loading data into chado problem!

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loading data into chado problem!

zhenyang guo
hi,everybody,here is a problem from a novice.

i am using the populated scripts from gmod to load the GFF file into chado .
warning comes out like 
 "
 DBD::Pg::db commit failed: ERROR:  insert or update on table "feature_relationship" violates foreign key constraint "feature_relationship_subject_id_fkey"
DETAIL:  Key (subject_id)=(3100) is not present in table "feature". at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh> line 6.

 "
since i am using gmod1.1, and bioperl has been updated to latest version.
I don't where the problem lies.

Also , I have several GFF files from similar species genbank files. but some can be loaded into chado ,while others cannot.

During the process of loading ,warning are like this:

"  There is a CDS feature with no parent (ID:polyprotein)  I think that is wrong!


There is a five_prime_UTR feature with no parent (ID:GenBank:five_prime_UTR:AY831695:1:169)  I think that is wrong!

this shouldn't happen in modified_uniquename at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2994
    Bio::GMOD::DB::Adapter::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)', 'orig_id', undef, 'organism_id', 25) called at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3953
    Bio::GMOD::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)', 'Bio::SeqFeature::Annotated=HASH(0xa22fec0)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 810


There is a five_prime_UTR feature with no parent (ID:GenBank:five_prime_UTR:AY831694:1:169)  I think that is wrong!

"
and so on,repeated warning.

i envelop  three GFF files ,in case you don't get what i mean.
thanks very much.


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Re: loading data into chado problem!

Scott Cain
Hi Zhenyang,

I see that you haven't fixed the multiple occurrences of
"ID=polyprotein".  Loading isn't going to work until that is fixed.
Converting GenBank entries to GFF3 frequently is not perfect, and this
appears to be one of those cases.  Other items:

* the warnings that say "I think that is wrong" are just warnings: the
data will still load as is (assuming nothing else is wrong).

* You probably need the --noexon flag if you aren't already using it.

Scott



On Thu, Jun 3, 2010 at 12:11 AM, zhenyang guo <[hidden email]> wrote:

> hi,everybody,here is a problem from a novice.
>
> i am using the populated scripts from gmod to load the GFF file into chado .
> warning comes out like
>  "
>  DBD::Pg::db commit failed: ERROR:  insert or update on table
> "feature_relationship" violates foreign key constraint
> "feature_relationship_subject_id_fkey"
> DETAIL:  Key (subject_id)=(3100) is not present in table "feature". at
> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh> line 6.
>
>  "
> since i am using gmod1.1, and bioperl has been updated to latest version.
> I don't where the problem lies.
>
> Also , I have several GFF files from similar species genbank files. but some
> can be loaded into chado ,while others cannot.
>
> During the process of loading ,warning are like this:
>
> "  There is a CDS feature with no parent (ID:polyprotein)  I think that is
> wrong!
>
>
> There is a five_prime_UTR feature with no parent
> (ID:GenBank:five_prime_UTR:AY831695:1:169)  I think that is wrong!
>
> this shouldn't happen in modified_uniquename at
> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2994
>
> Bio::GMOD::DB::Adapter::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
> 'orig_id', undef, 'organism_id', 25) called at
> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3953
>
> Bio::GMOD::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
> 'Bio::SeqFeature::Annotated=HASH(0xa22fec0)') called at
> /usr/local/bin/gmod_bulk_load_gff3.pl line 810
>
>
> There is a five_prime_UTR feature with no parent
> (ID:GenBank:five_prime_UTR:AY831694:1:169)  I think that is wrong!
>
> "
> and so on,repeated warning.
>
> i envelop  three GFF files ,in case you don't get what i mean.
> thanks very much.
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-schema mailing list
[hidden email]
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Re: loading data into chado problem!

Scott Cain
Hi Zhenyang,

Please keep responses on the mailing list so they can be archived.

You are correct that the genbank to gff script will only work on a
single genbank entry at a time.  I will fix the documentation to
reflect that fact (nobody has pointed out this flaw before).

I'm glad you got it working.

