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From: Doug H. <dh...@cs...> - 2005-10-05 10:38:20
|
In CL, trophectoderm cell should probably be trophoectodermal cell, making it consistent with the others in their adjectival state. With respect to the GO tem 'ectoderm cell fate sepcification'...I think if it more like [ectoderm] [cell fate specification] = refers to the tissue 'ectoderm' rather than [ectoderm cell] [fate specification] = refers to the cells of the ectoderm Does that have any bearing on this at all?? Perhaps it is neither here nor there... -Doug * * * * * * * * * * * * * * * * Doug Howe, Ph.D. ZFIN Scientific Curator Zebrafish Information Network 5291 University of Oregon Eugene, OR 97403-5291 Phone: (541) 346-0131 * * * * * * * * * * * * * * * * Alexander D. Diehl wrote: > Chris, > > Not to be too pedantic, but Stedman's Medical Dictionary, 27th > Edition, ISBN 068340007X, defines "poly" as "Abbreviated form and > colloquialism for polymorphonuclear leukocyte." Which matches the > usage I've read and heard by medical doctors. > > Of those three synonyms, only the first is exact, and the other two > are broad, or perhaps related, if we still allow that type. > > As to the second point, "syncytium" seems like an exact synonum. > > For the third point, you'd best enlist a developmental biologist. > > -- Alex > > > Chris Mungall wrote: > >> CL:0000096 "neutrophil" currently has the following synonyms: >> synonym: "neutrophil leukocyte" [] >> synonym: "poly" [] >> synonym: "polymorphonuclear leukocyte" [] >> >> The second is presumably some mistake? >> >> How complete is the synonym-typing in OBO-Cell? Exact synonyms are very >> useful for integration with GO. Do you think there are many untyped >> synonyms that should be upgraded to exacts? >> >> Can we add "syncytium" as an exact_synonym for: >> >> CL:0000228, "multinucleate cell" >> exact_synonym: "syncytial cell" [] >> >> The next comment is relatively minor - >> >> Are there any reasons why adjectival forms are sometimes used; for >> example, CL has: >> >> ectordermal cell >> endodermal cell >> >> but a non-adjectival form for: >> trophectoderm cell >> >> GO has >> >> "_ectoderm cell_ fate specification" >> >> Presumably they refer to the same thing >> >> I don't think we should manually specify both forms as synonyms in both >> ontologies - this can be done automatically. It may be an idea to use >> the >> same form as primary name in both ontologies though >> >> -- >> Chris >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: >> Power Architecture Resource Center: Free content, downloads, >> discussions, >> and more. http://solutions.newsforge.com/ibmarch.tmpl >> _______________________________________________ >> Obo-cell-type mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-cell-type >> >> > > |
From: Alexander D. D. <ad...@in...> - 2005-10-05 10:23:00
|
Chris, Not to be too pedantic, but Stedman's Medical Dictionary, 27th Edition, ISBN 068340007X, defines "poly" as "Abbreviated form and colloquialism for polymorphonuclear leukocyte." Which matches the usage I've read and heard by medical doctors. Of those three synonyms, only the first is exact, and the other two are broad, or perhaps related, if we still allow that type. As to the second point, "syncytium" seems like an exact synonum. For the third point, you'd best enlist a developmental biologist. -- Alex Chris Mungall wrote: >CL:0000096 "neutrophil" currently has the following synonyms: >synonym: "neutrophil leukocyte" [] >synonym: "poly" [] >synonym: "polymorphonuclear leukocyte" [] > >The second is presumably some mistake? > >How complete is the synonym-typing in OBO-Cell? Exact synonyms are very >useful for integration with GO. Do you think there are many untyped >synonyms that should be upgraded to exacts? > >Can we add "syncytium" as an exact_synonym for: > >CL:0000228, "multinucleate cell" >exact_synonym: "syncytial cell" [] > >The next comment is relatively minor - > >Are there any reasons why adjectival forms are sometimes used; for >example, CL has: > >ectordermal cell >endodermal cell > >but a non-adjectival form for: >trophectoderm cell > >GO has > >"_ectoderm cell_ fate specification" > >Presumably they refer to the same thing > >I don't think we should manually specify both forms as synonyms in both >ontologies - this can be done automatically. It may be an idea to use the >same form as primary name in both ontologies though > >-- >Chris > > >------------------------------------------------------- >This SF.Net email is sponsored by: >Power Architecture Resource Center: Free content, downloads, discussions, >and more. http://solutions.newsforge.com/ibmarch.tmpl >_______________________________________________ >Obo-cell-type mailing list >Obo...@li... >https://lists.sourceforge.net/lists/listinfo/obo-cell-type > > -- Alexander Diehl, Ph.D. Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: ad...@in... work: +1 (207) 288-6427 fax: +1 (207) 288-6131 |
From: Chris M. <cj...@fr...> - 2005-10-05 09:40:23
|
