search

PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
6 stars 5 forks source link

Integrate I2D (human) data #279

Closed IgorRodchenkov closed 5 years ago

IgorRodchenkov commented 6 years ago

Interologous Interaction Database (I2D)

IgorRodchenkov commented 6 years ago

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.

IgorRodchenkov commented 6 years ago

News: @gbader, @jvwong - IID is a major replacement of the I2D; see PMID:26516188

And these probably contain (integrate) other PSI data sources IntAct, BioGRID, HPRD, which we have been using already...

IgorRodchenkov commented 6 years ago

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
gbader commented 6 years ago

Should we forget about i2d?

On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, notifications@github.com 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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/cpath2/issues/279#issuecomment-380613720, or mute the thread https://github.com/notifications/unsubscribe-auth/AA8X5-GSiGma03lxa_2zGs-dcLxb_Y4tks5tnoEtgaJpZM4Oz6xx .

IgorRodchenkov commented 6 years ago

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 notifications@github.com wrote:

Should we forget about i2d?

On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, notifications@github.com 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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/cpath2/issues/279#issuecomment-380613720, or mute the thread https://github.com/notifications/unsubscribe-auth/AA8X5-GSiGma03lxa_2zGs-dcLxb_Y4tks5tnoEtgaJpZM4Oz6xx .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

IgorRodchenkov commented 6 years ago

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 rodche@gmail.com 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 notifications@github.com wrote:

Should we forget about i2d?

On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, notifications@github.com 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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/cpath2/issues/ 279#issuecomment-380613720, or mute the thread https://github.com/notifications/unsubscribe- auth/AA8X5-GSiGma03lxa_2zGs-dcLxb_Y4tks5tnoEtgaJpZM4Oz6xx .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/cpath2/issues/279#issuecomment-381262469, or mute the thread https://github.com/notifications/unsubscribe-auth/AA8fwYNi9aOpMOjQr3oSacdOgskpQKDsks5toRVzgaJpZM4Oz6xx .

IgorRodchenkov commented 6 years ago

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 rodche@gmail.com 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 rodche@gmail.com 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 notifications@github.com wrote:

Should we forget about i2d?

On Wed, Apr 11, 2018, 6:18 PM Igor Rodchenkov, notifications@github.com 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 https://github.com/PathwayCommons/cpath2/issues/279# issuecomment-380613720, or mute the thread https://github.com/notifications/unsubscribe-auth/AA8X5- GSiGma03lxa_2zGs-dcLxb_Y4tks5tnoEtgaJpZM4Oz6xx .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/cpath2/issues/279#issuecomment-381262469, or mute the thread https://github.com/notifications/unsubscribe-auth/AA8fwYNi9aOpMOjQr3oSacdOgskpQKDsks5toRVzgaJpZM4Oz6xx .

IgorRodchenkov commented 5 years ago

I2D is also part of IntAct.