From feedback_submission at filetta.cshl.edu Mon Aug 1 14:42:53 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 1 Aug 2005 14:42:53 -0400 Subject: Feedback on POC Message-ID: <200508011842.j71Igrng019506@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: Correct the spelling of "triploid" in definition (last word) term: primary endosperm cell PO:0000038 name: pankaj email: pj37 at cornell.edu organization: cu send_feedback: Send your feedback From feedback_submission at filetta.cshl.edu Mon Aug 1 14:48:45 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 1 Aug 2005 14:48:45 -0400 Subject: Feedback on POC Message-ID: <200508011848.j71Imjkg019695@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: is pro embry a single word? I see its use a two words vs single word two words: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&session_id=6529b1122921588&search_constraint=terms&query=pro+embryo single word: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&session_id=3235b1122922042&search_constraint=terms&query=proembryo We need consistency name: pankaj email: pj37 at cornell.edu organization: cu send_feedback: Send your feedback From Leszek at missouri.edu Mon Aug 1 16:34:41 2005 From: Leszek at missouri.edu (Vincent, Leszek) Date: Mon, 1 Aug 2005 15:34:41 -0500 Subject: Feedback on POC Message-ID: My understanding & my references indicate 'proembryo' is one word. - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Skype VoIP: phytosynergy; Fax:(573) 884-7850; Email: Leszek at missouri.edu Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 (www.plantontology.org) *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of feedback_submission at filetta.cshl.edu Sent: Monday, August 01, 2005 1:49 PM To: po-dev Subject: Feedback on POC *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: is pro embry a single word? I see its use a two words vs single word two words: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&sessio n_id=6529b1122921588&search_constraint=terms&query=pro+embryo single word: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&sessio n_id=3235b1122922042&search_constraint=terms&query=proembryo We need consistency name: pankaj email: pj37 at cornell.edu organization: cu send_feedback: Send your feedback From feedback_submission at filetta.cshl.edu Tue Aug 2 10:33:35 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Tue, 2 Aug 2005 10:33:35 -0400 Subject: Feedback on POC Message-ID: <200508021433.j72EXZCD030639@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0006318&show_associations=terms In this particular example we see that PO:0006318 : floret (sensu Poaceae) is a prt of PO:0009051 : spikelet. From the definition of PO:0009051 : spikelet, it appears a sensu Poaceae term and teh term lacks is_a relationship. Can someone confirm that spikelet is found only in grass inflorescence and not in any other taxa. If it is found elsewhere also, we need a non sensu generic term of which the current (so called sensu term) will be an instance (is_a relationship to a parent). name: Pankaj email: pj37 at cornell.edu organization: CU send_feedback: Send your feedback From fzqhd at umsl.edu Tue Aug 2 11:06:57 2005 From: fzqhd at umsl.edu (Felipe Zapata) Date: Tue, 2 Aug 2005 10:06:57 -0500 Subject: Feedback on POC In-Reply-To: <200508021433.j72EXZCD030639@filetta.cshl.org> References: <200508021433.j72EXZCD030639@filetta.cshl.org> Message-ID: You can call spikelet to the inflorescence of other monocots (e.g. some sedges) as weel. But I think we included "sensu Poaceae" for the necessity to specify only the Poaceae spikelet (gramene annotations). If go along the "sensu" style for the rest of plants having spikelet we'll hit again the multiplicative crisis as there will be reasons to consider spikelets for each taxon unique and different and not as a generic term for describing a unit of packed flowers plus their bracts. F On Aug 2, 2005, at 9:33 AM, feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: http://www.plantontology.org/amigo/go.cgi? > view=details&search_constraint=terms&depth=0&query=PO: > 0006318&show_associations=terms > > In this particular example we see that PO:0006318 : floret (sensu > Poaceae) is a prt of PO:0009051 : spikelet. From the definition > of PO:0009051 : spikelet, it appears a sensu Poaceae term and teh > term lacks is_a relationship. Can someone confirm that spikelet is > found only in grass inflorescence and not in any other taxa. If it > is found elsewhere also, we need a non sensu generic term of which > the current (so called sensu term) will be an instance (is_a > relationship to a parent). > > > > name: Pankaj > > email: pj37 at cornell.edu > > organization: CU > > send_feedback: Send your feedback > > .............. Felipe Zapata University of Missouri St. Louis Department of Biology 8001 Natural Bridge Rd. St. Louis, MO 63121 USA p.314.516.6200 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Fri Aug 5 11:58:54 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 05 Aug 2005 11:58:54 -0400 Subject: term: columella Message-ID: <42F38CBE.6030403@cornell.edu> Please correct me if I am wrong. As I understand it the term PO:0020130 : central root cap is a region in the root cap and its synonym "columella cells" is inappropriate. Also I see that a similar term PO:0020132 : columella root cap cell exists, so the synonym "columella cells" should actually be added to PO:0020132 : columella root cap cell and removed from PO:0020130 : central root cap. A renaming of the term PO:0020132 : columella root cap cell to "central root cap cell" will help, thus maintaining consistency with parent term. Additional parent term for PO:0020132 : columella root cap cell is a must as follows. PO:0020130 : central root cap ---part_of--PO:0020132 : columella root cap cell For consistency the renaming is suggested for PO:0020133 : columella root cap initial to "central root cap initial" ----------------------- Just to clarify the usage of word "columella" My understanding is that the term "columella" is popularly called as : The central part of root cap in which the cells are arranged in longitudinal files (ref: Essau). We are using the same definition for defining the "central root cap" (syn columella cells) and they are the same structure we are talking about. However there is a confusion by use of the word "columella" in the term PO:0020014 "columella" A rod-like element of the sexine/ectexine, either supporting the tectum or a caput. To make it very clear we are talking about root cap columella in one place and pollen wall columella in another can we do the renaming of PO:0020014 "columella" to "pollen wall columella" -Pankaj From katica at acoma.Stanford.EDU Fri Aug 5 15:44:33 2005 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Fri, 5 Aug 2005 12:44:33 -0700 (PDT) Subject: term: columella In-Reply-To: <42F38CBE.6030403@cornell.edu> References: <42F38CBE.6030403@cornell.edu> Message-ID: My two cents: On Fri, 5 Aug 2005, Pankaj Jaiswal wrote: > > > > Please correct me if I am wrong. > > As I understand it the term PO:0020130 : central root cap is a region in > the root cap and its synonym "columella cells" is inappropriate. Also I see > that a similar term PO:0020132 : columella root cap cell exists, so the > synonym "columella cells" should actually be added to PO:0020132 : columella > root cap cell and removed from PO:0020130 : central root cap. Central root cap IS columella, hence synonym 'columella cells'; I would perhaps remove cells from this synonym. (BTW, that's why the definitions in PO and in Esau are the same.) > > A renaming of the term PO:0020132 : columella root cap cell to "central root > cap cell" will help, thus maintaining consistency with parent term. > Additional parent term for PO:0020132 : columella root cap cell is a must as > follows. > > PO:0020130 : central root cap > ---part_of--PO:0020132 : columella root cap cell > > For consistency the renaming is suggested for PO:0020133 : columella root > cap initial to "central root cap initial" This term 'PO:0020132 : columella root cap cell' resides only under tissue (meristem) and cell node. When making these nodes, we agreed that terms from tissue and cell node would not be propagated initially elsewhere in the ontology, unless there is specific reason for that (mostly annotation requirements). So, unless we have such a reason, this term could stay where it is right now. New name, 'central root cap cell' is fine, but these cells are called 'columella root cap cells' in the literature, and I am inclined to keep it as such; perhaps adding a synonym 'central root cap cell' would serve the purpose. > ----------------------- > > Just to clarify the usage of word "columella" > > My understanding is that the term "columella" is popularly called as : The > central part of root cap in which the cells are arranged in longitudinal > files (ref: Essau). We are using the same definition for defining the > "central root cap" (syn columella cells) and they are the same structure we > are talking about. > > However there is a confusion by use of the word "columella" in the term > PO:0020014 "columella" A rod-like element of the sexine/ectexine, either > supporting the tectum or a caput. > > > To make it very clear we are talking about root cap columella in one place > and pollen wall columella in another can we do the renaming of > > PO:0020014 "columella" to "pollen wall columella" This is unnecessary, in my opinion, since the lineage of the term 'columella' as in pollen wall is sufficient to distinguish it from columella in the root cap. This is preciselly why the hierarchical structure of ontology is useful, i.e., term lineage (parentage) adds up to the sum total of information about a term, beside its name and definition. Otherwise, we would have opted for a flat structure, something like a dictionary. Note: this is different from having two terms with same name and same or similar definitions. Here, we have two terms (term and a synonym of another term) with different definitions, describing very different concepts, which makes it legitimate to keep them as they are. Katica > > -Pankaj > > > -- -------------------------------------------------------------------------- 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 Fri Aug 5 16:30:32 2005 From: Leszek at missouri.edu (Vincent, Leszek) Date: Fri, 5 Aug 2005 15:30:32 -0500 Subject: term: columella Message-ID: Pankaj & colleagues - Please see my comments below - prefixed with XX. - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Skype VoIP: phytosynergy; Fax:(573) 884-7850; Email: Leszek at missouri.edu Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 (www.plantontology.org) *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Pankaj Jaiswal Sent: Friday, August 05, 2005 10:59 AM To: po-dev at plantontology.org Subject: term: columella Please correct me if I am wrong. As I understand it the term PO:0020130 : central root cap is a region in the root cap and its synonym "columella cells" is inappropriate. Also I see that a similar term PO:0020132 : columella root cap cell exists, so the synonym "columella cells" should actually be added to PO:0020132 : columella root cap cell and removed from PO:0020130 : central root cap. XX I concur with this reasoning in that "central root cap" is a tissue (a region) etc. & that the synonym would be more appropriate in the relocated position. A renaming of the term PO:0020132 : columella root cap cell to "central root cap cell" will help, thus maintaining consistency with parent term. Additional parent term for PO:0020132 : columella root cap cell is a must as follows. PO:0020130 : central root cap ---part_of--PO:0020132 : columella root cap cell For consistency the renaming is suggested for PO:0020133 : columella root cap initial to "central root cap initial" XX I see the renaming issue differently. The term "columella root cap cell" 'feels' grammatically awkward to me. A preferable form could be "root cap columella cell" - this conveys the components/complexity of the compound term a lot better - for me! Furthermore, the revised term name would convey the desired improved consistency to which you refer. ----------------------- Just to clarify the usage of word "columella" My understanding is that the term "columella" is popularly called as : The central part of root cap in which the cells are arranged in longitudinal files (ref: Essau). We are using the same definition for defining the "central root cap" (syn columella cells) and they are the same structure we are talking about. However there is a confusion by use of the word "columella" in the term PO:0020014 "columella" A rod-like element of the sexine/ectexine, either supporting the tectum or a caput. To make it very clear we are talking about root cap columella in one place and pollen wall columella in another can we do the renaming of PO:0020014 "columella" to "pollen wall columella" XX This change would be very helpful. -Pankaj From peter.stevens at mobot.org Sat Aug 6 19:58:22 2005 From: peter.stevens at mobot.org (Peter Stevens) Date: Sat, 6 Aug 2005 19:58:22 -0400 Subject: term: columella In-Reply-To: <42F38CBE.6030403@cornell.edu> References: <42F38CBE.6030403@cornell.edu> Message-ID: Seems OK to mre, but I would suggest not having "pollen wall coluella" as the name of the term: if we are in the pollen wall part of the ontology, "columella" alone will do the trick if the root "columella" has been obsoleted. Applying any principle of qualifying terms based on the particular part of the plant where they are to be found will ultimately lead to wholesale "renaming" of terms. However, there is also a term "columella" used in fruits that applies to the central axis that persists after the rest of the fruit wall has separated and/or fallen off. If we were to keep this term, then qualification might be needed, but again, one would be be in a totally different part of the ontology - qualification would then be driven by the needs of our particular controlled vocabulary.... P. > > > > >Please correct me if I am wrong. > >As I understand