CL:0000096 "neutrophil" currently has the following synonyms: synonym: "neutrophil leukocyte" [] synonym: "poly" [] synonym: "polymorphonuclear leukocyte" [] The second is presumably some mistake? How complete is the synonym-typing in OBO-Cell? Exact synonyms are very useful for integration with GO. Do you think there are many untyped synonyms that should be upgraded to exacts? Can we add "syncytium" as an exact_synonym for: CL:0000228, "multinucleate cell" exact_synonym: "syncytial cell" [] The next comment is relatively minor - Are there any reasons why adjectival forms are sometimes used; for example, CL has: ectordermal cell endodermal cell but a non-adjectival form for: trophectoderm cell GO has "_ectoderm cell_ fate specification" Presumably they refer to the same thing I don't think we should manually specify both forms as synonyms in both ontologies - this can be done automatically. It may be an idea to use the same form as primary name in both ontologies though -- Chris |
From: Kara D. <ka...@ge...> - 2005-09-30 06:04:41
|
** Registration and Abstract deadline October 11 ** 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) -Mike Tyers (Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto). Advance registration and abstract submission will be available from August 6 - October 11. For more information, including links to registration, housing, and abstract submission, please see the meeting web site at: http://biocurator.org/intnlbiocurator.html Everyone is strongly encouraged to submit an abstract for either a poster or an oral presentation. 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 |
From: Michael A. (Genetics) <ma...@ge...> - 2005-09-29 09:52:11
|
OK thanks will fix. Michael |
From: Midori H. <mi...@eb...> - 2005-09-29 09:45:55
|
Hi, Is this list the best way to report errors or request changes in the cell type ontology? The error I noticed is that spheroplast (CL:0000524) is_a prokaryotic cell (CL:0000520); this is wrong because, as the definition notes, spheroplasts can be made from fungal cells as well as bacteria. Midori |
From: Kara D. <ka...@ge...> - 2005-09-12 10:51:56
|
** Second 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) -Mike Tyers (Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 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 |
From: sue r. <rh...@ac...> - 2005-09-12 10:19:32
|
> Not added as isa animal cell: > nitrogen fixing cell Thanks for taking care of the fix. What are some examples of nitrogen fixing animal cell? I thought this was done by microbes and plants... Sue > Michael > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Obo-cell-type mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-cell-type > -- ----------------------------------------------------------------------------- Sue Rhee rh...@ac... 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: Chris M. <cj...@fr...> - 2005-09-06 12:20:24
|
Looks good, thanks! |
From: Michael A. (Genetics) <ma...@ge...> - 2005-09-05 06:12:28
|
Opps mea culpa. Namespace glitch now fixed. Sue: Many of those on yr list were already isa animal cell but I have added some of them: These were already isa animal cell eye photoreceptor cell lymph gland crystal cell secondary pigment cell fusimotor neuron R4 photoreceptor cell R6 photoreceptor cell chlamydospore embryonic crystal cell posterior cone cell (sensu Endoptyeygota) corona radiata cell anterior cone cell (sensu Endoptyeygota) R7 photoreceptor cell equatorial cone cell (sensu Endoptyeygota) R2 photoreceptor cell R1 photoreceptor cell cumulus cell primary pigment cell R8 photoreceptor cell stratum granulosum cell leading edge cell R5 photoreceptor cell cardioblast R3 photoreceptor cell cone cell (sensu Endoptyeygota) tertiary pigment cell This was already a fungal cell: chlamydospore This was already a prokaryote cell: heterocyst Added as childs of animal cell: somatic stem cell leading edge cell cystoblast urothelial cell Not added as isa animal cell: nitrogen fixing cell Michael |
From: Michael A. (G. <ma...@ge...> - 2005-09-01 02:43:46
|
I will fix this over the w/end when home. Bah ! Michael |
From: sue r. <rh...@ac...> - 2005-08-31 10:45:37
|
Mike or Jonathan, These seem to be animal cells. Can either of you fix these? eye photoreceptor cell eye photoreceptor cell lymph gland crystal cell lymph gland crystal cell secondary pigment cell secondary pigment cell fusimotor neuron fusimotor neuron R4 photoreceptor cell R4 photoreceptor cell R6 photoreceptor cell R6 photoreceptor cell somatic stem cell somatic stem cell chlamydospore chlamydospore embryonic crystal cell embryonic crystal cell posterior cone cell (sensu Endoptyeygota) posterior cone cell (sensu Endoptyeygota) corona radiata cell corona radiata cell anterior cone cell (sensu Endoptyeygota) anterior cone cell (sensu Endoptyeygota) R7 photoreceptor cell R7 photoreceptor cell equatorial cone cell (sensu Endoptyeygota) equatorial cone cell (sensu Endoptyeygota) R2 photoreceptor cell R2 photoreceptor cell R1 photoreceptor cell R1 photoreceptor cell cumulus cell cumulus cell cystoblast cystoblast primary pigment cell primary pigment cell R8 photoreceptor cell R8 photoreceptor cell stratum granulosum cell stratum granulosum cell leading edge cell leading edge cell heterocyst heterocyst urothelial cell urothelial cell R5 photoreceptor cell R5 photoreceptor cell nitrogen fixing cell nitrogen fixing cell cardioblast cardioblast R3 photoreceptor cell R3 photoreceptor cell cone cell (sensu Endoptyeygota) cone cell (sensu Endoptyeygota) tertiary pigment cell tertiary pigment cell Sue On Mon, 29 Aug 2005, Chris Mungall wrote: > > Did someone confuse their cell and GO obo-edit configs? There are some GO > IDs in cell.obo - presumably these should be switched to unique CL IDs? > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Obo-cell-type mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-cell-type > -- ----------------------------------------------------------------------------- Sue Rhee rh...@ac... 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: Chris M. <cj...@ma...> - 2005-08-29 09:30:45
