identifier) and the term definition (which could > also > be internationalized). > > I think that the CGIAR plant crop centers (and the ICIS project, and the > Generation CP) can probably help out in this regard given our broad > multi-national constituency, and extensive network of ESL national > research > partners. If we collectively design the schemata to accommodate such > flexibility, then perhaps national partners from major non-English > speaking > research constituencies will offer to do the translation into their own > languages(?). Big task, I know, but doable... > > BTW, though English is one of the world's most widely spoken languages, I > wouldn't automatically assume that American English is the dominant > form... > Considering the size of some major ESL countries in the British Empire, > like > India ;-))) > > Richard > > > > -----Original Message----- > From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] > Sent: Thursday, April 29, 2004 8:56 AM > To: POC-dev > Subject: friendly reminders > > Here are a few friendly reminders. > > -please do not use characters like ! # $ in the definitions. > -The main term should always have an American english spelling if > required. > -the synonyms can have British spellings. > -Same goes with definitions. Try using the American English spellings. > -do not use short forms of words like "str." for "structure" in the > definition. Always use full form. > -Always prefix /suffix the desired term mane if its a combination of noun > and an adjective. e.g. "indehiscent fruits". Having only "indehiscent" as > term name is insufficient. > > There are some more things, which I will post later on. I did some of the > changes but asombody has to go through them again. > > Cheers > > Pankaj > > ************************ > Pankaj Jaiswal, PhD > G15-Bradfiled Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > > -- Pankaj Jaiswal Gramene Database www.gramene.org