iproclass dataset, loading error about bio2rdf-scripts HOT 4 CLOSED

Hi Paul,
Indeed - that looks like a problem in the parsing.
https://github.com/micheldumontier/bio2rdf-scripts/blob/iproclass/iproclass/iproclass.php

wanna look into it?

m.

Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford
University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

On Tue, Mar 11, 2014 at 9:04 AM, Paul Rigor [email protected]:

Has anyone encountered the following issues while loading the iproclass
dataset into virtuoso (version 7.1.0)? There seems to be a malformed quad
with multiple an invalid uniprot ids.

==Error message excerpts below==

Loading /var/preserve/bio2rdf/mirror/release/3/iproclass/t2.txt into
http://bio2rdf.org/iproclass ...
Skipping line:1 ... Problem in: http://purl.org/dc/terms/identifier"iproclass:uniprot:75070738; 440648385; 116242084; 381277118; 223014445;
262343945; 393660255; 545765794; 326200806; 171675572; 122938060;
313267586; 381269698; 381235637; 375070038; 223011463; 168252164;
306976300; 71012654; 290544683; 552099586; 71015856; 223009293; 298367672;
381220965; 381263594; 118122797; 71017146; 283047974; 513791906; 410062122;
356476889; 126038553; 381220321; 545755337; 133712399; 119221318; 32892886;
150023363; 545773508; 71011533; 119035042; 71016641; 342840601; 410061422;
375067798; 545760936; 440652669; 94980847; 396580364; 302376750; 305655998;
545772752; 40848968; 349501937; 440653985; 302375924; 513789232; 381237709;
306976986; 385257755; 51894941; 213990019; 194580074; 290758436; 375066580;
57904139; 381242007; 218454552; 350282678; 381250715; 151334971; 381254929;
378744438; 528078892; 187960896; 224036663; 126038572; 156077456; 545
760754; 393190388; 151334146; 496528315; 32348620; 381265624; 381267696;
381244919; 315021963; 359468606; 513790394; 334738648; 309752115;
381239417; 381231017; 381248909; 61652721; 189179453; 171675936; 401710617;
375068736; 381220237; 381225039; 51450507; 545770162; 301505924; 223008761;
305654864; 71017217; 171674984; 156455294; 440653369; 310776622; 381246333;
530848012; 393660591; 83266850; 223010427; 150023474; 213493011; 344267169;
150023044; 381270944; 545750325; 310776398; 381257225; 69065120; 145967460;
82492497; 444328782; 545765990; 32894300; 381251835; 251765638; 71008964;
381275452; 381226551; 240252114; 187961162; 223008985; 32894958; 381259913;
381236995; 61393516; 215883812; 171674718; 545752705; 381219971; 381243953;
83266934; 381249791; 347809526; 410064684; 385254773; 440647993; 116241692;
156455696; 381242301; 430728523; 302320751; 332379800; 381252255;
530926823; 513789526; 381273716; 381242483; 442565814; 381224437;
401711107; 375067490; 381230709; 381232823; 545753489; 223009489;
381248937"^^http://www.w3.org/2001/XMLSchema#string
http://bio2rdf.org/bio2rdf.dataset:bio2rdf-iproclass-20131213 .

Loading /var/preserve/bio2rdf/mirror/release/3/iproclass/t2.txt into
http://bio2rdf.org/iproclass ...
Skipping line:1 ... Problem in:
http://bio2rdf.org/bio2rdf_vocabulary:namespace "iproclass"^^
http://www.w3.org/2001/XMLSchema#string
http://bio2rdf.org/bio2rdf.dataset:bio2rdf-iproclass-20131213 .