|
Did someone confuse their cell and GO obo-edit configs? There are some GO IDs in cell.obo - presumably these should be switched to unique CL IDs? |
From: Suzanna L. <su...@fr...> - 2005-05-16 18:14:48
|
Hi Sue, Now that we are both in the same room (wave), we should definitely take this opportunity to talk to one another. It seems to me that there is some confusion here and that many of the concerns stem from the confusion. -S On Apr 26, 2005, at 6:13 PM, Sue Rhee wrote: > I can think of two pragmatic issues at hand with respect to the > possibility of obsoleting cell type terms in PO. One is whether the > scope > of the cell type node within PO is comparable to that of the plant cell > type node within CL. The other is how quickly the databases using PO > can > switch to using CL for the cell types. Before these two issues are > addressed, we cannot obsolete the cell type node within PO. > > Regarding the first issue, PO's current goal is to accomodate plants > within the angiosperm taxa only. This means that we may not cover cell > types in lower plants that might be useful to have in a more generic > cell > type onology. On the other hand, even within this subdomain of plant > taxanomy, we could have some quite granular terms (e.g. that are > applicable to only a few species) that might be too specific for the > scope > of CL. I'm amenable to changing the scope of either or both of the > ontologies to allow the mutual exclusivity of the two ontologies in > terms > of primary terms, but this is something that needs to be agreed upon > all > pertinent developers of both of the ontologies. > > Regarding the second issue, it took TAIR 8 months to switch from TAIR > anatomy to PO structure ontology, with plenty of time to plan for it. > So > this is probably something we need to plan quite a bit in advance.. > > Sue > > > On Mon, 25 Apr 2005, Pankaj Jaiswal wrote: > >> >> >> Chris Mungall wrote: >> >> >>> >>> Regarding PO and CL - at the plant ontology meeting I suggested >>> simply >>> removing all cell terms from PO - is there any need to duplicate >>> them? >>> >> >> >> I agree on maintaining the cell types in cell.ontology, but the BIG >> questions are: >> #1 How many different ontologies are we expecting a database to use >> in >> their annotations? >> #2 What is the border line for each ontology, so that we do not >> overlap? >> #3 Is it good for the users or is it confusing? Users being both the >> actual wetlab scientists and the curators. >> # Is there a better way of semantically using an integrated version >> of >> all the required ontologies, despite being maintained independently? >> >> -Pankaj >> >> >> >> > > ----------------------------------------------------------------------- > ------ > Sue Rhee rh...@ac... > 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: Sue R. <rh...@ac...> - 2005-05-16 16:49:55
|
Sure:-) That'd be great. Maybe we could have the discussion over beer at the British Bankers Club? Sue On Mon, 16 May 2005, Suzanna Lewis wrote: > Hi Sue, > > Now that we are both in the same room (wave), we should > definitely take this opportunity to talk to one another. > It seems to me that there is some confusion here and that > many of the concerns stem from the confusion. > > -S > > On Apr 26, 2005, at 6:13 PM, Sue Rhee wrote: > > > I can think of two pragmatic issues at hand with respect to the > > possibility of obsoleting cell type terms in PO. One is whether the > > scope > > of the cell type node within PO is comparable to that of the plant cell > > type node within CL. The other is how quickly the databases using PO > > can > > switch to using CL for the cell types. Before these two issues are > > addressed, we cannot obsolete the cell type node within PO. > > > > Regarding the first issue, PO's current goal is to accomodate plants > > within the angiosperm taxa only. This means that we may not cover cell > > types in lower plants that might be useful to have in a more generic > > cell > > type onology. On the other hand, even within this subdomain of plant > > taxanomy, we could have some quite granular terms (e.g. that are > > applicable to only a few species) that might be too specific for the > > scope > > of CL. I'm amenable to changing the scope of either or both of the > > ontologies to allow the mutual exclusivity of the two ontologies in > > terms > > of primary terms, but this is something that needs to be agreed upon > > all > > pertinent developers of both of the ontologies. > > > > Regarding