From john.richter at aya.yale.edu Wed Dec 1 02:24:13 2004
From: john.richter at aya.yale.edu (John Day-Richter)
Date: Wed, 01 Dec 2004 00:24:13 -0700
Subject: pls help (PR#46)
In-Reply-To: <96EC66889610D611BA9500A0C9DCFB2E01026359@ems8042-01.monsanto.com>
References: <96EC66889610D611BA9500A0C9DCFB2E01026359@ems8042-01.monsanto.com>
Message-ID: <41AD719D.2000409@aya.yale.edu>
One more thing you might be interested in...
The configuration manager doesn't let you add new types. It merely
allows you to *assign icons* to types. The icons you specify in the
configuration manager will never cause a new type to appear in the
ontology. In fact, you'll never see your icons unless you load an
ontology that happens to contain a relationship types whose id matches
one of the ids you entered in the configuration manager.
-John
AUGUSTINE, ALICE CLARA [AG/8042] wrote:
>Dear Katica,
>Thank you for getting back to me so quickly.
>This has really helped me.
>
>Cheers
>Clare :)
>
>
>-----Original Message-----
>From: Katica Ilic [mailto:jitterbug at plantontology.org]
>Sent: Wednesday, December 01, 2004 9:08 AM
>To: alice.clara.augustine at monsanto.com
>Cc: po-dev at plantontology.org; john.richter at aya.yale.edu
>Subject: Re: pls help (PR#46)
>
>Hi Alice,
>
>I already forwarded your message to John Richter and am waiting to hear from
>him.
>
>In the meantime, I tried few things in DAG-edit myself, and, contrary to what I
>told you earlier, when I used Advance Option (while saving or loading files), it
>worked, meaning the new relationship type was saved (after I closed DAG-edit).
>However, this relationship type (inverse_of) did not show up under the Edit
>menu, when I scrolled to 'Change relationship type to' (there are only three
>previous relationship types there). Also, adding new relationship types through
>the Configuration Manager did not work at all.
>
>So here is a summary of what worked (using Advanced option window):
>
>In 'Define term relationship symbols' I added NEWTYPE by clicking on 'Add', then
>added Relationship type symbol (I randomly chose &), then below, added
>Relationship type name (which was 'inverse_of'), and in the last box, added
>description (inverse of).
>
>As I said, I am waiting to hear from John and will forward his response to you
>immediately.
>
>Katica
>
>
>
>
>>Dear Katica,
>>Thank you for getting back to me so quickly.
>>I am using ver 1.418 desktop.
>>Could you go through the steps of adding relationship types using the
>>
>>
>DAG-edit
>
>
>>configuration manager (in Plugins). I was not too successful.
>>
>>As an urgent request, could you please find out from any of your colleagues
>>
>>
>and
>
>
>>help me out as soon as possible?
>>
>>Thank you
>>Regards
>>Clare
>>PS: I believe Pankaj is on holiday, which is why I have not written to him.
>>I did write to John Richter, but I have not heard from him either (I'm
>>
>>
>assuming
>
>
>>he is on a thanksgiving holiday).
>>
>>-----Original Message-----
>>From: Katica Ilic [mailto:jitterbug at plantontology.org]
>>Sent: Tuesday, November 30, 2004 11:26 PM
>>To: alice.clara.augustine at monsanto.com
>>Cc: po-dev at plantontology.org
>>Subject: Re: pls help (PR#46)
>>
>>Hi Alice,
>>
>>I am not sure I know the exact answer to your question, but I would rather
>>
>>
>try
>
>
>>adding the new relationship types in the DAG-edit configuration manager (in
>>Plugins), and not in advanced option. However, adding the Icon path for new
>>realatioship types is more complicated and I would need to ask John Richter
>>about this.
>>
>>Just to make it easier, can you tell me if you are using the most recent
>>
>>
>version
>
>
>>of DAG-edit (desktop or Unix) and also did you download plugins as well
>>(http://sourceforge.net/project/showfiles.php?group_id=36855).
>>
>>I'll look into this and get back to you soon.
>>
>>Katica
>>
>>
>>
>>>------_=_NextPart_001_01C4D686.43009590
>>>Content-Type: text/plain
>>>
>>>Dear Katica,
>>>
>>>I use DAG-Edit version 1.418.
>>>I have problems adding new relationship types.
>>>On your documentation you refer to (Clicking the "Advanced Options" button
>>>allows you to specify the symbol table used to specify relationship types
>>>
>>>
>>using
>>
>>
>>>the legacy GO Flat File Format encodings)........I could not find this
>>>
>>>
>>option.
>>
>>
>>>I tried doing it via the configuration manager too......but did not have too
>>>much luck.
>>>Could you please guide me?
>>>
>>>Regards
>>>Alice Clare
>>>
>>>------_=_NextPart_001_01C4D686.43009590
>>>Content-Type: text/html
>>>Content-Transfer-Encoding: quoted-printable
>>>
>>>
>>>
>>>
>>>>>charset=3Dus-ascii">
>>>>>5.5.2654.19">
>>>pls help
>>>
>>>
>>>
>>>Dear >>SIZE=3D2 FACE=3D"Arial">Katica>>FACE=3D"Arial">, &n=
>>>bsp;
>>>
>>>I use DAG-Edit version =
>>>1.418.
>>>
>>>I have problems adding =
>>>new relationship types.
>>>
>>>On your documentation you =
>>>refer to (Clicking the "Advanced Options" button =
>>>allows you to specify the symbol table used to specify relationship =
>>>types using the legacy GO Flat File Format encodings)........I could =
>>>not find this option.
>>>
>>>I tried doing it via the configuration manager =
>>>too......but did not have too much luck.
>>>
>>>Could you please guide me?
>>>
>>>Regards
>>>
>>>Alice Clare
>>>
>>>
>>>
>>>------_=_NextPart_001_01C4D686.43009590--
>>>
>>>
>>>
>>>
>>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.
>>
>>
>>
>
>
>
From john.richter at aya.yale.edu Wed Dec 1 02:24:13 2004
From: john.richter at aya.yale.edu (John Day-Richter)
Date: Wed, 01 Dec 2004 00:24:13 -0700
Subject: pls help (PR#46)
In-Reply-To: <96EC66889610D611BA9500A0C9DCFB2E01026359@ems8042-01.monsanto.com>
References: <96EC66889610D611BA9500A0C9DCFB2E01026359@ems8042-01.monsanto.com>
Message-ID: <41AD719D.2000409@aya.yale.edu>
One more thing you might be interested in...
The configuration manager doesn't let you add new types. It merely
allows you to *assign icons* to types. The icons you specify in the
configuration manager will never cause a new type to appear in the
ontology. In fact, you'll never see your icons unless you load an
ontology that happens to contain a relationship types whose id matches
one of the ids you entered in the configuration manager.
-John
AUGUSTINE, ALICE CLARA [AG/8042] wrote:
>Dear Katica,
>Thank you for getting back to me so quickly.
>This has really helped me.
>
>Cheers
>Clare :)
>
>
>-----Original Message-----
>From: Katica Ilic [mailto:jitterbug at plantontology.org]
>Sent: Wednesday, December 01, 2004 9:08 AM
>To: alice.clara.augustine at monsanto.com
>Cc: po-dev at plantontology.org; john.richter at aya.yale.edu
>Subject: Re: pls help (PR#46)
>
>Hi Alice,
>
>I already forwarded your message to John Richter and am waiting to hear from
>him.
>
>In the meantime, I tried few things in DAG-edit myself, and, contrary to what I
>told you earlier, when I used Advance Option (while saving or loading files), it
>worked, meaning the new relationship type was saved (after I closed DAG-edit).
>However, this relationship type (inverse_of) did not show up under the Edit
>menu, when I scrolled to 'Change relationship type to' (there are only three
>previous relationship types there). Also, adding new relationship types through
>the Configuration Manager did not work at all.
>
>So here is a summary of what worked (using Advanced option window):
>
>In 'Define term relationship symbols' I added NEWTYPE by clicking on 'Add', then
>added Relationship type symbol (I randomly chose &), then below, added
>Relationship type name (which was 'inverse_of'), and in the last box, added
>description (inverse of).
>
>As I said, I am waiting to hear from John and will forward his response to you
>immediately.
>
>Katica
>
>
>
>
>>Dear Katica,
>>Thank you for getting back to me so quickly.
>>I am using ver 1.418 desktop.
>>Could you go through the steps of adding relationship types using the
>>
>>
>DAG-edit
>
>
>>configuration manager (in Plugins). I was not too successful.
>>
>>As an urgent request, could you please find out from any of your colleagues
>>
>>
>and
>
>
>>help me out as soon as possible?
>>
>>Thank you
>>Regards
>>Clare
>>PS: I believe Pankaj is on holiday, which is why I have not written to him.
>>I did write to John Richter, but I have not heard from him either (I'm
>>
>>
>assuming
>
>
>>he is on a thanksgiving holiday).
