From feedback_submission at filetta.cshl.edu Tue Apr 12 14:53:58 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Tue, 12 Apr 2005 14:53:58 -0400 Subject: Feedback on POC Message-ID: <200504121853.j3CIrwvZ010398@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: I looked over the list of groups working on botanical terminology issues and found it interesting that the Botanical Society of America was not asked to participate. I presume this is an oversight. name: Tom Rost email: tlrost at ucdavis.edu organization: Section of Plant Biology, University of California, Davis send_feedback: Send your feedback From feedback_submission at filetta.cshl.edu Wed Apr 20 04:02:29 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Wed, 20 Apr 2005 04:02:29 -0400 Subject: Feedback on POC Message-ID: <200504200802.j3K82TAu021243@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: To whom it may concern: This message proposes a refinement of the anatomical ontology. In dicotelydons, the petiole, like the stem, consists of a dermal, fundamental (ground) and vascular system. Its epidermis consists in one layer of cells and contains elongated epidermal cells and stomatal complexes, although the latter occur less frequently in petioles than in leaf lamina. Under the epidermal layer is the ground tissue of which the outer region is the cortex and the inner region is the pith. These two regions are interconnected by the interfascicular parenchyma. In the vascular system (stele), the vascular bundles (xylem and phloem) are separated by this interfascicular parenchyma. The pith is located in the very centre of the stele. This organisation can be summarized as follows, from the outside in: Petiole ? dermal system - epidermis - stomatal complex ? cortex ? vascular system - phloem - xylem - interfascicular parenchyma - pith As there is presently no subdivision under the term ?petiole?, would it be possible to add these categories in the ontology tree? Definitions of the terminology used above are similar to those listed in the current ontology but are here applied for petioles. Do not hesitate to contact us back if you need any additional information regarding this proposal. Ruth De Groodt Bj?rn De Meyer Pierre Hilson name: Ruth De Groodt email: ruth.degroodt at psb.ugent.be organization: VIB - Department of Plant Systems Biology send_feedback: Send your feedback From pj37 at cornell.edu Wed Apr 20 10:59:53 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 20 Apr 2005 10:59:53 -0400 Subject: [Obo-cell-type] GO and Cell ontologies In-Reply-To: <42666B81.9090503@ebi.ac.uk> References: <42666B81.9090503@ebi.ac.uk> Message-ID: <42666E69.9020400@cornell.edu> If you all agree, for plants perspective, my suggestion is that all the plant cell instances and their nomenclature be made consistent with the terms coming from Plant Ontology project. This will help us to create equivalences in a automated way if not manually. Synergid http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0000191&show_associations=terms Egg cell http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0020094&show_associations=terms Pankaj J Clark wrote: > Hi Michael, > > That all seems good to me. > > From the plant perspective I have checked a couple of text books and > the 'egg cell' is always referred to fully as the 'egg cell' not just > the 'egg'. The 'synergids' can be referred to as 'synergids' or > 'synergid cells' so 'synergid' would be fine. > > Hope that helps, > > Jen > > > Michael Ashburner (Genetics) wrote: > >> Both the GO and OBO CELL lists will have seen traffic recently concerning >> the fact that GO and CL are out of synchrony with respect to the >> semantics >> and relationships of cell types. We must be committed to resolving >> these problems. >> I see this as proceeding in several steps. >> >> Step 1. Address the semantic differences between GO and CL with respect >> to cell types, and differences in synonomy. >> These are the major subjects of this email and I thank Chris & Mikel >> Aranguren for most of the examples. >> >> I would like comments on these proposed changes to both CL and GO, >> from Jonathan, >> Sue Rhee and GO folk. Then, I and perhaps Jane will coordinate the >> changes >> to the two ontologies. >> >> The next step will be to resolve differences in >> relationship/parenthood