Some questions about installing the Intermine

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Some questions about installing the Intermine

clemsonyfu
Hi, I'm a newbie, I met several problems when I tried to install the intermine in a CentOS PC box.

I installed the malariamine example successfully. I need to 1) add my own data, 2) integrate the gbrowse/jbrowse with the intermine.

1. I first deleted all of the files in the directory intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/gff and intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/fasta, I copied my own files to the two directories.
when I tried to run (cd ~/intermine_0_97/malariamine/integrate; ant -Dsource=malaria-gff -v), I got:

java.lang.IllegalArgumentException: no class found in model for: Source (original GFF record type: source) for record: <GFF3Record: sequenceID: NC_012985.2 source: RefSeq type: source start: 1 end: 1226704 score: null strand: + phase: null attributes: {organism=[Candidatus Liberibacter asiaticus str. psy62], mol_type=[genomic DNA], strain=[psy62], db_xref=[taxon:537021]}>
at org.intermine.bio.dataconversion.GFF3Converter.process(GFF3Converter.java:173)
at org.intermine.bio.dataconversion.GFF3Converter.parse(GFF3Converter.java:126)
at org.intermine.bio.task.GFF3ConverterTask.execute(GFF3ConverterTask.java:241)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
at org.intermine.task.Integrate.performAction(Integrate.java:135)
at org.intermine.task.Integrate.execute(Integrate.java:127)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
at org.apache.tools.ant.Main.runBuild(Main.java:758)
at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

2. How to setup the gbrowse?
First, I copied the whole directory from ~/intermine_0_97/flymine/gbrowse/ to ~/intermine_0_97/malariamine/.

Then I followed the instructions in the document http://intermine.org/wiki/GBrowseConfiguration. I don't know where is the file build.properties.<mine>. I put it to ~/intermine_0_97/malariamine/gbrowse/build.properties.malariamine, and run ant write-gff. I get only error:

write-gff:

BUILD FAILED
java.lang.RuntimeException: no chromosomes found
at org.intermine.bio.gbrowse.WriteGFFTask.writeGFF(WriteGFFTask.java:271)
at org.intermine.bio.gbrowse.WriteGFFTask.execute(WriteGFFTask.java:110)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
at org.apache.tools.ant.Main.runBuild(Main.java:758)
at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

Anybody can help me to install the intermine? Thanks!!!

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Re: Some questions about installing the Intermine

Julie Sullivan
Hi,

1. It looks like the parser found the word "Source" in the third column, which
is reserved for "type" (eg. gene, chromosome).  Do you have column headers in
your file?

I would recommend going through our tutorial.  It has a section on loading GFF3
files and gives an example of what the parser expects the data files to look like:

        http://www.intermine.org/wiki/GettingStarted

2. The docs were wrong, sorry!  Those properties should be in your
~/.intermine/malariamine.properties file.

You won't be able to run GBrowse on your local mine until you have genomic data
successfully loaded into your database, hence the "no chromosomes found" error.

Cheers,
Julie

On 07/28/2011 09:46 PM, clemsonyfu wrote:

> Hi, I'm a newbie, I met several problems when I tried to install the
> intermine in a CentOS PC box.
>
> I installed the malariamine example successfully. I need to 1) add my own
> data, 2) integrate the gbrowse/jbrowse with the intermine.
>
> 1. I first deleted all of the files in the directory
> intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/gff and
> intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/fasta, I copied
> my own files to the two directories.
> when I tried to run (cd ~/intermine_0_97/malariamine/integrate; ant
> -Dsource=malaria-gff -v), I got:
>
> java.lang.IllegalArgumentException: no class found in model for: Source
> (original GFF record type: source) for record:<GFF3Record: sequenceID:
> NC_012985.2 source: RefSeq type: source start: 1 end: 1226704 score: null
> strand: + phase: null attributes: {organism=[Candidatus Liberibacter
> asiaticus str. psy62], mol_type=[genomic DNA], strain=[psy62],
> db_xref=[taxon:537021]}>
>   at
> org.intermine.bio.dataconversion.GFF3Converter.process(GFF3Converter.java:173)
> at
> org.intermine.bio.dataconversion.GFF3Converter.parse(GFF3Converter.java:126)
>   at
> org.intermine.bio.task.GFF3ConverterTask.execute(GFF3ConverterTask.java:241)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>   at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>   at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
>   at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>   at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>   at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
>   at org.intermine.task.Integrate.performAction(Integrate.java:135)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
>   at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
>   at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
>   at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
>   at org.apache.tools.ant.Target.execute(Target.java:357)
> at org.apache.tools.ant.Target.performTasks(Target.java:385)
>   at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
>   at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>   at org.apache.tools.ant.Main.runBuild(Main.java:758)
> at org.apache.tools.ant.Main.startAnt(Main.java:217)
>   at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
>
> 2. How to setup the gbrowse?
> First, I copied the whole directory from ~/intermine_0_97/flymine/gbrowse/
> to ~/intermine_0_97/malariamine/.
>
> Then I followed the instructions in the document
> http://intermine.org/wiki/GBrowseConfiguration. I don't know where is the
> file build.properties.<mine>. I put it to
> ~/intermine_0_97/malariamine/gbrowse/build.properties.malariamine, and run
> ant write-gff. I get only error:
>
> write-gff:
>
> BUILD FAILED
> java.lang.RuntimeException: no chromosomes found
> at org.intermine.bio.gbrowse.WriteGFFTask.writeGFF(WriteGFFTask.java:271)
>   at org.intermine.bio.gbrowse.WriteGFFTask.execute(WriteGFFTask.java:110)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>   at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>   at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
>   at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>   at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>   at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
> at org.apache.tools.ant.Main.runBuild(Main.java:758)
>   at org.apache.tools.ant.Main.startAnt(Main.java:217)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
>   at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
>
> Anybody can help me to install the intermine? Thanks!!!
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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Re: Some questions about installing the Intermine

