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* large xml database
@ 2010-10-30 21:49 Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-30 22:06 ` Re: large xml database Andreas Joseph Krogh <andreak@officenet.no>
2010-10-31 00:26 ` Re: large xml database James Cloos <cloos@jhcloos.com>
2010-10-31 06:08 ` Re: large xml database Lutz Steinborn <l.steinborn@4c-ag.de>
0 siblings, 3 replies; 12+ messages in thread
From: Viktor Bojović @ 2010-10-30 21:49 UTC (permalink / raw)
To: pgsql-sql
Hi,
i have very big XML documment which is larger than 50GB and want to import
it into databse, and transform it to relational schema.
When splitting this documment to smaller independent xml documments i get
~11.1mil XML documents.
I have spent lots of time trying to get fastest way to transform all this
data but every time i give up because it takes too much time. Sometimes more
than month it would take if not stopped.
I have tried to insert each line as varchar into database and parse it using
plperl regex..
also i have tried to store every documment as XML and parse it, but it is
also to slow.
i have tried to store every documment as varchar but it is also slow when
using regex to get data.
many tries have failed because 8GB of ram and 10gb of swap were not enough.
also sometimes i get that more than 2^32 operations were performed, and
functions stopped to work.
i wanted just to ask if someone knows how to speed this up.
thanx in advance
--
---------------------------------------
Viktor Bojović
---------------------------------------
Wherever I go, Murphy goes with me
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
@ 2010-10-30 22:06 ` Andreas Joseph Krogh <andreak@officenet.no>
2010-10-30 22:42 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
2 siblings, 1 reply; 12+ messages in thread
From: Andreas Joseph Krogh @ 2010-10-30 22:06 UTC (permalink / raw)
To: pgsql-sql
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
On 10/30/2010 11:49 PM, Viktor Bojović wrote:
> Hi,
> i have very big XML documment which is larger than 50GB and want to import
> it into databse, and transform it to relational schema.
> When splitting this documment to smaller independent xml documments i get
> ~11.1mil XML documents.
> I have spent lots of time trying to get fastest way to transform all this
> data but every time i give up because it takes too much time. Sometimes more
> than month it would take if not stopped.
> I have tried to insert each line as varchar into database and parse it using
> plperl regex..
> also i have tried to store every documment as XML and parse it, but it is
> also to slow.
> i have tried to store every documment as varchar but it is also slow when
> using regex to get data.
>
> many tries have failed because 8GB of ram and 10gb of swap were not enough.
> also sometimes i get that more than 2^32 operations were performed, and
> functions stopped to work.
>
> i wanted just to ask if someone knows how to speed this up.
>
> thanx in advance
Use a SAX-parser and handle the endElement(String name) events to insert
the element's content into your db.
- --
Andreas Joseph Krogh <andreak@officenet.no>
Senior Software Developer / CTO
Public key: http://home.officenet.no/~andreak/public_key.asc
- ------------------------+---------------------------------------------+
OfficeNet AS | The most difficult thing in the world is to |
Rosenholmveien 25 | know how to do a thing and to watch |
1414 Trollåsen | somebody else doing it wrong, without |
NORWAY | comment. |
| |
Tlf: +47 24 15 38 90 | |
Fax: +47 24 15 38 91 | |
Mobile: +47 909 56 963 | |
- ------------------------+---------------------------------------------+
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^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-30 22:06 ` Re: large xml database Andreas Joseph Krogh <andreak@officenet.no>
@ 2010-10-30 22:42 ` Rob Sargent <robjsargent@gmail.com>
0 siblings, 0 replies; 12+ messages in thread
From: Rob Sargent @ 2010-10-30 22:42 UTC (permalink / raw)
To: Andreas Joseph Krogh <andreak@officenet.no>; +Cc: pgsql-sql
Andreas Joseph Krogh wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA256
>
> On 10/30/2010 11:49 PM, Viktor Bojović wrote:
>
>> Hi,
>> i have very big XML documment which is larger than 50GB and want to import
>> it into databse, and transform it to relational schema.
>> When splitting this documment to smaller independent xml documments i get
>> ~11.1mil XML documents.
>> I have spent lots of time trying to get fastest way to transform all this
>> data but every time i give up because it takes too much time. Sometimes more
>> than month it would take if not stopped.
>> I have tried to insert each line as varchar into database and parse it using
>> plperl regex..
>> also i have tried to store every documment as XML and parse it, but it is
>> also to slow.
>> i have tried to store every documment as varchar but it is also slow when
>> using regex to get data.
>>
>> many tries have failed because 8GB of ram and 10gb of swap were not enough.
>> also sometimes i get that more than 2^32 operations were performed, and
>> functions stopped to work.
>>
>> i wanted just to ask if someone knows how to speed this up.
>>
>> thanx in advance
>>
>
> Use a SAX-parser and handle the endElement(String name) events to insert
> the element's content into your db.
>
>
If you still have the 11 million subfiles, I would start there, sax
parse as above and maybe make make csv files, then load those with bulk
as begin/end transaction on each data item discovered will hurt.
Can the subfiles be segregated into specific data types, or at least
holder of specific data types such that they releate to a specific
subset of your new db/schema? This will play into what get's loaded
first and who depends on whom w.r.t. foreign keys etc.
You can parallelize marginally with multiple threads (hoping to split
file read from sax paring from element construction from save/network)
but more boxes would be the way to go. Partitioning remains a problem.
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
@ 2010-10-31 00:26 ` James Cloos <cloos@jhcloos.com>
2010-10-31 19:53 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2 siblings, 1 reply; 12+ messages in thread
From: James Cloos @ 2010-10-31 00:26 UTC (permalink / raw)
To: Viktor Bojović <viktor.bojovic@gmail.com>; +Cc: pgsql-sql
>>>>> "VB" == Viktor Bojović <viktor.bojovic@gmail.com> writes:
VB> i have very big XML documment which is larger than 50GB and want to
VB> import it into databse, and transform it to relational schema.
Were I doing such a conversion, I'd use perl to convert the xml into
something which COPY can grok. Any other language, script or compiled,
would work just as well. The goal is to avoid having to slurp the whole
xml structure into memory.
-JimC
--
James Cloos <cloos@jhcloos.com> OpenPGP: 1024D/ED7DAEA6
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 00:26 ` Re: large xml database James Cloos <cloos@jhcloos.com>
@ 2010-10-31 19:53 ` Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 20:42 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
0 siblings, 1 reply; 12+ messages in thread
From: Viktor Bojović @ 2010-10-31 19:53 UTC (permalink / raw)
To: James Cloos <cloos@jhcloos.com>; +Cc: pgsql-sql
On Sun, Oct 31, 2010 at 2:26 AM, James Cloos <cloos@jhcloos.com> wrote:
> >>>>> "VB" == Viktor Bojović <viktor.bojovic@gmail.com> writes:
>
> VB> i have very big XML documment which is larger than 50GB and want to
> VB> import it into databse, and transform it to relational schema.
