R_ExportWikiData

(I know, awful name but will change it once we have agreement.)

This is the sister code of the R_WikidataBot and creates teh required csv file from the Reactome Graph Database.

##Code

The code is written in Java and uses the Graph Database and corresponding API.

Usage

Arguments

The following arguments are required

• -h "host" The neo4j host for the ReactomeDB
• -b "port" The neo4j port
• -u "user" The neoj4 username
• -p "password" The neo4j password
• -o "outfilename" The full path for the output file to be written

Zero or one of the following "pathway" arguments are also expected to identify which Pathway(s) are to be exported

• -t "toplevelpath" A single integer argument that is the databaseIdentifier for a Pathway
• -s "species" A single integer argument that is the databaseIdentifier for a Species
• -m "multiple" A comma-separated list of integers that are the databaseIdentifiers of several Pathways

Output depending on "pathway" argument

• no specific pathway argument

The output when no specific path way argument is specified will be the csv file containing an entry for every pathway in the Reactome DB.

• -t dbid

The output for the argument -t will be the csv file with a single entry corresponding to the pathway specified.

• -s dbid

The output for the argument -s will be the csv file with a one entry corresponding to each pathway in the species specified.

• -m dbid1,dbid2,dbid3

The output for the argument -m will be the csv file with a one entry corresponding to each pathway specified.

Output file

The code generates a comma separated value (.csv) file where each line refers to a Pathway and therefore a single Wikisdata entry. The entries expected are:

Species_code,Reactome_Id,Name,Description,[publication1;publication2;..],goterm,None

where

• Species_code is the three letter abbreviation of the species used by Reactome e.g. HSA
• Reactome_Id is the Reactome Stable Indentifier for the pathway
• Name the Reactome Display Name
• Description a sentence based on Name stating that this is an instance of this pathway in the given species
• [publication1;..] a semi-colon separated list of the pmid URL of each referenced publication
• goterm teh relevant term as GO:nnnn
• None - to indicate the end of the entry

Restricting output

Before outputting data the code checks that the Pathway meets any restrictions that have been placed in the private static boolean is_appropriate(Pathway path) function. This allows the user to tailor the output.

TO DO

Currently the code only supports the Homo sapiens species as it hard codes the 'HSA' entry in the output.

1. Support all species
2. Support a reaction that is not a Pathway