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From: Don G. <gil...@bi...> - 2005-03-03 19:38:21
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Dear MOD folks, Do you think we should arrange to have a common URL to locate genome data? The value to this is making it easier for anyone looking for dna, protein, feature data for a given genome (or all of them). Common urls would be something like this: my.org/genome?species=x [&version=y] == dna fasta my.org/proteome?species=x ... == protein fasta my.org/transcriptome? ... == transcript fasta and I guess add gff or include it as option above ? my.org/genomefeatures?... I would vote for keeping the above options fairly simple, not necessarily comprehensive for all possible data choices. Also I'd suggest a common URL for information (e.g. a web page that lists the particulars for a MOD). my.org/genomes/help or equivalent One can think of variants on the above: my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ... The main thing is some agreement and folks who will implement this. = Don Gilbert From: Kara Dolinski <ka...@ge...> | Thanks for the info, and thanks for the reminder about Lincoln's idea; | I had totally forgotten about it! I think it's a great idea--it'd be | fabulous to have a standard URL to get these common files that we all | provide. No matter how hard we all try, it is still pretty darn hard | to make it easy for people to navigate our ftp sites. A | standard/common URL to get at least the basic files would do wonders. | I think beginning with DNA and protein fasta files for all ORFs + a gff | file would be a great start. | | Should we send a message to a gmod list and see if we can decide on the | URL, then work on implementation? Should be pretty straightforward to | do, I think.... | | -Kara On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote: > > Kara, > > Find drosophila genome data including gff at > http://flybase.net/annot/#Data > the gff section (for each of two species). > > Lincoln Stein thought we (mods) should all be serving bulk genome data > sets thru > a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx, > yeastgenome.org/genome/...). > I don't recall what the specific url was, but if we all used the same > one, it would > make it easier to find these things. > > Ah, notes help - October GMOD meeting - you were there also? > sample standard urls something like this: > my.org/genome?species=x [&version=y] == dna fasta > my.org/proteome?species=x ... == protein fasta > my.org/transcriptome? ... == transcript fasta > > and I guess add gff or include it as option above ? > my.org/genomefeatures?... > > I'm not sure what options we would be expected to all support. |
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From: Aaron J. M. <am...@pc...> - 2005-03-04 00:12:20
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FYI, if/when a consensus is reached, the ApiDB databases (PlasmoDB, ToxoDB, CryptoDB, etc.) will follow suit. I'd be happy with the virtual path based solution, and even happier if it was extended to include the possibility for different formats: my.org/genome # dna fasta, current version my.org/genome/v4.4 # dna fasta, version 4.4 my.org/proteome/v4.3 # protein fasta, version 4.3 my.org/proteome/v4.3/gff # GFF of protein-encoding (CDS) features my.org/proteome/gff/v4.3 # same, order shouldn't matter my.org/v4.3/gff/proteome # same, ditto I'd argue that "v4.3" and such strings be very "weakly typed", i.e. they're just tags that represent different instances of the dataset. This way I can also get: my.org/proteome/gff/glimmerM/v4.3 my.org/proteome/gff/twinscan/v4.4 While this last bit looks hard, it actually isn't with the right Apache configuration ... but maybe this is overkill? And it leaves open the problem of how would one find out what possible datasets/tags/formats are available (besides a separate download index HTML page) ... should my.org/proteome/list provide a flat list of available URLs? -Aaron Don Gilbert wrote: > Dear MOD folks, > > Do you think we should arrange to have a common URL to locate genome > data? The value to this is making it easier for anyone looking for > dna, protein, feature data for a given genome (or all of them). > > Common urls would be something like this: > my.org/genome?species=x [&version=y] == dna fasta > my.org/proteome?species=x ... == protein fasta > my.org/transcriptome? ... == transcript fasta > > and I guess add gff or include it as option above ? > my.org/genomefeatures?... > > I would vote for keeping the above options fairly simple, not > necessarily comprehensive for all possible data choices. > Also I'd suggest a common URL for information (e.g. a web page > that lists the particulars for a MOD). > my.org/genomes/help or equivalent > > One can think of variants on the above: > my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ... > The main thing is some agreement and folks who will > implement this. > > = Don Gilbert > > From: Kara Dolinski <ka...