From phismith at buffalo.edu  Sat Aug  1 06:58:05 2009
From: phismith at buffalo.edu (Barry Smith)
Date: Sat, 01 Aug 2009 09:58:05 -0400
Subject: [Annotation] Example of one of the problems in cellular
	component
In-Reply-To: <29af5e2d0907310627x4c2fa9dag5a0054a44163d464@mail.gmail.co
 m>
References: <29af5e2d0907310627x4c2fa9dag5a0054a44163d464@mail.gmail.com>
Message-ID: <20090801141012.401235B003A@mweb1.acsu.buffalo.edu>


>>
>>
>>---------- Forwarded message ----------
>>From: Rachael Huntley <huntley at ebi.ac.uk>
>>Date: Fri, Jul 31, 2009 at 5:50 AM
>>Subject: [Annotation] GPI-anchored proteins
>>To: annotation at genome.stanford.edu
>>
>>
>>Hi all,
>>
>>I'm after some advice. I'm a little confused about these two terms,
>>with respect to GPI-anchored proteins;
>>
>>GO:0031224 intrinsic to membrane - Located in a membrane such that
>>some covalently attached portion of the gene product, for example part
>>of a peptide sequence or some other covalently attached moiety such as
>>a GPI anchor, spans or is embedded in one or both leaflets of the
>>membrane. Note that proteins intrinsic to membranes cannot be removed
>>without disrupting the membrane, e.g. by detergent.
>>
>>GO:0019898 extrinsic to membrane - Loosely bound to one surface of a
>>membrane, but not integrated into the hydrophobic region. Note that
>>proteins extrinsic to membranes can be removed by treatments that do
>>not disrupt the membrane, such as salt solutions.
>>This term can be used instead of these obsolete terms: GO:0015025
>>GPI-anchored membrane-bound receptor (consider GO:0019898)
>>
>>Both mention GPI anchor, the first (intrinsic to membrane) in the
>>definition and the second as a suggestion to use extrinsic to membrane
>>instead of the obsolete GO:0015025 GPI-anchored membrane-bound
>>receptor
>>
>>I don't know much about GPI-anchored proteins, but from what I can
>>gather they can be extracted by detergent-solubilizing a membrane
>>(PMID:19374451) which would suggest use of the term GO:0031224
>>intrinsic to membrane. However, the GPI-anchor can be disrupted by
>>phospholipase C, thus releasing the associated protein, which would
>>suggest use of the term GO:0019898 extrinsic to membrane.
>>
>>Additionally, GO:0031224 intrinsic to membrane has the child
>>GO:0031225 anchored to membrane (Def: Tethered to a membrane by a
>>covalently attached anchor, such as a lipid moiety, that is embedded
>>in the membrane. When used to describe a protein, indicates that none
>>of the peptide sequence is embedded in the membrane.) which would be a
>>term I would use for GPI-anchored proteins.
>>
>>Can anyone suggest whether GPI-anchored proteins should be annotated
>>to extrinsic or intrinsic to membrane. Either way, it looks as though
>>the ontology could be refined in this area.
>>
>>Thanks for your help.
>>
>>Rachael.
>>
>>--
>>GOA and IntAct Curator
>>European Bioinformatics Institute
>>Welcome Trust Genome Campus
>>Hinxton
>>Cambridge, CB10 1SD
>>UK
>>
>>Tel: 01223 492515
>>Fax: 01223 494468

>At 09:27 AM 7/31/2009, Alan Ruttenberg wrote:
>Nice discussion. I'll note, however, that an adjective can't be a
>place. Taj Mahal, versus Tah Mahalish. Or "above the Taj Mahal" (a
>location) versus "floating above the Taj Mahal" (a relation to a
>location).
>
>Cellular components are either places that things can be located in,
>or substances that are part_of cells.
>And GO:0031225: anchored to membrane
>
>Is neither of these - it is a state of affairs or disposition or something.
>
>-Alan

I agree with Alan that there are cellular component terms which need 
cleaning up. However, I note that, according to BFO, objects can have 
both other objects and also holes (cavities) as parts. Thus for 
instance your gut and your nostrils are parts of you. This is one of 
the reasons why it is wrong to see organisms as sums of molecules, for example.
BS
BS 


From maria at genome.stanford.edu  Mon Aug 10 19:16:30 2009
From: maria at genome.stanford.edu (Maria Costanzo)
Date: Mon, 10 Aug 2009 22:16:30 -0400
Subject: [Annotation] use of new PAMGO terms
Message-ID: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>