clemsonyfu
my data file looks like:
==========================================================================
##gff-version 3
#!gff-spec-version 1.14
#!source-version NCBI C++ formatter 0.2
##Type DNA NC_012985.2
NC_012985.2 RefSeq source 1 1226704 . + . organism=Candidatus Liberibacter asiaticus str. psy62;mol_type=genomic DNA;strain=psy62;db_xref=taxon:537021
NC_012985.2 RefSeq gene 36 407 . + . locus_tag=CLIBASIA_00005;db_xref=GeneID:8210255
NC_012985.2 RefSeq CDS 36 404 . + 0 locus_tag=CLIBASIA_00005;transl_table=11;product=hypothetical protein;protein_id=YP_003064535.1;db_xref=GI:254780122;db_xref=GeneID:8210255;exon_number=1
NC_012985.2 RefSeq start_codon 36 38 . + 0 locus_tag=CLIBASIA_00005;transl_table=11;product=hypothetical protein;protein_id=YP_003064535.1;db_xref=GI:254780122;db_xref=GeneID:8210255;exon_number=1
NC_012985.2 RefSeq stop_codon 405 407 . + 0 locus_tag=CLIBASIA_00005;transl_table=11;product=hypothetical protein;protein_id=YP_003064535.1;db_xref=GI:254780122;db_xref=GeneID:8210255;exon_number=1
NC_012985.2 RefSeq gene 497 820 . + . locus_tag=CLIBASIA_00010;db_xref=GeneID:8209098
NC_012985.2 RefSeq CDS 497 817 . + 0 locus_tag=CLIBASIA_00010;transl_table=11;product=hypothetical protein;protein_id=YP_003064536.1;db_xref=GI:254780123;db_xref=GeneID:8209098;exon_number=1
NC_012985.2 RefSeq start_codon 497 499 . + 0 locus_tag=CLIBASIA_00010;transl_table=11;product=hypothetical protein;protein_id=YP_003064536.1;db_xref=GI:254780123;db_xref=GeneID:8209098;exon_number=1
NC_012985.2 RefSeq stop_codon 818 820 . + 0 locus_tag=CLIBASIA_00010;transl_table=11;product=hypothetical protein;protein_id=YP_003064536.1;db_xref=GI:254780123;db_xref=GeneID:8209098;exon_number=1
NC_012985.2 RefSeq gene 948 2114 . + . locus_tag=CLIBASIA_00015;db_xref=GeneID:8209099
==========================================================================
It seems that the type supported for GFF3 format are only gene and mRNA in the document (http://www.intermine.org/wiki/GettingStarted#a8.2GFF3files). My data contains some types which are not supported, such as 'source'.

It seems that the exception was thrown by GFF3Converter.process (intermine_0_97/bio/core/main/src/org/intermine/bio/dataconversion/GFF3Converter.java).
The requested class is org.intermine.model.bio.Source, but it was not found.
The classes seem locate in directory intermine_0_97/malariamine/dbmodel/build/gen/src/org/intermine/model/bio.
The directory intermine_0_97/malariamine/dbmodel/build/ was generated when I run the command  'cd ~/intermine_0_97/malariamine/dbmodel && ant build-db'.
The source files of the types are listed in intermine_0_97/malariamine/dbmodel/resources/so_term_list.txt and is configed by section so-model in intermine_0_97/malariamine/dbmodel/build.xml.

How can I support type  'source'? Do I need to edit file intermine_0_97/bio/sources/so/data/so_2_4_4.obo?


On Fri, Jul 29, 2011 at 3:57 AM, Julie Sullivan <[hidden email]> wrote:
Hi,

1. It looks like the parser found the word "Source" in the third column, which is reserved for "type" (eg. gene, chromosome).  Do you have column headers in your file?

I would recommend going through our tutorial.  It has a section on loading GFF3 files and gives an example of what the parser expects the data files to look like:

       http://www.intermine.org/wiki/GettingStarted

2. The docs were wrong, sorry!  Those properties should be in your ~/.intermine/malariamine.properties file.

You won't be able to run GBrowse on your local mine until you have genomic data successfully loaded into your database, hence the "no chromosomes found" error.

Cheers,
Julie


On 07/28/2011 09:46 PM, clemsonyfu wrote:
Hi, I'm a newbie, I met several problems when I tried to install the
intermine in a CentOS PC box.

I installed the malariamine example successfully. I need to 1) add my own
data, 2) integrate the gbrowse/jbrowse with the intermine.

1. I first deleted all of the files in the directory
intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/gff and
intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/fasta, I copied
my own files to the two directories.
when I tried to run (cd ~/intermine_0_97/malariamine/integrate; ant
-Dsource=malaria-gff -v), I got:

java.lang.IllegalArgumentException: no class found in model for: Source
(original GFF record type: source) for record:<GFF3Record: sequenceID:
NC_012985.2 source: RefSeq type: source start: 1 end: 1226704 score: null
strand: + phase: null attributes: {organism=[Candidatus Liberibacter
asiaticus str. psy62], mol_type=[genomic DNA], strain=[psy62],
db_xref=[taxon:537021]}>
 at
org.intermine.bio.dataconversion.GFF3Converter.process(GFF3Converter.java:173)
at
org.intermine.bio.dataconversion.GFF3Converter.parse(GFF3Converter.java:126)
 at
org.intermine.bio.task.GFF3ConverterTask.execute(GFF3ConverterTask.java:241)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
 at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:616)
at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
 at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
 at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
 at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
 at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
 at org.intermine.task.Integrate.performAction(Integrate.java:135)
at org.intermine.task.Integrate.execute(Integrate.java:127)
 at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
 at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
 at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
 at org.apache.tools.ant.Target.execute(Target.java:357)
at org.apache.tools.ant.Target.performTasks(Target.java:385)
 at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
 at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
 at org.apache.tools.ant.Main.runBuild(Main.java:758)
at org.apache.tools.ant.Main.startAnt(Main.java:217)
 at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

2. How to setup the gbrowse?
First, I copied the whole directory from ~/intermine_0_97/flymine/gbrowse/
to ~/intermine_0_97/malariamine/.

Then I followed the instructions in the document
http://intermine.org/wiki/GBrowseConfiguration. I don't know where is the
file build.properties.<mine>. I put it to
~/intermine_0_97/malariamine/gbrowse/build.properties.malariamine, and run
ant write-gff. I get only error:

write-gff:

BUILD FAILED
java.lang.RuntimeException: no chromosomes found
at org.intermine.bio.gbrowse.WriteGFFTask.writeGFF(WriteGFFTask.java:271)
 at org.intermine.bio.gbrowse.WriteGFFTask.execute(WriteGFFTask.java:110)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
 at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:616)
at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
 at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
 at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
 at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
 at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
at org.apache.tools.ant.Main.runBuild(Main.java:758)
 at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
 at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

Anybody can help me to install the intermine? Thanks!!!




_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: Some questions about installing the Intermine

Julie Sullivan


On 08/01/2011 11:50 PM, clemsonyfu wrote:

> my data file looks like:
> ==========================================================================
> ##gff-version 3
> #!gff-spec-version 1.14
> #!source-version NCBI C++ formatter 0.2
> ##Type DNA NC_012985.2
> NC_012985.2 RefSeq source 1 1226704 . + . organism=Candidatus Liberibacter
> asiaticus str. psy62;mol_type=genomic DNA;strain=psy62;db_xref=taxon:537021
> NC_012985.2 RefSeq gene 36 407 . + .
> locus_tag=CLIBASIA_00005;db_xref=GeneID:8210255
> ==========================================================================
> It seems that the type supported for GFF3 format are only gene and mRNA in
> the document (http://www.intermine.org/wiki/GettingStarted#a8.2GFF3files).
> My data contains some types which are not supported, such as 'source'.

Yes, that 3rd column has to be a valid sequence ontology term; that's an invalid
GFF3 file.  I would remove that line.

> intermine_0_97/malariamine/dbmodel/build.xml.
>
> How can I support type  'source'? Do I need to edit
> file intermine_0_97/bio/sources/so/data/so_2_4_4.obo?

No, you don't want to edit the OBO file, that loads the sequence ontology terms
and their relationships.

You can add classes to the model by editing the model XML files.  I would
recommend going through our tutorial here:

        http://intermine.org/wiki/GettingStarted

It doesn't take too long and it does a step by step of editing the model and
loading a GFF3 file.  I think it might make things clearer!

Cheers,
Julie

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dev mailing list
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