add male fruitless stacks about vfb

[dosumis]

We have Python code for adding the individuals to the DB. Just need a ref for source + table of name + type.

[dosumis]

If these have not been added yet, can you provide a tsv of names, types and file paths? Otherwise please close. Cheers, David

[dosumis]

Where are we with this? Can we fit it into a December release. (Assuming we can so assigning to December release Milestone)

[mmc46]

This information (except for types) was sent to Nestor in July 2013, so I'm assuming it's somewhere in Edinburgh. I can provide it again if need be.

See https://gist.github.com/mmc46/ca968041d4ef37f766a2
for tsv files for original stacks and thumbnail images.

Files are here
https://www.dropbox.com/s/icpmzhrscczt79u/CanonicalClones-4xd-quant.JFRC2-M.tar.gz?dl=0
https://www.dropbox.com/s/dulv4ekvmtti42w/CanonicalClones-4xd-quant.JFRC2.mzpng-M.tar.gz?dl=0

[Robbie1977]

@dosumis can we start the ID's from VFB_00016227 as we have a massive gap or are we keeping this for anything?
Tzumins data is the next at VFB_00020000

[dosumis]

Individuals for these are now in the OWL. Have kept short names for now, but we should probably harmonise names with others from same dataset. (Note - having serious doubts about sustainability of keeping long, descriptive names for individuals). Committed to Sandbox, so should be visible there shortly.

[Robbie1977]

Something the ontserver doesn't like:
uk.ac.ebi.brain.error.ClassExpressionException: org.semanticweb.owlapi.expression.ParserException: Encountered C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 at line 1 column 62. Expected one of:
Class name
Object property name
Data property name
not
inverse
Self
(
{

at uk.ac.ebi.brain.core.Brain.parseClassExpression(Brain.java:1215)
at uk.ac.ebi.brain.core.Brain.getInstances(Brain.java:1746)
at uk.ac.ed.vfb.dao.client_server.server_includes.DLQUeryEngineBrainInd.askQuery(DLQUeryEngineBrainInd.java:41)
at uk.ac.ed.vfb.dao.client_server.server_includes.DLQueryServer.askQuery(DLQueryServer.java:94)
at uk.ac.ed.vfb.dao.client_server.Server$ClientHandler.run(Server.java:151)

Caused by: org.semanticweb.owlapi.expression.ParserException: Encountered C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 at line 1 column 62. Expected one of:
Class name
Object property name
Data property name
not
inverse
Self
(
{

at org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.createException(ManchesterOWLSyntaxEditorParser.java:2772)
at org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseObjectRestriction(ManchesterOWLSyntaxEditorParser.java:745)
at org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseNonNaryClassExpression(ManchesterOWLSyntaxEditorParser.java:709)
at org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseUnion(ManchesterOWLSyntaxEditorParser.java:625)
at org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseIntersection(ManchesterOWLSyntaxEditorParser.java:603)
at org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseClassExpression(ManchesterOWLSyntaxEditorParser.java:591)
at uk.ac.ebi.brain.core.Brain.parseClassExpression(Brain.java:1213)
... 4 more

java.lang.NullPointerException
at uk.ac.ed.vfb.dao.client_server.server_includes.DLQUeryEngineBrainInd.askQuery(DLQUeryEngineBrainInd.java:47)
at uk.ac.ed.vfb.dao.client_server.server_includes.DLQueryServer.askQuery(DLQueryServer.java:94)
at uk.ac.ed.vfb.dao.client_server.Server$ClientHandler.run(Server.java:151)

[Robbie1977]

The new individuals OWL does seem odd as previously:
Declaration(Class(http://flybase.org/reports/FBti0016783))
AnnotationAssertion(rdfs:label http://flybase.org/reports/FBti0016783 "P{GawB}GH146"^^xsd:string)
Declaration(Class(http://flybase.org/reports/FBti0132502))
AnnotationAssertion(rdfs:label http://flybase.org/reports/FBti0132502 "P{GAL4}G0239"^^xsd:string)

Where as the new one has just Declaration - might be further on but seems odd:
Declaration(Class(http://flybase.org/reports/FBti0016783))
Declaration(Class(http://flybase.org/reports/FBti0132502))
Declaration(Class(http://flybase.org/reports/FBti0143413))

[Robbie1977]

@dosumis if you can give me a list of vfbIDs to the file names I can add them in ready.

[dosumis]

Looks like failure to merge in a support file. Could be an issue with shell
script arising from branch merge to master I did this aft. Will fix
tomorrow morning, and send mapping at same time.
On 18 Feb 2015 20:53, "Robbie1977" [email protected] wrote:

@dosumis https://github.com/dosumis if you can give me a list of vfbIDs
to the file names I can add them in ready.

—
Reply to this email directly or view it on GitHub
#177 (comment).

[dosumis]

Found the problem. While trying to fix the reasoning bug, I switched out shortFormIDs with leading digits - as I suspected one problem may be a bug in shortForm parsing. Have updated individual build code to reflect this. Rebuilding now.

BTW - the apparent difference in content you flagged is just a difference in line ordering. The same axioms are in the new file - just not in the same place.

[dosumis]

Mapping here: https://gist.github.com/dosumis/410663ada7e1778f44ad

[dosumis]

Still problems with OWL gen. Fixing now.

[Robbie1977]

Files added to new file system

[Robbie1977]

Definitely still not happy:
http://vfbsandbox.inf.ed.ac.uk/logs/

Files are all live on sandbox:
http://vfbsandbox.inf.ed.ac.uk/owl/VFBi_00017910/

[Robbie1977]

BTW Would rather solve #442 than add to VFB DB.

[dosumis]

Still seeing: Encountered C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 at line 1 column 62. Expected one of: Class name Object property name Data property name not inverse Self

But this looks fine in the file.

Are you sure it's running the latest. I did post an interim version that was still broken ealier this afternoon.

One thing we need to fix. The VFB build shell script is not failing when jobs in the middle of the script fail. Posting of bad files is mainly due to that (although I think not in this case). Will fix tomorrow - or you could have a go if you have time.

[Robbie1977]

Have you forced the ontology server to restart - should auto restart when owl changed plus also worth restarting tomcat to be sure - all done from jenkins.
I'll check now.

[Robbie1977]

Still giving a similar error
It updated and decompressed the individual owl file 19-Feb-2015 18:29:42

[Robbie1977]

The individuals file is working OK if deployed on jenkins think you must of had a merge issue.
There is a process to deploy it - could link automatically if you like?

Live on the sandbox server if you want to check everything is there.

[dosumis]

Deploy from Jenkins to Sandbox would be good. But we need to work on the Jenkins shell script first. Needs to be set up to return false if intermediate jobs fail.

[Robbie1977]

All ready just need to either add to VFB DB or bypass to owl - going to take a look at feasibility this weekend.
http://vfbsandbox.inf.ed.ac.uk/site/tools/view_stack/3rdPartyStack.htm?tpbid=VFB_00017893

[Robbie1977]

New individuals lacking some details:

Declaration(NamedIndividual(http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017893))
AnnotationAssertion(Annotation(http://www.geneontology.org/formats/oboInOwl#hasDbXref "PMID:20832311"^^xsd:string) http://purl.obolibrary.org/obo/IAO_0000115 http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017893 ""^^xsd:string)
AnnotationAssertion(rdfs:label http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017893 "aDT-b_M"^^xsd:string)
ClassAssertion(owl:Thing http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017893)

Previous example:
Declaration(NamedIndividual(http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017892))
AnnotationAssertion(Annotation(http://www.geneontology.org/formats/oboInOwl#hasDbXref "PMID:20832311"^^xsd:string) http://purl.obolibrary.org/obo/IAO_0000115 http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017892 "An example of an adult fruitless aDT-a lineage clone in the adult brain"^^xsd:string)
AnnotationAssertion(rdfs:label http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017892 "aDT-a_M"^^xsd:string)
ClassAssertion(http://purl.obolibrary.org/obo/FBbt_00110414 http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017892)
ClassAssertion(ObjectSomeValuesFrom(http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/FBbt_00003624) http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017892)
ClassAssertion(ObjectSomeValuesFrom(http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/FBbt_00007004) http://vfbsandbox3.inf.ed.ac.uk/owl/VFB_00017892)

No Definition for one plus is there no more data for them?

[Robbie1977]

@mmc46 do we have the FlyCircuit ids?

[dosumis]

Hi Robbie, I'll provide the FlyCircuit id mapping. (roll on ditching the VFB postgres DB...)

[Robbie1977]

@dosumis Could we include the remote URI in the OWL?

[dosumis]

Scratch that these things are from FlyCircuit - so request makes no sense.

Yes, it is possible to include the remote URI in the OWL.

My first instinct was to use the standard xref annotation property. The axioms have value = string that is conventionally structured as DB:accession. This is what we already use, along with a standard recipe, for rolling linkouts. We could (ab)use this field by adding values of the form (source:full_url), but this will be messy to parse. So, I'm inclined to add a new annotation property for data_source_link with string value = full URL. This can be generated from a recipe specified in the data_source table of the VFB_owl database.

[Robbie1977]

So to clarify these are from CacheroOstrovsky2010 and the external link should be http://flybase.org/reports/FBrf0211926.html or would http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:start be more useful as the Publication would be in the definition.

@dosumis can we change to FBrf (when available) rather than PMID just to be more consistent.

[mmc46]

The source should be http://flybase.org/reports/FBrf0211926.html.

On 23 Feb 2015, at 14:19, Robbie1977 [email protected] wrote:

So to clarify these are from CacheroOstrovsky2010 and the external link should be http://flybase.org/reports/FBrf0211926.html or would http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:start be more useful as the Publication would be in the definition.

@dosumis can we change to FBrf (when available) rather than PMID just to be more consistent.

—
Reply to this email directly or view it on GitHub.

[Robbie1977]

@mmc46 This is only for the source link - usually the link to the original data and the paper is already in the references. The wiki page does a better job of explaining the alignment and giving links to original data and hence I think is a more useful link?

[mmc46]

I can see that it would be useful, but possibly confusing because the wiki page gives info on the registration of the original data, not on the bridged one that we have on the site (and the only place where the template is named is in the command in the 'Registration parameters' section).

Regardless, the link to the wiki could be added here.

http://www.virtualflybrain.org/site/vfb_site/image_data_downloads.htm

[Robbie1977]

Then how about an internal link to the correct section of the image data downloads page.

[mmc46]

Ok.
For consistency, should we do the same to the rest of the image data in the downloads page?

[Robbie1977]

Agreed but this is only where the original data is not directly available
online.

On Mon Feb 23 2015 at 4:08:23 PM mmc46 [email protected] wrote:

Ok.
For consistency, should we do the same to the rest of the image data in
the downloads page?

—
Reply to this email directly or view it on GitHub
#177 (comment).