>
> Were I doing such a conversion, I'd use perl to convert the xml into
> something which COPY can grok. Any other language, script or compiled,
> would work just as well. The goal is to avoid having to slurp the whole
> xml structure into memory.
>
> -JimC
> --
> James Cloos <cloos@jhcloos.com> OpenPGP: 1024D/ED7DAEA6
>
The insertion into dabase is not very big problem.
I insert it as XML docs, or as varchar lines or as XML docs in varchar
format. Usually i use transaction and commit after block of 1000 inserts and
it goes very fast. so insertion is over after few hours.
But the problem occurs when i want to transform it inside database from
XML(varchar or XML format) into tables by parsing.
That processing takes too much time in database no matter if it is stored as
varchar lines, varchar nodes or XML data type.
--
---------------------------------------
Viktor Bojović
---------------------------------------
Wherever I go, Murphy goes with me
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 00:26 ` Re: large xml database James Cloos <cloos@jhcloos.com>
2010-10-31 19:53 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
@ 2010-10-31 20:42 ` Rob Sargent <robjsargent@gmail.com>
2010-10-31 21:16 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
0 siblings, 1 reply; 12+ messages in thread
From: Rob Sargent @ 2010-10-31 20:42 UTC (permalink / raw)
To: Viktor Bojovic' <viktor.bojovic@gmail.com>; +Cc: James Cloos <cloos@jhcloos.com>; pgsql-sql
Viktor Bojovic' wrote:
>
>
> On Sun, Oct 31, 2010 at 2:26 AM, James Cloos <cloos@jhcloos.com
> <mailto:cloos@jhcloos.com>> wrote:
>
> >>>>> "VB" == Viktor Bojovic' <viktor.bojovic@gmail.com
> <mailto:viktor.bojovic@gmail.com>> writes:
>
> VB> i have very big XML documment which is larger than 50GB and
> want to
> VB> import it into databse, and transform it to relational schema.
>
> Were I doing such a conversion, I'd use perl to convert the xml into
> something which COPY can grok. Any other language, script or compiled,
> would work just as well. The goal is to avoid having to slurp the
> whole
> xml structure into memory.
>
> -JimC
> --
> James Cloos <cloos@jhcloos.com <mailto:cloos@jhcloos.com>>
> OpenPGP: 1024D/ED7DAEA6
>
>
> The insertion into dabase is not very big problem.
> I insert it as XML docs, or as varchar lines or as XML docs in varchar
> format. Usually i use transaction and commit after block of 1000
> inserts and it goes very fast. so insertion is over after few hours.
> But the problem occurs when i want to transform it inside database
> from XML(varchar or XML format) into tables by parsing.
> That processing takes too much time in database no matter if it is
> stored as varchar lines, varchar nodes or XML data type.
>
> --
> ---------------------------------------
> Viktor Bojovic'
> ---------------------------------------
> Wherever I go, Murphy goes with me
Are you saying you first load the xml into the database, then parse that
xml into instance of objects (rows in tables)?
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 00:26 ` Re: large xml database James Cloos <cloos@jhcloos.com>
2010-10-31 19:53 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 20:42 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
@ 2010-10-31 21:16 ` Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 21:26 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
0 siblings, 1 reply; 12+ messages in thread
From: Viktor Bojović @ 2010-10-31 21:16 UTC (permalink / raw)
To: Rob Sargent <robjsargent@gmail.com>; +Cc: James Cloos <cloos@jhcloos.com>; pgsql-sql
On Sun, Oct 31, 2010 at 9:42 PM, Rob Sargent <robjsargent@gmail.com> wrote:
>
>
>
> Viktor Bojovic' wrote:
>
>>
>>
>> On Sun, Oct 31, 2010 at 2:26 AM, James Cloos <cloos@jhcloos.com <mailto:
>> cloos@jhcloos.com>> wrote:
>>
>> >>>>> "VB" == Viktor Bojovic' <viktor.bojovic@gmail.com
>>
>> <mailto:viktor.bojovic@gmail.com>> writes:
>>
>> VB> i have very big XML documment which is larger than 50GB and
>> want to
>> VB> import it into databse, and transform it to relational schema.
>>
>> Were I doing such a conversion, I'd use perl to convert the xml into
>> something which COPY can grok. Any other language, script or compiled,
>> would work just as well. The goal is to avoid having to slurp the
>> whole
>> xml structure into memory.
>>
>> -JimC
>> --
>> James Cloos <cloos@jhcloos.com <mailto:cloos@jhcloos.com>>
>>
>> OpenPGP: 1024D/ED7DAEA6
>>
>>
>> The insertion into dabase is not very big problem.
>> I insert it as XML docs, or as varchar lines or as XML docs in varchar
>> format. Usually i use transaction and commit after block of 1000 inserts and
>> it goes very fast. so insertion is over after few hours.
>> But the problem occurs when i want to transform it inside database from
>> XML(varchar or XML format) into tables by parsing.
>> That processing takes too much time in database no matter if it is stored
>> as varchar lines, varchar nodes or XML data type.
>>
>> --
>> ---------------------------------------
>> Viktor Bojovic'
>>
>> ---------------------------------------
>> Wherever I go, Murphy goes with me
>>
>
> Are you saying you first load the xml into the database, then parse that
> xml into instance of objects (rows in tables)?
>
>
Yes. That way takes less ram then using twig or simple xml, so I tried using
postgre xml functions or regexes.
--
---------------------------------------
Viktor Bojović
---------------------------------------
Wherever I go, Murphy goes with me
Attachments:
[application/x-gzip] 100001.xml.gz (2.8K, ../../AANLkTimQC=tg6g3vsYb5X55MUHcaAOmMH_xZskxQNFBz@mail.gmail.com/3-100001.xml.gz)
download
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 00:26 ` Re: large xml database James Cloos <cloos@jhcloos.com>
2010-10-31 19:53 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 20:42 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
2010-10-31 21:16 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
@ 2010-10-31 21:26 ` Rob Sargent <robjsargent@gmail.com>
2010-10-31 22:52 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
0 siblings, 1 reply; 12+ messages in thread
From: Rob Sargent @ 2010-10-31 21:26 UTC (permalink / raw)
To: Viktor Bojović <viktor.bojovic@gmail.com>; +Cc: pgsql-sql
Viktor Bojović wrote:
>
>
> On Sun, Oct 31, 2010 at 9:42 PM, Rob Sargent <robjsargent@gmail.com
> <mailto:robjsargent@gmail.com>> wrote:
>
>
>
>
> Viktor Bojovic' wrote:
>
>
>
> On Sun, Oct 31, 2010 at 2:26 AM, James Cloos
> <cloos@jhcloos.com <mailto:cloos@jhcloos.com>
> <mailto:cloos@jhcloos.com <mailto:cloos@jhcloos.com>>> wrote:
>
> >>>>> "VB" == Viktor Bojovic' <viktor.bojovic@gmail.com
> <mailto:viktor.bojovic@gmail.com>
>
> <mailto:viktor.bojovic@gmail.com
> <mailto:viktor.bojovic@gmail.com>>> writes:
>
> VB> i have very big XML documment which is larger than 50GB and
> want to
> VB> import it into databse, and transform it to relational
> schema.
