Integrate I2D (human) data #279
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So, we'll simply run the Paxtools' psimi-converter to auto-convert these data to BioPAX Level3 (see also cli command: toLevel3), to integrate into PC10 - the same way we process IntAct, BioGRID, etc.. Nothing else to do. |
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Looks, there are syntax errors in I2D PSI-MI XML data (JAXB fails; the same command/tool does not fail when dealing with HPRD, IntAct, BioGRID, etc., PSI-MI data)...
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Should we forget about i2d?
…On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, ***@***.***> wrote:
Looks, there are syntax errors in I2D PSI-MI XML data (JAXB fails; the
same command/tool does not fail when dealing with HPRD, IntAct, BioGRID,
etc., PSI-MI data)...
java -Xmx16g -jar paxtools.jar toLevel3 i2d.psimi.xml i2d.owl
Exception in thread "main" java.lang.RuntimeException: Failed to convert i2d.psimi.xmlto BioPAX L3
at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:233)
at org.biopax.paxtools.Main$Command$6.run(Main.java:66)
at org.biopax.paxtools.Main.main(Main.java:22)
Caused by: java.lang.IllegalArgumentException: You must give a non null JAXB Source.
at psidev.psi.mi.xml.converter.impl253.SourceConverter.fromJaxb(SourceConverter.java:52)
at psidev.psi.mi.xml.converter.impl253.EntryConverter.fromJaxb(EntryConverter.java:100)
at psidev.psi.mi.xml.converter.impl253.EntrySetConverter.fromJaxb(EntrySetConverter.java:85)
at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.convertInMemory(PsimiXmlReader253.java:124)
at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.read(PsimiXmlReader253.java:73)
at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:65)
at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:50)
at org.biopax.paxtools.converter.psi.PsiToBiopax3Converter.convert(PsiToBiopax3Converter.java:104)
at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:221)
... 2 more
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Igor J. sent me another link to i2d human data v2.9; I am trying that...
Also, he said they will release IID in PSI-MI eventually... I2D hasn’t been updated for quite a while.
… On Apr 13, 2018, at 5:15 PM, Gary Bader ***@***.***> wrote:
Should we forget about i2d?
On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, ***@***.***>
wrote:
> Looks, there are syntax errors in I2D PSI-MI XML data (JAXB fails; the
> same command/tool does not fail when dealing with HPRD, IntAct, BioGRID,
> etc., PSI-MI data)...
>
> java -Xmx16g -jar paxtools.jar toLevel3 i2d.psimi.xml i2d.owl
>
> Exception in thread "main" java.lang.RuntimeException: Failed to convert i2d.psimi.xmlto BioPAX L3
> at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:233)
> at org.biopax.paxtools.Main$Command$6.run(Main.java:66)
> at org.biopax.paxtools.Main.main(Main.java:22)
> Caused by: java.lang.IllegalArgumentException: You must give a non null JAXB Source.
> at psidev.psi.mi.xml.converter.impl253.SourceConverter.fromJaxb(SourceConverter.java:52)
> at psidev.psi.mi.xml.converter.impl253.EntryConverter.fromJaxb(EntryConverter.java:100)
> at psidev.psi.mi.xml.converter.impl253.EntrySetConverter.fromJaxb(EntrySetConverter.java:85)
> at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.convertInMemory(PsimiXmlReader253.java:124)
> at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.read(PsimiXmlReader253.java:73)
> at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:65)
> at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:50)
> at org.biopax.paxtools.converter.psi.PsiToBiopax3Converter.convert(PsiToBiopax3Converter.java:104)
> at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:221)
> ... 2 more
>
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Well, that one is also broken too; so I give up on I2D - will wait for *IID*
PSI-MI (to try it later, in PC11, probably).
…On Fri, Apr 13, 2018 at 5:20 PM, Igor R ***@***.***> wrote:
Igor J. sent me another link to i2d human data v2.9; I am trying that...
Also, he said they will release IID in PSI-MI eventually... I2D hasn’t
been updated for quite a while.
On Apr 13, 2018, at 5:15 PM, Gary Bader ***@***.***> wrote:
Should we forget about i2d?
On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, ***@***.***>
wrote:
> Looks, there are syntax errors in I2D PSI-MI XML data (JAXB fails; the
> same command/tool does not fail when dealing with HPRD, IntAct, BioGRID,
> etc., PSI-MI data)...
>
> java -Xmx16g -jar paxtools.jar toLevel3 i2d.psimi.xml i2d.owl
>
> Exception in thread "main" java.lang.RuntimeException: Failed to convert
i2d.psimi.xmlto BioPAX L3
> at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:233)
> at org.biopax.paxtools.Main$Command$6.run(Main.java:66)
> at org.biopax.paxtools.Main.main(Main.java:22)
> Caused by: java.lang.IllegalArgumentException: You must give a non null
JAXB Source.