>>
>>-----Original Message-----
>>From: Katica Ilic [mailto:jitterbug at plantontology.org]
>>Sent: Tuesday, November 30, 2004 11:26 PM
>>To: alice.clara.augustine at monsanto.com
>>Cc: po-dev at plantontology.org
>>Subject: Re: pls help (PR#46)
>>
>>Hi Alice,
>>
>>I am not sure I know the exact answer to your question, but I would rather
>>
>>
>try
>
>
>>adding the new relationship types in the DAG-edit configuration manager (in
>>Plugins), and not in advanced option. However, adding the Icon path for new
>>realatioship types is more complicated and I would need to ask John Richter
>>about this.
>>
>>Just to make it easier, can you tell me if you are using the most recent
>>
>>
>version
>
>
>>of DAG-edit (desktop or Unix) and also did you download plugins as well
>>(http://sourceforge.net/project/showfiles.php?group_id=36855).
>>
>>I'll look into this and get back to you soon.
>>
>>Katica
>>
>>
>>
>>>------_=_NextPart_001_01C4D686.43009590
>>>Content-Type: text/plain
>>>
>>>Dear Katica,
>>>
>>>I use DAG-Edit version 1.418.
>>>I have problems adding new relationship types.
>>>On your documentation you refer to (Clicking the "Advanced Options" button
>>>allows you to specify the symbol table used to specify relationship types
>>>
>>>
>>using
>>
>>
>>>the legacy GO Flat File Format encodings)........I could not find this
>>>
>>>
>>option.
>>
>>
>>>I tried doing it via the configuration manager too......but did not have too
>>>much luck.
>>>Could you please guide me?
>>>
>>>Regards
>>>Alice Clare
>>>
>>>------_=_NextPart_001_01C4D686.43009590
>>>Content-Type: text/html
>>>Content-Transfer-Encoding: quoted-printable
>>>
>>>
>>>
>>>
>>>>>charset=3Dus-ascii">
>>>>>5.5.2654.19">
>>>pls help
>>>
>>>
>>>
>>>Dear >>SIZE=3D2 FACE=3D"Arial">Katica>>FACE=3D"Arial">, &n=
>>>bsp;
>>>
>>>I use DAG-Edit version =
>>>1.418.
>>>
>>>I have problems adding =
>>>new relationship types.
>>>
>>>On your documentation you =
>>>refer to (Clicking the "Advanced Options" button =
>>>allows you to specify the symbol table used to specify relationship =
>>>types using the legacy GO Flat File Format encodings)........I could =
>>>not find this option.
>>>
>>>I tried doing it via the configuration manager =
>>>too......but did not have too much luck.
>>>
>>>Could you please guide me?
>>>
>>>Regards
>>>
>>>Alice Clare
>>>
>>>
>>>
>>>------_=_NextPart_001_01C4D686.43009590--
>>>
>>>
>>>
>>>
>>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.
>>
>>
>>
>
>
>
From guido.mathieu at taxa.be Wed Dec 1 12:54:00 2004
From: guido.mathieu at taxa.be (Guido Mathieu)
Date: Wed, 1 Dec 2004 18:54:00 +0100
Subject: Inflorescence - peduncle
Message-ID: <200412011754.iB1Hs35r025626@outmx018.isp.belgacom.be>
As can be seen in the PO browser the peduncle is considered as an integral part
of the inflorescence.
According to the Angiosperm Phylogeny Website / Glossary, the peduncle is
defined as: the stalk of an inflorescence, i.e. that 'part of the axis of an
inflorescence' below the insertion of any flowers or inflorescence branches.
Personally I completely agree with all this but I see so many literature (&
Internet) references where the peduncle is considered as:
'the portion of stem' above the leaves and below the lowest branching point of
the inflorescence, i.e. a part of the stem and not of the inflorescence. The
difference is extremely important when measurements are recorded. I would be
very pleased to hear some good arguments to defend the PO point of view.
Thanks!
Guido.
Dr. Guido Mathieu
Peperomia Research Group
Department of Biology
Ghent University
K.L. Ledeganckstraat 35,
B-9000 Gent. Belgium
From alice.clara.augustine at monsanto.com Wed Dec 1 21:21:28 2004
From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042])
Date: Wed, 1 Dec 2004 20:21:28 -0600
Subject: pls help (PR#46)
Message-ID: <96EC66889610D611BA9500A0C9DCFB2E0102635B@ems8042-01.monsanto.com>
Thank you very much Katica for contacting John for us.
We have moved all our ontologies to the OBO format.
I don't know of anyone in our group is going to the PAG XIII meeting in
San Diego this winter. I will find out from Mike Edgerton if he is attending.
Regards
Clare/Alice
-----Original Message-----
From: Katica Ilic [mailto:jitterbug at plantontology.org]
Sent: Thursday, December 02, 2004 1:01 AM
To: alice.clara.augustine at monsanto.com
Cc: john.richter at aya.yale.edu; po-internal at plantontology.org
Subject: Re: pls help (PR#46)
Hi Alice,
You are very welcome! I hope you got both e-mails from John. As you can see, the
key here seems to be in using the OBO format. So unless you have a compelling
reason to stick to the old GO flat files, I wholeheartedly recommend OBO format.
POC is switching to OBO too.
Please don't hesitate to contact me again if you need help with DAG edit or for
any other questions related to the Plant Ontologies.
Best Regards,
Katica
P.S. Are you or anyone else from your group coming to the PAG XIII meeting in
San Diego this winter?
> Dear Katica,
> Thank you for getting back to me so quickly.
> This has really helped me.
>
> Cheers
> Clare :)
>
From katica at acoma.Stanford.EDU Thu Dec 2 01:12:47 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Wed, 1 Dec 2004 22:12:47 -0800 (PST)
Subject: pls help (PR#46)
In-Reply-To: <96EC66889610D611BA9500A0C9DCFB2E0102635B@ems8042-01.monsanto.com>
Message-ID:
Hi Alice,
No problem, any time! Please don't hesitate to contact me. John
sometimes doesn't respond right away, but since I know him, he can't
refuse my 'inquiry'.
Too bad you are not coming to tha PAG in January; I hope we would meet at
some other meetings in near future.
Best regards,
Katica
On Wed, 1 Dec 2004, AUGUSTINE, ALICE CLARA [AG/8042]
wrote:
> Thank you very much Katica for contacting John for us.
> We have moved all our ontologies to the OBO format.
>
> I don't know of anyone in our group is going to the PAG XIII meeting in
> San Diego this winter. I will find out from Mike Edgerton if he is attending.
>
> Regards
> Clare/Alice
>
>
> -----Original Message-----
> From: Katica Ilic [mailto:jitterbug at plantontology.org]
> Sent: Thursday, December 02, 2004 1:01 AM
> To: alice.clara.augustine at monsanto.com
> Cc: john.richter at aya.yale.edu; po-internal at plantontology.org
> Subject: Re: pls help (PR#46)
>
>
> Hi Alice,
>
> You are very welcome! I hope you got both e-mails from John. As you can see, the
> key here seems to be in using the OBO format. So unless you have a compelling
> reason to stick to the old GO flat files, I wholeheartedly recommend OBO format.
> POC is switching to OBO too.
>
> Please don't hesitate to contact me again if you need help with DAG edit or for
> any other questions related to the Plant Ontologies.
>
> Best Regards,
>
> Katica
>
> P.S. Are you or anyone else from your group coming to the PAG XIII meeting in
> San Diego this winter?
>
>
> > Dear Katica,
> > Thank you for getting back to me so quickly.
> > This has really helped me.
> >
> > Cheers
> > Clare :)
> >
>
--------------------------------------------------------------------------
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 simon at arabidopsis.info Thu Dec 2 05:37:57 2004
From: simon at arabidopsis.info (Simon Jupp)
Date: Thu, 02 Dec 2004 10:37:57 +0000
Subject: [Fwd: Need info...]
Message-ID: <41AEF085.6060003@arabidopsis.info>
An HTML attachment was scrubbed...
URL:
From r.bruskiewich at cgiar.org Thu Dec 2 17:36:43 2004
From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI))
Date: Thu, 02 Dec 2004 14:36:43 -0800
Subject: [Fwd: Need info...]
Message-ID: <2A491C94FFBC5843A212A69CBEA5CEC718A6D1@IRRIMAIL.IRRI.CGIARAD.ORG>
Hi Simon,
We've been applying the EAV to our rice mutants and have noted the same
issue. We'd be pleased to work with you on this. I think Mike Cherry might
have done the most recent PATO attribute curation. We should ask Mike
Ashburner for guidance on this.
Richard
-----Original Message-----
From: Simon Jupp
To: po-dev at plantontology.org
Sent: 12/2/2004 6:37 PM
Subject: [Fwd: Need info...]
{This message has already been sent out on the obo-phenotypes list, but
thought it may also be relavent here as I have some terms that may need
including in PO.}
Hi,
I am writing from the Nottingham Arabidopsis Stock Center (NASC) , we
are currently curating over 5000 phenotype descriptions using a
combination of Plant ontology and PATO. We are using an EAV model to
describe the various phenotypes and are finding that some of the value
terms we ant to use are missing from PATO, we already have a list of at
least 20 new terms that we would like including. Is there a term
submission procedure, what is the current state of PATO?