@ge...> > | Thanks for the info, and thanks for the reminder about Lincoln's idea; > | I had totally forgotten about it! I think it's a great idea--it'd be > | fabulous to have a standard URL to get these common files that we all > | provide. No matter how hard we all try, it is still pretty darn hard > | to make it easy for people to navigate our ftp sites. A > | standard/common URL to get at least the basic files would do wonders. > | I think beginning with DNA and protein fasta files for all ORFs + a gff > | file would be a great start. > | > | Should we send a message to a gmod list and see if we can decide on the > | URL, then work on implementation? Should be pretty straightforward to > | do, I think.... > | > | -Kara > > On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote: > > >>Kara, >> >>Find drosophila genome data including gff at >>http://flybase.net/annot/#Data >>the gff section (for each of two species). >> >>Lincoln Stein thought we (mods) should all be serving bulk genome data >>sets thru >>a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx, >>yeastgenome.org/genome/...). >>I don't recall what the specific url was, but if we all used the same >>one, it would >>make it easier to find these things. >> >>Ah, notes help - October GMOD meeting - you were there also? >> sample standard urls something like this: >> my.org/genome?species=x [&version=y] == dna fasta >> my.org/proteome?species=x ... == protein fasta >> my.org/transcriptome? ... == transcript fasta >> >>and I guess add gff or include it as option above ? >> my.org/genomefeatures?... >> >>I'm not sure what options we would be expected to all support. > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel |
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From: Todd H. <ha...@cs...> - 2005-03-04 13:58:24
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Hi Don -
I definitely think the MODs should implement this as discussed at the last
meeting. Currently, WormBase uses an Apache handler to map URLs to files --
or if need be, database dump scripts.
Currently, we have
/genome
/proteome
/transcriptome
/laboratories // a list of labs and IDs, admittedly worm specific
When appropriate, URLs also accept a "species=" parameter.
I'd also like to suggest two additional URLs:
/version // The current version or release of the MOD
/defaults // A key=value listing of appropriate defaults for the MOD
These last two options are used by my Bio::GMOD module which aims to provide
a unified perl API to the MODs. (I haven't officially announced the module
yet while I polish some details and add some documentation).
Todd
> On 3/3/05 12:38 PM, Don Gilbert wrote:
>
> Dear MOD folks,
>
> Do you think we should arrange to have a common URL to locate genome
> data? The value to this is making it easier for anyone looking for
> dna, protein, feature data for a given genome (or all of them).
>
> Common urls would be something like this:
> my.org/genome?species=x [&version=y] == dna fasta
> my.org/proteome?species=x ... == protein fasta
> my.org/transcriptome? ... == transcript fasta
>
> and I guess add gff or include it as option above ?
> my.org/genomefeatures?...
>
> I would vote for keeping the above options fairly simple, not
> necessarily comprehensive for all possible data choices.
> Also I'd suggest a common URL for information (e.g. a web page
> that lists the particulars for a MOD).
> my.org/genomes/help or equivalent
>
> One can think of variants on the above:
> my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ...
> The main thing is some agreement and folks who will
> implement this.
>
> = Don Gilbert
>
> From: Kara Dolinski <ka...@ge...>
> | Thanks for the info, and thanks for the reminder about Lincoln's idea;
> | I had totally forgotten about it! I think it's a great idea--it'd be
> | fabulous to have a standard URL to get these common files that we all
> | provide. No matter how hard we all try, it is still pretty darn hard
> | to make it easy for people to navigate our ftp sites. A
> | standard/common URL to get at least the basic files would do wonders.
> | I think beginning with DNA and protein fasta files for all ORFs + a gff
> | file would be a great start.
> |
> | Should we send a message to a gmod list and see if we can decide on the
> | URL, then work on implementation? Should be pretty straightforward to
> | do, I think....
> |
> | -Kara
>
> On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote:
>
>>
>> Kara,
>>
>> Find drosophila genome data including gff at
>> http://flybase.net/annot/#Data
>> the gff section (for each of two species).
