[Go] generic GO slim question
Hannick, Linda
lhannick at jcvi.org
Tue Jun 16 09:47:29 PDT 2009
We were just discussing this same issue, in the context of updating our
go slims. Another category of interest for us is metagenomic. A
metagenomics slim would have a definite prokaryotic slant; the question
for us: would it be different from a prokaryotic slim?
Another question: How many slims are in use or were developed for
specific purposes, and not shared with the GO community as groups move
on to the next project? Could we mount a drive to collect them, if they
exist?
Linda
> Judith Blake wrote:
>> Val,
>>
>> I agree with Jane. It would be excellent if we could provide updated
slims
>> for 'all' and then a very few subsets. The question would be...
>>
>> Eucaryotic/prokaryotic?
>>
>> Multi-cellular/single-celled?
>>
>> Both? One or the other?
>>
>>
>>
>> Judy
>>
>>
>> On 6/15/09 11:13 AM, "Jane Lomax" <jane at ebi.ac.uk> wrote:
>>
>> Hi Val - I totally agree with you about the generic GO slim -
it's
>> embarrassingly out-of-date. I think the problem is partly that
>> no-one has
>> committed to work on it.
>>
>> Do you have time in the next couple of weeks so you and I can sit
>> down and
>> at least improve it a bit?
>>
>> I think in the long term seprate multi-cellular
organism/single-celled
>> organism etc slims are the way to go. But think there will always
be a
>> place for a generic slim too.
>>
>> Jane
>>
>>
>> On Sun, 14 Jun 2009, Valerie Wood wrote:
>>
>> >
>> > How was it decided which terms to include in the generic GO
slim?
>> >
>> > There have been discussions previously about what makes a
useful
>> and relevent
>> > generic GO slim (but no agreement). However, it seems that at
the
>> very least
>> > the terms should be i) general, and ii) high level terms which
>> constitute
>> > major cellular processes (and therefore areas of research)
should be
>> > included.
>> >
>> > So, I was wondering why the following terms are in the slim (I
>> have included
>> > the TOTAL number of annotations for all organisms in
parenthases)
>> >
>> > i) plastid translation [1]
>> > ii) lead ion binding [2]
>> > iii) cytoplasmic chromosome [28]
>> > iv) neurotransmitter transporter [55]
>> >
>> > Conversely the following biologically important "general" terms
>> (at least
>> > from a single celled organism perprective) , are absent from
the
>> generic GO
>> > slim
>> >
>> > i) DNA replication [1685]
>> > ii) DNA repair [1934]
>> > iii) transmembrane transport [814]
>> > iv) ribosome biogenesis [1849]
>> > v) cytokinesis [1049]
>> > vi) cytoskeletal organization [2311]
>> > and others.
>> >
>> > In addition, there is an obsolete molecular function term in
the slim
>> > (chaperone regulator activity)
>> >
>> > I wondered whether the contents of the slim need to be to make
it
>> more
>> > useful. I realise it isn't easy to make a slim which is good
for all
>> > organisms. If this is the case perhaps we should consider
>> abandoning the
>> > "generic generic" slim and define more useful individual
generic
>> slims for
>> > prokaryotes, eukaryotic unicellular, and multicellular orgs?
>> >
>> > We might not agree about the utility of a "generic slim" but
>> these are used
>> > a lot as they are the default slims used by AmiGO, and the
>> Princeton generic
>> > GO term mapper.......They should provide a good overview of the
>> known biology
>> > of any organism. They should probably provide a starting point
>> for people
>> > who wish to refine to make their own slim and include more
>> specific terms
>> > for their area of interest, and remove terms which are not
>> useful. I am
>> > trying to write a tutorial which includes how to select terms
for
>> a slim to
>> > give complete coverage for their organism, and refine to make a
>> more specific
>> > slim, but the the generic slim doesn't seem to provide very
good
>> example for
>> > a starting point.
>> >
>> > Val
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>>
>> --
>> 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
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
------------------------------------------------------------------------
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>
>
------------------------------
Message: 2
Date: Mon, 15 Jun 2009 09:51:56 -0700 (PDT)
From: vanauken at caltech.edu
Subject: [Go] Reporting invalid PubMed IDs - central location?
To: gohelp at genome.stanford.edu, go at genome.stanford.edu
Cc: maglott at ncbi.nlm.nih.gov
Message-ID:
<2321.128.112.116.185.1245084716.squirrel at webmail.caltech.edu>
Content-Type: text/plain;charset=iso-8859-1
Dear Donna,
Thank you for writing to the GO and raising the issue about reporting
invalid PubMed IDs.
I have cc'ed the general GO mailing list on this email to see if it
would
be possible to set up a central place to report invalid PMIDs, or if
someone might perhaps have another suggestion for how to communicate
this
information to the various MODs efficiently.