Loading /var/preserve/bio2rdf/mirror/release/3/iproclass/t2.txt into
http://bio2rdf.org/iproclass ...
Skipping line:1 ... Problem in:
http://bio2rdf.org/bio2rdf_vocabulary:identifier "uniprot:75070738;
440648385; 116242084; 381277118; 223014445; 262343945; 393660255;
545765794; 326200806; 171675572; 122938060; 313267586; 381269698;
381235637; 375070038; 223011463; 168252164; 306976300; 71012654; 290544683;
552099586; 71015856; 223009293; 298367672; 381220965; 381263594; 118122797;
71017146; 283047974; 513791906; 410062122; 356476889; 126038553; 381220321;
545755337; 133712399; 119221318; 32892886; 150023363; 545773508; 71011533;
119035042; 71016641; 342840601; 410061422; 375067798; 545760936; 440652669;
94980847; 396580364; 302376750; 305655998; 545772752; 40848968; 349501937;
440653985; 302375924; 513789232; 381237709; 306976986; 385257755; 51894941;
213990019; 194580074; 290758436; 375066580; 57904139; 381242007; 218454552;
350282678; 381250715; 151334971; 381254929; 378744438; 528078892;
187960896; 224036663; 126038572 ; 156077456; 545760754; 393190388;
151334146; 496528315; 32348620; 381265624; 381267696; 381244919; 315021963;
359468606; 513790394; 334738648; 309752115; 381239417; 381231017;
381248909; 61652721; 189179453; 171675936; 401710617; 375068736; 381220237;
381225039; 51450507; 545770162; 301505924; 223008761; 305654864; 71017217;
171674984; 156455294; 440653369; 310776622; 381246333; 530848012;
393660591; 83266850; 223010427; 150023474; 213493011; 344267169; 150023044;
381270944; 545750325; 310776398; 381257225; 69065120; 145967460; 82492497;
444328782; 545765990; 32894300; 381251835; 251765638; 71008964; 381275452;
381226551; 240252114; 187961162; 223008985; 32894958; 381259913; 381236995;
61393516; 215883812; 171674718; 545752705; 381219971; 381243953; 83266934;
381249791; 347809526; 410064684; 385254773; 440647993; 116241692;
156455696; 381242301; 430728523; 302320751; 332379800; 381252255;
530926823; 513789526; 381273716; 381242483; 442565814; 381224437;
401711107; 375067490; 381230 709; 381232823; 545753489; 223009489;
381248937"^^http://www.w3.org/2001/XMLSchema#string
http://bio2rdf.org/bio2rdf.dataset:bio2rdf-iproclass-20131213 .

Reply to this email directly or view it on GitHubhttps://github.com//issues/353
.

from bio2rdf-scripts.

Sure thing, I just pulled that branch. I'll keep you posted.
~Paul

On Tue, Mar 11, 2014 at 9:43 AM, Michel Dumontier
[email protected]:

Hi Paul,
Indeed - that looks like a problem in the parsing.

https://github.com/micheldumontier/bio2rdf-scripts/blob/iproclass/iproclass/iproclass.php

wanna look into it?

m.

Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford
University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
Group
http://dumontierlab.com

On Tue, Mar 11, 2014 at 9:04 AM, Paul Rigor <[email protected]

wrote:

Has anyone encountered the following issues while loading the iproclass
dataset into virtuoso (version 7.1.0)? There seems to be a malformed quad
with multiple an invalid uniprot ids.

==Error message excerpts below==

Loading /var/preserve/bio2rdf/mirror/release/3/iproclass/t2.txt into
http://bio2rdf.org/iproclass ...
Skipping line:1 ... Problem in: http://purl.org/dc/terms/identifier"iproclass:uniprot:75070738;
440648385; 116242084; 381277118; 223014445;
262343945; 393660255; 545765794; 326200806; 171675572; 122938060;
313267586; 381269698; 381235637; 375070038; 223011463; 168252164;
306976300; 71012654; 290544683; 552099586; 71015856; 223009293;
298367672;
381220965; 381263594; 118122797; 71017146; 283047974; 513791906;
410062122;
356476889; 126038553; 381220321; 545755337; 133712399; 119221318;
32892886;
150023363; 545773508; 71011533; 119035042; 71016641; 342840601;
410061422;
375067798; 545760936; 440652669; 94980847; 396580364; 302376750;
305655998;
545772752; 40848968; 349501937; 440653985; 302375924; 513789232;
381237709;
306976986; 385257755; 51894941; 213990019; 194580074; 290758436;
375066580;
57904139; 381242007; 218454552; 350282678; 381250715; 151334971;
381254929;
378744438; 528078892; 187960896; 224036663; 126038572; 156077456; 545
760754; 393190388; 151334146; 496528315; 32348620; 381265624; 381267696;
381244919; 315021963; 359468606; 513790394; 334738648; 309752115;
381239417; 381231017; 381248909; 61652721; 189179453; 171675936;
401710617;
375068736; 381220237; 381225039; 51450507; 545770162; 301505924;
223008761;
305654864; 71017217; 171674984; 156455294; 440653369; 310776622;
381246333;
530848012; 393660591; 83266850; 223010427; 150023474; 213493011;
344267169;
150023044; 381270944; 545750325; 310776398; 381257225; 69065120;
145967460;
82492497; 444328782; 545765990; 32894300; 381251835; 251765638; 71008964;
381275452; 381226551; 240252114; 187961162; 223008985; 32894958;
381259913;
381236995; 61393516; 215883812; 171674718; 545752705; 381219971;
381243953;
83266934; 381249791; 347809526; 410064684; 385254773; 440647993;
116241692;
156455696; 381242301; 430728523; 302320751; 332379800; 381252255;
530926823; 513789526; 381273716; 381242483; 442565814; 381224437;
401711107; 375067490; 381230709; 381232823; 545753489; 223009489;
381248937"^^http://www.w3.org/2001/XMLSchema#string
http://bio2rdf.org/bio2rdf.dataset:bio2rdf-iproclass-20131213 .