the second issue, it took TAIR 8 months to switch from TAIR > > anatomy to PO structure ontology, with plenty of time to plan for it. > > So > > this is probably something we need to plan quite a bit in advance.. > > > > Sue > > > > > > On Mon, 25 Apr 2005, Pankaj Jaiswal wrote: > > > >> > >> > >> Chris Mungall wrote: > >> > >> > >>> > >>> Regarding PO and CL - at the plant ontology meeting I suggested > >>> simply > >>> removing all cell terms from PO - is there any need to duplicate > >>> them? > >>> > >> > >> > >> I agree on maintaining the cell types in cell.ontology, but the BIG > >> questions are: > >> #1 How many different ontologies are we expecting a database to use > >> in > >> their annotations? > >> #2 What is the border line for each ontology, so that we do not > >> overlap? > >> #3 Is it good for the users or is it confusing? Users being both the > >> actual wetlab scientists and the curators. > >> # Is there a better way of semantically using an integrated version > >> of > >> all the required ontologies, despite being maintained independently? > >> > >> -Pankaj > >> > >> > >> > >> > > > > ----------------------------------------------------------------------- > > ------ > > Sue Rhee rh...@ac... > > 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. > > ----------------------------------------------------------------------- > > ------ > > > ----------------------------------------------------------------------------- Sue Rhee rh...@ac... 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: Pankaj J. <pj...@co...> - 2005-05-05 08:53:47
|
Sorry for the late reply, I agree with Sue, but there is another problem. If we remove the cell types from PO or for that reason in any anatomy ontology, then there is no mechanism (at least in the present day) we can connect to say X-cell is a part_of Y-Tissue/organ from plant/fly/any_organism. As an alternative, I still strongly believe, that all the cell types be maintained in individual organism/clade specific anatomy ontologies and whenever required, a complete but flat vocabulary of cell type (aka cell ontology) be created. This will also help to maintain the sensu aspects. However we may lose the comparative aspects, the moment we go down the sensu path. -Pankaj Sue Rhee wrote: > I can think of two pragmatic issues at hand with respect to the > possibility of obsoleting cell type terms in PO. One is whether the scope > of the cell type node within PO is comparable to that of the plant cell > type node within CL. The other is how quickly the databases using PO can > switch to using CL for the cell types. Before these two issues are > addressed, we cannot obsolete the cell type node within PO. > > Regarding the first issue, PO's current goal is to accomodate plants > within the angiosperm taxa only. This means that we may not cover cell > types in lower plants that might be useful to have in a more generic cell > type onology. On the other hand, even within this subdomain of plant > taxanomy, we could have some quite granular terms (e.g. that are > applicable to only a few species) that might be too specific for the scope > of CL. I'm amenable to changing the scope of either or both of the > ontologies to allow the mutual exclusivity of the two ontologies in terms > of primary terms, but this is something that needs to be agreed upon all > pertinent developers of both of the ontologies. > > Regarding the second issue, it took TAIR 8 months to switch from TAIR > anatomy to PO structure ontology, with plenty of time to plan for it. So > this is probably something we need to plan quite a bit in advance.. > > Sue > > > On Mon, 25 Apr 2005, Pankaj Jaiswal wrote: > > >> >>Chris Mungall wrote: >> >> >> >>>Regarding PO and CL - at the plant ontology meeting I suggested simply >>>removing all cell terms from PO - is there any need to duplicate them? >>> >> >> >>I agree on maintaining the cell types in cell.ontology, but the BIG >>questions are: >> #1 How many different ontologies are we expecting a database to use in >>their annotations? >> #2 What is the border line for each ontology, so that we do not overlap? >> #3 Is it good for the users or is it confusing? Users being both the >>actual wetlab scientists and the curators. >> # Is there a better way of semantically using an integrated version of >>all the required ontologies, despite being maintained independently? >> >>-Pankaj >> |
From: Sue R. <rh...@ac...> - 2005-04-27 15:54:11
|
Wasn't there an email thread recently that Jonathan Bard answered that sort of supports the view that the CL is focused on model organisms? I'd like to look into that email more carefully but can't seem to find it on the obo-cell-type archive. If someone has this, can you forward it to me? I don't have real concrete argument either for or against setting a limitation on granularity right now... Sue On Wed, 27 Apr 2005, Michael Ashburner (Genetics) wrote: > Sue - Chris raises am interesting point in his reply to you: > > Your second point raises an important question: just how specific is too > specific for CL? Do we have a formal means of deciding this? > > The answer is no we no not have such a means. However, I see no problem > in CL wrt granularity. If a term is needed it should be there. > > > > Michael > ----------------------------------------------------------------------------- Sue Rhee rh...@ac... 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: Michael A. (Genetics) <ma...@ge...> - 2005-04-27 01:33:48