>
> Were I doing such a conversion, I'd use perl to convert the
> xml into
> something which COPY can grok. Any other language, script
> or compiled,
> would work just as well. The goal is to avoid having to
> slurp the
> whole
> xml structure into memory.
>
> -JimC
> --
> James Cloos <cloos@jhcloos.com <mailto:cloos@jhcloos.com>
> <mailto:cloos@jhcloos.com <mailto:cloos@jhcloos.com>>>
>
> OpenPGP: 1024D/ED7DAEA6
>
>
> The insertion into dabase is not very big problem.
> I insert it as XML docs, or as varchar lines or as XML docs in
> varchar format. Usually i use transaction and commit after
> block of 1000 inserts and it goes very fast. so insertion is
> over after few hours.
> But the problem occurs when i want to transform it inside
> database from XML(varchar or XML format) into tables by parsing.
> That processing takes too much time in database no matter if
> it is stored as varchar lines, varchar nodes or XML data type.
>
> --
> ---------------------------------------
> Viktor Bojovic'
>
> ---------------------------------------
> Wherever I go, Murphy goes with me
>
>
> Are you saying you first load the xml into the database, then
> parse that xml into instance of objects (rows in tables)?
>
>
> Yes. That way takes less ram then using twig or simple xml, so I tried
> using postgre xml functions or regexes.
>
>
>
> --
> ---------------------------------------
> Viktor Bojović
> ---------------------------------------
> Wherever I go, Murphy goes with me
Is the entire load a set of "entry" elements as your example contains?
This I believe would parse nicely into a tidy but non-trivial schema
directly without the "middle-man" of having xml in db (unless of course
you prefer xpath to sql ;) )
The single most significant caveat I would have for you is Beware:
Biologists involved. Inconsistency (at least overloaded concepts)
almost assured :). EMBL too is suspect imho, but I've been out of that
arena for a while.
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 00:26 ` Re: large xml database James Cloos <cloos@jhcloos.com>
2010-10-31 19:53 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 20:42 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
2010-10-31 21:16 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 21:26 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
@ 2010-10-31 22:52 ` Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 23:07 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
0 siblings, 1 reply; 12+ messages in thread
From: Viktor Bojović @ 2010-10-31 22:52 UTC (permalink / raw)
To: Rob Sargent <robjsargent@gmail.com>; +Cc: pgsql-sql
On Sun, Oct 31, 2010 at 10:26 PM, Rob Sargent <robjsargent@gmail.com> wrote:
> Viktor Bojović wrote:
>
>>
>>
>> On Sun, Oct 31, 2010 at 9:42 PM, Rob Sargent <robjsargent@gmail.com<mailto:
>> robjsargent@gmail.com>> wrote:
>>
>>
>>
>>
>> Viktor Bojovic' wrote:
>>
>>
>>
>> On Sun, Oct 31, 2010 at 2:26 AM, James Cloos
>> <cloos@jhcloos.com <mailto:cloos@jhcloos.com>
>> <mailto:cloos@jhcloos.com <mailto:cloos@jhcloos.com>>> wrote:
>>
>> >>>>> "VB" == Viktor Bojovic' <viktor.bojovic@gmail.com
>> <mailto:viktor.bojovic@gmail.com>
>>
>> <mailto:viktor.bojovic@gmail.com
>> <mailto:viktor.bojovic@gmail.com>>> writes:
>>
>> VB> i have very big XML documment which is larger than 50GB and
>> want to
>> VB> import it into databse, and transform it to relational
>> schema.
>>
>> Were I doing such a conversion, I'd use perl to convert the
>> xml into
>> something which COPY can grok. Any other language, script
>> or compiled,
>> would work just as well. The goal is to avoid having to
>> slurp the
>> whole
>> xml structure into memory.
>>
>> -JimC
>> --
>> James Cloos <cloos@jhcloos.com <mailto:cloos@jhcloos.com>
>> <mailto:cloos@jhcloos.com <mailto:cloos@jhcloos.com>>>
>>
>>
>> OpenPGP: 1024D/ED7DAEA6
>>
>>
>> The insertion into dabase is not very big problem.
>> I insert it as XML docs, or as varchar lines or as XML docs in
>> varchar format. Usually i use transaction and commit after
>> block of 1000 inserts and it goes very fast. so insertion is
>> over after few hours.
>> But the problem occurs when i want to transform it inside
>> database from XML(varchar or XML format) into tables by parsing.
>> That processing takes too much time in database no matter if
>> it is stored as varchar lines, varchar nodes or XML data type.
>>
>> -- ---------------------------------------
>> Viktor Bojovic'
>>
>> ---------------------------------------
>> Wherever I go, Murphy goes with me
>>
>>
>> Are you saying you first load the xml into the database, then
>> parse that xml into instance of objects (rows in tables)?
>>
>>
>> Yes. That way takes less ram then using twig or simple xml, so I tried
>> using postgre xml functions or regexes.
>>
>>
>>
>> --
>> ---------------------------------------
>> Viktor Bojović
>> ---------------------------------------
>> Wherever I go, Murphy goes with me
>>
> Is the entire load a set of "entry" elements as your example contains?
> This I believe would parse nicely into a tidy but non-trivial schema
> directly without the "middle-man" of having xml in db (unless of course you
> prefer xpath to sql ;) )
>
> The single most significant caveat I would have for you is Beware:
> Biologists involved. Inconsistency (at least overloaded concepts) almost
> assured :). EMBL too is suspect imho, but I've been out of that arena for a
> while.
>
>
Unfortunately some elements are always missing, so I had to create script
which scanned whole document of swissprot and trembl , and stored it into
file to use it as a template to build a code generator if I find a best
parser for this purpose. To parse all elements it in one day I should use
parser which is capable to parse at least 128 entry blocks for an second @
2.4GHz. You are right about inconsistency, im constantly have problems with
PDB files.
btw.
you have mentioned "This I believe would parse nicely into a tidy but
non-trivial schema directly", does it mean that postgre has a support for
restoring the database schema from xml files?