it the term PO:0020130 : central root cap is a >region in the root cap and its synonym "columella cells" is >inappropriate. Also I see that a similar term PO:0020132 : >columella root cap cell exists, so the synonym "columella cells" >should actually be added to PO:0020132 : columella root cap cell >and removed from PO:0020130 : central root cap. > >A renaming of the term PO:0020132 : columella root cap cell to >"central root cap cell" will help, thus maintaining consistency with >parent term. Additional parent term for PO:0020132 : columella root >cap cell is a must as follows. > >PO:0020130 : central root cap >---part_of--PO:0020132 : columella root cap cell > >For consistency the renaming is suggested for PO:0020133 : >columella root cap initial to "central root cap initial" > >----------------------- > >Just to clarify the usage of word "columella" > >My understanding is that the term "columella" is popularly called as >: The central part of root cap in which the cells are arranged in >longitudinal files (ref: Essau). We are using the same definition >for defining the "central root cap" (syn columella cells) and they >are the same structure we are talking about. > >However there is a confusion by use of the word "columella" in the >term PO:0020014 "columella" A rod-like element of the >sexine/ectexine, either supporting the tectum or a caput. > > >To make it very clear we are talking about root cap columella in one >place and pollen wall columella in another can we do the renaming of > >PO:0020014 "columella" to "pollen wall columella" > >-Pankaj From pj37 at cornell.edu Mon Aug 8 11:06:25 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 08 Aug 2005 11:06:25 -0400 Subject: term: columella In-Reply-To: References: <42F38CBE.6030403@cornell.edu> Message-ID: <42F774F1.1050405@cornell.edu> Peter Stevens wrote: > Seems OK to mre, but I would suggest not having "pollen wall coluella" > as the name of the term: if we are in the pollen wall part of the > ontology, "columella" alone will do the trick if the root "columella" > has been obsoleted. Applying any principle of qualifying terms based on The root columella is not obsolete, we have renamed the term to PO:0020130 : central root cap. > the particular part of the plant where they are to be found will > ultimately lead to wholesale "renaming" of terms. However, there is also > a term "columella" used in fruits that applies to the central axis that > persists after the rest of the fruit wall has separated and/or fallen > off. If we were to keep this term, then qualification might be needed, > but again, one would be be in a totally different part of the ontology - > qualification would then be driven by the needs of our particular > controlled vocabulary.... > The example given by you is an excellent one considering the ambiguous usage of the anatomical terms in the classical literature. Therefore to me, it is more or less suggesting us to create the terms with their anatomical location attributes (pointing to the composite terms). This is so because even though the definition and the parent-child relationships in an ontology tree, make a term unique if the same term name is used, it is often confusing for the users if they are looking at the term only and not at the definition or the term's lineage. Often the stand alone terms are easy to suggest what they are based on their uniqueness, but not always as in the case of columella. > P. > > >> >> >> >> >> >> Please correct me if I am wrong. >> >> As I understand it the term PO:0020130 : central root cap is a >> region in the root cap and its synonym "columella cells" is >> inappropriate. Also I see that a similar term PO:0020132 : columella >> root cap cell exists, so the synonym "columella cells" should actually >> be added to PO:0020132 : columella root cap cell and removed from >> PO:0020130 : central root cap. >> >> A renaming of the term PO:0020132 : columella root cap cell to >> "central root cap cell" will help, thus maintaining consistency with >> parent term. Additional parent term for PO:0020132 : columella root >> cap cell is a must as follows. >> >> PO:0020130 : central root cap >> ---part_of--PO:0020132 : columella root cap cell >> >> For consistency the renaming is suggested for PO:0020133 : columella >> root cap initial to "central root cap initial" >> >> ----------------------- >> >> Just to clarify the usage of word "columella" >> >> My understanding is that the term "columella" is popularly called as : >> The central part of root cap in which the cells are arranged in >> longitudinal files (ref: Essau). We are using the same definition for >> defining the "central root cap" (syn columella cells) and they are the >> same structure we are talking about. >> >> However there is a confusion by use of the word "columella" in the >> term PO:0020014 "columella" A rod-like element of the >> sexine/ectexine, either supporting the tectum or a caput. >> >> >> To make it very clear we are talking about root cap columella in one >> place and pollen wall columella in another can we do the renaming of >> >> PO:0020014 "columella" to "pollen wall columella" >> >> -Pankaj > > > From katica at acoma.Stanford.EDU Mon Aug 8 12:01:08 2005 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Mon, 8 Aug 2005 09:01:08 -0700 (PDT) Subject: term: columella In-Reply-To: <42F774F1.1050405@cornell.edu> References: <42F38CBE.6030403@cornell.edu> <42F774F1.1050405@cornell.edu> Message-ID: What we have here is a term and a non-related synonym with the same name (assuming that 'columella cells' would be changed to 'columella'). So, it's a simple question: Is it confusing for our users to have 'columella' as synonym of 'central root cap' and also as a term (someplace else in the ontology) with its synonym 'sexine 1'. These four terms came out in AmiGO when searching for 'columella': PO Term Synonyms central root cap columella cells columella sexine 1 columella root cap cell NONE columella root cap initial NONE I can't speak for ontology users, but my guess is that it's more or less obvious for an average user. It would be useful and interesting to hear from ontology users on this topic. Katica On Mon, 8 Aug 2005, Pankaj Jaiswal wrote: > Peter Stevens wrote: > >> Seems OK to mre, but I would suggest not having "pollen wall coluella" as >> the name of the term: if we are in the pollen wall part of the ontology, >> "columella" alone will do the trick if the root "columella" has been >> obsoleted. Applying any principle of qualifying terms based on > > The root columella is not obsolete, we have renamed the term to PO:0020130 : > central root cap. > > >> the particular part of the plant where they are to be found will ultimately >> lead to wholesale "renaming" of terms. However, there is also a term >> "columella" used in fruits that applies to the central axis that persists >> after the rest of the fruit wall has separated and/or fallen off. If we >> were to keep this term, then qualification might be needed, but again, one >> would be be in a totally different part of the ontology - qualification >> would then be driven by the needs of our particular controlled >> vocabulary.... >> > > The example given by you is an excellent one considering the ambiguous usage > of the anatomical terms in the classical literature. Therefore to me, it is > more or less suggesting us to create the terms with their anatomical location > attributes (pointing to the composite terms). This is so because even though > the definition and the parent-child relationships in an ontology tree, make a > term unique if the same term name is used, it is often confusing for the > users if they are looking at the term only and not at the definition or the > term's lineage. Often the stand alone terms are easy to suggest what they are > based on their uniqueness, but not always as in the case of columella. > > > >> P. >> >> >>> >>> >>> >>> >>> Please correct me if I am wrong. >>> >>> As I understand it the term PO:0020130 : central root cap is a region in >>> the root cap and its synonym "columella cells" is inappropriate. Also I >>> see that a similar term PO:0020132 : columella root cap cell exists, so >>> the synonym "columella cells" should actually be added to PO:0020132 : >>> columella root cap cell and removed from PO:0020130 : central root cap. >>> >>> A renaming of the term PO:0020132 : columella root cap cell to "central >>> root cap cell" will help, thus maintaining consistency with parent term. >>> Additional parent term for PO:0020132 : columella root cap cell is a must >>> as follows. >>> >>> PO:0020130 : central root cap >>> ---part_of--PO:0020132 : columella root cap cell >>> >>> For consistency the renaming is suggested for PO:0020133 : columella root >>> cap initial to "central root cap initial" >>> >>> ----------------------- >>> >>> Just to clarify the usage of word "columella" >>> >>> My understanding is that the term "columella" is popularly called as : The >>> central part of root cap in which the cells are arranged in longitudinal >>> files (ref: Essau). We are using the same definition for defining the >>> "central root cap" (syn columella cells) and they are the same structure >>> we are talking about. >>> >>> However there is a confusion by use of the word "columella" in the term >>> PO:0020014 "columella" A rod-like element of the sexine/ectexine, either >>> supporting the tectum or a