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ICGC DCC - Import Resources

This details the updating of static resources used by the importer modules. This is done offline because these files have been known to change schemas and break the import process. Doing it this way leads to greater runtime stability

Last Updated:

File Date
cancer_gene_census.tsv Oct 9th, 2015
pathway_hier.txt Oct 9th, 2015
uniprot_2_reactome.txt Oct 9th, 2015
pathway_2_summation.txt Oct 9th, 2015

Update the files.

Reactome Pathway Resources

Refer to this wiki page for complete information.

curl http://www.reactome.org/ReactomeRESTfulAPI/RESTfulWS/pathwayHierarchy/homo+sapiens > pathway_hierarchy.txt
curl http://www.reactome.org/download/current/UniProt2Reactome.txt > uniprot_2_reactome.txt
curl http://www.reactome.org/download/current/pathway2summation.txt > pathway_2_summation.txt

Verify Resources.

Unfortunately, the updated files are usually not in the right format or consistency. So some manual work is needed to make them compatible with ETL component. Based on previous experiences, these are some items to look out for:

cancer_gene_census.tsv file might have csv header. Just replace the commas with tab character in a text editor.

Reactome names are present in pathway_hierarchy.txt but missing from pathway_2_summation.txt. You'd need to resolve them using uniprot_2_reactome.txt. Start by copying the lines with '???' from the end of previous pathway_2_summation.txt to the new verison. For each one of those, search for the REACT_[id] in the file to see if the data is provided in the current version. If so, delete the lines.

Currently, the following reactome names are inconsistent between the reactome data files and have been resolved with other methods:

The following reactome names are present in pathway_hierarchy.txt but missing from pathway_2_summation.txt and have been resolved using uniprot_2_reactome.txt:

  • PI3K Cascade
  • RNA Polymerase II Transcription
  • S6K1-mediated signalling
  • Switching of origins to a post-replicative state
  • mTOR signalling

The following reactome names are present in pathway_hierarchy.txt but missing from pathway_2_summation.txt and uniprot_2_reactome.txt have been resolved using reactome.org website:

  • Acetylcholine Binding And Downstream Events
  • Cell Cycle
  • Cell junction organization
  • Mitotic G1-G1/S phases
  • Mitotic G2-G2/M phases
  • RNA Polymerase II Transcription
  • Regulation of mitotic cell cycle
  • Transmembrane transport of small molecules
  • mTORC1-mediated signalling
  • Infectious disease
  • Vesicle-mediated transport

The following reactome ids are present in uniprot_2_reactome.txt but missing from the other 2 files.

  • REACT_790
  • REACT_1451
  • REACT_330
  • REACT_2204
  • REACT_1156
  • REACT_329
  • REACT_22107
  • REACT_22201
  • REACT_1178
  • REACT_63
  • REACT_6772
  • REACT_1993
  • REACT_1156

Update the contents at the following paths

Run dcc-import tests

dcc-import modules heavily depends on the jar resource, so running the unit tests is the first step to catch issues with updates bundle. Run the tests and try to resolve the issues. You might get an error similar to following:

java.lang.NullPointerException: Cannot find reactome id for pathway segment with reactome name 'Infectious disease' and segment 'PathwaySegment(reactomeId=null, reactomeName=Infectious disease, diagrammed=true)'

In which case, you might need to go to reactome website and search for the missing reactome name and finding the corresponding reactome id such as REACT_355497 and add the combination to the buttom of pathway_2_summation.txt.

Run all Import tests

cd dcc-import
mvn clean package

Update this document.

Reflect the changes and their date.