Best,
--Kimberly Van Auken
Database Curator, WormBase
www.wormbase.org
www.geneontology.org
> Subject: validating PubMed ids in the gene association files
> Date: Mon, 15 Jun 2009 12:18:49 -0400
>
> Hello all,
> In our processing of gene_association files on the ftp site for Entrez
> Gene, we periodically (and rarely) find PubMed uids that are not
valid.
>
> Is there a central location to which we can report these invalid
PubMed
> uids that can be checked by each data source?
>
> We are hoping for one reporting site, rather than gmod-specific ones.
>
> Thanks for your help,
>
> Donna Maglott maglott at ncbi.nlm.nih.gov
>
------------------------------------------------------------------------
------
> ? National Center for Biotechnology Information???
> ?National Library of Medicine, NIH?????????? ? ?? phone:??
301-435-5895
> ? Building 45, Room 4As.47C ???????????????????????
> fax:????301-480-0109
> ? Bethesda, MD 20892-6510
>
------------------------------------------------------------------------
------
>
>
>
>
------------------------------
Message: 3
Date: Mon, 15 Jun 2009 18:00:52 UT
From: midori at ebi.ac.uk
Subject: [Go] SourceForge Update
To: go at genome.stanford.edu, go-curator-tracker at genome.stanford.edu
Message-ID: <200906151800.n5FI0qD4031444 at pigeon.ebi.ac.uk>
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Message: 4
Date: Mon, 15 Jun 2009 13:14:13 -0500
From: Jim Hu <jimhu at tamu.edu>
Subject: Re: [Go] Reporting invalid PubMed IDs - central location?
To: vanauken at caltech.edu
Cc: maglott at ncbi.nlm.nih.gov, GO consortium <go at genome.stanford.edu>,
GO Help List <gohelp at genome.stanford.edu>
Message-ID: <11FB5077-6B8D-40A2-9154-4E8D29B25BF7 at tamu.edu>
Content-Type: text/plain; charset="us-ascii"; Format="flowed";
DelSp="yes"
It might actually be possible to build this into the validation
scripts, but if it's really rare, that may not be worth it.
E-Utils will accept single queries with large numbers of PMIDs, and
the PMIDs in a gaf could be checked locally against the xml return.
After doing this the first time, one could make the script only check
new annotations, so the query wouldn't even have to be ridiculously
huge.
Jim
On Jun 15, 2009, at 11:51 AM, vanauken at caltech.edu wrote:
> Dear Donna,
>
> Thank you for writing to the GO and raising the issue about reporting
> invalid PubMed IDs.
>
> I have cc'ed the general GO mailing list on this email to see if it
> would
> be possible to set up a central place to report invalid PMIDs, or if
> someone might perhaps have another suggestion for how to communicate
> this
> information to the various MODs efficiently.
>
> Best,
> --Kimberly Van Auken
>
> Database Curator, WormBase
> www.wormbase.org
> www.geneontology.org
>
>
>
>> Subject: validating PubMed ids in the gene association files
>> Date: Mon, 15 Jun 2009 12:18:49 -0400
>>
>> Hello all,
>> In our processing of gene_association files on the ftp site for
>> Entrez
>> Gene, we periodically (and rarely) find PubMed uids that are not
>> valid.
>>
>> Is there a central location to which we can report these invalid
>> PubMed
>> uids that can be checked by each data source?
>>
>> We are hoping for one reporting site, rather than gmod-specific ones.
>>
>> Thanks for your help,
>>
>> Donna Maglott maglott at ncbi.nlm.nih.gov
>>
------------------------------------------------------------------------
------
>> National Center for Biotechnology Information
>> National Library of Medicine, NIH phone:
>> 301-435-5895
>> Building 45, Room 4As.47C
>> fax: 301-480-0109
>> Bethesda, MD 20892-6510
>>
------------------------------------------------------------------------
------
>>
>>
>>
>>
>
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
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------------------------------
Message: 5
Date: Tue, 16 Jun 2009 10:26:52 +0100
From: Valerie Wood <val at sanger.ac.uk>
Subject: Re: [Go] generic GO slim question
To: Midori Harris <midori at ebi.ac.uk>
Cc: GO mailing list <go at genome.stanford.edu>
Message-ID: <4A37655C.5070500 at sanger.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Can we have a Wiki page dedicated to GO slim and put all of these
suggestions in a list.
I will do it but I don't know the best place for it to live.
Val
Midori Harris wrote:
> On a tangentially related note, we shoud consider making the generic
> slim(s) is_a-complete. (I brought this up on the ontology editors'
> list a few month ago, but it fell off the radar.)