--
---------------------------------------
Viktor Bojović
---------------------------------------
Wherever I go, Murphy goes with me
entry[]->sequence[]
entry[]->feature[]
entry[]->reference[]
entry[]->feature[]->location[]->position[]->status
entry[]->dbReference[]->property[]
entry[]->reference[]->citation[]->last
entry[]->comment[]->text[]->status
entry[]->geneLocation[]->type
entry[]->comment[]->experiments[]
entry[]->comment[]->conflict[]->sequence[]
entry[]->comment[]->subcellularLocation[]->orientation[]->status
entry[]->protein[]->domain[]->alternativeName[]->fullName[]
entry[]->evidence[]->category
entry[]->feature[]->location[]->begin[]->status
entry[]->reference[]->citation[]->volume
entry[]->feature[]->evidence
entry[]->dbReference[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]
entry[]->version
entry[]->comment[]->location[]->sequence
entry[]->sequence[]->version
entry[]->proteinExistence[]
entry[]->reference[]->scope[]
entry[]->reference[]->source[]->plasmid[]
entry[]->reference[]->citation[]->dbReference[]
entry[]->comment[]->locationType
entry[]->protein[]->domain[]
entry[]->reference[]->citation[]->publisher
entry[]->gene[]->name[]
entry[]->protein[]->domain[]->alternativeName[]->ref
entry[]->comment[]->conflict[]
entry[]->evidence[]
entry[]->sequence[]->modified
entry[]->comment[]->conflict[]->sequence[]->id
entry[]->keyword[]->id
entry[]->comment[]->redoxPotential[]->evidence
entry[]->comment[]->link[]
entry[]->feature[]->location[]->position[]
entry[]->reference[]->citation[]->dbReference[]->id
entry[]->organismHost[]->dbReference[]->key
entry[]->organism[]->lineage[]
entry[]->organismHost[]->name[]->type
entry[]->comment[]->location[]->position[]->evidence
entry[]->proteinExistence[]->type
entry[]->protein[]->component[]->alternativeName[]->shortName[]
entry[]->reference[]->citation[]->editorList[]->person[]
entry[]->comment[]->isoform[]->sequence[]->type
entry[]->organismHost[]->dbReference[]->type
entry[]->sequence[]->checksum
entry[]->gene[]
entry[]->gene[]->name[]->type
entry[]->dbReference[]->id
entry[]->comment[]->phDependence[]->evidence
entry[]->comment[]->interactant[]
entry[]->dbReference[]->property[]->type
entry[]->protein[]->alternativeName[]->fullName[]
entry[]->protein[]->component[]->recommendedName[]->shortName[]
entry[]->protein[]->allergenName[]
entry[]->comment[]->kinetics[]->KM[]
entry[]->comment[]->absorption[]
entry[]->comment[]->error
entry[]->protein[]->component[]->recommendedName[]
entry[]->comment[]->link[]->uri
entry[]->comment[]->location[]
entry[]->comment[]->location[]->position[]
entry[]->feature[]->location[]->begin[]
entry[]->comment[]->isoform[]->sequence[]->ref
entry[]->protein[]->component[]->alternativeName[]
entry[]->feature[]->location[]->end[]->position
entry[]->reference[]->citation[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]->name
entry[]->comment[]->name
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entry[]->sequence[]->precursor
entry[]->sequence[]->mass
entry[]->evidence[]->date
entry[]->protein[]->component[]->alternativeName[]->ref
entry[]->comment[]->subcellularLocation[]->location[]
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entry[]->comment[]->method
entry[]->feature[]->location[]->position[]->position
entry[]->comment[]->interactant[]->intactId
entry[]->feature[]->location[]->end[]->status
entry[]->protein[]->alternativeName[]->shortName[]
entry[]->comment[]->absorption[]->text[]->evidence
entry[]->comment[]->kinetics[]->text[]
entry[]->protein[]->domain[]->recommendedName[]->shortName[]
entry[]->protein[]
entry[]->organism[]->lineage[]->taxon[]
entry[]->protein[]->domain[]->recommendedName[]
entry[]->keyword[]
entry[]->reference[]->citation[]->city
entry[]->protein[]->component[]->recommendedName[]->ref
entry[]->reference[]->source[]->tissue[]
entry[]->comment[]->kinetics[]
entry[]->comment[]->temperatureDependence[]
entry[]->reference[]->citation[]->dbReference[]->type
entry[]->comment[]->type
entry[]->comment[]->conflict[]->sequence[]->resource
entry[]->comment[]->isoform[]->note[]
entry[]->comment[]->subcellularLocation[]->orientation[]
entry[]->comment[]->absorption[]->max[]->evidence
entry[]->comment[]->subcellularLocation[]->topology[]
entry[]->protein[]->recommendedName[]->fullName[]
entry[]->feature[]->id
entry[]->comment[]->subcellularLocation[]->topology[]->status
entry[]->reference[]->citation[]->first
entry[]->dbReference[]
entry[]->comment[]->isoform[]->name[]
entry[]->accession[]
entry[]->feature[]->location[]
entry[]->protein[]->component[]->allergenName[]
entry[]->comment[]->molecule[]
entry[]->comment[]->text[]
entry[]->protein[]->component[]->recommendedName[]->fullName[]
entry[]->comment[]->phDependence[]
entry[]->comment[]->interactant[]->label[]
entry[]->comment[]->isoform[]->sequence[]
entry[]->reference[]->citation[]->authorList[]
entry[]->comment[]->isoform[]
entry[]->sequence[]->fragment
entry[]->feature[]->location[]->end[]
entry[]->reference[]->citation[]->number
entry[]->comment[]->location[]->end[]->status
entry[]->organism[]
entry[]->protein[]->component[]->alternativeName[]->fullName[]
entry[]->organismHost[]->dbReference[]->id
entry[]->protein[]->alternativeName[]
entry[]->reference[]->citation[]->date
entry[]->protein[]->domain[]->alternativeName[]->shortName[]
entry[]->reference[]->citation[]->editorList[]->person[]->name
entry[]->dbReference[]->property[]->value
entry[]->protein[]->domain[]->alternativeName[]
entry[]->reference[]->citation[]->title[]
entry[]->comment[]->subcellularLocation[]
entry[]->comment[]->mass
entry[]->protein[]->component[]
entry[]->reference[]->citation[]->dbReference[]->key
entry[]->protein[]->recommendedName[]->shortName[]
entry[]->organismHost[]->name[]
entry[]->reference[]->source[]->strain[]
entry[]->comment[]->conflict[]->type
entry[]->organism[]->name[]
entry[]->reference[]->citation[]->institute
entry[]->comment[]->evidence
entry[]->feature[]->original[]
entry[]->protein[]->domain[]->recommendedName[]->fullName[]
entry[]->name[]
entry[]->comment[]->location[]->begin[]->position
entry[]->organism[]->dbReference[]
entry[]->reference[]->citation[]
entry[]->organism[]->name[]->type
entry[]->reference[]->source[]
entry[]->organismHost[]->dbReference[]
entry[]->reference[]->citation[]->country
entry[]
entry[]->dbReference[]->key
entry[]->feature[]->ref
entry[]->protein[]->alternativeName[]->ref