Scott


On Thu, Jun 3, 2010 at 10:00 AM, zhenyang guo <[hidden email]> wrote:

> thanks ,Scott, actually I tried  --noexon  before . Since the sequences  i
> am trying to load are of single-stranded (+)RNA virus , I don't think that
> helps .
> Anyway ,i have a solution now ,with two other scripts combining some
> commands .with these ,genbank file are splited  into single record ,which is
> transformed to GFF afterward .
>
> The following is about the solution webpage "
> http://159.226.126.177/mediawiki/index.php/Load_Multi-entry_GenBank_flatfile_into_Chado_database"
> .
> I can sent you the two scripts ,if you need that.
>
>
> 2010/6/3 Scott Cain <[hidden email]>
>>
>> Hi Zhenyang,
>>
>> I see that you haven't fixed the multiple occurrences of
>> "ID=polyprotein".  Loading isn't going to work until that is fixed.
>> Converting GenBank entries to GFF3 frequently is not perfect, and this
>> appears to be one of those cases.  Other items:
>>
>> * the warnings that say "I think that is wrong" are just warnings: the
>> data will still load as is (assuming nothing else is wrong).
>>
>> * You probably need the --noexon flag if you aren't already using it.
>>
>> Scott
>>
>>
>>
>> On Thu, Jun 3, 2010 at 12:11 AM, zhenyang guo <[hidden email]>
>> wrote:
>> > hi,everybody,here is a problem from a novice.
>> >
>> > i am using the populated scripts from gmod to load the GFF file into
>> > chado .
>> > warning comes out like
>> >  "
>> >  DBD::Pg::db commit failed: ERROR:  insert or update on table
>> > "feature_relationship" violates foreign key constraint
>> > "feature_relationship_subject_id_fkey"
>> > DETAIL:  Key (subject_id)=(3100) is not present in table "feature". at
>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
>> > line 6.
>> >
>> >  "
>> > since i am using gmod1.1, and bioperl has been updated to latest
>> > version.
>> > I don't where the problem lies.
>> >
>> > Also , I have several GFF files from similar species genbank files. but
>> > some
>> > can be loaded into chado ,while others cannot.
>> >
>> > During the process of loading ,warning are like this:
>> >
>> > "  There is a CDS feature with no parent (ID:polyprotein)  I think that
>> > is
>> > wrong!
>> >
>> >
>> > There is a five_prime_UTR feature with no parent
>> > (ID:GenBank:five_prime_UTR:AY831695:1:169)  I think that is wrong!
>> >
>> > this shouldn't happen in modified_uniquename at
>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2994
>> >
>> >
>> > Bio::GMOD::DB::Adapter::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
>> > 'orig_id', undef, 'organism_id', 25) called at
>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3953
>> >
>> >
>> > Bio::GMOD::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
>> > 'Bio::SeqFeature::Annotated=HASH(0xa22fec0)') called at
>> > /usr/local/bin/gmod_bulk_load_gff3.pl line 810
>> >
>> >
>> > There is a five_prime_UTR feature with no parent
>> > (ID:GenBank:five_prime_UTR:AY831694:1:169)  I think that is wrong!
>> >
>> > "
>> > and so on,repeated warning.
>> >
>> > i envelop  three GFF files ,in case you don't get what i mean.
>> > thanks very much.
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> > lucky parental unit.  See the prize list and enter to win:
>> > http://p.sf.net/sfu/thinkgeek-promo
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Re: loading data into chado problem!

Scott Cain
Hi Zhenyang,

When I wrote before that the genbank to gff3 script won't work on
multiple entry genbank files, that was incorrect: it will.  The
limitation is the assumption that they are from the same organism,
because, as you noted, the organism information for subsequent entries
will be incorrect.  The script also make the assumption that the
genbank entries will be "well annotated" like a refseq entry.

Basically, it boils down to the fact that it is hard to do genbank to
gff3 conversion, and the result frequently requires some modification.

Scott


On Thu, Jun 3, 2010 at 10:07 AM, Scott Cain <[hidden email]> wrote:

> Hi Zhenyang,
>
> Please keep responses on the mailing list so they can be archived.
>
> You are correct that the genbank to gff script will only work on a
> single genbank entry at a time.  I will fix the documentation to
> reflect that fact (nobody has pointed out this flaw before).
>
> I'm glad you got it working.
>
> Scott
>
>
> On Thu, Jun 3, 2010 at 10:00 AM, zhenyang guo <[hidden email]> wrote:
>> thanks ,Scott, actually I tried  --noexon  before . Since the sequences  i
>> am trying to load are of single-stranded (+)RNA virus , I don't think that
>> helps .
>> Anyway ,i have a solution now ,with two other scripts combining some
>> commands .with these ,genbank file are splited  into single record ,which is
>> transformed to GFF afterward .
>>
>> The following is about the solution webpage "
>> http://159.226.126.177/mediawiki/index.php/Load_Multi-entry_GenBank_flatfile_into_Chado_database"
>> .
>> I can sent you the two scripts ,if you need that.
>>
>>
>> 2010/6/3 Scott Cain <[hidden email]>
>>>
>>> Hi Zhenyang,
>>>
>>> I see that you haven't fixed the multiple occurrences of
>>> "ID=polyprotein".  Loading isn't going to work until that is fixed.
>>> Converting GenBank entries to GFF3 frequently is not perfect, and this
>>> appears to be one of those cases.  Other items:
>>>
>>> * the warnings that say "I think that is wrong" are just warnings: the
>>> data will still load as is (assuming nothing else is wrong).
>>>
>>> * You probably need the --noexon flag if you aren't already using it.
>>>
>>> Scott
>>>
>>>
>>>
>>> On Thu, Jun 3, 2010 at 12:11 AM, zhenyang guo <[hidden email]>
>>> wrote:
>>> > hi,everybody,here is a problem from a novice.
>>> >
>>> > i am using the populated scripts from gmod to load the GFF file into
>>> > chado .
>>> > warning comes out like
>>> >  "
>>> >  DBD::Pg::db commit failed: ERROR:  insert or update on table
>>> > "feature_relationship" violates foreign key constraint
>>> > "feature_relationship_subject_id_fkey"
>>> > DETAIL:  Key (subject_id)=(3100) is not present in table "feature". at
>>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
>>> > line 6.
>>> >
>>> >  "
>>> > since i am using gmod1.1, and bioperl has been updated to latest
>>> > version.
>>> > I don't where the problem lies.
>>> >
>>> > Also , I have several GFF files from similar species genbank files. but
>>> > some
>>> > can be loaded into chado ,while others cannot.
>>> >
>>> > During the process of loading ,warning are like this:
>>> >
>>> > "  There is a CDS feature with no parent (ID:polyprotein)  I think that
>>> > is
>>> > wrong!
>>> >
>>> >
>>> > There is a five_prime_UTR feature with no parent
>>> > (ID:GenBank:five_prime_UTR:AY831695:1:169)  I think that is wrong!
>>> >
>>> > this shouldn't happen in modified_uniquename at
>>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2994
>>> >
>>> >
>>> > Bio::GMOD::DB::Adapter::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
>>> > 'orig_id', undef, 'organism_id', 25) called at
>>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3953
>>> >
>>> >
>>> > Bio::GMOD::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
>>> > 'Bio::SeqFeature::Annotated=HASH(0xa22fec0)') called at
>>> > /usr/local/bin/gmod_bulk_load_gff3.pl line 810
>>> >
>>> >
>>> > There is a five_prime_UTR feature with no parent
>>> > (ID:GenBank:five_prime_UTR:AY831694:1:169)  I think that is wrong!
>>> >
>>> > "
>>> > and so on,repeated warning.
>>> >
>>> > i envelop  three GFF files ,in case you don't get what i mean.
>>> > thanks very much.
>>> >
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
>>> > ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> > lucky parental unit.  See the prize list and enter to win:
>>> > http://p.sf.net/sfu/thinkgeek-promo
>>> > _______________________________________________
>>> > Gmod-schema mailing list
>>> > [hidden email]
>>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Re: loading data into chado problem!

zhenyang guo
yeah, you are right ,Scott .
Things always come out ,then we can do better.
It indeed can be attributed to imperfect genbank annotation  partly. Importantly ,things must be taken into consideration from many aspects.  I think it will grow more and more good with further modification ,most of which are of your industrious works.

2010/6/3 Scott Cain <[hidden email]>
Hi Zhenyang,

When I wrote before that the genbank to gff3 script won't work on
multiple entry genbank files, that was incorrect: it will.  The
limitation is the assumption that they are from the same organism,
because, as you noted, the organism information for subsequent entries
will be incorrect.  The script also make the assumption that the
genbank entries will be "well annotated" like a refseq entry.