between >> GO and CL and to resolve the proplems of 1 to many mappings from GO to >> CL. >> >> We will then need to bring the GO and CL definitions into synchrony. >> >> When we think we have done all of these, I guess the next will be for >> Chris >> to re-run his scripts and see what we have missed. >> >> Then, I hope, we will be in a very good state for cross-product computes. >> >> Thankyou for your help - Michael >> ====================================================================== >> Changes to CL: >> >> 1. REMOVE all _ and replaced by spaces. >> 2. CORRECT spelling 'sperm cel' (synonym of CL:0000019). >> 3. CHANGE default-namespace: to 'cell' from 'cell_ontology'. >> 4. CHANGE all 'fat cell' to 'apidocyte' (with 'fat cell' as synonym) >> to bring in line with GO use. >> 5. ADD parent 'cardioblast ; CL:NEW' for 'cardioblast (sensu Arthropoda) >> 6. ADD as isa child of 'crystal cell': >> embryonic crystal cell >> lymph gland crystal cell >> 7. ADD new cell type: >> heterocyst, isa 'prokaryotic cell'; isa 'nitrogen fixing cell ; >> CL:NEW' >> definition: A differentiated cell that functions as a site of >> nitrogen fixation under aerobic conditions. >> chlamydospore, isa a 'fungal cell'; isa 'asexual spore' >> definition: An asexual 1-celled spore (primarily for >> perennation, not dissemination) originating endogenously and singly >> within part of a pre-existing cell, by the contraction of the >> protoplast and possessing >> an inner secondary and oftened thickened hyaline or brown wall, usually >> impregnated with hydrophobic material. definition_reference: >> ISBN:085199377X >> 8. ADD 'female gametophyte egg cell' as isa child of 'egg cell' >> 9. CHANGE 'epithelial cell of trachea' to 'tracheal epithelial cell' >> 10. ADD as develops_from 'granulosa_cell': >> cumulus cell ; CL:NEW >> stratum granulosum cell ; CL:NEW >> with 'corona radiata cell ; CL:NEW' as being an isa cumulus cell >> This all from Gray's page 123. >> 11. ADD 'male gametophyte sperm cell ; CL:NEW' as isa of 'sperm cell >> (sensu Viridiplantae' >> 12. [removed] >> 13. CHANGE 'central cell' > 'female gametophyte central cell' (plant >> cell) >> 14. ADD 'NT cell' as synonym of 'natural killer cell' >> 15. ADD 'fusimotor neuron' >> is_a 'motor neuron' >> def: A subset of motor neurons that innervates intrafusal muscle >> fibers and has small diameter axons. PMID:15582775 >> 16. MAKE 'osteoclast' and 'macrophage' both is_a's of 'monocyte' >> 17. ADD 'eye photoreceptor cell ; CL:NEW' as isa 'photoreceptor cell' >> 18. ADD 'retinal cone cell ; CL:NEW' as isa 'cone cell' >> 19. MAKE 'trichome' also an isa of 'hair cell' >> 20. CHANGE: 'blood platelet' > 'platlet' [I presume there is no other >> type of platlet ?] >> 21. GO uses 'sperm', CL used 'spermatozoan'. I suggest CL changes the >> primary term >> to 'sperm' >> 22. GO uses 'striated muscle cell'; CL has only 'obliquely striated >> muscle cell'. Is there any other type of striated muscle cell ? If so >> CL should change. >> ========================================================================= >> Need to decide with GO: >> >> 0. B cell vs B-cell vs B lymphocyte >> T cell vs T-cell vs T lymphocyte >> T-helper vs helper T' etc >> natural killer vs NK etc >> >> ========================================================================= >> Problems to be discussed with GO: >> >> 1. GO has the term 'thymocyte differentiation' defined as: >> '* Processes by which a relatively unspecialized hemopoietic stem cell >> acquires the specialized features of a thymocyte, a lymphocyte found >> in the thymus.' >> >> How does this fit into CL ? >> >> 2. [removed] >> 3. I suggest all GO instances of 'mesoderm cell' be changed to >> 'mesodermal cell' [similarly ectoderm, endoderm cell, if such exist in >> GO] >> >> 4. GO to change 'tracheal cell *' to 'tracheal epithelial cell *' >> 5. GO to change 'ovarian cumulus cell differentiation' to 'cumulus >> cell differentiation' >> 6. GO to change 'auditory hair cell' to 'auditory receptor cell' >> 7. GO to change 'branch cell fate determination (sensu Insecta) -> >> branched_duct_epithelial_cell fate determination (sensu Insecta)' >> 8. Is the GO usage of 'hemocyte' arthropod specific ? In this case >> GO needs to change 'hemocyte differentiation (sensu Arthropoda)' by >> removing >> the sensu. >> 