entry[]->geneLocation[]->name[]->status
entry[]->comment[]->event[]
entry[]->comment[]->isoform[]->id[]
entry[]->evidence[]->key
entry[]->comment[]->kinetics[]->Vmax[]
entry[]->dataset
entry[]->protein[]->recommendedName[]->ref
entry[]->reference[]->citation[]->authorList[]->person[]
entry[]->comment[]->organismsDiffer[]
entry[]->comment[]->conflict[]->sequence[]->version
entry[]->reference[]->source[]->transposon[]
entry[]->geneLocation[]
entry[]->reference[]->citation[]->db
entry[]->reference[]->citation[]->locator[]
entry[]->organism[]->dbReference[]->key
entry[]->comment[]->conflict[]->ref
entry[]->modified
entry[]->sequence[]->length
entry[]->comment[]->location[]->begin[]->status
entry[]->comment[]->temperatureDependence[]->evidence
entry[]->reference[]->key
entry[]->comment[]->kinetics[]->KM[]->evidence
entry[]->created
entry[]->comment[]->redoxPotential[]
entry[]->comment[]->absorption[]->max[]
entry[]->evidence[]->attribute
entry[]->comment[]->location[]->end[]->position
entry[]->comment[]->kinetics[]->text[]->evidence
entry[]->comment[]
entry[]->organism[]->dbReference[]->type
entry[]->comment[]->subcellularLocation[]->location[]->status
entry[]->comment[]->location[]->position[]->position
entry[]->comment[]->event[]->type
entry[]->reference[]->citation[]->authorList[]->person[]->name
entry[]->feature[]->location[]->begin[]->position
entry[]->reference[]->citation[]->name
entry[]->reference[]->citation[]->editorList[]
entry[]->feature[]->description
entry[]->organism[]->dbReference[]->id
entry[]->protein[]->domain[]->recommendedName[]->ref
entry[]->comment[]->location[]->begin[]
entry[]->protein[]->recommendedName[]
entry[]->feature[]->type
entry[]->organismHost[]
entry[]->comment[]->absorption[]->text[]
entry[]->feature[]->variation[]
entry[]->geneLocation[]->name[]
entry[]->evidence[]->type
entry[]->comment[]->interactant[]->id[]
entry[]->protein[]->cdAntigenName[]
entry[]->sequence[]
entry[]->feature[]
entry[]->reference[]
entry[]->dbReference[]->property[]
entry[]->reference[]->citation[]->last
entry[]->comment[]->text[]->status
entry[]->comment[]->experiments[]
entry[]->geneLocation[]->type
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entry[]->evidence[]->category
entry[]->reference[]->citation[]->volume
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entry[]->dbReference[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]
entry[]->version
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entry[]->gene[]->name[]->evidence
entry[]->proteinExistence[]
entry[]->reference[]->scope[]
entry[]->reference[]->source[]->plasmid[]
entry[]->reference[]->citation[]->dbReference[]
entry[]->reference[]->citation[]->publisher
entry[]->gene[]->name[]
entry[]->evidence[]
entry[]->reference[]->evidence
entry[]->sequence[]->modified
entry[]->keyword[]->id
entry[]->organismHost[]->dbReference[]->key
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entry[]->reference[]->citation[]->dbReference[]->id
entry[]->organismHost[]->name[]->type
entry[]->organism[]->lineage[]
entry[]->proteinExistence[]->type
entry[]->reference[]->citation[]->editorList[]->person[]
entry[]->organismHost[]->dbReference[]->type
entry[]->sequence[]->checksum
entry[]->gene[]
entry[]->gene[]->name[]->type
entry[]->dbReference[]->evidence
entry[]->dbReference[]->id
entry[]->reference[]->source[]->tissue[]->evidence
entry[]->comment[]->interactant[]
entry[]->protein[]->recommendedName[]->fullName[]->evidence
entry[]->dbReference[]->property[]->type
entry[]->feature[]->location[]->begin[]
entry[]->protein[]->submittedName[]->ref
entry[]->feature[]->location[]->end[]->position
entry[]->reference[]->citation[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]->name
entry[]->sequence[]->precursor
entry[]->sequence[]->mass
entry[]->evidence[]->date
entry[]->comment[]->subcellularLocation[]->location[]
entry[]->feature[]->status
entry[]->feature[]->location[]->position[]->position
entry[]->comment[]->interactant[]->intactId
entry[]->feature[]->location[]->end[]->status
entry[]->protein[]
entry[]->protein[]->submittedName[]->fullName[]
entry[]->organism[]->lineage[]->taxon[]
entry[]->keyword[]
entry[]->reference[]->citation[]->city
entry[]->reference[]->source[]->tissue[]
entry[]->reference[]->citation[]->dbReference[]->type
entry[]->comment[]->type
entry[]->comment[]->subcellularLocation[]->topology[]
entry[]->protein[]->recommendedName[]->fullName[]
entry[]->feature[]->id
entry[]->comment[]->subcellularLocation[]->topology[]->status
entry[]->reference[]->citation[]->first
entry[]->dbReference[]
entry[]->accession[]
entry[]->feature[]->location[]
entry[]->comment[]->molecule[]
entry[]->comment[]->text[]
entry[]->comment[]->interactant[]->label[]
entry[]->reference[]->citation[]->authorList[]
entry[]->sequence[]->fragment
entry[]->reference[]->source[]->plasmid[]->evidence
entry[]->feature[]->location[]->end[]
entry[]->reference[]->citation[]->number
entry[]->organism[]
entry[]->organismHost[]->dbReference[]->id
entry[]->reference[]->citation[]->date
entry[]->dbReference[]->property[]->value
entry[]->reference[]->citation[]->editorList[]->person[]->name
entry[]->reference[]->citation[]->title[]
entry[]->comment[]->subcellularLocation[]
entry[]->reference[]->citation[]->dbReference[]->key
entry[]->organismHost[]->name[]
entry[]->reference[]->source[]->strain[]
entry[]->organism[]->name[]
entry[]->comment[]->evidence
entry[]->reference[]->citation[]->institute
entry[]->name[]
entry[]->organism[]->dbReference[]
entry[]->reference[]->citation[]
entry[]->organism[]->name[]->type
entry[]->reference[]->source[]
entry[]->organismHost[]->dbReference[]
entry[]
entry[]->dbReference[]->key
entry[]->reference[]->citation[]->country
entry[]->geneLocation[]->name[]->status
entry[]->evidence[]->key
entry[]->dataset
entry[]->protein[]->recommendedName[]->ref
entry[]->reference[]->citation[]->authorList[]->person[]
entry[]->keyword[]->evidence
entry[]->comment[]->organismsDiffer[]
entry[]->reference[]->source[]->transposon[]
entry[]->reference[]->citation[]->db
entry[]->geneLocation[]
entry[]->organism[]->dbReference[]->key
entry[]->modified
entry[]->sequence[]->length
entry[]->reference[]->key
entry[]->created
entry[]->geneLocation[]->evidence
entry[]->evidence[]->attribute
entry[]->comment[]
entry[]->organism[]->dbReference[]->type
entry[]->comment[]->subcellularLocation[]->location[]->status
