wikipathways / reactome2gpml-converter Goto Github PK
View Code? Open in Web Editor NEWConverts Reactome pathways to GPML format
License: Other
Converts Reactome pathways to GPML format
License: Other
a clear from this recent curation event in WP4082:
Problems with converting megapathways from Version 53
In the current GPML created some labels have redundant spaces at the end of labels, e.g. in WP3579:
<DataNode TextLabel="PC " GraphId="cdb40" Type="Metabolite" GroupRef="bbf32">
<Attribute Key="cellular_location" Value="endoplasmic reticulum membrane" />
<Attribute Key="complex_id" Value="R-ALL-5684863" />
<Attribute Key="copies_num" Value="1" />
<Graphics CenterX="240.0" CenterY="1851.0" Width="100.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="ChEBI" ID="CHEBI:16110" />
</DataNode>
Duplicates found in complex component list should be store instead of deleted
Names of GPML files should be changed to reactomeID.gpml i.s.o. pathway title. (lots of special characters)
WP2767 does not have any elements: http://wikipathways.org/index.php/Pathway:WP2767
reported by Anders
This is the error I get using the converter.
GKBReader.createRenderableFromType(): java.lang.ClassNotFoundException: org.gk.render.RenderableEntitySet
java.lang.ClassNotFoundException: org.gk.render.RenderableEntitySet
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:191)
at org.gk.persistence.GKBReader.createRenderableFromType(GKBReader.java:648)
at org.gk.persistence.GKBReader.createRenderableFromElement(GKBReader.java:632)
at org.gk.persistence.GKBReader.openNodes(GKBReader.java:474)
at org.gk.persistence.GKBReader.openProcess(GKBReader.java:398)
at org.gk.persistence.GKBReader.openProcess(GKBReader.java:312)
at org.gk.persistence.DiagramGKBReader.openProcess(DiagramGKBReader.java:68)
at org.gk.persistence.DiagramGKBReader.openDiagram(DiagramGKBReader.java:62)
at org.reactome.convert.common.AbstractConverterFromReactome.queryPathwayDiagram(AbstractConverterFromReactome.java:199)
at org.gk.gpml.ReactometoGPML2013.convertPathway(ReactometoGPML2013.java:489)
at org.gk.gpml.CLIConverter.convertReactomeToGPML(CLIConverter.java:126)
at org.gk.gpml.CLIConverter.convertReactomeToGPMLByID(CLIConverter.java:162)
at org.gk.gpml.CLIConverter.main(CLIConverter.java:42)
The renderable entity set (equivalent to the Pathway Class on our end) seems to be missing.
List of non renderable pathways in version 50 : https://cloud.bigcat.maastrichtuniversity.nl/public.php?service=files&t=e5900286773689ce08820c088bd57f5e
The pathway http://test2.wikipathways.org/index.php/Pathway:WP2655 does not display in my browser.
Identical references on interactions and anchor points seem repetitive. For cases with references on one or more interactions leading to an anchor point, the anchor point also lists the same references, which makes the pathways look busier than necessary and doesn’t really add any information. Is it OK to skip the references at the level of the anchor and keep them just for the incoming interactions? See the attached for an example. Note that I dragged the horizontal interaction (with the anchors) up a bit to show the references clearer.
This PW has been updated to version 65, but doesn't exist in 66. However, the description mentions that it will be created in the future. I'll leave the pathway in for now, have to check version 67 for presence of PW.
Hi Anwesha,
After reviewing about half of the pathways, here’s what I found:
Thanks,
Kristina
How can I compile the source code, and how do I run the converter? What do I need to do to set up MySQL? Etc.
All proteins annotated with datasource uniprot-swissprot should be annotated with uniprot-trembl
It seems to coincide with nodes that have “Reference Entity” listed as “Unkown:Unknown" in Reactome. I don’t recall if this was the case with the human converted pathways also. Could we still add the node, just with an empty xref, but with the same label as Reactome?
Example: http://www.wikipathways.org/index.php/Pathway:WP3111
Instead of:
<Xref Database="ChEBI" ID="15379" />
Please output the identifiers as:
<Xref Database="ChEBI" ID="CHEBI:15379" />
Optimize layout of complex components to save space
Another 2 exceptions, which I've seen for version 66 but also previous ones:
"java.lang.IllegalArgumentException : no DataSource known for PubChem Compound "
&
"java.lang.IllegalArgumentException : no DataSource known for NCBI Nucleotide "
Have to check out why the datasource annotation is not working in this case...
one pathway with serious issues: http://www.wikipathways.org/index.php/Pathway:WP2972
Complex nodes and their component should be linked using a dynamic property complex_id. This can be used to connect the components in the RDF and in the ComplexViz Plugin.
... pointing the /home/... Please use relative paths.
Some of the plant pathways in the list seem to have a diagram. Check out what might be wrong : https://cloud.bigcat.maastrichtuniversity.nl/public.php?service=files&t=16fe7b31fb69cb5c3efcf26427b81cf4
.svn/ folders should not be there, but please also remove folder with autogenerated content, like bin/, and the SVN folders like trunk/ and branches/.