>
> m
>
> On Mon, 15 Jun 2009, Sue Rhee wrote:
>
>> It would also be awesome to figure out a way to eliminate 'Other XXX'
>> from the GO slim terms. I've heard many confusions and complaints
>> about these from users.
>>
>> Cheers,
>> Sue
>>
>> Judith Blake wrote:
>>
>>> Val,
>>>
>>> I agree with Jane. It would be excellent if we could provide
>>> updated slims for 'all' and then a very few subsets. The question
>>> would be...
>>>
>>> Eucaryotic/prokaryotic?
>>>
>>> Multi-cellular/single-celled?
>>>
>>> Both? One or the other?
>>>
>>>
>>>
>>> Judy
>>>
>>>
>>> On 6/15/09 11:13 AM, "Jane Lomax" <jane at ebi.ac.uk> wrote:
>>>
>>> Hi Val - I totally agree with you about the generic GO slim -
it's
>>> embarrassingly out-of-date. I think the problem is partly that
>>> no-one has
>>> committed to work on it.
>>>
>>> Do you have time in the next couple of weeks so you and I can
sit
>>> down and
>>> at least improve it a bit?
>>>
>>> I think in the long term seprate multi-cellular
>>> organism/single-celled
>>> organism etc slims are the way to go. But think there will
>>> always be a
>>> place for a generic slim too.
>>>
>>> Jane
>>>
>>>
>>> On Sun, 14 Jun 2009, Valerie Wood wrote:
>>>
>>> >
>>> > How was it decided which terms to include in the generic GO
slim?
>>> >
>>> > There have been discussions previously about what makes a
useful
>>> and relevent
>>> > generic GO slim (but no agreement). However, it seems that at
the
>>> very least
>>> > the terms should be i) general, and ii) high level terms which
>>> constitute
>>> > major cellular processes (and therefore areas of research)
>>> should be
>>> > included.
>>> >
>>> > So, I was wondering why the following terms are in the slim (I
>>> have included
>>> > the TOTAL number of annotations for all organisms in
parenthases)
>>> >
>>> > i) plastid translation [1]
>>> > ii) lead ion binding [2]
>>> > iii) cytoplasmic chromosome [28]
>>> > iv) neurotransmitter transporter [55]
>>> >
>>> > Conversely the following biologically important "general"
terms
>>> (at least
>>> > from a single celled organism perprective) , are absent from
the
>>> generic GO
>>> > slim
>>> >
>>> > i) DNA replication [1685]
>>> > ii) DNA repair [1934]
>>> > iii) transmembrane transport [814]
>>> > iv) ribosome biogenesis [1849]
>>> > v) cytokinesis [1049]
>>> > vi) cytoskeletal organization [2311]
>>> > and others.
>>> >
>>> > In addition, there is an obsolete molecular function term in
>>> the slim
>>> > (chaperone regulator activity)
>>> >
>>> > I wondered whether the contents of the slim need to be to make
it
>>> more
>>> > useful. I realise it isn't easy to make a slim which is good
>>> for all
>>> > organisms. If this is the case perhaps we should consider
>>> abandoning the
>>> > "generic generic" slim and define more useful individual
generic
>>> slims for
>>> > prokaryotes, eukaryotic unicellular, and multicellular orgs?
>>> >
>>> > We might not agree about the utility of a "generic slim" but
>>> these are used
>>> > a lot as they are the default slims used by AmiGO, and the
>>> Princeton generic
>>> > GO term mapper.......They should provide a good overview of
the
>>> known biology
>>> > of any organism. They should probably provide a starting
point
>>> for people
>>> > who wish to refine to make their own slim and include more
>>> specific terms
>>> > for their area of interest, and remove terms which are not
>>> useful. I am
>>> > trying to write a tutorial which includes how to select terms
for
>>> a slim to
>>> > give complete coverage for their organism, and refine to make
a
>>> more specific
>>> > slim, but the the generic slim doesn't seem to provide very
good
>>> example for
>>> > a starting point.
>>> >
>>> > Val
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>>
>>> --
>>> 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
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>
>>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
------------------------------
Message: 6
Date: Tue, 16 Jun 2009 10:56:33 +0100 (BST)
From: Midori Harris <midori at ebi.ac.uk>
Subject: Re: [Go] generic GO slim question
To: Valerie Wood <val at sanger.ac.uk>
Cc: GO mailing list <go at genome.stanford.edu>
Message-ID: <Pine.LNX.4.64.0906161055210.12083 at pigeon.ebi.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Here you go:
http://wiki.geneontology.org/index.php/GO_slim_overhaul
linked to main ontology development page
m
On Tue, 16 Jun 2009, Valerie Wood wrote:
> Can we have a Wiki page dedicated to GO slim and put all of these
suggestions
> in a list.