I am also working with the current GO tools and AMIGO to build an
ontology browser and search method that combines PO and PATO. Is anyone
else doing similar work and interested in collaboration?
Cheers,
Simon Jupp
NASC,
Nottingham,
UK
This message has been scanned but we cannot guarantee that it and any
attachments are free from viruses or other damaging content: you are
advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK
legislation.
From jitterbug at plantontology.org Thu Dec 2 18:05:20 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Thu, 2 Dec 2004 18:05:20 -0500
Subject: User's request - new term in PATO (fwd) (PR#48)
Message-ID: <200412022305.iB2N5KUq005605@brie4.cshl.org>
Hi Simon,
I am really not aware of any term submission procedure for the PATO. As for the
current state of the Phenotype Attribute Ontology, you should contact Dr.
Michael Ashburner (ma11 at gen.cam.ac.uk), since his group created this ontology
and is currently maintaining it. You can also e-mail the OBO phenotype group
(obo-phenotype at lists.sourceforge.net).
If you have new terms to suggest for the Plant Ontology, please send us the list
of terms. We will consider thoroughly each term and will get back to you with
the list of introduced terms and explanation in case a term may not belong to
the Plant Structure Ontology, but rather to other Biological Ontologies (for
instance, Gene Ontology).
I would be very interested to learn more about the ontology browser you are
working on.
I look forward to hearing from you.
Best regards,
Katica
>
> ---------- Forwarded message ----------
> Date: Thu, 02 Dec 2004 10:37:57 +0000
> From: Simon Jupp
> Reply-To: po-dev at plantontology.org, Simon Jupp
> To: po-dev at plantontology.org
> Subject: [Fwd: Need info...]
>
>
> {This message has already been sent out on the obo-phenotypes list, but
> thought it may also be relavent here as I have some terms that may need
> including in PO.}
>
> Hi,
>
> I am writing from the Nottingham Arabidopsis Stock Center (NASC) , we are
> currently curating over 5000 phenotype descriptions using a combination
> of Plant ontology and PATO.? We are using an EAV model to describe the
> various phenotypes and are finding that some of the value terms we ant to
> use are missing from PATO, we already have a list of at least 20 new
> terms that we would like including.? Is there a term submission
> procedure, what is the current state of PATO?
>
> I am also working with the current GO tools and AMIGO to build an
> ontology browser and search method that combines PO and PATO.? Is anyone
> else doing similar work and interested in collaboration?
>
> Cheers,
> Simon Jupp
>
> NASC,
> Nottingham,
> UK
>
> This message has been scanned but we cannot guarantee that it and any
> attachments are free from viruses or other damaging content: you are
> advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>
>
>
>
>
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.
From r.bruskiewich at cgiar.org Fri Dec 3 02:14:28 2004
From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI))
Date: Thu, 02 Dec 2004 23:14:28 -0800
Subject: User's request - new term in PATO (fwd) (PR#48)
Message-ID: <2A491C94FFBC5843A212A69CBEA5CEC718A6DF@IRRIMAIL.IRRI.CGIARAD.ORG>
How about inviting Nottingham to join the POC as a full (international)
partner, Katica, so that they can freely debate whether or not a term
belongs in PO or not, based on their own expertise...
Richard :-))?
-----Original Message-----
From: Katica Ilic [mailto:jitterbug at plantontology.org]
Sent: Friday, 2004 December 03 7:05 AM
To: simon at arabidopsis.info
Cc: po-dev at plantontology.org
Subject: Re: User's request - new term in PATO (fwd) (PR#48)
Hi Simon,
I am really not aware of any term submission procedure for the PATO. As for
the
current state of the Phenotype Attribute Ontology, you should contact Dr.
Michael Ashburner (ma11 at gen.cam.ac.uk), since his group created this
ontology
and is currently maintaining it. You can also e-mail the OBO phenotype group
(obo-phenotype at lists.sourceforge.net).
If you have new terms to suggest for the Plant Ontology, please send us the
list
of terms. We will consider thoroughly each term and will get back to you
with
the list of introduced terms and explanation in case a term may not belong
to
the Plant Structure Ontology, but rather to other Biological Ontologies (for
instance, Gene Ontology).
I would be very interested to learn more about the ontology browser you are
working on.
I look forward to hearing from you.
Best regards,
Katica
>
> ---------- Forwarded message ----------
> Date: Thu, 02 Dec 2004 10:37:57 +0000
> From: Simon Jupp
> Reply-To: po-dev at plantontology.org, Simon Jupp
> To: po-dev at plantontology.org
> Subject: [Fwd: Need info...]
>
>
> {This message has already been sent out on the obo-phenotypes list, but
> thought it may also be relavent here as I have some terms that may need
> including in PO.}
>
> Hi,
>
> I am writing from the Nottingham Arabidopsis Stock Center (NASC) , we are
> currently curating over 5000 phenotype descriptions using a combination
> of Plant ontology and PATO.? We are using an EAV model to describe the
> various phenotypes and are finding that some of the value terms we ant to
> use are missing from PATO, we already have a list of at least 20 new
> terms that we would like including.? Is there a term submission
> procedure, what is the current state of PATO?
>
> I am also working with the current GO tools and AMIGO to build an
> ontology browser and search method that combines PO and PATO.? Is anyone
> else doing similar work and interested in collaboration?
>
> Cheers,
> Simon Jupp
>
> NASC,
> Nottingham,
> UK
>
> This message has been scanned but we cannot guarantee that it and any
> attachments are free from viruses or other damaging content: you are
> advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>
>
>
>
>
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.
From paulien.adamse at wur.nl Fri Dec 3 02:28:50 2004
From: paulien.adamse at wur.nl (Adamse, Paulien)
Date: Fri, 3 Dec 2004 08:28:50 +0100
Subject: User's request - new term in PATO (fwd) (PR#48)
Message-ID:
As one of the partners of PlaNet they are "official" collaborators already, in fact Beatrice Schildknecht, from Nottingham, also attended the POC meeting in San Diego las year. So did I, unfortunately I will not be able to come this year.
I started using EAV in www.watdb.nl and will have that visible there in a few weeks. Also used PATO, but have a hard time using the tree structure of it.
Dr Paulien Adamse
BU Bioscience
Plant Research International,
P.O. Box 16,
6700 AA Wageningen,
The Netherlands.
Tel: +31 317 477001/476850
FAX: +31 317 418094
paulien.adamse at wur.nl
www.plant.wageningen-ur.nl
-----Original Message-----
From: Bruskiewich, Richard (IRRI) [mailto:r.bruskiewich at cgiar.org]
Sent: vrijdag 3 december 2004 08:14
To: 'Katica Ilic'; simon at arabidopsis.info
Subject: RE: User's request - new term in PATO (fwd) (PR#48)
How about inviting Nottingham to join the POC as a full (international) partner, Katica, so that they can freely debate whether or not a term belongs in PO or not, based on their own expertise...
Richard :-))?
-----Original Message-----
From: Katica Ilic [mailto:jitterbug at plantontology.org]
Sent: Friday, 2004 December 03 7:05 AM
To: simon at arabidopsis.info
Cc: po-dev at plantontology.org
Subject: Re: User's request - new term in PATO (fwd) (PR#48)
Hi Simon,
I am really not aware of any term submission procedure for the PATO. As for the current state of the Phenotype Attribute Ontology, you should contact Dr.
Michael Ashburner (ma11 at gen.cam.ac.uk), since his group created this ontology and is currently maintaining it. You can also e-mail the OBO phenotype group (obo-phenotype at lists.sourceforge.net).
If you have new terms to suggest for the Plant Ontology, please send us the list of terms. We will consider thoroughly each term and will get back to you with the list of introduced terms and explanation in case a term may not belong to the Plant Structure Ontology, but rather to other Biological Ontologies (for instance, Gene Ontology).
I would be very interested to learn more about the ontology browser you are working on.
I look forward to hearing from you.
Best regards,
Katica
>
> ---------- Forwarded message ----------
> Date: Thu, 02 Dec 2004 10:37:57 +0000
> From: Simon Jupp
> Reply-To: po-dev at plantontology.org, Simon Jupp
>
> To: po-dev at plantontology.org
> Subject: [Fwd: Need info...]
>
>
> {This message has already been sent out on the obo-phenotypes list,
> but thought it may also be relavent here as I have some terms that may
> need including in PO.}
>
> Hi,
>
> I am writing from the Nottingham Arabidopsis Stock Center (NASC) , we
> are currently curating over 5000 phenotype descriptions using a
> combination of Plant ontology and PATO.? We are using an EAV model to
> describe the various phenotypes and are finding that some of the value
> terms we ant to use are missing from PATO, we already have a list of
> at least 20 new terms that we would like including.? Is there a term
> submission procedure, what is the current state of PATO?
>
> I am also working with the current GO tools and AMIGO to build an
> ontology browser and search method that combines PO and PATO.? Is
> anyone else doing similar work and interested in collaboration?
>
> Cheers,
> Simon Jupp
>
> NASC,
> Nottingham,
> UK
>
> This message has been scanned but we cannot guarantee that it and any
> attachments are free from viruses or other damaging content: you are
> advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>
>
>
>
>
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.