entry[]->protein[]->submittedName[]
entry[]->reference[]->citation[]->authorList[]->person[]->name
entry[]->reference[]->citation[]->name
entry[]->feature[]->location[]->begin[]->position
entry[]->reference[]->source[]->strain[]->evidence
entry[]->feature[]->description
entry[]->reference[]->citation[]->editorList[]
entry[]->organism[]->dbReference[]->id
entry[]->protein[]->submittedName[]->fullName[]->evidence
entry[]->protein[]->recommendedName[]
entry[]->feature[]->type
entry[]->organismHost[]
entry[]->organism[]->evidence
entry[]->evidence[]->type
entry[]->geneLocation[]->name[]
entry[]->comment[]->interactant[]->id[]
Attachments:
[text/plain] sp.nodes.txt (8.0K, ../../AANLkTi=iQkAA3Bc0ua-ZauXwfFJg+eLqvEb4rb+NFaj2@mail.gmail.com/3-sp.nodes.txt)
download | inline:
entry[]->sequence[]
entry[]->feature[]
entry[]->reference[]
entry[]->feature[]->location[]->position[]->status
entry[]->dbReference[]->property[]
entry[]->reference[]->citation[]->last
entry[]->comment[]->text[]->status
entry[]->geneLocation[]->type
entry[]->comment[]->experiments[]
entry[]->comment[]->conflict[]->sequence[]
entry[]->comment[]->subcellularLocation[]->orientation[]->status
entry[]->protein[]->domain[]->alternativeName[]->fullName[]
entry[]->evidence[]->category
entry[]->feature[]->location[]->begin[]->status
entry[]->reference[]->citation[]->volume
entry[]->feature[]->evidence
entry[]->dbReference[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]
entry[]->version
entry[]->comment[]->location[]->sequence
entry[]->sequence[]->version
entry[]->proteinExistence[]
entry[]->reference[]->scope[]
entry[]->reference[]->source[]->plasmid[]
entry[]->reference[]->citation[]->dbReference[]
entry[]->comment[]->locationType
entry[]->protein[]->domain[]
entry[]->reference[]->citation[]->publisher
entry[]->gene[]->name[]
entry[]->protein[]->domain[]->alternativeName[]->ref
entry[]->comment[]->conflict[]
entry[]->evidence[]
entry[]->sequence[]->modified
entry[]->comment[]->conflict[]->sequence[]->id
entry[]->keyword[]->id
entry[]->comment[]->redoxPotential[]->evidence
entry[]->comment[]->link[]
entry[]->feature[]->location[]->position[]
entry[]->reference[]->citation[]->dbReference[]->id
entry[]->organismHost[]->dbReference[]->key
entry[]->organism[]->lineage[]
entry[]->organismHost[]->name[]->type
entry[]->comment[]->location[]->position[]->evidence
entry[]->proteinExistence[]->type
entry[]->protein[]->component[]->alternativeName[]->shortName[]
entry[]->reference[]->citation[]->editorList[]->person[]
entry[]->comment[]->isoform[]->sequence[]->type
entry[]->organismHost[]->dbReference[]->type
entry[]->sequence[]->checksum
entry[]->gene[]
entry[]->gene[]->name[]->type
entry[]->dbReference[]->id
entry[]->comment[]->phDependence[]->evidence
entry[]->comment[]->interactant[]
entry[]->dbReference[]->property[]->type
entry[]->protein[]->alternativeName[]->fullName[]
entry[]->protein[]->component[]->recommendedName[]->shortName[]
entry[]->protein[]->allergenName[]
entry[]->comment[]->kinetics[]->KM[]
entry[]->comment[]->absorption[]
entry[]->comment[]->error
entry[]->protein[]->component[]->recommendedName[]
entry[]->comment[]->link[]->uri
entry[]->comment[]->location[]
entry[]->comment[]->location[]->position[]
entry[]->feature[]->location[]->begin[]
entry[]->comment[]->isoform[]->sequence[]->ref
entry[]->protein[]->component[]->alternativeName[]
entry[]->feature[]->location[]->end[]->position
entry[]->reference[]->citation[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]->name
entry[]->comment[]->name
entry[]->comment[]->location[]->end[]
entry[]->sequence[]->precursor
entry[]->sequence[]->mass
entry[]->evidence[]->date
entry[]->protein[]->component[]->alternativeName[]->ref
entry[]->comment[]->subcellularLocation[]->location[]
entry[]->feature[]->status
entry[]->comment[]->method
entry[]->feature[]->location[]->position[]->position
entry[]->comment[]->interactant[]->intactId
entry[]->feature[]->location[]->end[]->status
entry[]->protein[]->alternativeName[]->shortName[]
entry[]->comment[]->absorption[]->text[]->evidence
entry[]->comment[]->kinetics[]->text[]
entry[]->protein[]->domain[]->recommendedName[]->shortName[]
entry[]->protein[]
entry[]->organism[]->lineage[]->taxon[]
entry[]->protein[]->domain[]->recommendedName[]
entry[]->keyword[]
entry[]->reference[]->citation[]->city
entry[]->protein[]->component[]->recommendedName[]->ref
entry[]->reference[]->source[]->tissue[]
entry[]->comment[]->kinetics[]
entry[]->comment[]->temperatureDependence[]
entry[]->reference[]->citation[]->dbReference[]->type
entry[]->comment[]->type
entry[]->comment[]->conflict[]->sequence[]->resource
entry[]->comment[]->isoform[]->note[]
entry[]->comment[]->subcellularLocation[]->orientation[]
entry[]->comment[]->absorption[]->max[]->evidence
entry[]->comment[]->subcellularLocation[]->topology[]
entry[]->protein[]->recommendedName[]->fullName[]
entry[]->feature[]->id
entry[]->comment[]->subcellularLocation[]->topology[]->status
entry[]->reference[]->citation[]->first
entry[]->dbReference[]
entry[]->comment[]->isoform[]->name[]
entry[]->accession[]
entry[]->feature[]->location[]
entry[]->protein[]->component[]->allergenName[]
entry[]->comment[]->molecule[]
entry[]->comment[]->text[]
entry[]->protein[]->component[]->recommendedName[]->fullName[]
entry[]->comment[]->phDependence[]
entry[]->comment[]->interactant[]->label[]
entry[]->comment[]->isoform[]->sequence[]
entry[]->reference[]->citation[]->authorList[]
entry[]->comment[]->isoform[]
entry[]->sequence[]->fragment
entry[]->feature[]->location[]->end[]
entry[]->reference[]->citation[]->number
entry[]->comment[]->location[]->end[]->status
entry[]->organism[]
entry[]->protein[]->component[]->alternativeName[]->fullName[]
entry[]->organismHost[]->dbReference[]->id
entry[]->protein[]->alternativeName[]
entry[]->reference[]->citation[]->date
entry[]->protein[]->domain[]->alternativeName[]->shortName[]
entry[]->reference[]->citation[]->editorList[]->person[]->name
entry[]->dbReference[]->property[]->value
entry[]->protein[]->domain[]->alternativeName[]
entry[]->reference[]->citation[]->title[]
entry[]->comment[]->subcellularLocation[]
entry[]->comment[]->mass
entry[]->protein[]->component[]
entry[]->reference[]->citation[]->dbReference[]->key
entry[]->protein[]->recommendedName[]->shortName[]
entry[]->organismHost[]->name[]