> at psidev.psi.mi.xml.converter.impl253.SourceConverter.
fromJaxb(SourceConverter.java:52)
> at psidev.psi.mi.xml.converter.impl253.EntryConverter.
fromJaxb(EntryConverter.java:100)
> at psidev.psi.mi.xml.converter.impl253.EntrySetConverter.
fromJaxb(EntrySetConverter.java:85)
> at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.convertInMemory(
PsimiXmlReader253.java:124)
> at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.read(
PsimiXmlReader253.java:73)
> at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:65)
> at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:50)
> at org.biopax.paxtools.converter.psi.PsiToBiopax3Converter.
convert(PsiToBiopax3Converter.java:104)
> at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:221)
> ... 2 more
>
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> <https://github.com/PathwayCommons/cpath2/issues/
279#issuecomment-380613720>,
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<#279 (comment)>,
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Does it make sense to build a from IID (TSV format) to BioPAX converter
from scratch?
I could start this (next IID PSIMITAB version will likely arrive in several
weeks...)
Example data:
uniprot1^Iuniprot2^Isymbol1^Isymbol2^Imethods^Ipmids^Idbs^Ievidence
type^Iadipose tissue^Iadrenal gland^Iamygdala^Ibone^Ibone
marrow^Ibrain^Idorsal root ganglia^Ieye^Iheart^Ihindgut^
Ihypothalamus^Ikidney^IQ96DB2^IQ96EY1^IHDAC11^IDNAJA3^Iaffinity
chromatography technology,anti tag coimmunoprecipitation^
I23752268^Ibiogrid,intact^Iexp^IG^IG^IG^IG^IG^IG^IG^I-^
IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^IG^I
...
Otherwise, let's postpone adding IID/I2D untill PC10 (December?)
IR.
…On Sat, Apr 14, 2018 at 1:18 AM, Igo R ***@***.***> wrote:
Well, that one is also broken too; so I give up on I2D - will wait for
*IID* PSI-MI (to try it later, in PC11, probably).
On Fri, Apr 13, 2018 at 5:20 PM, Igor R ***@***.***> wrote:
> Igor J. sent me another link to i2d human data v2.9; I am trying that...
> Also, he said they will release IID in PSI-MI eventually... I2D hasn’t
> been updated for quite a while.
>
>
>
>
>
> On Apr 13, 2018, at 5:15 PM, Gary Bader ***@***.***> wrote:
>
> Should we forget about i2d?
>
> On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, ***@***.***>
> wrote:
>
> > Looks, there are syntax errors in I2D PSI-MI XML data (JAXB fails; the
> > same command/tool does not fail when dealing with HPRD, IntAct, BioGRID,
> > etc., PSI-MI data)...
> >
> > java -Xmx16g -jar paxtools.jar toLevel3 i2d.psimi.xml i2d.owl
> >
> > Exception in thread "main" java.lang.RuntimeException: Failed to
> convert i2d.psimi.xmlto BioPAX L3
> > at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:233)
> > at org.biopax.paxtools.Main$Command$6.run(Main.java:66)
> > at org.biopax.paxtools.Main.main(Main.java:22)
> > Caused by: java.lang.IllegalArgumentException: You must give a non
> null JAXB Source.
> > at psidev.psi.mi.xml.converter.impl253.SourceConverter.fromJaxb
> (SourceConverter.java:52)
> > at psidev.psi.mi.xml.converter.impl253.EntryConverter.fromJaxb(
> EntryConverter.java:100)
> > at psidev.psi.mi.xml.converter.impl253.EntrySetConverter.fromJa
> xb(EntrySetConverter.java:85)
> > at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.convertInMemory(
> PsimiXmlReader253.java:124)
> > at psidev.psi.mi.xml.io.impl.PsimiXmlReader253.read(PsimiXmlRea
> der253.java:73)
> > at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:65)
> > at psidev.psi.mi.xml.PsimiXmlReader.read(PsimiXmlReader.java:50)
> > at org.biopax.paxtools.converter.psi.PsiToBiopax3Converter.conv
> ert(PsiToBiopax3Converter.java:104)
> > at org.biopax.paxtools.PaxtoolsMain.toLevel3(PaxtoolsMain.java:221)
> > ... 2 more
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#279#
> issuecomment-380613720>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AA8X5-
> GSiGma03lxa_2zGs-dcLxb_Y4tks5tnoEtgaJpZM4Oz6xx>
> > .
> >
>
> —
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> <#279 (comment)>,
> or mute the thread
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>
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I2D is also part of IntAct. |
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Interologous Interaction Database (I2D)
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