Loading /var/preserve/bio2rdf/mirror/release/3/iproclass/t2.txt into
http://bio2rdf.org/iproclass ...
Skipping line:1 ... Problem in:
http://bio2rdf.org/bio2rdf_vocabulary:namespace "iproclass"^^
http://www.w3.org/2001/XMLSchema#string
http://bio2rdf.org/bio2rdf.dataset:bio2rdf-iproclass-20131213 .

Loading /var/preserve/bio2rdf/mirror/release/3/iproclass/t2.txt into
http://bio2rdf.org/iproclass ...
Skipping line:1 ... Problem in:
http://bio2rdf.org/bio2rdf_vocabulary:identifier "uniprot:75070738;
440648385; 116242084; 381277118; 223014445; 262343945; 393660255;
545765794; 326200806; 171675572; 122938060; 313267586; 381269698;
381235637; 375070038; 223011463; 168252164; 306976300; 71012654;
290544683;
552099586; 71015856; 223009293; 298367672; 381220965; 381263594;
118122797;
71017146; 283047974; 513791906; 410062122; 356476889; 126038553;
381220321;
545755337; 133712399; 119221318; 32892886; 150023363; 545773508;
71011533;
119035042; 71016641; 342840601; 410061422; 375067798; 545760936;
440652669;
94980847; 396580364; 302376750; 305655998; 545772752; 40848968;
349501937;
440653985; 302375924; 513789232; 381237709; 306976986; 385257755;
51894941;
213990019; 194580074; 290758436; 375066580; 57904139; 381242007;
218454552;
350282678; 381250715; 151334971; 381254929; 378744438; 528078892;
187960896; 224036663; 126038572 ; 156077456; 545760754; 393190388;
151334146; 496528315; 32348620; 381265624; 381267696; 381244919;
315021963;
359468606; 513790394; 334738648; 309752115; 381239417; 381231017;
381248909; 61652721; 189179453; 171675936; 401710617; 375068736;
381220237;
381225039; 51450507; 545770162; 301505924; 223008761; 305654864;
71017217;
171674984; 156455294; 440653369; 310776622; 381246333; 530848012;
393660591; 83266850; 223010427; 150023474; 213493011; 344267169;
150023044;
381270944; 545750325; 310776398; 381257225; 69065120; 145967460;
82492497;
444328782; 545765990; 32894300; 381251835; 251765638; 71008964;
381275452;
381226551; 240252114; 187961162; 223008985; 32894958; 381259913;
381236995;
61393516; 215883812; 171674718; 545752705; 381219971; 381243953;
83266934;
381249791; 347809526; 410064684; 385254773; 440647993; 116241692;
156455696; 381242301; 430728523; 302320751; 332379800; 381252255;
530926823; 513789526; 381273716; 381242483; 442565814; 381224437;
401711107; 375067490; 381230 709; 381232823; 545753489; 223009489;
381248937"^^http://www.w3.org/2001/XMLSchema#string
http://bio2rdf.org/bio2rdf.dataset:bio2rdf-iproclass-20131213 .

Reply to this email directly or view it on GitHub<
https://github.com/bio2rdf/bio2rdf-scripts/issues/353>
.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/353#issuecomment-37318417
.

from bio2rdf-scripts.

Paul, any progress on this issue?

from bio2rdf-scripts.

new files have been issued. http://download.bio2rdf.org/release/3/iproclass/

from bio2rdf-scripts.