9. GO should add neuroblast_(sensu_Nematoda_and_Protostomia), >> neuroblast_(sensu_Vertebrata) as childs of neuroblast [cell] * terms >> 10. GO should add erythrocyte_(sensu_Mammalia), >> erythrocyte_(sensu_non-Mammalia) as >> childs of of erythrocyte * terms >> 11. Does GO need epidermal_cell_(sensu_Insecta) * as childs of >> epidermal cell * terms ? >> 12. ditto glial cell (sensu Nematoda and Protostomia) as childs of >> glial cell * terms ? >> 13. ditto pigment cell (sensu Nematoda and Protostomia), pigment cell >> (sensu Vertebrata) as childs of pigment cell * terms ? >> 14. The following terms in GO have 'cell' as a suffix. This suffix >> should be removed >> from all terms: >> basophil cell >> egg cell >> hemocyte cell >> neuroblast cell >> neuron cell >> oocyte cell >> spermatid cell >> spermatocyte cell >> synergid cell >> trichome cell >> 15. CL uses 'photoreceptor cell'; GO uses 'photoreceptor'. Are these >> the same? >> We need to normalize. Suggestions ? Same is true of GO's >> 'mechanoreceptor' and CL's >> 'mechanoreceptor cell'. CL should probably >> add R1..R8 as isa of 'eye photoreceptor cell' >> 16. GO has 'cone cell' and 'retinal cone cell' ... are these different >> ? i.e. >> are their any non-retinal cone cells ? CL just has 'retinal cone cell' >> 17. GO has both 'glia cell' and 'glial cell'. Change all former to >> 'glial cell' >> 18. GO has 'border cell', CL has 'border follicle cell'. I suggest GO >> uses >> the latter term. >> 19. [removed] >> 20. GO has 'cardioblast', CL 'cardioblast (sensu Arthropoda)'. Are all >> cardioblasts Arthropod, which case CL can change and drop the sensu. >> If not >> then GO needs to change. >> 21. Go has both 'leukocyte cell' and 'leukocyte'. I suggest we change all >> former to latter. >> 22. GO has both 'mesoderm cell' & 'mesodermal cell'. I suggest we >> change all >> former to latter. >> 23. GO should change all 'neuronal cell' to 'neuron' >> 24. GO has 'spermatogonial cell', CL has 'spermatogonium'. I suggest >> GO changes to latter >> =========================================================================== >> >> These are NOT problems [this list mainly for Chris]: >> >> rhabdomere development .. The reason being is that 'rhabdomere' is >> part_of a photoreceptor cell >> missing seed ... not a cell >> missing sex ... not a cell >> synonym stalk cell .. I think GO & CL are consistent >> synonym pigment cell .. I think GO & CL are consistent >> synonym nurse cell .. I think GO & CL are consistent >> synonym muscle cell .. I think GO & CL are consistent >> missing cell homeostatic ... not a cell >> missing cell mass cell ... eh ? >> missing positive ... eh ? >> missing host cell ... not a cell type >> missing epidermal cell ... GO & CL consistent >> missing endothelial cell ... GO & CL consistent >> missing epithelial cell ... GO & CL consistent >> missing crest cell .. no GO has only 'neural crest cell' >> consistent with CL >> missing heterophilic cell ... not a cell type >> missing homophilic cell ... not a cell type >> missing inductive cell ... not a cell type >> missing kinase C ... not a cell type >> missing antipodal cell ... GO & CL consistent >> missing central cell ... GO & CL consistent >> missing crystal cell ... GO & CL consistent >> missing dendritic cell ... GO & CL consistent >> missing female gamete ... GO & CL consistent >> missing female sex ... eh ? >> missing female germ cell ... GO & CL consistent >> missing follicle cell ... GO & CL consistent >> missing garland cell ... GO & CL consistent >> missing germ cell ... GO & CL consistent >> missing guard cell ... GO & CL consistent >> missing guard mother cell ... GO & CL consistent >> missing hyphal cell ... GO & CL consistent >> missing male gamete ... GO & CL consistent >> missing male germ cell ... GO & CL consistent >> missing male sex ... not a cell >> missing mast cell... GO & CL consistent >> missing microglial cell... GO & CL consistent >> missing mother cell .. not in GO, though 'guard mother' >> and 'ganglion mother' are and are consistent with CL >> missing phospholipase C ... not a cell >> missing ocellus ... not a cell >> missing neural crest cell ... GO & CL consistent >> missing pericardial cell ... GO & CL consistent >> missing pole cell ... GO & CL consistent >> missing protein kinase C ... not a cell >> missing retinal cone