caput. >>> >>> >>> To make it very clear we are talking about root cap columella in one place >>> and pollen wall columella in another can we do the renaming of >>> >>> PO:0020014 "columella" to "pollen wall columella" >>> >>> -Pankaj >> >> >> > > -- -------------------------------------------------------------------------- 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 Aug 8 12:02:18 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 08 Aug 2005 12:02:18 -0400 Subject: term: columella In-Reply-To: References: <42F38CBE.6030403@cornell.edu> Message-ID: <42F7820A.6090903@cornell.edu> katica at acoma.Stanford.EDU wrote: > > My two cents: > > On Fri, 5 Aug 2005, Pankaj Jaiswal wrote: > >> >> >> >> >> Please correct me if I am wrong. >> >> As I understand it the term PO:0020130 : central root cap is a >> region in the root cap and its synonym "columella cells" is >> inappropriate. Also I see that a similar term PO:0020132 : columella >> root cap cell exists, so the synonym "columella cells" should actually >> be added to PO:0020132 : columella root cap cell and removed from >> PO:0020130 : central root cap. > > > Central root cap IS columella, hence synonym 'columella cells'; I would > perhaps remove cells from this synonym. (BTW, that's why the definitions > in PO and in Esau are the same.) > >> >> A renaming of the term PO:0020132 : columella root cap cell to >> "central root cap cell" will help, thus maintaining consistency with >> parent term. Additional parent term for PO:0020132 : columella root >> cap cell is a must as follows. >> >> PO:0020130 : central root cap >> ---part_of--PO:0020132 : columella root cap cell >> >> For consistency the renaming is suggested for PO:0020133 : columella >> root cap initial to "central root cap initial" > > > This term 'PO:0020132 : columella root cap cell' resides only under > tissue (meristem) and cell node. When making these nodes, we agreed that > terms > from tissue and cell node would not be propagated initially elsewhere in > the ontology, unless there is specific reason for that (mostly > annotation requirements). So, unless we have such a reason, this term > could stay where it is right now. > If the term is under tissue and cell and it is a specific type of cell found only in roots it is valid to have it as part of the root where it is actually found. -Pankaj From katica at acoma.Stanford.EDU Mon Aug 8 12:16:29 2005 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Mon, 8 Aug 2005 09:16:29 -0700 (PDT) Subject: term: columella In-Reply-To: <42F7820A.6090903@cornell.edu> References: <42F38CBE.6030403@cornell.edu> <42F7820A.6090903@cornell.edu> Message-ID: On Mon, 8 Aug 2005, Pankaj Jaiswal wrote: >> This term 'PO:0020132 : columella root cap cell' resides only under tissue >> (meristem) and cell node. When making these nodes, we agreed that terms >> from tissue and cell node would not be propagated initially elsewhere in >> the ontology, unless there is specific reason for that (mostly annotation >> requirements). So, unless we have such a reason, this term could stay where >> it is right now. >> > If the term is under tissue and cell and it is a specific type of cell found > only in roots it is valid to have it as part of the root where it is actually > found. This is valid, I thought of this myself when I wrote this comment, but this should be true for entire ontology, that is, we should make sure that this rule is applied everywhere in the ontology, not just in a few cases. Katica > -Pankaj > > > -- -------------------------------------------------------------------------- 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 peter.stevens at mobot.org Wed Aug 10 14:37:58 2005 From: peter.stevens at mobot.org (Peter Stevens) Date: Wed, 10 Aug 2005 14:37:58 -0400 Subject: First International Biocurator Meeting, Asilomar, CA, December 8-11, 2005 In-Reply-To: References: Message-ID: So I suppose curators (e.g., me) in herbaria and zoological museums are not biocurators... It seems a rather unfortunate choice of a name! P. >** First announcement ** >First International Biocurator Meeting, Asilomar, CA, December 8-11, 2005 > >The goal of this meeting is to create a forum for curators and developers of >biological databases to discuss their work, promote collaborations, and foster >a sense of community in this very active and growing area of research. >Confirmed plenary speakers include Rolf Apweiler (EBI), Russ Altman (Stanford >University), and Mike Tyers (University of Toronto). > >Advance registration will be available from August 6 - October 1, and abstract >submission will be open from August 6 - October 11. > >For more information, please see the meeting web site at: > >http://biocurator.org/intnlbiocurator.html > >The meeting organizers would like to thank the Genetics Society of America for >their support. > >Organizing Comittee: >Richard Bruskiewich -International Rice Research Institute, the Philippines >Maria Costanzo -Saccharomyces Genome Database, Stanford University, USA >Kara Dolinski -Saccharomyces Genome Database, Princeton University, USA >Takashi Gojobori -Center for Information Biology and DNA Data Bank of Japan, >National Institute of Genetics, Japan >Win Hide -South African National Bioinformatics Institute, University of the >Western Cape, South Africa >Doug Howe -Zebrafish Information Network, University of Oregon, USA >Sean May -NASC, the European Arabidopsis Stock Centre, UK >Gillian Millburn -FlyBase, University of Cambridge, UK >Sima Misra -FlyBase and BDGP, University of California, Berkeley, USA >Mary Polacco -USDA ARS and University of Missouri, USA >Sue Rhee -The Arabidopsis Information Resource, Carnegie Institution, USA >Simon Twigger -Rat Genome Database, Medical College of Wisconsin at Milwaukee, >USA >Yukiko Yamazaki -Oryzabase, Genetic Informatics Laboratory, Center for Genetic >Resource Information, National Institute of Genetics, Japan > > >_______________________________________________ >Biocurator mailing list >Biocurator at acoma.stanford.edu >http://aztec.stanford.edu/mailman/listinfo/biocurator From rhee at acoma.Stanford.EDU Wed Aug 10 16:00:57 2005 From: rhee at acoma.Stanford.EDU (sue rhee) Date: Wed, 10 Aug 2005 13:00:57 -0700 (PDT) Subject: First International Biocurator Meeting, Asilomar, CA, December 8-11, 2005 In-Reply-To: References: Message-ID: Peter, I would say that any curator of biological data (whether they are in databases or in other types of collections) are biocurators. A curator of DNA samples from Egyptian mummies is coming to the meeting, for example. I hope the phrase 'biological databases' will not deter you from being interested in coming. While the majority of the talks will be based on curating digital data that have been coming out en masse in the last decade but I think the issues of curation will be more broadly applicable. Sue On Wed, 10 Aug 2005, Peter Stevens wrote: > So I suppose curators (e.g., me) in herbaria and zoological museums are not > biocurators... It seems a rather unfortunate choice of a name! > > P. > > >> ** First announcement ** >> First International Biocurator Meeting, Asilomar, CA, December 8-11, 2005 >> >> The goal of this meeting is to create a forum for curators and developers >> of >> biological databases to discuss their work, promote collaborations, and >> foster >> a sense of community in this very active and growing area of research. >> Confirmed plenary speakers include Rolf Apweiler (EBI), Russ Altman >> (Stanford >> University), and Mike Tyers (University of Toronto). >> >> Advance registration will be available from August 6 - October 1, and >> abstract >> submission will be open from August 6 - October 11. >> >> For more information, please see the meeting web site at: >> >> http://biocurator.org/intnlbiocurator.html >> >> The meeting organizers would like to thank the Genetics Society of America >> for >> their support. >> >> Organizing Comittee: >> Richard Bruskiewich -International Rice Research Institute, the Philippines >> Maria Costanzo -Saccharomyces Genome Database, Stanford University, USA >> Kara Dolinski -Saccharomyces Genome Database, Princeton University, USA >> Takashi Gojobori -Center for Information Biology and DNA Data Bank of >> Japan, >> National Institute of Genetics, Japan >> Win Hide -South African National Bioinformatics Institute, University of >> the >> Western Cape, South Africa >> Doug Howe -Zebrafish Information Network, University of Oregon, USA >> Sean May -NASC, the European Arabidopsis Stock Centre, UK >> Gillian Millburn -FlyBase, University of Cambridge, UK >> Sima Misra -FlyBase and BDGP, University of California, Berkeley, USA >> Mary Polacco -USDA ARS and University of Missouri, USA >> Sue Rhee -The Arabidopsis Information Resource, Carnegie Institution, USA >> Simon Twigger -Rat Genome Database, Medical College of Wisconsin at >> Milwaukee, >> USA >> Yukiko Yamazaki -Oryzabase, Genetic Informatics Laboratory, Center for >> Genetic >> Resource Information, National Institute of Genetics, Japan >> >> >> _______________________________________________ >> Biocurator mailing list >> Biocurator at acoma.stanford.edu >> http://aztec.stanford.edu/mailman/listinfo/biocurator > -- ----------------------------------------------------------------------------- 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. -----------------------------------------------------------------------------