From katica at acoma.Stanford.EDU Fri Dec 3 13:51:03 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 3 Dec 2004 10:51:03 -0800 (PST)
Subject: User's request - new term in PATO (fwd) (PR#48)
In-Reply-To:
Message-ID:
Paulien,
Thank you for clarifying this to Richard. BTW, do you know if
anyone from PlaNet is coming to the PAG XIII in January? I haven't
heard from them yet.
Also, would you continue collaboration on the POC now that you took the
new
position? I see you are using EAV, so you shouldn't be far from PO, right?
:-)
Katica
On Fri, 3 Dec 2004, Adamse, Paulien wrote:
> As one of the partners of PlaNet they are "official" collaborators already, in fact Beatrice Schildknecht, from Nottingham, also attended the POC meeting in San Diego las year. So did I, unfortunately I will not be able to come this year.
>
> I started using EAV in www.watdb.nl and will have that visible there in a few weeks. Also used PATO, but have a hard time using the tree structure of it.
>
> Dr Paulien Adamse
> BU Bioscience
> Plant Research International,
> P.O. Box 16,
> 6700 AA Wageningen,
> The Netherlands.
>
> Tel: +31 317 477001/476850
> FAX: +31 317 418094
> paulien.adamse at wur.nl
> www.plant.wageningen-ur.nl
>
>
> -----Original Message-----
> From: Bruskiewich, Richard (IRRI) [mailto:r.bruskiewich at cgiar.org]
> Sent: vrijdag 3 december 2004 08:14
> To: 'Katica Ilic'; simon at arabidopsis.info
> Subject: RE: User's request - new term in PATO (fwd) (PR#48)
>
> How about inviting Nottingham to join the POC as a full (international) partner, Katica, so that they can freely debate whether or not a term belongs in PO or not, based on their own expertise...
>
> Richard :-))?
>
> -----Original Message-----
> From: Katica Ilic [mailto:jitterbug at plantontology.org]
> Sent: Friday, 2004 December 03 7:05 AM
> To: simon at arabidopsis.info
> Cc: po-dev at plantontology.org
> Subject: Re: User's request - new term in PATO (fwd) (PR#48)
>
> Hi Simon,
>
> I am really not aware of any term submission procedure for the PATO. As for the current state of the Phenotype Attribute Ontology, you should contact Dr.
> Michael Ashburner (ma11 at gen.cam.ac.uk), since his group created this ontology and is currently maintaining it. You can also e-mail the OBO phenotype group (obo-phenotype at lists.sourceforge.net).
>
> If you have new terms to suggest for the Plant Ontology, please send us the list of terms. We will consider thoroughly each term and will get back to you with the list of introduced terms and explanation in case a term may not belong to the Plant Structure Ontology, but rather to other Biological Ontologies (for instance, Gene Ontology).
>
> I would be very interested to learn more about the ontology browser you are working on.
>
> I look forward to hearing from you.
>
> Best regards,
>
> Katica
> >
> > ---------- Forwarded message ----------
> > Date: Thu, 02 Dec 2004 10:37:57 +0000
> > From: Simon Jupp
> > Reply-To: po-dev at plantontology.org, Simon Jupp
> >
> > To: po-dev at plantontology.org
> > Subject: [Fwd: Need info...]
> >
> >
> > {This message has already been sent out on the obo-phenotypes list,
> > but thought it may also be relavent here as I have some terms that may
> > need including in PO.}
> >
> > Hi,
> >
> > I am writing from the Nottingham Arabidopsis Stock Center (NASC) , we
> > are currently curating over 5000 phenotype descriptions using a
> > combination of Plant ontology and PATO.? We are using an EAV model to
> > describe the various phenotypes and are finding that some of the value
> > terms we ant to use are missing from PATO, we already have a list of
> > at least 20 new terms that we would like including.? Is there a term
> > submission procedure, what is the current state of PATO?
> >
> > I am also working with the current GO tools and AMIGO to build an
> > ontology browser and search method that combines PO and PATO.? Is
> > anyone else doing similar work and interested in collaboration?
> >
> > Cheers,
> > Simon Jupp
> >
> > NASC,
> > Nottingham,
> > UK
> >
> > This message has been scanned but we cannot guarantee that it and any
> > attachments are free from viruses or other damaging content: you are
> > advised to perform your own checks. Email communications with the
> > University of Nottingham may be monitored as permitted by UK legislation.
> >
> >
> >
> >
> >
> 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.
>
>
>
>
--------------------------------------------------------------------------
Katica Ilic katica at acoma.stanford.edu
The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington FAX: (650) 325-6857
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------
From katica at acoma.Stanford.EDU Fri Dec 3 13:51:03 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 3 Dec 2004 10:51:03 -0800 (PST)
Subject: User's request - new term in PATO (fwd) (PR#48)
In-Reply-To:
Message-ID:
Paulien,
Thank you for clarifying this to Richard. BTW, do you know if
anyone from PlaNet is coming to the PAG XIII in January? I haven't
heard from them yet.
Also, would you continue collaboration on the POC now that you took the
new
position? I see you are using EAV, so you shouldn't be far from PO, right?
:-)
Katica
On Fri, 3 Dec 2004, Adamse, Paulien wrote:
> As one of the partners of PlaNet they are "official" collaborators already, in fact Beatrice Schildknecht, from Nottingham, also attended the POC meeting in San Diego las year. So did I, unfortunately I will not be able to come this year.
>
> I started using EAV in www.watdb.nl and will have that visible there in a few weeks. Also used PATO, but have a hard time using the tree structure of it.
>
> Dr Paulien Adamse
> BU Bioscience
> Plant Research International,
> P.O. Box 16,
> 6700 AA Wageningen,
> The Netherlands.
>
> Tel: +31 317 477001/476850
> FAX: +31 317 418094
> paulien.adamse at wur.nl
> www.plant.wageningen-ur.nl
>
>
> -----Original Message-----
> From: Bruskiewich, Richard (IRRI) [mailto:r.bruskiewich at cgiar.org]
> Sent: vrijdag 3 december 2004 08:14
> To: 'Katica Ilic'; simon at arabidopsis.info
> Subject: RE: User's request - new term in PATO (fwd) (PR#48)
>
> How about inviting Nottingham to join the POC as a full (international) partner, Katica, so that they can freely debate whether or not a term belongs in PO or not, based on their own expertise...
>
> Richard :-))?
>
> -----Original Message-----
> From: Katica Ilic [mailto:jitterbug at plantontology.org]
> Sent: Friday, 2004 December 03 7:05 AM
> To: simon at arabidopsis.info
> Cc: po-dev at plantontology.org
> Subject: Re: User's request - new term in PATO (fwd) (PR#48)
>
> Hi Simon,
>
> I am really not aware of any term submission procedure for the PATO. As for the current state of the Phenotype Attribute Ontology, you should contact Dr.
> Michael Ashburner (ma11 at gen.cam.ac.uk), since his group created this ontology and is currently maintaining it. You can also e-mail the OBO phenotype group (obo-phenotype at lists.sourceforge.net).
>
> If you have new terms to suggest for the Plant Ontology, please send us the list of terms. We will consider thoroughly each term and will get back to you with the list of introduced terms and explanation in case a term may not belong to the Plant Structure Ontology, but rather to other Biological Ontologies (for instance, Gene Ontology).
>
> I would be very interested to learn more about the ontology browser you are working on.
>
> I look forward to hearing from you.
>
> Best regards,
>
> Katica
> >
> > ---------- Forwarded message ----------
> > Date: Thu, 02 Dec 2004 10:37:57 +0000
> > From: Simon Jupp
> > Reply-To: po-dev at plantontology.org, Simon Jupp
> >
> > To: po-dev at plantontology.org
> > Subject: [Fwd: Need info...]
> >
> >
> > {This message has already been sent out on the obo-phenotypes list,
> > but thought it may also be relavent here as I have some terms that may
> > need including in PO.}
> >
> > Hi,
> >
> > I am writing from the Nottingham Arabidopsis Stock Center (NASC) , we
> > are currently curating over 5000 phenotype descriptions using a
> > combination of Plant ontology and PATO.? We are using an EAV model to
> > describe the various phenotypes and are finding that some of the value
> > terms we ant to use are missing from PATO, we already have a list of
> > at least 20 new terms that we would like including.? Is there a term
> > submission procedure, what is the current state of PATO?
> >
> > I am also working with the current GO tools and AMIGO to build an
> > ontology browser and search method that combines PO and PATO.? Is
> > anyone else doing similar work and interested in collaboration?
> >
> > Cheers,
> > Simon Jupp
> >
> > NASC,
> > Nottingham,
> > UK
> >
> > This message has been scanned but we cannot guarantee that it and any
> > attachments are free from viruses or other damaging content: you are
> > advised to perform your own checks. Email communications with the
> > University of Nottingham may be monitored as permitted by UK legislation.
> >
> >
> >
> >
> >
> 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.