|
Sue - Chris raises am interesting point in his reply to you: Your second point raises an important question: just how specific is too specific for CL? Do we have a formal means of deciding this? The answer is no we no not have such a means. However, I see no problem in CL wrt granularity. If a term is needed it should be there. Michael |
From: Chris M. <cj...@fr...> - 2005-04-26 18:41:01
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On Tue, 26 Apr 2005, Sue Rhee wrote: > I can think of two pragmatic issues at hand with respect to the > possibility of obsoleting cell type terms in PO. One is whether the scope > of the cell type node within PO is comparable to that of the plant cell > type node within CL. The other is how quickly the databases using PO can > switch to using CL for the cell types. Before these two issues are > addressed, we cannot obsolete the cell type node within PO. > > Regarding the first issue, PO's current goal is to accomodate plants > within the angiosperm taxa only. This means that we may not cover cell > types in lower plants that might be useful to have in a more generic cell > type onology. On the other hand, even within this subdomain of plant > taxanomy, we could have some quite granular terms (e.g. that are > applicable to only a few species) that might be too specific for the scope > of CL. I'm amenable to changing the scope of either or both of the > ontologies to allow the mutual exclusivity of the two ontologies in terms > of primary terms, but this is something that needs to be agreed upon all > pertinent developers of both of the ontologies. The fact that the angiosperm partition of CL would be more complete than the non-angiosperm plant partition should not be a problem in itself However I can imagine a potential problem: are there any cases of "A derives_from B" in angiosperms with "A derives_from C" in gymnosperms, where B != C? If so, this could spell trouble for the proposed merger; the current solution to this problem of introducing sensu terms is problematic. Your second point raises an important question: just how specific is too specific for CL? Do we have a formal means of deciding this? I don't think this is problematic though. PO could extend CL, adding more specific cells but managing them as part of PO. It's possible to configure obo-edit so that this would appear as one ontology. But you're right, the respective ontologies have to agree on what the boundary is > Regarding the second issue, it took TAIR 8 months to switch from TAIR > anatomy to PO structure ontology, with plenty of time to plan for it. So > this is probably something we need to plan quite a bit in advance.. Is the issue a software one, or is it to do with mapping existing IDs? I don't think this should be too problematic compared to your first issue > Sue > > > On Mon, 25 Apr 2005, Pankaj Jaiswal wrote: > > > > > > > Chris Mungall wrote: > > > > > > > > > > Regarding PO and CL - at the plant ontology meeting I suggested simply > > > removing all cell terms from PO - is there any need to duplicate them? > > > > > > > > > I agree on maintaining the cell types in cell.ontology, but the BIG > > questions are: > > #1 How many different ontologies are we expecting a database to use in > > their annotations? > > #2 What is the border line for each ontology, so that we do not overlap? > > #3 Is it good for the users or is it confusing? Users being both the > > actual wetlab scientists and the curators. > > # Is there a better way of semantically using an integrated version of > > all the required ontologies, despite being maintained independently? > > > > -Pankaj > > > > > > > > > > ----------------------------------------------------------------------------- > Sue Rhee rh...@ac... > 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: Sue R. <rh...@ac...> - 2005-04-26 18:13:31
|
I can think of two pragmatic issues at hand with respect to the possibility of obsoleting cell type terms in PO. One is whether the scope of the cell type node within PO is comparable to that of the plant cell type node within CL. The other is how quickly the databases using PO can switch to using CL for the cell types. Before these two issues are addressed, we cannot obsolete the cell type node within PO. Regarding the first issue, PO's current goal is to accomodate plants within the angiosperm taxa only. This means that we may not cover cell types in lower plants that might be useful to have in a more generic cell type onology. On the other hand, even within this subdomain of plant taxanomy, we could have some quite granular terms (e.g. that are applicable to only a few species) that might be too specific for the scope of CL. I'm amenable to changing the scope of either or both of the ontologies to allow the mutual exclusivity of the two ontologies in terms of primary terms, but this is something that needs to be agreed upon all pertinent developers of both of the ontologies. Regarding the second issue, it took TAIR 8 months to switch from TAIR anatomy to PO structure ontology, with plenty of time to plan for it. So this is probably something we need to plan quite a bit in advance.. Sue On Mon, 25 Apr 2005, Pankaj Jaiswal wrote: > > > Chris Mungall wrote: > > > > > > Regarding PO and CL - at the plant ontology meeting I suggested simply > > removing all cell terms from PO - is there any need to duplicate them? > > > > > I agree on maintaining the cell types in cell.ontology, but the BIG > questions are: > #1 How many different ontologies are we expecting a database to use in > their annotations? > #2 What is the border line for each ontology, so that we do not overlap? > #3 Is it good for the users or is it confusing? Users being both the > actual wetlab scientists and the curators. > # Is there a better way of semantically using an integrated version of > all the required ontologies, despite being maintained independently? > > -Pankaj > > > > ----------------------------------------------------------------------------- Sue Rhee rh...@ac... 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: Michael A. (Genetics) <ma...@ge...> - 2005-04-26 07:21:37
|
Thankyou all for your input. The following summarises where we are. Next Monday (May Day) I will make the changes to CL and ask Jane to do likewise to GO unless we hear onjections to any. Michael * Action for CL ** Action for GO ========================================================================= missing extrathymic T-cell missing thymic T-cell missing negative extrathymic T-cell missing negative thymic T-cell missing positive extrathymic T-cell missing positive thymic T-cell ... no change to CL/GO needed; not a cell type but a cell location X-Sender: ad...@po... Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing edge cell .. no action parse problem missing thymocyte .. no change to CL; GO in process of obsoleting/merging this term X-Sender: ad...@po... Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing natural killer cell *.. is in CL. CL to add 'NK T-cell' & 'NK T cell' & 'NK T lymphocyte' as synonyms. missing NK T-cell .. see above X-Sender: ad...@po... Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing B-1 B-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 helper cell missing cytotoxic T-cell missing gamma-delta T-cell missing killer cell missing regulatory T-cell *CL to change all 'B_cell' 'T_cell' > 'B cell' 'T cell' with 'B-cell', 'B lymphocyte' as synonmyms. *CL to change 'helper T cell' > 'T-helper cell' with former as synonym. **GO also to change 'B-cell' etc > 'B cell' etc with 'B cell', 'B lymphocyte' etc as synonyms. *CL will not add terms above until Alex reports back. # 8. Is the GO usage of 'hemocyte' arthropod specific ? In this case GO needs to change 'hemocyte differentiation (sensu Arthropoda)' by removing the sensu. *CL will change 'hemocyte' and 'prohemocyte' to ditto (sensu Arthropoda' X-Sender: ad...@po... Date: Wed, 20 Apr 2005 12:39:21 -0400 # missing azurophil .. not a cell type but a class of granule; parse error # GO has already changed 'neuron cell differentiation' > 'neuron differentiation' From: J Clark <jc...@eb...> Date: Mon, 18 Apr 2005 17:32:25 +0100 # basophil cell hemocyte cell neuroblast cell neuron cell oocyte cell spermatid cell spermatocyte cell synergid cell trichome cell missing cystoblast cell **GO to remove 'cell' from all of these. Note that 'egg cell' has been kept because that is plant useage. CL will keep 'egg cell' with the same meaning. From: J Clark <jc...@eb...> Date: Wed, 20 Apr 2005 15:47:29 +0100 # 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' .. photorecptor and photoreceptor cell are not the same thing. The 'receptor' can be a single cell or the entire stucture (the eye is a photoreceptor, so are its rods and cones); ditto mechanoreceptor. CL no change except: *GO: ADD 'eye photoreceptor cell ; CL:NEW' as isa 'photoreceptor cell' *GO: ADD 'non-eye photoreceptor cell' non-eye photoreceptor cell # 11. ADD 'male gametophyte sperm cell ; CL:NEW' as isa of 'sperm cell (sensu Viridiplantae' Sue argues that this is redundant: 'We feel that this is somewhat redundant since all Viridiplantae sperm cells come from the gametophyte.' Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rh...@ac...> If so it is presumably redundant in GO: GO:0048235 : male gametophyte sperm cell **GO to act # > missing pollen not a cell but an organism (male gametophyte) Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rh...@ac...> .. no action # These are Sue's comments Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rh...@ac...> ... which indicate that a change to GO, rather than CL, is required: > missing abaxial cell This is too vague a concept as a cell type and should not be included in CL. > missing gametophyte central cell not necessary. female gametophyte central cell is sufficient. i believe that hermaphrodite gametophyte does not make a central cell. Also if 'central cell' is not used in other systems, the adjective 'female gametophyte' may not be necessary as part of the term name. > missing gametophyte egg cell i don't think we need to make a distinction between gametophyte egg cell and female gametophyte egg cell. > missing gametophyte sperm cell not necessary. we could add it as a synonym of sperm cell (sensu Viridiplantae) > missing male gametophyte sperm cell not necessary. # > missing primary endosperm perhaps endosperm cell might be needed. will look into this further and update the ontology. Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rh...@ac...> *CL to add # > missing primary cell this probably comes from 'primary cell wall' and doesn't need to be added as a cell type. > missing secondary cell this comes from 'secondary cell wall' and doesn't need to be added as a cell type. Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rh...@ac...> .. no action parse problems # > missing pollen germ cell this is not necessary as it's the same as male gametophyte sperm cell. also it is not a very good synonym. *CL to make synonym **GO is this then needed ?? Date: Wed, 20 Apr 2005 17:41:29 -0700 (PDT) From: Sue Rhee <rh...@ac...> # *CL. 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 *CL. MAKE 'osteoclast' and 'macrophage' both is_a's of 'monocyte' *CL. change 'spermatozoan' to 'sperm' *CL. ADD parent 'cardioblast ; CL:NEW' for 'cardioblast (sensu Arthropoda) *CL. CORRECT spelling 'sperm cel' (synonym of CL:0000019). *CL. REMOVE all _ and replaced by spaces. *CL. CHANGE default-namespace: to 'cell' from 'cell_ontology'. *CL. CHANGE 'epithelial cell of trachea' to 'tracheal epithelial cell' *CL: make 'trichome' also an isa of 'hair cell' *CL to addroot epidermal cell *CL. CHANGE: 'blood platelet' > 'platelet' *CL. ADD 'retinal cone cell ; CL:NEW' as isa 'cone cell' *CL. 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 *CL. ADD as isa child of 'crystal cell': embryonic crystal cell lymph gland crystal cell *CL: add 'cystoblast' as child of 'germ cell'; make 'nurse cell' a developsfrom child *CL: add 'somatic stem cell' as child of 'stem cell' *CL. 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 *CL to change 'leukocyte cell' > 'leukocyte' *CL: correct spelling of 'iridiophore' to 'iridophore' *CL: add 'primary pigment cell' 'secondary pigment cell' 'tertiary pigment cell'as childs of 'visual pigment cell (sensu Nematoda ..' *CL: add 'cone cell (sensu Endoptyeygota)' as child of 'crystallin accumulating cell' with children 'posterior, anterior, polar & equatorial cone cell (sens E)' *CL: add 'leading edge cell' as child of 'epithelial cell' with defn: 'A cell at the front of a migrating epithelial sheet.' *CL: add 'urothelial cell' as child of 'epithelial cell' with defn: 'A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria'. *CL: Add 'ameboid cell' as a child of ; make 'chemotactic ameoba' a child of it. defn: 'A cell that migrates by extension and retraction of a pseudopodium.' # **GO to change 'tracheal cell *' to 'tracheal epithelial cell *' **GO to change 'ovarian cumulus cell differentiation' to 'cumulus cell differentiation' **GO to change 'auditory hair cell' to 'auditory receptor cell' **GO to change 'branch cell fate determination (sensu Insecta) -> branched_duct_epithelial_cell fate determination (sensu Insecta)' **GO change 'glia cell' to 'glial cell'. **GO change 'border cell' to 'border follicle cell'. **GO. change 'leukocyte cell' to 'leukocyte'. **GO: change 'mesoderm cell' to 'mesodermal cell' **GO: change 'endoderm cell' to 'endodermal cell' **GO: change 'neuronal cell' to 'neuron' **GO; add neuroblast_(sensu_Nematoda_and_Protostomia), neuroblast_(sensu_Vertebrata) as childs of neuroblast [cell] * terms **GO; add erythrocyte_(sensu_Mammalia), erythrocyte_(sensu_non-Mammalia) as childs of of erythrocyte * terms **GO add epidermal_cell_(sensu_Insecta) * as childs of epidermal cell * terms ? **GO: ditto glial cell (sensu Nematoda and Protostomia) as childs of glial cell * terms ? **GO: ditto pigment cell (sensu Nematoda and Protostomia), pigment cell (sensu Vertebrata) as childs of pigment cell * terms ? **GO: male 'iridophore differentiation' and 'xanthophore differentiation' childs of 'melanocyte differentiation', not sibs **GO: to change 'apidocyte' to 'fat cell' .. JB argued that 'apidocyte' as not understood by vertebrates. CL uses 'fat cell' with 'apidocyte' as a syn. # > 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. Delivery-date: Fri, 22 Apr 2005 10:05:07 +0100 From: Jonathan Bard <jb...@st...> Striated muscle comes in two flavours - normal (default, longitudinal striations) and obliquely striated - a c elegans speciality (I suppose it is seen in other nematodes and such organisms)# *CL: add 'striated muscle cell' as parent of 'obliquely striated muscle cell # missing embryonic crystal cell missing embryonic hemocyte missing embryonic plasmatocyte missing lymph gland crystal cell missing lymph gland hemocyte missing lymph gland plasmatocyte *CL: add these terms as there is, indeed, two such pops in flies # Outstanding terms missing from CL. Any helpers ? missing aortic cell (sensu Insecta) missing autophagic cell missing blood cell missing early stripe melanocyte missing gland cell missing inner cell mass cell missing larval midgut cell missing late stripe melanocyte missing stripe melanocyte missing mass cell missing mystery cell fate missing organ precursor cell missing precursor cell missing sensory organ precursor cell missing polarized epithelial cell ... is there such a thing as an unpolarized epithelial cell ?? These all have similar constyct '<place> cell' missing axial mesoderm cell missing lateral mesoderm cell missing intermediate mesoderm cell missing paraxial mesoderm cell missing salivary gland cell missing tracheal cell missing trophectoderm cell missing retinal cell missing heart proper cell missing cardiac cell missing midgut cell # |