entry[]->reference[]->source[]->strain[]
entry[]->comment[]->conflict[]->type
entry[]->organism[]->name[]
entry[]->reference[]->citation[]->institute
entry[]->comment[]->evidence
entry[]->feature[]->original[]
entry[]->protein[]->domain[]->recommendedName[]->fullName[]
entry[]->name[]
entry[]->comment[]->location[]->begin[]->position
entry[]->organism[]->dbReference[]
entry[]->reference[]->citation[]
entry[]->organism[]->name[]->type
entry[]->reference[]->source[]
entry[]->organismHost[]->dbReference[]
entry[]->reference[]->citation[]->country
entry[]
entry[]->dbReference[]->key
entry[]->feature[]->ref
entry[]->protein[]->alternativeName[]->ref
entry[]->geneLocation[]->name[]->status
entry[]->comment[]->event[]
entry[]->comment[]->isoform[]->id[]
entry[]->evidence[]->key
entry[]->comment[]->kinetics[]->Vmax[]
entry[]->dataset
entry[]->protein[]->recommendedName[]->ref
entry[]->reference[]->citation[]->authorList[]->person[]
entry[]->comment[]->organismsDiffer[]
entry[]->comment[]->conflict[]->sequence[]->version
entry[]->reference[]->source[]->transposon[]
entry[]->geneLocation[]
entry[]->reference[]->citation[]->db
entry[]->reference[]->citation[]->locator[]
entry[]->organism[]->dbReference[]->key
entry[]->comment[]->conflict[]->ref
entry[]->modified
entry[]->sequence[]->length
entry[]->comment[]->location[]->begin[]->status
entry[]->comment[]->temperatureDependence[]->evidence
entry[]->reference[]->key
entry[]->comment[]->kinetics[]->KM[]->evidence
entry[]->created
entry[]->comment[]->redoxPotential[]
entry[]->comment[]->absorption[]->max[]
entry[]->evidence[]->attribute
entry[]->comment[]->location[]->end[]->position
entry[]->comment[]->kinetics[]->text[]->evidence
entry[]->comment[]
entry[]->organism[]->dbReference[]->type
entry[]->comment[]->subcellularLocation[]->location[]->status
entry[]->comment[]->location[]->position[]->position
entry[]->comment[]->event[]->type
entry[]->reference[]->citation[]->authorList[]->person[]->name
entry[]->feature[]->location[]->begin[]->position
entry[]->reference[]->citation[]->name
entry[]->reference[]->citation[]->editorList[]
entry[]->feature[]->description
entry[]->organism[]->dbReference[]->id
entry[]->protein[]->domain[]->recommendedName[]->ref
entry[]->comment[]->location[]->begin[]
entry[]->protein[]->recommendedName[]
entry[]->feature[]->type
entry[]->organismHost[]
entry[]->comment[]->absorption[]->text[]
entry[]->feature[]->variation[]
entry[]->geneLocation[]->name[]
entry[]->evidence[]->type
entry[]->comment[]->interactant[]->id[]
entry[]->protein[]->cdAntigenName[]
[text/plain] tr.nodes.txt (4.9K, ../../AANLkTi=iQkAA3Bc0ua-ZauXwfFJg+eLqvEb4rb+NFaj2@mail.gmail.com/4-tr.nodes.txt)
download | inline:
entry[]->sequence[]
entry[]->feature[]
entry[]->reference[]
entry[]->dbReference[]->property[]
entry[]->reference[]->citation[]->last
entry[]->comment[]->text[]->status
entry[]->comment[]->experiments[]
entry[]->geneLocation[]->type
entry[]->feature[]->location[]->begin[]->status
entry[]->evidence[]->category
entry[]->reference[]->citation[]->volume
entry[]->feature[]->evidence
entry[]->dbReference[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]
entry[]->version
entry[]->sequence[]->version
entry[]->gene[]->name[]->evidence
entry[]->proteinExistence[]
entry[]->reference[]->scope[]
entry[]->reference[]->source[]->plasmid[]
entry[]->reference[]->citation[]->dbReference[]
entry[]->reference[]->citation[]->publisher
entry[]->gene[]->name[]
entry[]->evidence[]
entry[]->reference[]->evidence
entry[]->sequence[]->modified
entry[]->keyword[]->id
entry[]->organismHost[]->dbReference[]->key
entry[]->feature[]->location[]->position[]
entry[]->reference[]->citation[]->dbReference[]->id
entry[]->organismHost[]->name[]->type
entry[]->organism[]->lineage[]
entry[]->proteinExistence[]->type
entry[]->reference[]->citation[]->editorList[]->person[]
entry[]->organismHost[]->dbReference[]->type
entry[]->sequence[]->checksum
entry[]->gene[]
entry[]->gene[]->name[]->type
entry[]->dbReference[]->evidence
entry[]->dbReference[]->id
entry[]->reference[]->source[]->tissue[]->evidence
entry[]->comment[]->interactant[]
entry[]->protein[]->recommendedName[]->fullName[]->evidence
entry[]->dbReference[]->property[]->type
entry[]->feature[]->location[]->begin[]
entry[]->protein[]->submittedName[]->ref
entry[]->feature[]->location[]->end[]->position
entry[]->reference[]->citation[]->type
entry[]->reference[]->citation[]->authorList[]->consortium[]->name
entry[]->sequence[]->precursor
entry[]->sequence[]->mass
entry[]->evidence[]->date
entry[]->comment[]->subcellularLocation[]->location[]
entry[]->feature[]->status
entry[]->feature[]->location[]->position[]->position
entry[]->comment[]->interactant[]->intactId
entry[]->feature[]->location[]->end[]->status
entry[]->protein[]
entry[]->protein[]->submittedName[]->fullName[]
entry[]->organism[]->lineage[]->taxon[]
entry[]->keyword[]
entry[]->reference[]->citation[]->city
entry[]->reference[]->source[]->tissue[]
entry[]->reference[]->citation[]->dbReference[]->type
entry[]->comment[]->type
entry[]->comment[]->subcellularLocation[]->topology[]
entry[]->protein[]->recommendedName[]->fullName[]
entry[]->feature[]->id
entry[]->comment[]->subcellularLocation[]->topology[]->status
entry[]->reference[]->citation[]->first
entry[]->dbReference[]
entry[]->accession[]
entry[]->feature[]->location[]
entry[]->comment[]->molecule[]
entry[]->comment[]->text[]
entry[]->comment[]->interactant[]->label[]
entry[]->reference[]->citation[]->authorList[]
entry[]->sequence[]->fragment
entry[]->reference[]->source[]->plasmid[]->evidence
entry[]->feature[]->location[]->end[]
entry[]->reference[]->citation[]->number
entry[]->organism[]
entry[]->organismHost[]->dbReference[]->id
entry[]->reference[]->citation[]->date
entry[]->dbReference[]->property[]->value
entry[]->reference[]->citation[]->editorList[]->person[]->name
entry[]->reference[]->citation[]->title[]
entry[]->comment[]->subcellularLocation[]
entry[]->reference[]->citation[]->dbReference[]->key
entry[]->organismHost[]->name[]
entry[]->reference[]->source[]->strain[]
entry[]->organism[]->name[]
entry[]->comment[]->evidence
entry[]->reference[]->citation[]->institute
entry[]->name[]
entry[]->organism[]->dbReference[]
entry[]->reference[]->citation[]
entry[]->organism[]->name[]->type
entry[]->reference[]->source[]
entry[]->organismHost[]->dbReference[]
entry[]