cell ... GO & CL consistent >> missing smooth muscle cell ... GO & CL consistent >> missing spermatid nuclear ... eh ? .. spermatid is in CL >> missing stem cell ... GO & CL consistent >> missing tryptophan hydroxylase ... not a cell >> >> >> =========================================================================== >> >> These cells are already in CL: >> >> natural killer cell differentiation (CL:0000623) >> =========================================================================== >> >> >> GO has these cell types not in CL - ideas on what >> to do ?. I have grouped the immunology terms at top. There may be some >> redundancy with what is above. >> >> >> missing B-1 B-cell >> missing NK T-cell >> missing T-helper 1 cell >> missing T-helper 2 cell >> missing T-helper cell >> missing activated T-cell >> missing alpha-beta T-cell >> missing extrathymic T-cell >> missing helper cell >> missing cytotoxic T-cell >> missing gamma-delta T-cell >> missing immune cell >> missing killer cell >> missing myeloid blood cell >> missing natural killer cell >> missing negative extrathymic T-cell >> missing negative thymic T-cell >> missing positive extrathymic T-cell >> missing positive thymic T-cell >> missing thymic T-cell >> missing thymocyte >> missing regulatory T-cell >> >> missing abaxial cell >> missing ameboid cell >> missing anterior cone cell >> missing aortic cell (sensu Insecta) >> missing autophagic cell >> missing axial mesoderm cell >> missing azurophil >> missing blood cell >> missing cardiac cell >> missing cystoblast cell >> missing early stripe melanocyte >> missing edge cell >> missing embryonic crystal cell >> missing embryonic hemocyte >> missing embryonic plasmatocyte >> missing equatorial cone cell >> missing eye photoreceptor cell >> missing gametophyte central cell >> missing gametophyte egg cell >> missing gametophyte sperm cell >> missing gland cell >> missing gland crystal cell >> missing gland hemocyte >> missing gland plasmatocyte >> missing heart proper cell >> missing inner cell mass cell >> missing intermediate mesoderm cell >> missing iridophore >> missing larval midgut cell >> missing late stripe melanocyte >> missing lateral mesoderm cell >> missing leading edge cell >> missing leukocyte >> missing lymph gland crystal cell >> missing lymph gland hemocyte >> missing lymph gland plasmatocyte >> missing male gametophyte sperm cell >> missing mass cell >> missing midgut cell >> missing mystery cell fate >> missing non-eye photoreceptor cell >> missing organ precursor cell >> missing paraxial mesoderm cell >> missing polar cone cell >> missing polarized epithelial cell >> missing pollen >> missing pollen germ cell >> missing posterior cone cell >> missing precursor cell >> missing primary cell >> missing primary endosperm >> missing primary pigment cell >> missing retinal cell >> missing root epidermal cell >> missing salivary gland cell >> missing secondary cell >> missing secondary pigment cell >> missing sensory organ precursor cell >> missing somatic stem cell >> missing stripe melanocyte >> missing tertiary pigment cell >> missing tracheal cell >> missing trophectoderm cell >> missing urothelial cell >> >> >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: New Crystal Reports XI. >> Version 11 adds new functionality designed to reduce time involved in >> creating, integrating, and deploying reporting solutions. Free runtime >> info, >> new features, or free trial, at: http://www.businessobjects.com/devxi/728 >> _______________________________________________ >> Obo-cell-type mailing list >> Obo-cell-type at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-cell-type > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield 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 jitterbug at plantontology.org Fri Apr 22 18:10:49 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Fri, 22 Apr 2005 18:10:49 -0400 Subject: Feedback on POC: granular terms under 'petiole' (PR#56) Message-ID: <200504222210.j3MMAnAe015388@brie4.cshl.org> Dear Ruth, Thanks for the feedback and suggestion for improving current Plant Ontology structure. Term 'petiole' does not have any granular 'children' terms yet, since we deliberately chose not to have very detailed and elaborate ontology, at least not in the initial stage when we were focused on creating