Anwesha, can you please have a look at these two WikiPathways commits I made:
http://www.wikipathways.org/index.php?title=Pathway%3AWP2678&diff=78711&oldid=76870
http://www.wikipathways.org/index.php?title=Pathway%3AWP2792&diff=78712&oldid=77083
In both cases, the GPML has @GroupRef attributes that point to a Group element that does not exist.
Can you check in your code where this problem is coming from? The conversion or the Reactome data?
Warning! Requested path "rectangle-double" is not available with linetype of "Double". Using linetype of "Solid" instead
For example, if I compare http://www.wikipathways.org/index.php/Pathway:WP1849 with the original [0] then the arrows seem to be missing.
0.http://www.reactome.org/PathwayBrowser/#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=556833
The Reactome PW number for (https://www.wikipathways.org/index.php/Pathway:WP1898)[WP1898] doesn't exist anymore, nor is the title reflected anywhere. Have to check if part of the content is moved to another PW (after uploading to version 65 and 66).
Anwesha,
there are a number of ChEBI identifiers used in Reactome pathways which do not get annotated as @type="Metabolite" in the GPML.
What do you think of making a short list of known metabolites, so that when those IDs are identified the are marked as metabolite in the GPML?
That would solve a number of these errors (which are known upstream and haven't been fixed yet, it seems):
During the conversion of version 66, there was an exception printed out:
java.lang.ClassNotFoundExeption : org.gk.render.RenderableChemicalDrug .
Could this class be an update to the Reactome Schema?
Will work on printing an error report specifically for these exceptions, so we can locate them in the Reactome PW + schema, and go from there.
The SBGN interactions in the reactome pathways are not converted properly. ANy ideas about how we should go about converting them ?
For eg in the pathway http://test2.wikipathways.org/index.php/Pathway:WP2638
We see the following problem :
Reactome PW 166520 (Signaling by NTRKs) was in version 63, but became a meta PW for version 64.
This PW has 3 child PWs; one was already part of pathway collections, 1 is a new pathway, and 3rd (9034015) is not a GPML (nor are the children of this PW). Check if this 3rd pathway becomes part of the 65/66 version, and if not, where this is coming from.
We noticed one more thing about the new Reactome pathways, the GroupRefs are no longer alphanumeric, but instead look like this:
GroupRef="1416470.4872874213801427"
They used to look like this:
GroupRef="f1da6"
RNAs should be coloured in purple
The output GPML on WikiPathways is (r83141):
<DataNode TextLabel="DAG" GraphId="e667d" Type="Complex">
<Attribute Key="cellular_location" Value="plasma membrane" />
<Graphics CenterX="491.5" CenterY="29.0" Width="35.0" Height="22.0" ZOrder="32768" FontSize="10" Valign="Middle" ShapeType="RoundedRectangle" Color="a52a2a" />
<Xref Database="ChEBI" ID="R-HSA-CHEBI:17815" />
</DataNode>
However, "R-HSA-CHEBI:17815" is not a ChEBI identifier. I am not sure how to check the Reactome source and not sure if the problem is in the convertor code or in the Reactome pathway source.
Longer labels are not always multi-line, resulting in cutoff text. This is not a problem for all longer labels, some are written as multi-line labels as expected, so I don’t know if maybe this has to do with how the information in stored by Reactome. I’m attaching an example. For this particular example, the corresponding Reactome pathway does have a multi-line label.
"Glycerophospholipid biosynthesis": http://www.reactome.org/PathwayBrowser/#SPECIES=48895&DIAGRAM=5953473
reported by Egon
The GPML file is created, however it is empty.
There are no reported errors in the log file.
The PW still exists in Reactome; the parent PW is created (Metabolism of nucleotides, 15869), however this is a meta PW. The child pathways 'Purine salvage' and 'Pyrimidine salvage' are not created by the converter.
So, for now, I will keep the original PW at version 61 4082, and check if version 63/64/65/66 improve something in the conversion; If not, we should check the MySQL database to see what is going wrong here.
Which is needed for CI on our Jenkins server.
http://wikipathways.org/index.php/Pathway:WP1880
The protein "SLC26A1,2" has a Reactome ID and seems to be a complex but the complex components, proteins SLC26A1 and SLC26A2 are not listed at the bottom of the pathway where complexes are listed.
(Reported by Egon)
It has this GPML, but 111875 is not a valid Reactom ID according to identifiers.org:
<DataNode TextLabel="Ca2+" GraphId="a415d" Type="Metabolite">
<Attribute Key="cellular_location" Value="endoplasmic reticulum lumen" />
<Graphics CenterX="2809.0" CenterY="582.0" Width="50.0" Height="30.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="Reactome" ID="111875" />
</DataNode>
But there are more pathways with integer Reactome IDs.
Change datasource hyperlinks in the WikiPathways description
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