entry[]->dbReference[]->key
entry[]->reference[]->citation[]->country
entry[]->geneLocation[]->name[]->status
entry[]->evidence[]->key
entry[]->dataset
entry[]->protein[]->recommendedName[]->ref
entry[]->reference[]->citation[]->authorList[]->person[]
entry[]->keyword[]->evidence
entry[]->comment[]->organismsDiffer[]
entry[]->reference[]->source[]->transposon[]
entry[]->reference[]->citation[]->db
entry[]->geneLocation[]
entry[]->organism[]->dbReference[]->key
entry[]->modified
entry[]->sequence[]->length
entry[]->reference[]->key
entry[]->created
entry[]->geneLocation[]->evidence
entry[]->evidence[]->attribute
entry[]->comment[]
entry[]->organism[]->dbReference[]->type
entry[]->comment[]->subcellularLocation[]->location[]->status
entry[]->protein[]->submittedName[]
entry[]->reference[]->citation[]->authorList[]->person[]->name
entry[]->reference[]->citation[]->name
entry[]->feature[]->location[]->begin[]->position
entry[]->reference[]->source[]->strain[]->evidence
entry[]->feature[]->description
entry[]->reference[]->citation[]->editorList[]
entry[]->organism[]->dbReference[]->id
entry[]->protein[]->submittedName[]->fullName[]->evidence
entry[]->protein[]->recommendedName[]
entry[]->feature[]->type
entry[]->organismHost[]
entry[]->organism[]->evidence
entry[]->evidence[]->type
entry[]->geneLocation[]->name[]
entry[]->comment[]->interactant[]->id[]
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 00:26 ` Re: large xml database James Cloos <cloos@jhcloos.com>
2010-10-31 19:53 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 20:42 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
2010-10-31 21:16 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 21:26 ` Re: large xml database Rob Sargent <robjsargent@gmail.com>
2010-10-31 22:52 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
@ 2010-10-31 23:07 ` Rob Sargent <robjsargent@gmail.com>
0 siblings, 0 replies; 12+ messages in thread
From: Rob Sargent @ 2010-10-31 23:07 UTC (permalink / raw)
To: Viktor Bojović <viktor.bojovic@gmail.com>; +Cc: pgsql-sql
Skipping much of the included thread, urgently.
> btw.
> you have mentioned "This I believe would parse nicely into a tidy but
> non-trivial schema directly", does it mean that postgre has a support
> for restoring the database schema from xml files?
>
> --
> ---------------------------------------
> Viktor Bojović
> ---------------------------------------
> Wherever I go, Murphy goes with me
No. Sorry. Did not mean to imply that. If you had a xsd file from them
you might have a better chance. Have never looked but I but someone has
tried that sort of manipulation. Throw out the cardinality constraints
of course :).
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
@ 2010-10-31 06:08 ` Lutz Steinborn <l.steinborn@4c-ag.de>
2010-10-31 19:36 ` Re: large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2 siblings, 1 reply; 12+ messages in thread
From: Lutz Steinborn @ 2010-10-31 06:08 UTC (permalink / raw)
To: Viktor Bojović <viktor.bojovic@gmail.com>; +Cc: pgsql-sql
On Sat, 30 Oct 2010 23:49:29 +0200
Viktor Bojović <viktor.bojovic@gmail.com> wrote:
>
> many tries have failed because 8GB of ram and 10gb of swap were not enough.
> also sometimes i get that more than 2^32 operations were performed, and
> functions stopped to work.
>
we have a similar problem and we use the Amara xml Toolkit for python. To avoid
the big memory consumption use pushbind. A 30G bme catalog file takes a maximum
up to 20min to import. It might be faster because we are preparing complex
objects with an orm. So the time consumption depends how complex the catalog is.
If you use amara only to perform a conversion from xml to csv the final import
can be done much faster.
regards
--
Lutz
http://www.4c-gmbh.de
^ permalink raw reply [nested|flat] 12+ messages in thread
* Re: large xml database
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 06:08 ` Re: large xml database Lutz Steinborn <l.steinborn@4c-ag.de>
@ 2010-10-31 19:36 ` Viktor Bojović <viktor.bojovic@gmail.com>
0 siblings, 0 replies; 12+ messages in thread
From: Viktor Bojović @ 2010-10-31 19:36 UTC (permalink / raw)
To: Lutz Steinborn <l.steinborn@4c-ag.de>; +Cc: pgsql-sql
On Sun, Oct 31, 2010 at 7:08 AM, Lutz Steinborn <l.steinborn@4c-ag.de>wrote:
> On Sat, 30 Oct 2010 23:49:29 +0200
> Viktor Bojović <viktor.bojovic@gmail.com> wrote:
>
> >
> > many tries have failed because 8GB of ram and 10gb of swap were not
> enough.
> > also sometimes i get that more than 2^32 operations were performed, and
> > functions stopped to work.
> >
> we have a similar problem and we use the Amara xml Toolkit for python. To
> avoid
> the big memory consumption use pushbind. A 30G bme catalog file takes a
> maximum
> up to 20min to import. It might be faster because we are preparing complex
> objects with an orm. So the time consumption depends how complex the
> catalog is.
> If you use amara only to perform a conversion from xml to csv the final
> import
> can be done much faster.
>
> regards
>
> --
> Lutz
>
> http://www.4c-gmbh.de
>
>
Thanx Lutz, I will try to use that Amara and also I will try to parse it
with SAX.
I have tried twig and some other parsers but they consumed too much RAM.
--
---------------------------------------
Viktor Bojović
---------------------------------------
Wherever I go, Murphy goes with me
^ permalink raw reply [nested|flat] 12+ messages in thread
end of thread, other threads:[~2010-10-31 23:07 UTC | newest]
Thread overview: 12+ messages (download: mbox mbox.gz follow: Atom feed)
-- links below jump to the message on this page --
2010-10-30 21:49 large xml database Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-30 22:06 ` Andreas Joseph Krogh <andreak@officenet.no>
2010-10-30 22:42 ` Rob Sargent <robjsargent@gmail.com>
2010-10-31 00:26 ` James Cloos <cloos@jhcloos.com>
2010-10-31 19:53 ` Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 20:42 ` Rob Sargent <robjsargent@gmail.com>
2010-10-31 21:16 ` Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 21:26 ` Rob Sargent <robjsargent@gmail.com>
2010-10-31 22:52 ` Viktor Bojović <viktor.bojovic@gmail.com>
2010-10-31 23:07 ` Rob Sargent <robjsargent@gmail.com>
2010-10-31 06:08 ` Lutz Steinborn <l.steinborn@4c-ag.de>
2010-10-31 19:36 ` Viktor Bojović <viktor.bojovic@gmail.com>
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