> I will do it but I don't know the best place for it to live.
> Val
>
> Midori Harris wrote:
>
>> On a tangentially related note, we shoud consider making the generic
>> slim(s) is_a-complete. (I brought this up on the ontology editors'
list a
>> few month ago, but it fell off the radar.)
>>
>> m
>>
>> On Mon, 15 Jun 2009, Sue Rhee wrote:
>>
>>> It would also be awesome to figure out a way to eliminate 'Other
XXX' from
>>> the GO slim terms. I've heard many confusions and complaints about
these
>>> from users.
>>>
>>> Cheers,
>>> Sue
>>>
>>> Judith Blake wrote:
>>>
>>>> Val,
>>>>
>>>> I agree with Jane. It would be excellent if we could provide
updated
>>>> slims for 'all' and then a very few subsets. The question would
be...
>>>>
>>>> Eucaryotic/prokaryotic?
>>>>
>>>> Multi-cellular/single-celled?
>>>>
>>>> Both? One or the other?
>>>>
>>>>
>>>>
>>>> Judy
>>>>
>>>>
>>>> On 6/15/09 11:13 AM, "Jane Lomax" <jane at ebi.ac.uk> wrote:
>>>>
>>>> Hi Val - I totally agree with you about the generic GO slim -
it's
>>>> embarrassingly out-of-date. I think the problem is partly that
>>>> no-one has
>>>> committed to work on it.
>>>>
>>>> Do you have time in the next couple of weeks so you and I can
sit
>>>> down and
>>>> at least improve it a bit?
>>>>
>>>> I think in the long term seprate multi-cellular
>>>> organism/single-celled
>>>> organism etc slims are the way to go. But think there will
always be
>>>> a
>>>> place for a generic slim too.
>>>>
>>>> Jane
>>>>
>>>>
>>>> On Sun, 14 Jun 2009, Valerie Wood wrote:
>>>>
>>>> >
>>>> > How was it decided which terms to include in the generic GO
slim?
>>>> >
>>>> > There have been discussions previously about what makes a
useful
>>>> and relevent
>>>> > generic GO slim (but no agreement). However, it seems that at
the
>>>> very least
>>>> > the terms should be i) general, and ii) high level terms
which
>>>> constitute
>>>> > major cellular processes (and therefore areas of research)
should
>>>> be
>>>> > included.
>>>> >
>>>> > So, I was wondering why the following terms are in the slim
(I
>>>> have included
>>>> > the TOTAL number of annotations for all organisms in
parenthases)
>>>> >
>>>> > i) plastid translation [1]
>>>> > ii) lead ion binding [2]
>>>> > iii) cytoplasmic chromosome [28]
>>>> > iv) neurotransmitter transporter [55]
>>>> >
>>>> > Conversely the following biologically important "general"
terms
>>>> (at least
>>>> > from a single celled organism perprective) , are absent from
the
>>>> generic GO
>>>> > slim
>>>> >
>>>> > i) DNA replication [1685]
>>>> > ii) DNA repair [1934]
>>>> > iii) transmembrane transport [814]
>>>> > iv) ribosome biogenesis [1849]
>>>> > v) cytokinesis [1049]
>>>> > vi) cytoskeletal organization [2311]
>>>> > and others.
>>>> >
>>>> > In addition, there is an obsolete molecular function term in
the
>>>> slim
>>>> > (chaperone regulator activity)
>>>> >
>>>> > I wondered whether the contents of the slim need to be to
make it
>>>> more
>>>> > useful. I realise it isn't easy to make a slim which is good
for
>>>> all
>>>> > organisms. If this is the case perhaps we should consider
>>>> abandoning the
>>>> > "generic generic" slim and define more useful individual
generic
>>>> slims for
>>>> > prokaryotes, eukaryotic unicellular, and multicellular orgs?
>>>> >
>>>> > We might not agree about the utility of a "generic slim" but
>>>> these are used
>>>> > a lot as they are the default slims used by AmiGO, and the
>>>> Princeton generic
>>>> > GO term mapper.......They should provide a good overview of
the
>>>> known biology
>>>> > of any organism. They should probably provide a starting
point
>>>> for people
>>>> > who wish to refine to make their own slim and include more
>>>> specific terms
>>>> > for their area of interest, and remove terms which are not
>>>> useful. I am
>>>> > trying to write a tutorial which includes how to select terms
for
>>>> a slim to
>>>> > give complete coverage for their organism, and refine to make
a
>>>> more specific
>>>> > slim, but the the generic slim doesn't seem to provide very
good
>>>> example for
>>>> > a starting point.
>>>> >
>>>> > Val
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>>
>>>> --
>>>> 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
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>
------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>
>>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>
>
>
>
------------------------------
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Go mailing list
Go at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/go
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