a robust and extensible structure as a backbone to which granular terms can be added as needed. Our group is now considering your suggestion for adding more granular terms for 'petiole', and I have a couple of questions, to make sure that we can accommodate what you would like to see in this segment of the ontology, at the same time, making sure that we keep the Plant Ontology 'generic', encompassing both, dicots and monocots. I am assuming that these terms are required for functional genomics project that you might be involved and I wonder if a simpler solution that does not have, for instance 'interfascicular parenchyma' would work. I'll get back to you soon with the outline of the structure we are currently considering, but in the meantime, it would be useful if you can tell us few fords about the specific reasons for inquiring the structure you proposed and also how you use the Plant Ontology. Thank you again for sending us your suggestion. I look forward to hearing from you. Best regards, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Wed, 20 Apr 2005 04:02:29 -0400 > From: feedback_submission at filetta.cshl.edu > Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu > To: po-dev > Subject: Feedback on POC > > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: To whom it may concern: > > This message proposes a refinement of the anatomical ontology. > > In dicotelydons, the petiole, like the stem, consists of a dermal, fundamen= > tal (ground) and vascular system. Its epidermis consists in one layer of c= > ells and contains elongated epidermal cells and stomatal complexes, althoug= > h the latter occur less frequently in petioles than in leaf lamina. Under t= > he epidermal layer is the ground tissue of which the outer region is the co= > rtex and the inner region is the pith. These two regions are interconnected= > by the interfascicular parenchyma. In the vascular system (stele), the vas= > cular bundles (xylem and phloem) are separated by this interfascicular pare= > nchyma. The pith is located in the very centre of the stele. > > This organisation can be summarized as follows, from the outside in: > > Petiole > =B7=09dermal system > - epidermis > - stomatal complex > =B7=09cortex > =B7=09vascular system > - phloem > - xylem > - interfascicular parenchyma > - pith > > As there is presently no subdivision under the term =93petiole=94, would it= > be possible to add these categories in the ontology tree? Definitions of = > the terminology used above are similar to those listed in the current ontol= > ogy but are here applied for petioles. Do not hesitate to contact us back = > if you need any additional information regarding this proposal. > > > Ruth De Groodt > Bj=F6rn De Meyer > Pierre Hilson > > > name: Ruth De Groodt > > email: ruth.degroodt at psb.ugent.be > > organization: VIB - Department of Plant Systems Biology > > send_feedback: Send your feedback > > > From pj37 at cornell.edu Wed Apr 27 13:40:03 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 27 Apr 2005 13:40:03 -0400 Subject: Nodal root innstances (crown and seminal roots) Message-ID: <426FCE73.8010902@cornell.edu> Can we bring back the two instances of the nodal root, nodal root ; PO:0003005 ---%crown root ; PO:0003008 ---seminal root ; PO:0003009 These terms were merged to nodal root (PO:0003005) as synonyms. They were introduced to the anatomy.ontology in version 1.11 Their development is genetically controlled http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14980975 Also I need these terms for annotating the genes expressed in them #1 cDNA-AFLP analysis of inducible gene expression in rice seminal root tips under a water deficit doi:10.1016/S0378-1119(03)00713-3 http://www.paper.edu.cn/scholar/download.jsp?file=wuping-5 #2 The Crown rootless1 Gene in Rice Is Essential for Crown Root Formation and Is a Target of an AUXIN RESPONSE FACTOR in Auxin Signaling. Plant Cell. 2005 Apr 13 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15829602 -- ************************ Pankaj Jaiswal, PhD G15-Bradfield 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 feedback_submission at filetta.cshl.edu Thu Apr 28 16:41:12 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Thu, 28 Apr 2005 16:41:12 -0400 Subject: Feedback on POC Message-ID: <200504282041.j3SKfCZi004554@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/mailarch/index.html comments: refer:http://www.plantontology.org/mailarch/ Is it true there were no messages sent to the po or po-dev mailing lists in 2005 ?? I don't see any. on thsi archive on live site name: Pankaj email: pj37 at cornell.edu organization: CU send_feedback: Send your feedback From katica at acoma.Stanford.EDU Fri Apr 29 15:47:58 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 29 Apr 2005 12:47:58 -0700 (PDT) Subject: Question about PO term 'Whole plant' (fwd) Message-ID: ---------- Forwarded message ---------- Date: Fri, 29 Apr 2005 06:27:46 -0400 From: owner-po-dev at brie4.cshl.org To: katica at acoma.Stanford.EDU Subject: BOUNCE po-dev at brie4.cshl.org:[David Craigon ] Hello, I'd like to ask a naive question about the plant ontology. I was wondering why all terms were not "part-of" the "whole plant"? I'd like a section of the tree that goes something like: Whole plant-----above ground parts----leaves | | | |---------------------flowers (and so on) | |----below ground parts----roots That way as you move down the tree the areas of the plant gets more specific a la GO, and as you get to the bottom you get all the way down to cells. You could still have a cells, tissues, etc. category at the top as well, since each child term could be in both categories. What do you think? Is this too simplistic? David From jitterbug at plantontology.org Fri Apr 29 16:49:01 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Fri, 29 Apr 2005 16:49:01 -0400 Subject: Question about PO term 'Whole plant' (fwd) (PR#57) Message-ID: <200504292049.j3TKn1fg020723@brie4.cshl.org> Hi David, The term 'whole plant' was introduced to the PO for the purpose of facilitating annotations (when no other term could be used). It was introduced as a necessity, it is not really a botanical term, has vague meaning (and definition), and other terms that are available in the Plant Ontology should be used instead (such as sporophyte). Since we don't encourage users to use this term extensively, but rather scarcely, that is, only when absolutely necessary, we deliberately chose no to have any terms as children of 'whole plant'. Moreover, we have considered moving this term in a separate 'placeholder bin' in the ontology, so that it wouldn't appear as a top node. When creating this ontology, we decided that 'true'' top nodes (as an instance_of) of the Plant Structure are: cell tissue gametophyte sporophyte (we eliminated 'organ' to avoid redundancy in the ontology). Additional two nodes, 'in vitro cell, tissue and organ culture' and 'whole plant' are really 'satellite' nodes and are included to provide terms required for gene annotations. Terms that you listed are already in the ontology, they are children of the top node 'sporophyte', where they belong, as they are parts of the sporophyte. The 'above and below ground plant parts' division that you mentioned is not really relevant for the Plant Structure Ontology. I hope this clarifies the organization of the top nodes in the Plant Structure Ontology. If you would like to learn more about organizing principles of PO, please visit the following URL:http://www.plantontology.org/docs/otherdocs/principles_rationales.html. Best regards, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Fri, 29 Apr 2005 06:27:46 -0400 > From: owner-po-dev at brie4.cshl.org > To: katica at acoma.Stanford.EDU > Subject: BOUNCE po-dev at brie4.cshl.org:[David Craigon ] > > Hello, > I'd like to ask a naive question about the plant ontology. I was > wondering why all terms were not "part-of" the "whole plant"? I'd like a > section of the tree that goes something like: > > Whole plant-----above ground parts----leaves > | | > | |---------------------flowers (and so on) > | > |----below ground parts----roots > > That way as you move down the tree the areas of the plant gets more > specific a la GO, and as you get to the bottom you get all the way down > to cells. > > You could still have a cells, tissues, etc. category at the top as well, > since each child term could be in both categories. > > What do you think? Is this too simplistic? > > > David > > > Katica Ilic, TAIR Curator, E-mail: katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington Fax: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305, U.S.A.