>
>
>
>
--------------------------------------------------------------------------
Katica Ilic katica at acoma.stanford.edu
The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington FAX: (650) 325-6857
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------
From fzqhd at umsl.edu Fri Dec 3 14:02:27 2004
From: fzqhd at umsl.edu (Felipe Zapata)
Date: Fri, 3 Dec 2004 13:02:27 -0600
Subject: Inflorescence - peduncle
Message-ID:
Dr. Mathieu,
Part of your confusion is perhaps due to the inaccurate definitions for
inflorescence and stem that we adopted in POC. Updates to
APWeb-Glossary are in order for these terms (and few others), meanwhile
let me give you these 3 definitions hoping to clarify the issue.
Stem: the axial system of plants which is usually above ground and more
or less negatively geotropic, bears leaves and buds, is exogenous in
origin, often indeterminate in growth and with secondary thickening.
Inflorescence: That part of the axial system of plants that bears
flowers.
Peduncle: the stalk of an inforescene; that part of the inflorescence
below the first flower or inflorescence branch and above the last
foliage leaf.
Therefore, peduncle is part of inflorescence.
Felipe
From katica at acoma.Stanford.EDU Fri Dec 3 14:12:00 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 3 Dec 2004 11:12:00 -0800 (PST)
Subject: Inflorescence - peduncle
In-Reply-To: <200412011754.iB1Hs35r025626@outmx018.isp.belgacom.be>
Message-ID:
Dr. Mathieu,
Part of your confusion is perhaps due to the inaccurate definitions for
inflorescence and stem that we adopted in POC. Updates to
APWeb-Glossary are in order for these terms (and few others), meanwhile
let me give you these 3 definitions hoping to clarify the issue.
Stem: the axial system of plants which is usually above ground and more
or less negatively geotropic, bears leaves and buds, is exogenous in
origin, often indeterminate in growth and with secondary thickening.
Inflorescence: That part of the axial system of plants that bears
flowers.
Peduncle: the stalk of an inforescene; that part of the inflorescence
below the first flower or inflorescence branch and above the last
foliage leaf.
Therefore, peduncle is part of inflorescence.
Felipe
On Wed, 1 Dec 2004, Guido Mathieu wrote:
> As can be seen in the PO browser the peduncle is considered as an integral part
> of the inflorescence.
> According to the Angiosperm Phylogeny Website / Glossary, the peduncle is
> defined as: the stalk of an inflorescence, i.e. that 'part of the axis of an
> inflorescence' below the insertion of any flowers or inflorescence branches.
> Personally I completely agree with all this but I see so many literature (&
> Internet) references where the peduncle is considered as:
> 'the portion of stem' above the leaves and below the lowest branching point of
> the inflorescence, i.e. a part of the stem and not of the inflorescence. The
> difference is extremely important when measurements are recorded. I would be
> very pleased to hear some good arguments to defend the PO point of view.
>
> Thanks!
> Guido.
>
> Dr. Guido Mathieu
> Peperomia Research Group
> Department of Biology
> Ghent University
> K.L. Ledeganckstraat 35,
> B-9000 Gent. Belgium
>
--------------------------------------------------------------------------
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 guido.mathieu at taxa.be Sun Dec 5 06:08:44 2004
From: guido.mathieu at taxa.be (Guido Mathieu)
Date: Sun, 5 Dec 2004 12:08:44 +0100
Subject: Inflorescence - peduncle
In-Reply-To:
Message-ID: <200412051108.iB5B8sva020672@outmx004.isp.belgacom.be>
Hi Felipe,
> Part of your confusion is perhaps due to the inaccurate definitions for
inflorescence and stem that we adopted in POC.
Actually not. It is due to the consideration that definitions solely based on
'agreement' will stand as long as people are 'willing' to agree.
> 1. Stem: the axial system of plants which is usually above ground and more or
less negatively geotropic, bears leaves and buds, is exogenous in origin, often
indeterminate in growth and with secondary thickening.
> 2. Inflorescence: That part of the axial system of plants that bears flowers.
> 3. Peduncle: the stalk of an inflorescence; that part of the inflorescence
below the first flower or inflorescence branch and above the last foliage leaf.
> Therefore, peduncle is part of inflorescence.
Based on the definitions you provided (thanks!) one might reason even so:
1. The stem is the axial system of plants
2. The inflorescence is that part of the axial system that bears flowers
3. The peduncle doesn't bear flowers ('below the first flower')
Therefore the peduncle is not part of the inflorescence.
Don't get me wrong, I'm also in favour of considering the peduncle as an
integral part of the inflorescence. But just the definitions above are not
strong enough to support this.
It is not difficult to modify the definitions as:
1. Stem: the vegetative part of the axial system of plants bearing leaves and
buds...
2. Inflorescence: the fertile part of the axial system of plants consisting of a
common inflorescence axis and several flowers. The inflorescence axis consists
of a part below the first flower (the peduncle) and a flower bearing part (the
rachis)(*).
But, even this more nuanced definition just reflects an opinion. So, my initial
request still stands: 'to hear some 'arguments' to defend this point of view'.
(*)[It should be noticed that currently in the PO browser (and in the
APWeb-Glossary) there is some contradiction: rachis is considered as 'synonym'
of inflorescence axis and not as a 'part' of it. At the same time peduncle is
considered as a 'part' of the inflorescence axis while it is evidently not a
'part' of the rachis]
Guido.
Dr. Guido Mathieu
Peperomia Research Group
Department of Biology
Ghent University
K.L. Ledeganckstraat 35,
B-9000 Gent. Belgium
www.peperomia.net
From simon at arabidopsis.info Tue Dec 7 06:52:53 2004
From: simon at arabidopsis.info (Simon Jupp)
Date: Tue, 07 Dec 2004 11:52:53 +0000
Subject: POAmiGO
In-Reply-To:
References:
Message-ID: <41B59995.1080207@arabidopsis.info>
Hi Katica,
Could you please tell me who did the work on the POAmigo browser.
Thank You
Simon Jupp
NASC
This message has been scanned but we cannot guarantee that it and any
attachments are free from viruses or other damaging content: you are
advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.
From ware at cshl.edu Tue Dec 7 08:56:30 2004
From: ware at cshl.edu (Ware, Doreen)
Date: Tue, 7 Dec 2004 08:56:30 -0500
Subject: POAmiGO
Message-ID: <5F7E863301E72846B90A4CEBB15EAE66012A1B54@exch02>
Hi Simon,
Katica is away the next two days, so I will answer this. Shuly Avraham did
the work. I have copied her on the email.
Doreen
-----Original Message-----
From: Simon Jupp [mailto:simon at arabidopsis.info]
Sent: Tuesday, December 07, 2004 6:53 AM
To: po-dev at plantontology.org; Katica Ilic
Subject: Re: POAmiGO
Hi Katica,
Could you please tell me who did the work on the POAmigo browser.
Thank You
Simon Jupp
NASC
This message has been scanned but we cannot guarantee that it and any
attachments are free from viruses or other damaging content: you are
advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.
From shuly at cshl.edu Tue Dec 7 09:53:14 2004
From: shuly at cshl.edu (Shuly Avraham)
Date: Tue, 07 Dec 2004 09:53:14 -0500
Subject: POAmiGO
In-Reply-To: <41B59995.1080207@arabidopsis.info>
References: <41B59995.1080207@arabidopsis.info>
Message-ID: <41B5C3DA.1040903@cshl.edu>
Hi Simon,
I have installed and customized AmiGO for PO use.
Shuly.
Simon Jupp wrote:
> Hi Katica,
>
> Could you please tell me who did the work on the POAmigo browser.
>
> Thank You
> Simon Jupp
> NASC
>
> This message has been scanned but we cannot guarantee that it and any
> attachments are free from viruses or other damaging content: you are
> advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>
From pj37 at cornell.edu Tue Dec 7 11:17:50 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 07 Dec 2004 11:17:50 -0500
Subject: UniGene Library annotation --Question
Message-ID: <41B5D7AE.7000500@cornell.edu>
Can somebody help me identify which plant structure terms I shall use
for the following as described for the EXT library in GenBank records.
--------------------------------------
Organism: Oryza sativa subsp. japonica
Developmental stage: 3-5 leaves plantlets
Sex: hermaphrodite
Cultivar: Nipponbare
Tissue: shoot apex
Organ: shoot apex
Do you think that annotating to the following will be acceptable.
term: shoot apical meristem
Accession: PO:0020148
___________________________________
For the following
http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Os&LID=10901
Organism: Oryza sativa (japonica cultivar-group)
Developmental stage: two weeks old seedling
Cultivar: Lansheng
Organ: all plant
According to the recent suggestion, should this be annotated to
"whole plant" term or to the "sporophyte".
Personally I would like to annotate it to term "sporophyte" with an
additional annotation to the appropriate growth stage.
--------------------------------
Similar situation is for the following
http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Os&LID=11046
Organism: Oryza sativa
Developmental stage: Two-week-old rice seeding infested by brown
planthopper
Strain: B5 resistant variety to brown planthopper
Vector: pT-Adv
************************
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 katica at acoma.Stanford.EDU Tue Dec 7 16:21:58 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Tue, 7 Dec 2004 13:21:58 -0800 (PST)
Subject: UniGene Library annotation --Question
In-Reply-To: <41B5D7AE.7000500@cornell.edu>
Message-ID:
Pankaj,
On Tue, 7 Dec 2004, Pankaj Jaiswal wrote:
> Can somebody help me identify which plant structure terms I shall use
> for the following as described for the EXT library in GenBank records.
> --------------------------------------
>
>
>
> Organism: Oryza sativa subsp. japonica
> Developmental stage: 3-5 leaves plantlets
> Sex: hermaphrodite
> Cultivar: Nipponbare
> Tissue: shoot apex
> Organ: shoot apex
>
> Do you think that annotating to the following will be acceptable.
>
> term: shoot apical meristem
> Accession: PO:0020148
I am not sure about this, since you are suggesting a more granular term
than what they provided. It seems that having the term 'shoot apex' would
be useful, there are many publications where people use it.
> ___________________________________
>
> For the following
> http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Os&LID=10901
>
> Organism: Oryza sativa (japonica cultivar-group)
> Developmental stage: two weeks old seedling
> Cultivar: Lansheng
> Organ: all plant
>
> According to the recent suggestion, should this be annotated to
> "whole plant" term or to the "sporophyte".
>
> Personally I would like to annotate it to term "sporophyte" with an
> additional annotation to the appropriate growth stage.
>
Either one is fine, and since we should encourage people to use the most
appropriate term, sporophyte should be the one (in my humble opinion).
> --------------------------------
>
> Similar situation is for the following
>
> http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Os&LID=11046
>
> Organism: Oryza sativa
> Developmental stage: Two-week-old rice seeding infested by brown
> planthopper
> Strain: B5 resistant variety to brown planthopper
> Vector: pT-Ad
I am not sure here either, you can't pull out the proper dev stage
term, and they did't specify if they used the whole plant or not, and even
term sporophyte may not work out, since they didn't specify anything.
I don't thing that there is any term outh there taht I would be
entirely comfortable using in this particular case.
Katica
>
>
> ************************
> 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
> ************************
>
--------------------------------------------------------------------------
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 vcarollo at pw.usda.gov Tue Dec 7 16:43:52 2004
From: vcarollo at pw.usda.gov (Victoria Carollo)
Date: Tue, 07 Dec 2004 13:43:52 -0800
Subject: Wheat anatomy
In-Reply-To:
References: <41B5D7AE.7000500@cornell.edu>
Message-ID: <5.1.0.14.0.20041207134230.0494ff68@aggie.pw.usda.gov>
Hi Katica,
I'm wondering if the wheat terms I sent to you awhile back were of any
help? I know there were a few overlapping terms, and I don't want this to
get so far on the back-burner that I completely loose touch with you and
this effort.
Anything I can do to help the wheat effort?
Cheers,
Vickie
From shuly at cshl.edu Wed Dec 8 00:44:30 2004
From: shuly at cshl.edu (Shuly Avraham)
Date: Wed, 08 Dec 2004 00:44:30 -0500
Subject: [Fwd: Feedback on POC]
Message-ID: <41B694BE.2020606@cshl.edu>
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From ap343 at cornell.edu Wed Dec 8 09:27:45 2004
From: ap343 at cornell.edu (Anuradha Pujar)
Date: Wed, 8 Dec 2004 09:27:45 -0500 (EST)
Subject: Wheat anatomy
In-Reply-To: <5.1.0.14.0.20041207134230.0494ff68@aggie.pw.usda.gov>
References: <41B5D7AE.7000500@cornell.edu>
<5.1.0.14.0.20041207134230.0494ff68@aggie.pw.usda.gov>
Message-ID: <1316.128.253.246.53.1102516065.squirrel@128.253.246.53>
>Hi Katica,
I think i missed the mail with wheat terms that Victoria sent, can you
please send out to me again?
Thanks
anu
> Hi Katica,
>
> I'm wondering if the wheat terms I sent to you awhile back were of any
> help? I know there were a few overlapping terms, and I don't want this to
> get so far on the back-burner that I completely loose touch with you and
> this effort.
>
> Anything I can do to help the wheat effort?
>
> Cheers,
> Vickie
>
>
From katica at acoma.Stanford.EDU Wed Dec 8 02:31:27 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Tue, 7 Dec 2004 23:31:27 -0800
Subject: Wheat anatomy
References: <41B5D7AE.7000500@cornell.edu> <5.1.0.14.0.20041207134230.0494ff68@aggie.pw.usda.gov>
Message-ID: <000001c4dd59$abd705c0$6b2142ab@poc>
Hi Victoria,
I looked through your list back when I received it, just didn't have time to
reply. As I mentioned in my earlier e-mail, most of the terms (39 terms
exactly) are already in the PO. Remaining three terms are not in the PO, and
one sould be introduced, term pulvinus, to which I provided definition from
K Esau.
New term: pulvinus
Definition: An enlargement of the petiole of a leaf, or petiolule of a
leaflet, at its base. A structure that has a role in the movements of a leaf
or leaflet. (def from K Esau).
I need to see where exactly this term would go into Plant Structure
Ontology.
The last two are terms 'crease' and term 'beard'. I need to find out if
they can be synonyms of the existion terms.
Attached is the modified list. In bold are terms I searched in PO (all of
them); some terms have PO terms associated (in cases where PO terms have
slightly differnt names).
We now need to find out what are the other wheat specific terms that we
should add to the PO.
Any ideas?
Katica
----- Original Message -----
From: "Victoria Carollo"
To: ; "Katica Ilic"
Sent: Tuesday, December 07, 2004 1:43 PM
Subject: Wheat anatomy
>
> Hi Katica,
>
> I'm wondering if the wheat terms I sent to you awhile back were of any
> help? I know there were a few overlapping terms, and I don't want this to
> get so far on the back-burner that I completely loose touch with you and
> this effort.
>
> Anything I can do to help the wheat effort?
>
> Cheers,
> Vickie
>
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From katica at acoma.Stanford.EDU Wed Dec 8 14:19:41 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Wed, 8 Dec 2004 11:19:41 -0800 (PST)
Subject: Fw: Wheat anatomy (fwd)
Message-ID:
Hi Victoria,
I looked through your list shortly after I received it, just didn't
have time to reply. As I mentioned in my earlier e-mail, most of the terms
(39 terms exactly) are already in the PO. Remaining three terms are not in the PO,
and one sould be introduced, term pulvinus, to which I provided definition
from K Esau.
New term: pulvinus
Definition: An enlargement of the petiole of a leaf, or petiolule of a
leaflet, at its base. A structure that has a role in the movements of a
leaf
or leaflet. (def from K Esau).
I need to see where exactly this term would go into Plant Structure
Ontology.
The last two are terms 'crease' and term 'beard'. I need to find out if
they can be synonyms of the existing terms.
Attached is the modified list. In bold are terms I searched in PO (all of
them); some terms have PO terms associated (in cases where PO terms have
slightly differnt names).
We now need to find out if there are additional wheat specific terms
that we should add to the PO.
Any ideas?
Katica
> ----- Original Message -----
> From: "Victoria Carollo"
> To: ; "Katica Ilic"
> Sent: Tuesday, December 07, 2004 1:43 PM
> Subject: Wheat anatomy
>
>
> >
> > Hi Katica,
> >
> > I'm wondering if the wheat terms I sent to you awhile back were of any
> > help? I know there were a few overlapping terms, and I don't want this
to
> > get so far on the back-burner that I completely loose touch with you and
> > this effort.
> >
> > Anything I can do to help the wheat effort?
> >
> > Cheers,
> > Vickie
> >
>
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From vcarollo at pw.usda.gov Wed Dec 8 14:30:24 2004
From: vcarollo at pw.usda.gov (Victoria Carollo)
Date: Wed, 08 Dec 2004 11:30:24 -0800
Subject: Wheat anatomy
In-Reply-To: <000001c4dd59$abd705c0$6b2142ab@poc>
References: <41B5D7AE.7000500@cornell.edu>
<5.1.0.14.0.20041207134230.0494ff68@aggie.pw.usda.gov>
Message-ID: <5.1.0.14.0.20041208112833.043ee550@aggie.pw.usda.gov>
Hello Katica,
I forward the sheet to several wheat researchers that I know, and see if
they can come up with any. The 'crease' in a wheat grain is actually
quite important. Millers would LOVE it if we could breed wheat without
one, because of it less flour can be milled from the grain.
Cheers,
Vickie
At 11:31 PM 12/7/2004 -0800, you wrote:
>Hi Victoria,
>
>I looked through your list back when I received it, just didn't have time to
>reply. As I mentioned in my earlier e-mail, most of the terms (39 terms
>exactly) are already in the PO. Remaining three terms are not in the PO, and
>one sould be introduced, term pulvinus, to which I provided definition from
>K Esau.
>
>
>
>New term: pulvinus
>
>Definition: An enlargement of the petiole of a leaf, or petiolule of a
>leaflet, at its base. A structure that has a role in the movements of a leaf
>or leaflet. (def from K Esau).
>
>I need to see where exactly this term would go into Plant Structure
>Ontology.
>
> The last two are terms 'crease' and term 'beard'. I need to find out if
>they can be synonyms of the existion terms.
>
>Attached is the modified list. In bold are terms I searched in PO (all of
>them); some terms have PO terms associated (in cases where PO terms have
>slightly differnt names).
>
>We now need to find out what are the other wheat specific terms that we
>should add to the PO.
>
>Any ideas?
>
>Katica
>
>----- Original Message -----
>From: "Victoria Carollo"
>To: ; "Katica Ilic"
>Sent: Tuesday, December 07, 2004 1:43 PM
>Subject: Wheat anatomy
>
>
> >
> > Hi Katica,
> >
> > I'm wondering if the wheat terms I sent to you awhile back were of any
> > help? I know there were a few overlapping terms, and I don't want this to
> > get so far on the back-burner that I completely loose touch with you and
> > this effort.
> >
> > Anything I can do to help the wheat effort?
> >
> > Cheers,
> > Vickie
> >
o~o~o~o~o~o~o~o~o~o~o~o~o~o~o
Victoria Carollo, Ph.D.
Molecular Biologist / GrainGenes Curator
U.S. Department of Agriculture
800 Buchanan Street
Albany, CA 94710
voice: 510-559-5944 fax: 510-559-5818
Visit GrainGenes at http://wheat.pw.usda.gov
From lreiser at acoma.Stanford.EDU Wed Dec 8 14:36:22 2004
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Wed, 8 Dec 2004 11:36:22 -0800 (PST)
Subject: Wheat anatomy
In-Reply-To: <5.1.0.14.0.20041208112833.043ee550@aggie.pw.usda.gov>
Message-ID:
Vicky- is the crease the remnant of some other floral part? as the raphe
is derived from the funiculus of the ovule?
In other words- (no joke) is this a synonym of some other body part in
POC?
Leo
On Wed, 8 Dec 2004, Victoria Carollo wrote:
> Hello Katica,
>
> I forward the sheet to several wheat researchers that I know, and see if
> they can come up with any. The 'crease' in a wheat grain is actually
> quite important. Millers would LOVE it if we could breed wheat without
> one, because of it less flour can be milled from the grain.
>
> Cheers,
> Vickie
>
>
> At 11:31 PM 12/7/2004 -0800, you wrote:
> >Hi Victoria,
> >
> >I looked through your list back when I received it, just didn't have time to
> >reply. As I mentioned in my earlier e-mail, most of the terms (39 terms
> >exactly) are already in the PO. Remaining three terms are not in the PO, and
> >one sould be introduced, term pulvinus, to which I provided definition from
> >K Esau.
> >
> >
> >
> >New term: pulvinus
> >
> >Definition: An enlargement of the petiole of a leaf, or petiolule of a
> >leaflet, at its base. A structure that has a role in the movements of a leaf
> >or leaflet. (def from K Esau).
> >
> >I need to see where exactly this term would go into Plant Structure
> >Ontology.
> >
> > The last two are terms 'crease' and term 'beard'. I need to find out if
> >they can be synonyms of the existion terms.
> >
> >Attached is the modified list. In bold are terms I searched in PO (all of
> >them); some terms have PO terms associated (in cases where PO terms have
> >slightly differnt names).
> >
> >We now need to find out what are the other wheat specific terms that we
> >should add to the PO.
> >
> >Any ideas?
> >
> >Katica
> >
> >----- Original Message -----
> >From: "Victoria Carollo"
> >To: ; "Katica Ilic"
> >Sent: Tuesday, December 07, 2004 1:43 PM
> >Subject: Wheat anatomy
> >
> >
> > >
> > > Hi Katica,
> > >
> > > I'm wondering if the wheat terms I sent to you awhile back were of any
> > > help? I know there were a few overlapping terms, and I don't want this to
> > > get so far on the back-burner that I completely loose touch with you and
> > > this effort.
> > >
> > > Anything I can do to help the wheat effort?
> > >
> > > Cheers,
> > > Vickie
> > >
>
> o~o~o~o~o~o~o~o~o~o~o~o~o~o~o
>
> Victoria Carollo, Ph.D.
> Molecular Biologist / GrainGenes Curator
>
> U.S. Department of Agriculture
> 800 Buchanan Street
> Albany, CA 94710
> voice: 510-559-5944 fax: 510-559-5818
>
> Visit GrainGenes at http://wheat.pw.usda.gov
>
>
>
>
-------------------------------------------------------------------------------
Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
The Arabidopsis Information Resource FAX: (650) 325-6857
Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------
From pj37 at cornell.edu Wed Dec 8 15:11:17 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 08 Dec 2004 15:11:17 -0500
Subject: Fw: Wheat anatomy (fwd)
In-Reply-To:
References:
Message-ID: <41B75FE5.1070207@cornell.edu>
Katica Ilic wrote:
> Hi Victoria,
>
> I looked through your list shortly after I received it, just didn't
> have time to reply. As I mentioned in my earlier e-mail, most of the terms
> (39 terms exactly) are already in the PO. Remaining three terms are not in the PO,
> and one sould be introduced, term pulvinus, to which I provided definition
> from K Esau.
>
> New term: pulvinus
>
> Definition: An enlargement of the petiole of a leaf, or petiolule of a
> leaflet, at its base. A structure that has a role in the movements of a
> leaf
> or leaflet. (def from K Esau).
>
> I need to see where exactly this term would go into Plant Structure
> Ontology.
>
By your definition, it is the swollen part of the petiole. Whereas in
cereal crops, the leaf does not have a petiole. All they have is a leaf
sheath and leaf lamina. However sheath can be regarded as a structural
homolog of petiole. I guess the wheat people are calling is a different
structure found at the base of the leaf sheath and the structure seems
to play a role in gravitropism.. I looked at fig-1 of the following
reference
http://archiv.fgk.org/01/BLT/dispersion/
Kaufman et al http://www.jstor.org/view/00029122/di001875/00p0367d/0 are
calling it "Leaf sheath pulvinus".
Looks like it can have the following lineage in ontology
leaf
..[p] petiole
......[p] pulvinus (PO:new term)
..........[i] leaf sheath pulvinus (PO:new term)
..[p] leaf sheath
......[i] leaf sheath pulvinus (PO:new term)
More refs:
http://jxb.oupjournals.org/cgi/content/full/52/358/1029
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11537463&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8490136&dopt=Abstract
> The last two are terms 'crease' and term 'beard'. I need to find out if
> they can be synonyms of the existing terms.
>
If I am not wrong, the "beard" is a synonym for "awn".
"crease is a particular type of morphological character found in grains
of Triticeae. I suggest creating a new term.
Suggested lineage in PO
Seed
..[p]..crease
definition: the indentation on the ventral side of the seed as found in
the members of Triticeae
I found one more term "brush" under "seed"
It is often called as bristle, but in order to avoid having confusion
between bristle leaf and bristles found on seed, my suggestion is to
call it "seed bristle"
seed bristle: fine hairs on the distal end of the seed as found in the
members of Triticeae
Seed
..[p]..seed bristle (synonym: brush)
From tkellogg at umsl.edu Wed Dec 8 16:35:46 2004
From: tkellogg at umsl.edu (Kellogg, Elizabeth A.)
Date: Wed, 8 Dec 2004 15:35:46 -0600
Subject: Fw: Wheat anatomy (fwd)
Message-ID: <7953D8E2E57BF94393CA6B8D2599ADDF0525BF1F@STL-MAIL2.umsl.edu>
I'm not convinced of the identity between the pulvinus as the term is applied in eudicots and term applied in wheat. I looked at a couple of the references that Pankaj sent,and don't quite see what the structure is that they are referring to as pulvinus - it looks like a part of the internode to me, but maybe it's because I can't easily see the details of the photos.
The apex of the ovary in all Triticeae is covered with macrohairs, and these persist in the fruit. I guess this is what is called the brush. I don't think I've ever heard the term "bristle" applied to those hairs.
Toby
-----Original Message-----
From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal
Sent: Wed 12/8/2004 2:11 PM
To: po-dev at plantontology.org; Victoria
Cc:
Subject: Re: Fw: Wheat anatomy (fwd)
Katica Ilic wrote:
> Hi Victoria,
>
> I looked through your list shortly after I received it, just didn't
> have time to reply. As I mentioned in my earlier e-mail, most of the terms
> (39 terms exactly) are already in the PO. Remaining three terms are not in the PO,
> and one sould be introduced, term pulvinus, to which I provided definition
> from K Esau.
>
> New term: pulvinus
>
> Definition: An enlargement of the petiole of a leaf, or petiolule of a
> leaflet, at its base. A structure that has a role in the movements of a
> leaf
> or leaflet. (def from K Esau).
>
> I need to see where exactly this term would go into Plant Structure
> Ontology.
>
By your definition, it is the swollen part of the petiole. Whereas in
cereal crops, the leaf does not have a petiole. All they have is a leaf
sheath and leaf lamina. However sheath can be regarded as a structural
homolog of petiole. I guess the wheat people are calling is a different
structure found at the base of the leaf sheath and the structure seems
to play a role in gravitropism.. I looked at fig-1 of the following
reference
http://archiv.fgk.org/01/BLT/dispersion/
Kaufman et al http://www.jstor.org/view/00029122/di001875/00p0367d/0 are
calling it "Leaf sheath pulvinus".
Looks like it can have the following lineage in ontology
leaf
..[p] petiole
......[p] pulvinus (PO:new term)
..........[i] leaf sheath pulvinus (PO:new term)
..[p] leaf sheath
......[i] leaf sheath pulvinus (PO:new term)
More refs:
http://jxb.oupjournals.org/cgi/content/full/52/358/1029
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11537463&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8490136&dopt=Abstract
> The last two are terms 'crease' and term 'beard'. I need to find out if
> they can be synonyms of the existing terms.
>
If I am not wrong, the "beard" is a synonym for "awn".
"crease is a particular type of morphological character found in grains
of Triticeae. I suggest creating a new term.
Suggested lineage in PO
Seed
..[p]..crease
definition: the indentation on the ventral side of the seed as found in
the members of Triticeae
I found one more term "brush" under "seed"
It is often called as bristle, but in order to avoid having confusion
between bristle leaf and bristles found on seed, my suggestion is to
call it "seed bristle"
seed bristle: fine hairs on the distal end of the seed as found in the
members of Triticeae
Seed
..[p]..seed bristle (synonym: brush)
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From pj37 at cornell.edu Wed Dec 8 16:42:24 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 08 Dec 2004 16:42:24 -0500
Subject: Fw: Wheat anatomy (fwd)
In-Reply-To: <7953D8E2E57BF94393CA6B8D2599ADDF0525BF1F@STL-MAIL2.umsl.edu>
References: <7953D8E2E57BF94393CA6B8D2599ADDF0525BF1F@STL-MAIL2.umsl.edu>
Message-ID: <41B77540.5050708@cornell.edu>
Kellogg, Elizabeth A. wrote:
> I'm not convinced of the identity between the pulvinus as the term is applied in eudicots and term applied in wheat. I looked at a couple of the references that Pankaj sent,and don't quite see what the structure is that they are referring to as pulvinus - it looks like a part of the internode to me, but maybe it's because I can't easily see the details of the photos.
Please take a look at this. As shown by the authors it appears to be
like the basal part of leaf sheath, that is attached to the culm.
http://jxb.oupjournals.org/content/vol52/issue358/images/large/EB74058.23.1.jpeg
-Pankaj
From peter.stevens at mobot.org Wed Dec 8 16:07:04 2004
From: peter.stevens at mobot.org (Peter Stevens)
Date: Wed, 8 Dec 2004 17:07:04 -0400
Subject: Fw: Wheat anatomy (fwd)
In-Reply-To: <41B75FE5.1070207@cornell.edu>
References:
<41B75FE5.1070207@cornell.edu>
Message-ID:
At 3:11 PM -0500 12/8/04, Pankaj Jaiswal wrote:
>
>If I am not wrong, the "beard" is a synonym for "awn".
I don't know much about grasses, but I thought the "beard" was a tuft
of hairs at the base of the fruit; I have never heard of its
synonymisation with awn.
>
>"crease is a particular type of morphological character found in
>grains of Triticeae. I suggest creating a new term.
>
>Suggested lineage in PO
> Seed
> ..[p]..crease
>definition: the indentation on the ventral side of the seed as found
>in the members of Triticeae
I would make a plea for not using the positional term "ventral",
simply because this is used in two very differet senses. Dorsal and
ventral used early in development are equivalent to abaxial and
adaxial and the more colloquial lower and upper..... Could ventral
be replaced by adaxial or abaxial as appropriate?
As to the pulvinus, I couldn't access the illustration for some
reason, but it does sound a little weird.
P.
From jitterbug at plantontology.org Wed Dec 8 20:19:05 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Wed, 8 Dec 2004 20:19:05 -0500
Subject: Feedback on POC - Plant ontologies (PR#50)
Message-ID: <200412090119.iB91J5Uq026389@brie4.cshl.org>
Hi Alex,
We don't have a set of established standards for the all the other plant
ontologies, since so far they have developed independently from each other. I
am
referring here to species-specific plant ontologies. Plant Ontology Consortium
(POC) has adopted a set of rules and guiding principles that we have used for
creating the Plant Ontology.
We don't have a strict policy on accepting the other plant ontologies on the
POC.
This is collaborative project and we have a mandate to create and maintain the
Plant Ontology, which is a single ontology (which has two domains) describing
plant structures and growth/developmental stages for flowering plants. We don't
actively maintain species-specific ontologies at POC. Incorporation of the
species-specific ontologies into PO is something we have done initially when we
created our ontology (we started with three species-specific ontologies and
created a new, 'generic' plant onotology).
At the present time, we are incorporating new species-specific terms into PO,
but not the entire ontologies.
I hope this clarification helps.
Thank you for your interest in Plant Ontologies.
Best regards,
Katica
> Date: Wed, 8 Dec 2004 00:40:40 -0500
> Message-Id: <200412080540.iB85eeo0032373 at filetta.cshl.org>
> Subject: Feedback on POC
> To: Shuly Avraham
> From: feedback_submission at filetta.cshl.edu
> Content-type: text/plain
> MIME-Version: 1.0
>
> *** Feedback from Plant Ontology Live Site ***
>
> refer_to_url: http://www.plantontology.org/index.html
>
> comments: We are working on an ontology for genealogy managment systems. We
> would like to know if you have standards for plant related ontologies so
they
> all keep some level of consistancy (they are all related to plants). On the
> other hand We would like to know if you have policies for accpeting new plant
> related ontologies.
>
>
>
> name: alex
>
> email: a.garcia at imb.uq.edu.au
>
> organization: acpfg/imb/university of QLD, australia.
>
> send_feedback: Send your feedback
>
>
> --------------050102020700000903050401--
>
>
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.
From jitterbug at plantontology.org Wed Dec 8 21:07:22 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Wed, 8 Dec 2004 21:07:22 -0500
Subject: [Fwd: Re: PATO and EAV] (PR#49)
Message-ID: <200412090207.iB927MUq027094@brie4.cshl.org>
Hi Simon,
I am not familiar with CRAVE, I'll look into that a little later, thanks for the
links. I am leaving in a couple days and need to take care of some urgent
things. I am forwarding this email to Tanya Berardini, who is leading our TAIR
efforts on phenotype annotation.
Have a happy holiday season.
Katica
Hi,
>
> Thank you for all your speedy responses!
>
> Are any you familiar with CRAVE?
href="http://www.mgu.har.mrc.ac.uk/CRAVE/">http://www.mgu.har.mrc.ac.uk/CRAVE/ size="-1">) This group is using an Entity - Attribute - Assay - Value?
> ontology to characterise mouse phenotypes, where the entity comes from
> the various mouse specific ontologies and the attribute, assay and
> value comes from PATO.? They are generating many new PATO terms and Im
> hoping they will release a new version of PATO soon. I will be
> submitting a list of terms we think should be included on the
> obo-phenotypes list this week.?
>
> Although we have not been using assay values yet, I have seen many
> instances with our data where an assay term would be appropriate.? I
> have attached a document sent to me by Georgios Gkoutos from the
> Mammalian Genetics Unit which outline how the E-A-A-V model is being
> used with mice.? I believe it is more powerful at capturing information
> than EAV alone,? I would be interested to hear your views on this.?
>
>
> You will notice that some of the accession numbers in the latest PATO
> have
> changed, I have requested they release a full list of changes, as we
> have already curated hundreds of lines with accessions that are now
> obsolete!
>
> Simon
>
>
>
>
>
> Bruskiewich, Richard (IRRI) wrote:
> cite="mid2A491C94FFBC5843A212A69CBEA5CEC718A6D1 at IRRIMAIL.IRRI.CGIARAD.ORG"
> type="cite">
> Hi Simon,
>
> We've been applying the EAV to our rice mutants and have noted the same
> issue. We'd be pleased to work with you on this. I think Mike Cherry might
> have done the most recent PATO attribute curation. We should ask Mike
> Ashburner for guidance on this.
>
> Richard
>
> -----Original Message-----
> From: Simon Jupp
> To: class="moz-txt-link-abbreviated"
> href="mailto:po-dev at plantontology.org">po-dev at plantontology.org
> Sent: 12/2/2004 6:37 PM
> Subject: [Fwd: Need info...]
>
>
> {This message has already been sent out on the obo-phenotypes list, but
> thought it may also be relavent here as I have some terms that may need
> including in PO.}
>
> Hi,
>
> I am writing from the Nottingham Arabidopsis Stock Center (NASC) , we
> are currently curating over 5000 phenotype descriptions using a
> combination of Plant ontology and PATO. We are using an EAV model to
> describe the various phenotypes and are finding that some of the value
> terms we ant to use are missing from PATO, we already have a list of at
> least 20 new terms that we would like including. Is there a term
> submission procedure, what is the current state of PATO?
>
> I am also working with the current GO tools and AMIGO to build an
> ontology browser and search method that combines PO and PATO. Is anyone
> else doing similar work and interested in collaboration?
>
> Cheers,
> Simon Jupp
>
> NASC,
> Nottingham,
> UK
>
>
>
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>
>
>