Basically, it boils down to the fact that it is hard to do genbank to
gff3 conversion, and the result frequently requires some modification.

Scott


On Thu, Jun 3, 2010 at 10:07 AM, Scott Cain <[hidden email]> wrote:
> Hi Zhenyang,
>
> Please keep responses on the mailing list so they can be archived.
>
> You are correct that the genbank to gff script will only work on a
> single genbank entry at a time.  I will fix the documentation to
> reflect that fact (nobody has pointed out this flaw before).
>
> I'm glad you got it working.
>
> Scott
>
>
> On Thu, Jun 3, 2010 at 10:00 AM, zhenyang guo <[hidden email]> wrote:
>> thanks ,Scott, actually I tried  --noexon  before . Since the sequences  i
>> am trying to load are of single-stranded (+)RNA virus , I don't think that
>> helps .
>> Anyway ,i have a solution now ,with two other scripts combining some
>> commands .with these ,genbank file are splited  into single record ,which is
>> transformed to GFF afterward .
>>
>> The following is about the solution webpage "
>> http://159.226.126.177/mediawiki/index.php/Load_Multi-entry_GenBank_flatfile_into_Chado_database"
>> .
>> I can sent you the two scripts ,if you need that.
>>
>>
>> 2010/6/3 Scott Cain <[hidden email]>
>>>
>>> Hi Zhenyang,
>>>
>>> I see that you haven't fixed the multiple occurrences of
>>> "ID=polyprotein".  Loading isn't going to work until that is fixed.
>>> Converting GenBank entries to GFF3 frequently is not perfect, and this
>>> appears to be one of those cases.  Other items:
>>>
>>> * the warnings that say "I think that is wrong" are just warnings: the
>>> data will still load as is (assuming nothing else is wrong).
>>>
>>> * You probably need the --noexon flag if you aren't already using it.
>>>
>>> Scott
>>>
>>>
>>>
>>> On Thu, Jun 3, 2010 at 12:11 AM, zhenyang guo <[hidden email]>
>>> wrote:
>>> > hi,everybody,here is a problem from a novice.
>>> >
>>> > i am using the populated scripts from gmod to load the GFF file into
>>> > chado .
>>> > warning comes out like
>>> >  "
>>> >  DBD::Pg::db commit failed: ERROR:  insert or update on table
>>> > "feature_relationship" violates foreign key constraint
>>> > "feature_relationship_subject_id_fkey"
>>> > DETAIL:  Key (subject_id)=(3100) is not present in table "feature". at
>>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
>>> > line 6.
>>> >
>>> >  "
>>> > since i am using gmod1.1, and bioperl has been updated to latest
>>> > version.
>>> > I don't where the problem lies.
>>> >
>>> > Also , I have several GFF files from similar species genbank files. but
>>> > some
>>> > can be loaded into chado ,while others cannot.
>>> >
>>> > During the process of loading ,warning are like this:
>>> >
>>> > "  There is a CDS feature with no parent (ID:polyprotein)  I think that
>>> > is
>>> > wrong!
>>> >
>>> >
>>> > There is a five_prime_UTR feature with no parent
>>> > (ID:GenBank:five_prime_UTR:AY831695:1:169)  I think that is wrong!
>>> >
>>> > this shouldn't happen in modified_uniquename at
>>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2994
>>> >
>>> >
>>> > Bio::GMOD::DB::Adapter::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
>>> > 'orig_id', undef, 'organism_id', 25) called at
>>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3953
>>> >
>>> >
>>> > Bio::GMOD::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9fb18c8)',
>>> > 'Bio::SeqFeature::Annotated=HASH(0xa22fec0)') called at
>>> > /usr/local/bin/gmod_bulk_load_gff3.pl line 810
>>> >
>>> >
>>> > There is a five_prime_UTR feature with no parent
>>> > (ID:GenBank:five_prime_UTR:AY831694:1:169)  I think that is wrong!
>>> >
>>> > "
>>> > and so on,repeated warning.
>>> >
>>> > i envelop  three GFF files ,in case you don't get what i mean.
>>> > thanks very much.
>>> >
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
>>> > ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> > lucky parental unit.  See the prize list and enter to win:
>>> > http://p.sf.net/sfu/thinkgeek-promo
>>> > _______________________________________________
>>> > Gmod-schema mailing list
>>> > [hidden email]
>>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema