micheldumontier / pdb2rdf Goto Github PK

The UI proxy sometimes does no return anything. 

There is no crystal type

http://quebec.pdb.bio2rdf.org/describe/?url=http://bio2rdf.org/pdb:119D/crystal&
sid=14

@SubclassOf([Class])
@Label([String])
@Description([String])
... etc.

Make sure that the site at http://semanticscience.org/projects/pdb2rdf needs 
to be updated.

Links to the working version of the GUI also need to be checked.

no needed any more

Make the URIs for all records use only uppercase letters so that it's 
consistent with UniProt's URI patterns.

pdb2rdf currently looks horrible. Please fix me! 

The refinement category is not typed

see 
http://quebec.pdb.bio2rdf.org/describe/?url=http://bio2rdf.org/pdb:119D/refineme
nt&sid=14 for an example

There is no unit cell type

http://quebec.pdb.bio2rdf.org/describe/?url=http://bio2rdf.org/pdb:119D/crystal/
unitCell&sid=14

A downloadable version of PDB2RDF should be made available

Models need to always appears

All atoms should have a generic "atom" type added to them on top of the i.e.: 
pdb:NitrogenAtom type.

incorporate additional information about the refinement process

SLF4J Exception ... mutiple slf4j bindings. See exception:


SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in 
[jar:file:/home/jose/pdb2rdf-cli-0.0.9/lib/pdb2rdf-cli-0.0.9-jar-with-dependenci
es.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in 
[jar:file:/home/jose/pdb2rdf-cli-0.0.9/lib/slf4j-log4j12-1.5.8.jar!/org/slf4j/im
pl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.

Luego de borrar el slf4j-log4j12-1.5.8.jar de lib/ me encontre con este 
problemon::


java.lang.NullPointerException
        at com.dumontierlab.pdb2rdf.Pdb2Rdf$1.run(Pdb2Rdf.java:195)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
ERROR [pool-1-thread-11] (Pdb2Rdf.java:213) - Unable to parse input for PDB: 
null
java.lang.NullPointerException
        at com.dumontierlab.pdb2rdf.Pdb2Rdf$1.run(Pdb2Rdf.java:195)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
ERROR [pool-1-thread-2] (Pdb2Rdf.java:213) - Unable to parse input for PDB: null
java.lang.NullPointerException
        at com.dumontierlab.pdb2rdf.Pdb2Rdf$1.run(Pdb2Rdf.java:195)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
ERROR [pool-1-thread-5] (Pdb2Rdf.java:213) - Unable to parse input for PDB: null
java.lang.NullPointerException
        at com.dumontierlab.pdb2rdf.Pdb2Rdf$1.run(Pdb2Rdf.java:195)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
ERROR [pool-1-thread-11] (Pdb2Rdf.java:213) - Unable to parse input for PDB: 
null
java.lang.NullPointerException
        at com.dumontierlab.pdb2rdf.Pdb2Rdf$1.run(Pdb2Rdf.java:195)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)

All properties in dcelements are now found under the dcterms namespace

Currently the RDF produced utilizes pdb:CartesianCoordinateComponent as the 
type for the atom spatial locations X Y and Z parts. 
The types XCartesianComponent, YCartesianComponent and ZCartesianComponent 
must be added and associated with their respective atom spatial locations

Print stats to file.

The PDB2RDFui currently poses a query to the endpoint that has no types set 
in it.

Based on the following SELECT query produce the correct Construct query:
PREFIX dc: <http://purl.org/dc/terms/>
PREFIX pdb: <http://bio2rdf.org/pdb:>
SELECT* 
WHERE{
<http://bio2rdf.org/pdb:1Y26> dc:hasPart ?structure_deter.
?structure_deter pdb:hasProduct ?model.
?model a pdb:Model.
?model dc:hasPart ?atom_sl.
?atom a ?atomType.
?atom pdb:hasSpatialLocation ?atom_sl.
?atom_sl a pdb:AtomSpatialLocation.
?atom_sl pdb:hasXCoordinate ?xcoord.
?atom_sl pdb:hasYCoordinate ?ycoord.
?atom_sl pdb:hasZCoordinate ?zcoord.
?xcoord pdb:hasValue ?xval.
?ycoord pdb:hasValue ?yval.
?zcoord pdb:hasValue ?zval.
}LIMIT 1 

The pdb2rdf-cluster module throws a NullpointerException when started

needs to add Refinement class

Currently there is a pdb:hasPart relation between the atom URI 
(http://bio2rdf.org/pdb:1AM0/atomSpatialLocation_13) and its corresponding 
atom spatial location URI (http://bio2rdf.org/pdb:1AM0/atom_A6_N9) 

The statistics should be printed regardless of any errors. For example, if 
PDB2RDF has a out of memory error then the statistics should be produced for 
all files up to the one that produced the problem

Currently the -stats option in PDB2RDF mis-counts the number of instances of 
certain types.
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