>>
>> Lincoln Stein thought we (mods) should all be serving bulk genome data
>> sets thru
>> a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx,
>> yeastgenome.org/genome/...).
>> I don't recall what the specific url was, but if we all used the same
>> one, it would
>> make it easier to find these things.
>>
>> Ah, notes help - October GMOD meeting - you were there also?
>> sample standard urls something like this:
>> my.org/genome?species=x [&version=y] == dna fasta
>> my.org/proteome?species=x ... == protein fasta
>> my.org/transcriptome? ... == transcript fasta
>>
>> and I guess add gff or include it as option above ?
>> my.org/genomefeatures?...
>>
>> I'm not sure what options we would be expected to all support.
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
|
|
From: Todd H. <ha...@cs...> - 2005-03-04 14:36:49
|
Hi Don -
I definitely think the MODs should implement this as discussed at the last
meeting. Currently, WormBase uses an Apache handler to map URLs to files --
or if need be, database dump scripts.
Currently, we have
/genome
/proteome
/transcriptome
/laboratories // a list of labs and IDs, admittedly worm specific
When appropriate, URLs also accept a "species=" parameter.
I'd also like to suggest two additional URLs:
/version // The current version or release of the MOD
/defaults // A key=value listing of appropriate defaults for the MOD
These last two options are used by my Bio::GMOD module which aims to provide
a unified perl API to the MODs. (I haven't officially announced the module
yet while I polish some details and add some documentation).
Todd
> On 3/3/05 12:38 PM, Don Gilbert wrote:
>
> Dear MOD folks,
>
> Do you think we should arrange to have a common URL to locate genome
> data? The value to this is making it easier for anyone looking for
> dna, protein, feature data for a given genome (or all of them).
>
> Common urls would be something like this:
> my.org/genome?species=x [&version=y] == dna fasta
> my.org/proteome?species=x ... == protein fasta
> my.org/transcriptome? ... == transcript fasta
>
> and I guess add gff or include it as option above ?
> my.org/genomefeatures?...
>
> I would vote for keeping the above options fairly simple, not
> necessarily comprehensive for all possible data choices.
> Also I'd suggest a common URL for information (e.g. a web page
> that lists the particulars for a MOD).
> my.org/genomes/help or equivalent
>
> One can think of variants on the above:
> my.org/genomes/dna, genome/proteins, genome/gff, genomes/help, ...
> The main thing is some agreement and folks who will
> implement this.
>
> = Don Gilbert
>
> From: Kara Dolinski <ka...@ge...>
> | Thanks for the info, and thanks for the reminder about Lincoln's idea;
> | I had totally forgotten about it! I think it's a great idea--it'd be
> | fabulous to have a standard URL to get these common files that we all
> | provide. No matter how hard we all try, it is still pretty darn hard
> | to make it easy for people to navigate our ftp sites. A
> | standard/common URL to get at least the basic files would do wonders.
> | I think beginning with DNA and protein fasta files for all ORFs + a gff
> | file would be a great start.
> |
> | Should we send a message to a gmod list and see if we can decide on the
> | URL, then work on implementation? Should be pretty straightforward to
> | do, I think....
> |
> | -Kara
>
> On Mar 2, 2005, at 5:29 PM, Don Gilbert wrote:
>
>>
>> Kara,
>>
>> Find drosophila genome data including gff at
>> http://flybase.net/annot/#Data
>> the gff section (for each of two species).
>>
>> Lincoln Stein thought we (mods) should all be serving bulk genome data
>> sets thru
>> a common url (that is wormbase.org/genome/xxx, flybase.net/genome/xxx,
>> yeastgenome.org/genome/...).
>> I don't recall what the specific url was, but if we all used the same
>> one, it would
>> make it easier to find these things.
>>
>> Ah, notes help - October GMOD meeting - you were there also?
>> sample standard urls something like this:
>> my.org/genome?species=x [&version=y] == dna fasta
>> my.org/proteome?species=x ... == protein fasta
>> my.org/transcriptome? ... == transcript fasta
>>
>> and I guess add gff or include it as option above ?
>> my.org/genomefeatures?...
>>
>> I'm not sure what options we would be expected to all support.
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
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