Hi all,

We have some annotations for Candida albicans using the now-obsolete  
term 'growth or development of symbiont in host ; GO:0044412' and I  
need to replace them with one of these terms:

id: GO:0044114
name: development of symbiont in host
namespace: biological_process
def: "The progression of an organism from an initial condition to a  
later condition, occurring within the cells or tissues of the host  
organism. This may (but not necessarily) include a filamentous growth  
form, and also can include secretion of proteases and lipases to break  
down host tissue. The host is defined as the larger of the organisms  
involved in a symbiotic interaction." [GOC:jl, GOC:pamgo_curators]
comment: This term partially replaces the obsolete term 'growth or  
development of symbiont in host ; GO:0044412'. See also 'growth of  
symbiont in host ; GO:0044117'.
subset: gosubset_prok
is_a: GO:0044115 ! development of symbiont during interaction with host


id: GO:0044117
name: growth of symbiont in host
namespace: biological_process
def: "The increase in size or mass of an organism, occurring within  
the cells or tissues of the host organism. This may (but not  
necessarily) include a filamentous growth form, and also can include  
secretion of proteases and lipases to break down host tissue. The host  
is defined as the larger of the organisms involved in a symbiotic  
interaction." [GOC:jl, GOC:pamgo_curators]
comment: This term partially replaces the obsolete term 'growth or  
development of symbiont in host ; GO:0044412'. See also 'development  
of symbiont in host ; GO:0044114'.
subset: gosubset_prok
is_a: GO:0044116 ! growth of symbiont during interaction with host

It's not obvious to me which of these is appropriate for fungal growth  
in a mammalian host. In the host, the fungus grows either by budding  
of yeast-form cells, or by filamentous growth of hyphae, and growth  
may switch between the two forms. The comment for GO:0044114 suggests  
that filamentous growth could be a hallmark of development in the  
host, but it seems that filamentous growth in itself should not be  
considered development (and in keeping with this, the GO term  
'filamentous growth' doesn't have 'development' parentage). On the  
other hand, the definition of GO:0044117 doesn't really seem to fit  
fungal growth either. The size and mass of the fungal cells doesn't  
increase; the fungal burden in the host organism does. Any guidance  
would be appreciated!

Thanks,
Maria

From jane at ebi.ac.uk  Tue Aug 11 06:22:57 2009
From: jane at ebi.ac.uk (Jane Lomax)
Date: Tue, 11 Aug 2009 14:22:57 +0100
Subject: [Annotation] use of new PAMGO terms - growth v/s development
In-Reply-To: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>
References: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>
Message-ID: <4A8170B1.7020802@ebi.ac.uk>

Hi Maria - sorry, I should have cc'ed you guys on the discussion about 
those now obsolete terms - it was all done on the PAMGO list which is 
where the discussion of the multi-organism process (MOP) terms tends to 
go. I will remember next time.

Anyhow - I've been looking at these terms and I'm a bit confused about 
the terms in the main ontology:

- In the MOP node, formation of hypha is a type of developmental 
process, whereas in the main ontology we only have 'hyphal growth' which 
is not a child of development. I don't see why 'hyphal growth' isn't a 
child of 'developmental growth' - surely it's part of the development of 
a hypha? Perhaps we need a term 'hypha development' which would have the 
part 'hyphal growth' which in turn would be a child of both 'filamentous 
growth' and 'developmental growth'?

- The term 'growth of unicellular organism as a thread of attached 
cells' does not have any relationship to either 'reproduction of a 
single-celled organism' or 'cell division'. It should certainly be 
related to the former - but looking at the children of 'cell division', 
I can't see any single-celled organism processes...is this term just for 
multi-cellular org processes? If not, why does it not have 'reproduction 
of a single-celled organism' as a child?

Didn't really shed much light there, did I - just more questions!

cheers,

Jane

Maria Costanzo wrote:
> Hi all,
>
> We have some annotations for Candida albicans using the now-obsolete 
> term 'growth or development of symbiont in host ; GO:0044412' and I 
> need to replace them with one of these terms:
>
> id: GO:0044114
> name: development of symbiont in host
> namespace: biological_process
> def: "The progression of an organism from an initial condition to a 
> later condition, occurring within the cells or tissues of the host 
> organism. This may (but not necessarily) include a filamentous growth 
> form, and also can include secretion of proteases and lipases to break 
> down host tissue. The host is defined as the larger of the organisms 
> involved in a symbiotic interaction." [GOC:jl, GOC:pamgo_curators]
> comment: This term partially replaces the obsolete term 'growth or 
> development of symbiont in host ; GO:0044412'. See also 'growth of 
> symbiont in host ; GO:0044117'.
> subset: gosubset_prok
> is_a: GO:0044115 ! development of symbiont during interaction with host
>
>
> id: GO:0044117
> name: growth of symbiont in host
> namespace: biological_process
> def: "The increase in size or mass of an organism, occurring within 
> the cells or tissues of the host organism. This may (but not 
> necessarily) include a filamentous growth form, and also can include 
> secretion of proteases and lipases to break down host tissue. The host 
> is defined as the larger of the organisms involved in a symbiotic 
> interaction." [GOC:jl, GOC:pamgo_curators]
> comment: This term partially replaces the obsolete term 'growth or 
> development of symbiont in host ; GO:0044412'. See also 'development 
> of symbiont in host ; GO:0044114'.
> subset: gosubset_prok
> is_a: GO:0044116 ! growth of symbiont during interaction with host
>
> It's not obvious to me which of these is appropriate for fungal growth 
> in a mammalian host. In the host, the fungus grows either by budding 
> of yeast-form cells, or by filamentous growth of hyphae, and growth 
> may switch between the two forms. The comment for GO:0044114 suggests 
> that filamentous growth could be a hallmark of development in the 
> host, but it seems that filamentous growth in itself should not be 
> considered development (and in keeping with this, the GO term 
> 'filamentous growth' doesn't have 'development' parentage). On the 
> other hand, the definition of GO:0044117 doesn't really seem to fit 
> fungal growth either. The size and mass of the fungal cells doesn't 
> increase; the fungal burden in the host organism does. Any guidance 
> would be appreciated!
>
> Thanks,
> Maria
> _______________________________________________
> Annotation mailing list
> Annotation at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/annotation


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468


From midori at ebi.ac.uk  Tue Aug 11 06:33:15 2009
From: midori at ebi.ac.uk (Midori Harris)
Date: Tue, 11 Aug 2009 14:33:15 +0100 (BST)
Subject: [Annotation] use of new PAMGO terms - growth v/s development
In-Reply-To: <4A8170B1.7020802@ebi.ac.uk>
References: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>
	<4A8170B1.7020802@ebi.ac.uk>
Message-ID: <Pine.LNX.4.64.0908111431550.22083@pigeon.ebi.ac.uk>

I don't think 'cell division' was ever supposed to be restricted to 
multicellular organisms. We probably just overlooked those missing links 
...

m

On Tue, 11 Aug 2009, Jane Lomax wrote:

> Hi Maria - sorry, I should have cc'ed you guys on the discussion about those 
> now obsolete terms - it was all done on the PAMGO list which is where the 
> discussion of the multi-organism process (MOP) terms tends to go. I will 
> remember next time.
>
> Anyhow - I've been looking at these terms and I'm a bit confused about the 
> terms in the main ontology:
>
> - In the MOP node, formation of hypha is a type of developmental process, 
> whereas in the main ontology we only have 'hyphal growth' which is not a 
> child of development. I don't see why 'hyphal growth' isn't a child of 
> 'developmental growth' - surely it's part of the development of a hypha? 
> Perhaps we need a term 'hypha development' which would have the part 'hyphal 
> growth' which in turn would be a child of both 'filamentous growth' and 
> 'developmental growth'?
>
> - The term 'growth of unicellular organism as a thread of attached cells' 
> does not have any relationship to either 'reproduction of a single-celled 
> organism' or 'cell division'. It should certainly be related to the former - 
> but looking at the children of 'cell division', I can't see any single-celled 
> organism processes...is this term just for multi-cellular org processes? If 
> not, why does it not have 'reproduction of a single-celled organism' as a 
> child?
>
> Didn't really shed much light there, did I - just more questions!
>
> cheers,
>
> Jane
>
> Maria Costanzo wrote:
>> Hi all,
>> 
>> We have some annotations for Candida albicans using the now-obsolete term 
>> 'growth or development of symbiont in host ; GO:0044412' and I need to 
>> replace them with one of these terms:
>> 
>> id: GO:0044114
>> name: development of symbiont in host
>> namespace: biological_process
>> def: "The progression of an organism from an initial condition to a later 
>> condition, occurring within the cells or tissues of the host organism. This 
>> may (but not necessarily) include a filamentous growth form, and also can 
>> include secretion of proteases and lipases to break down host tissue. The 
>> host is defined as the larger of the organisms involved in a symbiotic 
>> interaction." [GOC:jl, GOC:pamgo_curators]
>> comment: This term partially replaces the obsolete term 'growth or 
>> development of symbiont in host ; GO:0044412'. See also 'growth of symbiont 
>> in host ; GO:0044117'.
>> subset: gosubset_prok
>> is_a: GO:0044115 ! development of symbiont during interaction with host
>> 
>> 
>> id: GO:0044117
>> name: growth of symbiont in host
>> namespace: biological_process
>> def: "The increase in size or mass of an organism, occurring within the 
>> cells or tissues of the host organism. This may (but not necessarily) 
>> include a filamentous growth form, and also can include secretion of 
>> proteases and lipases to break down host tissue. The host is defined as the 
>> larger of the organisms involved in a symbiotic interaction." [GOC:jl, 
>> GOC:pamgo_curators]
>> comment: This term partially replaces the obsolete term 'growth or 
>> development of symbiont in host ; GO:0044412'. See also 'development of 
>> symbiont in host ; GO:0044114'.
>> subset: gosubset_prok
>> is_a: GO:0044116 ! growth of symbiont during interaction with host
>> 
>> It's not obvious to me which of these is appropriate for fungal growth in a 
>> mammalian host. In the host, the fungus grows either by budding of 
>> yeast-form cells, or by filamentous growth of hyphae, and growth may switch 
>> between the two forms. The comment for GO:0044114 suggests that filamentous 
>> growth could be a hallmark of development in the host, but it seems that 
>> filamentous growth in itself should not be considered development (and in 
>> keeping with this, the GO term 'filamentous growth' doesn't have 
>> 'development' parentage). On the other hand, the definition of GO:0044117 
>> doesn't really seem to fit fungal growth either. The size and mass of the 
>> fungal cells doesn't increase; the fungal burden in the host organism does. 
>> Any guidance would be appreciated!
>> 
>> Thanks,
>> Maria
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation
>
>
>

From pgaudet at northwestern.edu  Tue Aug 11 06:58:03 2009
From: pgaudet at northwestern.edu (Pascale Gaudet)
Date: Tue, 11 Aug 2009 09:58:03 -0400
Subject: [Annotation] use of new PAMGO terms - growth v/s development
In-Reply-To: <Pine.LNX.4.64.0908111431550.22083@pigeon.ebi.ac.uk>
References: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>	<4A8170B1.7020802@ebi.ac.uk>
	<Pine.LNX.4.64.0908111431550.22083@pigeon.ebi.ac.uk>
Message-ID: <4A8178EB.2050606@northwestern.edu>

An HTML attachment was scrubbed...
URL: <http://fafner.stanford.edu/pipermail/annotation/attachments/20090811/988127a2/attachment.html>

From jane at ebi.ac.uk  Tue Aug 11 07:03:30 2009
From: jane at ebi.ac.uk (Jane Lomax)
Date: Tue, 11 Aug 2009 15:03:30 +0100
Subject: [Annotation] use of new PAMGO terms - growth v/s development
In-Reply-To: <4A8178EB.2050606@northwestern.edu>
References: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>	<4A8170B1.7020802@ebi.ac.uk>
	<Pine.LNX.4.64.0908111431550.22083@pigeon.ebi.ac.uk>
	<4A8178EB.2050606@northwestern.edu>
Message-ID: <4A817A32.7030501@ebi.ac.uk>

Pascale - not 'cell growth' - 'growth of unicellular organism as a 
thread of attached cells' [def: A filamentous growth process in which 
cells remain attached after division and form thread-like filaments that 
may penetrate into a solid growth medium such as an agar plate, 
exhibited by unicellular fungi under certain growth conditions.]

Jane


Pascale Gaudet wrote:
> Jane,
>
> I may have read too fast - but cell growth should *not* have any 
> relationship to 'reproduction of a single-celled organism' or 'cell 
> division'. Those are completely different processes. The cell can 
> increase in size without having to go through division.
>
> Pascale
>
> Midori Harris wrote:
>> I don't think 'cell division' was ever supposed to be restricted to 
>> multicellular organisms. We probably just overlooked those missing 
>> links ...
>>
>> m
>>
>> On Tue, 11 Aug 2009, Jane Lomax wrote:
>>
>>> Hi Maria - sorry, I should have cc'ed you guys on the discussion 
>>> about those now obsolete terms - it was all done on the PAMGO list 
>>> which is where the discussion of the multi-organism process (MOP) 
>>> terms tends to go. I will remember next time.
>>>
>>> Anyhow - I've been looking at these terms and I'm a bit confused 
>>> about the terms in the main ontology:
>>>
>>> - In the MOP node, formation of hypha is a type of developmental 
>>> process, whereas in the main ontology we only have 'hyphal growth' 
>>> which is not a child of development. I don't see why 'hyphal growth' 
>>> isn't a child of 'developmental growth' - surely it's part of the 
>>> development of a hypha? Perhaps we need a term 'hypha development' 
>>> which would have the part 'hyphal growth' which in turn would be a 
>>> child of both 'filamentous growth' and 'developmental growth'?
>>>
>>> - The term 'growth of unicellular organism as a thread of attached 
>>> cells' does not have any relationship to either 'reproduction of a 
>>> single-celled organism' or 'cell division'. It should certainly be 
>>> related to the former - but looking at the children of 'cell 
>>> division', I can't see any single-celled organism processes...is 
>>> this term just for multi-cellular org processes? If not, why does it 
>>> not have 'reproduction of a single-celled organism' as a child?
>>>
>>> Didn't really shed much light there, did I - just more questions!
>>>
>>> cheers,
>>>
>>> Jane
>>>
>>> Maria Costanzo wrote:
>>>> Hi all,
>>>>
>>>> We have some annotations for Candida albicans using the 
>>>> now-obsolete term 'growth or development of symbiont in host ; 
>>>> GO:0044412' and I need to replace them with one of these terms:
>>>>
>>>> id: GO:0044114
>>>> name: development of symbiont in host
>>>> namespace: biological_process
>>>> def: "The progression of an organism from an initial condition to a 
>>>> later condition, occurring within the cells or tissues of the host 
>>>> organism. This may (but not necessarily) include a filamentous 
>>>> growth form, and also can include secretion of proteases and 
>>>> lipases to break down host tissue. The host is defined as the 
>>>> larger of the organisms involved in a symbiotic interaction." 
>>>> [GOC:jl, GOC:pamgo_curators]
>>>> comment: This term partially replaces the obsolete term 'growth or 
>>>> development of symbiont in host ; GO:0044412'. See also 'growth of 
>>>> symbiont in host ; GO:0044117'.
>>>> subset: gosubset_prok
>>>> is_a: GO:0044115 ! development of symbiont during interaction with 
>>>> host
>>>>
>>>>
>>>> id: GO:0044117
>>>> name: growth of symbiont in host
>>>> namespace: biological_process
>>>> def: "The increase in size or mass of an organism, occurring within 
>>>> the cells or tissues of the host organism. This may (but not 
>>>> necessarily) include a filamentous growth form, and also can 
>>>> include secretion of proteases and lipases to break down host 
>>>> tissue. The host is defined as the larger of the organisms involved 
>>>> in a symbiotic interaction." [GOC:jl, GOC:pamgo_curators]
>>>> comment: This term partially replaces the obsolete term 'growth or 
>>>> development of symbiont in host ; GO:0044412'. See also 
>>>> 'development of symbiont in host ; GO:0044114'.
>>>> subset: gosubset_prok
>>>> is_a: GO:0044116 ! growth of symbiont during interaction with host
>>>>
>>>> It's not obvious to me which of these is appropriate for fungal 
>>>> growth in a mammalian host. In the host, the fungus grows either by 
>>>> budding of yeast-form cells, or by filamentous growth of hyphae, 
>>>> and growth may switch between the two forms. The comment for 
>>>> GO:0044114 suggests that filamentous growth could be a hallmark of 
>>>> development in the host, but it seems that filamentous growth in 
>>>> itself should not be considered development (and in keeping with 
>>>> this, the GO term 'filamentous growth' doesn't have 'development' 
>>>> parentage). On the other hand, the definition of GO:0044117 doesn't 
>>>> really seem to fit fungal growth either. The size and mass of the 
>>>> fungal cells doesn't increase; the fungal burden in the host 
>>>> organism does. Any guidance would be appreciated!
>>>>
>>>> Thanks,
>>>> Maria
>>>> _______________________________________________
>>>> Annotation mailing list
>>>> Annotation at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>
>>>
>>>
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468


From jane at ebi.ac.uk  Tue Aug 11 07:05:26 2009
From: jane at ebi.ac.uk (Jane Lomax)
Date: Tue, 11 Aug 2009 15:05:26 +0100
Subject: [Annotation] use of new PAMGO terms - growth v/s development
In-Reply-To: <4A8178EB.2050606@northwestern.edu>
References: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>	<4A8170B1.7020802@ebi.ac.uk>
	<Pine.LNX.4.64.0908111431550.22083@pigeon.ebi.ac.uk>
	<4A8178EB.2050606@northwestern.edu>
Message-ID: <4A817AA6.6060503@ebi.ac.uk>

...I guess I'm having a hard time discerning the distinction between 
'growth', development and 'reproduction' for unicellular organisms...



Pascale Gaudet wrote:
> Jane,
>
> I may have read too fast - but cell growth should *not* have any 
> relationship to 'reproduction of a single-celled organism' or 'cell 
> division'. Those are completely different processes. The cell can 
> increase in size without having to go through division.
>
> Pascale
>
> Midori Harris wrote:
>> I don't think 'cell division' was ever supposed to be restricted to 
>> multicellular organisms. We probably just overlooked those missing 
>> links ...
>>
>> m
>>
>> On Tue, 11 Aug 2009, Jane Lomax wrote:
>>
>>> Hi Maria - sorry, I should have cc'ed you guys on the discussion 
>>> about those now obsolete terms - it was all done on the PAMGO list 
>>> which is where the discussion of the multi-organism process (MOP) 
>>> terms tends to go. I will remember next time.
>>>
>>> Anyhow - I've been looking at these terms and I'm a bit confused 
>>> about the terms in the main ontology:
>>>
>>> - In the MOP node, formation of hypha is a type of developmental 
>>> process, whereas in the main ontology we only have 'hyphal growth' 
>>> which is not a child of development. I don't see why 'hyphal growth' 
>>> isn't a child of 'developmental growth' - surely it's part of the 
>>> development of a hypha? Perhaps we need a term 'hypha development' 
>>> which would have the part 'hyphal growth' which in turn would be a 
>>> child of both 'filamentous growth' and 'developmental growth'?
>>>
>>> - The term 'growth of unicellular organism as a thread of attached 
>>> cells' does not have any relationship to either 'reproduction of a 
>>> single-celled organism' or 'cell division'. It should certainly be 
>>> related to the former - but looking at the children of 'cell 
>>> division', I can't see any single-celled organism processes...is 
>>> this term just for multi-cellular org processes? If not, why does it 
>>> not have 'reproduction of a single-celled organism' as a child?
>>>
>>> Didn't really shed much light there, did I - just more questions!
>>>
>>> cheers,
>>>
>>> Jane
>>>
>>> Maria Costanzo wrote:
>>>> Hi all,
>>>>
>>>> We have some annotations for Candida albicans using the 
>>>> now-obsolete term 'growth or development of symbiont in host ; 
>>>> GO:0044412' and I need to replace them with one of these terms:
>>>>
>>>> id: GO:0044114
>>>> name: development of symbiont in host
>>>> namespace: biological_process
>>>> def: "The progression of an organism from an initial condition to a 
>>>> later condition, occurring within the cells or tissues of the host 
>>>> organism. This may (but not necessarily) include a filamentous 
>>>> growth form, and also can include secretion of proteases and 
>>>> lipases to break down host tissue. The host is defined as the 
>>>> larger of the organisms involved in a symbiotic interaction." 
>>>> [GOC:jl, GOC:pamgo_curators]
>>>> comment: This term partially replaces the obsolete term 'growth or 
>>>> development of symbiont in host ; GO:0044412'. See also 'growth of 
>>>> symbiont in host ; GO:0044117'.
>>>> subset: gosubset_prok
>>>> is_a: GO:0044115 ! development of symbiont during interaction with 
>>>> host
>>>>
>>>>
>>>> id: GO:0044117
>>>> name: growth of symbiont in host
>>>> namespace: biological_process
>>>> def: "The increase in size or mass of an organism, occurring within 
>>>> the cells or tissues of the host organism. This may (but not 
>>>> necessarily) include a filamentous growth form, and also can 
>>>> include secretion of proteases and lipases to break down host 
>>>> tissue. The host is defined as the larger of the organisms involved 
>>>> in a symbiotic interaction." [GOC:jl, GOC:pamgo_curators]
>>>> comment: This term partially replaces the obsolete term 'growth or 
>>>> development of symbiont in host ; GO:0044412'. See also 
>>>> 'development of symbiont in host ; GO:0044114'.
>>>> subset: gosubset_prok
>>>> is_a: GO:0044116 ! growth of symbiont during interaction with host
>>>>
>>>> It's not obvious to me which of these is appropriate for fungal 
>>>> growth in a mammalian host. In the host, the fungus grows either by 
>>>> budding of yeast-form cells, or by filamentous growth of hyphae, 
>>>> and growth may switch between the two forms. The comment for 
>>>> GO:0044114 suggests that filamentous growth could be a hallmark of 
>>>> development in the host, but it seems that filamentous growth in 
>>>> itself should not be considered development (and in keeping with 
>>>> this, the GO term 'filamentous growth' doesn't have 'development' 
>>>> parentage). On the other hand, the definition of GO:0044117 doesn't 
>>>> really seem to fit fungal growth either. The size and mass of the 
>>>> fungal cells doesn't increase; the fungal burden in the host 
>>>> organism does. Any guidance would be appreciated!
>>>>
>>>> Thanks,
>>>> Maria
>>>> _______________________________________________
>>>> Annotation mailing list
>>>> Annotation at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>
>>>
>>>
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468


From Peter.D'Eustachio at nyumc.org  Tue Aug 11 09:01:57 2009
From: Peter.D'Eustachio at nyumc.org (D'Eustachio, Peter)
Date: Tue, 11 Aug 2009 12:01:57 -0400
Subject: [Annotation] use of new PAMGO terms - growth v/s development
In-Reply-To: <4A817AA6.6060503@ebi.ac.uk>
Message-ID: <001F264FE3E0F14994BCFD1C3045AD0E3EDEF701@MSGWSDCPMB04.nyumc.org>

In principle, a cell can synthesize more of its components and enlarge (grow) or change its pattern of gene expression and its phenotypes (develop) without ever dividing into daughter cells (reproduce). On the other hand, there are lots of cases, and perhaps filament formation is one, where growth and development are causally linked to reproduction.

-----Original Message-----
From: annotation-bounces at genome.stanford.edu [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Jane Lomax
Sent: Tuesday, August 11, 2009 10:05 AM
To: pgaudet at northwestern.edu
Cc: pamgo-admin at vbi.vt.edu; CGD Curators; annotation at genome.stanford.edu
Subject: Re: [Annotation] use of new PAMGO terms - growth v/s development

...I guess I'm having a hard time discerning the distinction between
'growth', development and 'reproduction' for unicellular organisms...



Pascale Gaudet wrote:
> Jane,
>
> I may have read too fast - but cell growth should *not* have any
> relationship to 'reproduction of a single-celled organism' or 'cell
> division'. Those are completely different processes. The cell can
> increase in size without having to go through division.
>
> Pascale
>
> Midori Harris wrote:
>> I don't think 'cell division' was ever supposed to be restricted to
>> multicellular organisms. We probably just overlooked those missing
>> links ...
>>
>> m
>>
>> On Tue, 11 Aug 2009, Jane Lomax wrote:
>>
>>> Hi Maria - sorry, I should have cc'ed you guys on the discussion
>>> about those now obsolete terms - it was all done on the PAMGO list
>>> which is where the discussion of the multi-organism process (MOP)
>>> terms tends to go. I will remember next time.
>>>
>>> Anyhow - I've been looking at these terms and I'm a bit confused
>>> about the terms in the main ontology:
>>>
>>> - In the MOP node, formation of hypha is a type of developmental
>>> process, whereas in the main ontology we only have 'hyphal growth'
>>> which is not a child of development. I don't see why 'hyphal growth'
>>> isn't a child of 'developmental growth' - surely it's part of the
>>> development of a hypha? Perhaps we need a term 'hypha development'
>>> which would have the part 'hyphal growth' which in turn would be a
>>> child of both 'filamentous growth' and 'developmental growth'?
>>>
>>> - The term 'growth of unicellular organism as a thread of attached
>>> cells' does not have any relationship to either 'reproduction of a
>>> single-celled organism' or 'cell division'. It should certainly be
>>> related to the former - but looking at the children of 'cell
>>> division', I can't see any single-celled organism processes...is
>>> this term just for multi-cellular org processes? If not, why does it
>>> not have 'reproduction of a single-celled organism' as a child?
>>>
>>> Didn't really shed much light there, did I - just more questions!
>>>
>>> cheers,
>>>
>>> Jane
>>>
>>> Maria Costanzo wrote:
>>>> Hi all,
>>>>
>>>> We have some annotations for Candida albicans using the
>>>> now-obsolete term 'growth or development of symbiont in host ;
>>>> GO:0044412' and I need to replace them with one of these terms:
>>>>
>>>> id: GO:0044114
>>>> name: development of symbiont in host
>>>> namespace: biological_process
>>>> def: "The progression of an organism from an initial condition to a
>>>> later condition, occurring within the cells or tissues of the host
>>>> organism. This may (but not necessarily) include a filamentous
>>>> growth form, and also can include secretion of proteases and
>>>> lipases to break down host tissue. The host is defined as the
>>>> larger of the organisms involved in a symbiotic interaction."
>>>> [GOC:jl, GOC:pamgo_curators]
>>>> comment: This term partially replaces the obsolete term 'growth or
>>>> development of symbiont in host ; GO:0044412'. See also 'growth of
>>>> symbiont in host ; GO:0044117'.
>>>> subset: gosubset_prok
>>>> is_a: GO:0044115 ! development of symbiont during interaction with
>>>> host
>>>>
>>>>
>>>> id: GO:0044117
>>>> name: growth of symbiont in host
>>>> namespace: biological_process
>>>> def: "The increase in size or mass of an organism, occurring within
>>>> the cells or tissues of the host organism. This may (but not
>>>> necessarily) include a filamentous growth form, and also can
>>>> include secretion of proteases and lipases to break down host
>>>> tissue. The host is defined as the larger of the organisms involved
>>>> in a symbiotic interaction." [GOC:jl, GOC:pamgo_curators]
>>>> comment: This term partially replaces the obsolete term 'growth or
>>>> development of symbiont in host ; GO:0044412'. See also
>>>> 'development of symbiont in host ; GO:0044114'.
>>>> subset: gosubset_prok
>>>> is_a: GO:0044116 ! growth of symbiont during interaction with host
>>>>
>>>> It's not obvious to me which of these is appropriate for fungal
>>>> growth in a mammalian host. In the host, the fungus grows either by
>>>> budding of yeast-form cells, or by filamentous growth of hyphae,
>>>> and growth may switch between the two forms. The comment for
>>>> GO:0044114 suggests that filamentous growth could be a hallmark of
>>>> development in the host, but it seems that filamentous growth in
>>>> itself should not be considered development (and in keeping with
>>>> this, the GO term 'filamentous growth' doesn't have 'development'
>>>> parentage). On the other hand, the definition of GO:0044117 doesn't
>>>> really seem to fit fungal growth either. The size and mass of the
>>>> fungal cells doesn't increase; the fungal burden in the host
>>>> organism does. Any guidance would be appreciated!
>>>>
>>>> Thanks,
>>>> Maria
>>>> _______________________________________________
>>>> Annotation mailing list
>>>> Annotation at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>
>>>
>>>
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>>


--
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468

_______________________________________________
Annotation mailing list
Annotation at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/annotation

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From btyler at vbi.vt.edu  Tue Aug 11 07:10:47 2009
From: btyler at vbi.vt.edu (Brett Tyler)
Date: Tue, 11 Aug 2009 10:10:47 -0400
Subject: [Annotation] [pamgo-admin] Re: use of new PAMGO terms - growth v/s
 development
In-Reply-To: <4A8170B1.7020802@ebi.ac.uk>
References: <BE1B52FF-0CE1-4E22-A6B6-B327BAF88C3C@genome.stanford.edu>
	<4A8170B1.7020802@ebi.ac.uk>
Message-ID: <p06240851c6a72a5ce5ec@[128.173.101.124]>

Folks,

Its seems to me that formation of hypha (i.e. filamentous growth 
form) as a developmental process should be reserved for a change of 
state, e.g. germination of a spore to produce a hyphal germ tube, 
switch from a yeast form to a hyphal form, or differentiation into a 
specialized hyphal form (e.g. invasive hyphae of some plant 
pathogens).

A simple expansion of hyphal biomass should be considered hyphal 
growth, and thus fall under growth of symbiont in host when it occurs 
inside host tissue.

The definition of growth of symbiont in host should definitely be 
expanded to include an increase in the number of cells and/or 
increase in size or mass of a collection of pseudohyphae.

I'd also comment that "and also can include secretion of proteases 
and lipases to break down host tissue" seems too specific as well as 
unrelated to growth and perhaps should be modified to "and also may 
be accompanied by break down of host tissue"

Cheers

Brett



At 2:22 PM +0100 8/11/09, Jane Lomax wrote:
>Hi Maria - sorry, I should have cc'ed you guys on the discussion 
>about those now obsolete terms - it was all done on the PAMGO list 
>which is where the discussion of the multi-organism process (MOP) 
>terms tends to go. I will remember next time.
>
>Anyhow - I've been looking at these terms and I'm a bit confused 
>about the terms in the main ontology:
>
>- In the MOP node, formation of hypha is a type of developmental 
>process, whereas in the main ontology we only have 'hyphal growth' 
>which is not a child of development. I don't see why 'hyphal growth' 
>isn't a child of 'developmental growth' - surely it's part of the 
>development of a hypha? Perhaps we need a term 'hypha development' 
>which would have the part 'hyphal growth' which in turn would be a 
>child of both 'filamentous growth' and 'developmental growth'?
>
>- The term 'growth of unicellular organism as a thread of attached 
>cells' does not have any relationship to either 'reproduction of a 
>single-celled organism' or 'cell division'. It should certainly be 
>related to the former - but looking at the children of 'cell 
>division', I can't see any single-celled organism processes...is 
>this term just for multi-cellular org processes? If not, why does it 
>not have 'reproduction of a single-celled organism' as a child?
>
>Didn't really shed much light there, did I - just more questions!
>
>cheers,
>
>Jane
>
>Maria Costanzo wrote:
>>  Hi all,
>>
>>  We have some annotations for Candida albicans using the 
>>now-obsolete term 'growth or development of symbiont in host ; 
>>GO:0044412' and I need to replace them with one of these terms:
>>
>>  id: GO:0044114
>>  name: development of symbiont in host
>>  namespace: biological_process
>>  def: "The progression of an organism from an initial condition to 
>>a later condition, occurring within the cells or tissues of the 
>>host organism. This may (but not necessarily) include a filamentous 
>>growth form, and also can include secretion of proteases and 
>>lipases to break down host tissue. The host is defined as the 
>>larger of the organisms involved in a symbiotic interaction." 
>>[GOC:jl, GOC:pamgo_curators]
>>  comment: This term partially replaces the obsolete term 'growth or 
>>development of symbiont in host ; GO:0044412'. See also 'growth of 
>>symbiont in host ; GO:0044117'.
>>  subset: gosubset_prok
>>  is_a: GO:0044115 ! development of symbiont during interaction with host
>>
>>
>>  id: GO:0044117
>>  name: growth of symbiont in host
>>  namespace: biological_process
>>  def: "The increase in size or mass of an organism, occurring 
>>within the cells or tissues of the host organism. This may (but not 
>>necessarily) include a filamentous growth form, and also can 
>>include secretion of proteases and lipases to break down host 
>>tissue. The host is defined as the larger of the organisms involved 
>>in a symbiotic interaction." [GOC:jl, GOC:pamgo_curators]
>>  comment: This term partially replaces the obsolete term 'growth or 
>>development of symbiont in host ; GO:0044412'. See also 
>>'development of symbiont in host ; GO:0044114'.
>>  subset: gosubset_prok
>>  is_a: GO:0044116 ! growth of symbiont during interaction with host
>>
>>  It's not obvious to me which of these is appropriate for fungal 
>>growth in a mammalian host. In the host, the fungus grows either by 
>>budding of yeast-form cells, or by filamentous growth of hyphae, 
>>and growth may switch between the two forms. The comment for 
>>GO:0044114 suggests that filamentous growth could be a hallmark of 
>>development in the host, but it seems that filamentous growth in 
>>itself should not be considered development (and in keeping with 
>>this, the GO term 'filamentous growth' doesn't have 'development' 
>>parentage). On the other hand, the definition of GO:0044117 doesn't 
>>really seem to fit fungal growth either. The size and mass of the 
>>fungal cells doesn't increase; the fungal burden in the host 
>>organism does. Any guidance would be appreciated!
>>
>>  Thanks,
>>  Maria
>>  _______________________________________________
>>  Annotation mailing list
>>  Annotation at geneontology.org
>>  http://fafner.stanford.edu/mailman/listinfo/annotation
>
>
>--
>Dr Jane Lomax
>GO Editorial Office
>EMBL-EBI
>Wellcome Trust Genome Campus
>Hinxton
>Cambridgeshire, UK
>CB10 1SD
>
>p: +44 1223 492516
>f: +44 1223 494468
>
>*******************************************************************************
>      Virginia Bioinformatics Institute PAMGO Admin Mailing List
>*******************************************************************************

-- 
*****************
Brett Tyler
Professor
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Washington Street
Blacksburg, VA 24061-0477

Telephone: (540) 231-7318
Fax: (540) 231-2606
Email: bmtyler at vt.edu
Web: https://www.vbi.vt.edu/article/articleview/141

Administrative Assistant:
Emily Alberts
Telephone:  (540) 231-9417
Email: ealberts at vbi.vt.edu
*****************

From midori at ebi.ac.uk  Wed Aug 19 04:00:31 2009
From: midori at ebi.ac.uk (midori at ebi.ac.uk)
Date: Wed, 19 Aug 2009 11:00:31 UT
Subject: [Annotation] SourceForge Annotation Tracker Update
Message-ID: <200908191100.n7JB0VoN004765@pigeon.ebi.ac.uk>

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From midori at ebi.ac.uk  Thu Aug 20 04:00:32 2009
From: midori at ebi.ac.uk (midori at ebi.ac.uk)
Date: Thu, 20 Aug 2009 11:00:32 UT
Subject: [Annotation] SourceForge Annotation Tracker Update
Message-ID: <200908201100.n7KB0W58023717@pigeon.ebi.ac.uk>

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