From: Chris M. <cj...@fr...> - 2005-04-25 12:18:21
|
On Mon, 25 Apr 2005, Pankaj Jaiswal wrote: > > > Chris Mungall wrote: > > > > > > Regarding PO and CL - at the plant ontology meeting I suggested simply > > removing all cell terms from PO - is there any need to duplicate them? > > > > > I agree on maintaining the cell types in cell.ontology, but the BIG > questions are: These are good questions - before answering, consider the fact that in OBO we currently conflate 'reference' and 'application' ontologies - they are one and the same thing. But we have the ability to do things such as provide an automatically derived cut of GO (an application ontology) which excludes animal development terms for use by PO annotation-curators and PO end-users (but of course GO-editos would always use the reference ontology). This may or may not be a good thing in this particular case. Personally I think it is a good idea to have no overlap between any clade-specific reference anatomy ontology and the cell type ontology. We can always make an application ontology for each species that combines the two. In fact we really do this now with GO - is it 3 ontologies or 1? From a curators point of view there are 3. But from an application point of view it can be treated as 1. > #1 How many different ontologies are we expecting a database to use in > their annotations? it depends on the kind of annotation.. is this important? > #2 What is the border line for each ontology, so that we do not overlap? in this particular case, the border line between CL, cellular component and a structure in any one clade-specific anatomical ontology should be clear > #3 Is it good for the users or is it confusing? Users being both the > actual wetlab scientists and the curators. it needn't be confusing - it can be presented as the same ontology or different ontologies, depending in what is appropriate for the application. > # Is there a better way of semantically using an integrated version of > all the required ontologies, despite being maintained independently? Not sure what you mean - if the ontologies are non-overlapping then integrating them should be much easier. Of course there is still the problem of overlap between species-specific anatomical ontologies, and relationships between cell types and anatomical structures - this is a fairly thorny one, and it's being addressed by the XSPAN and SAEL projects > -Pankaj > > > > > |
From: Pankaj J. <pj...@co...> - 2005-04-25 07:04:15
|
Chris Mungall wrote: > > Regarding PO and CL - at the plant ontology meeting I suggested simply > removing all cell terms from PO - is there any need to duplicate them? > I agree on maintaining the cell types in cell.ontology, but the BIG questions are: #1 How many different ontologies are we expecting a database to use in their annotations? #2 What is the border line for each ontology, so that we do not overlap? #3 Is it good for the users or is it confusing? Users being both the actual wetlab scientists and the curators. # Is there a better way of semantically using an integrated version of all the required ontologies, despite being maintained independently? -Pankaj |
From: Mikel E. A. <mik...@cs...> - 2005-04-24 08:54:09
|
That sounds fine for me Mikel Michael Ashburner (Genetics) wrote: >Chris > >Yes, the first step is to get CL, GO and PO in synch with respect to >semantics and definitions. Then, as you say, you & Mikel can get to work >and we will then go thru fixing the relationships. > >I will fix the namespace. > >I agree with you wrt to PO, but that is their decision. If they decide >not to, then I suggest that we give Katica write access to CL. > >Michael > > >------------------------------------------------------- >SF email is sponsored by - The IT Product Guide >Read honest & candid reviews on hundreds of IT Products from real users. >Discover which products truly live up to the hype. Start reading now. >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >_______________________________________________ >Obo-cell-type mailing list >Obo...@li... >https://lists.sourceforge.net/lists/listinfo/obo-cell-type > > -- Mikel Egana Aranguren --------------------------------------- http://www.sindominio.net/~pik Manchester University Computer Science --------------------------------------- |
From: Michael A. (G. <ma...@ge...> - 2005-04-23 00:26:28
|
Chris Yes, the first step is to get CL, GO and PO in synch with respect to semantics and definitions. Then, as you say, you & Mikel can get to work and we will then go thru fixing the relationships. I will fix the namespace. I agree with you wrt to PO, but that is their decision. If they decide not to, then I suggest that we give Katica write access to CL. Michael |