Question: Reactome pathway names from IDs?
0
3.8 years ago by
enricoferrero570
Switzerland
enricoferrero570 wrote:

I have a bunch of Reactome ID that I'd like to annotate with Reactome pathway names.

Is there a way to do this through biomaRt?

If not, is reactome.db my best option? I found this in the package manual:

Mappings were based on data provided by: Reactome http://www.reactome.org/download/current/sql.gz & http://www.reactome.org/download/current/sql_dn.gz With a date stamp from the source of: 2010- Dec-21

Is reactome.db kept up to date with Reactome?

Thank you,

biomart reactome reactome.db id • 977 views
ADD COMMENTlink
modified 3.8 years ago by James W. MacDonald51k • written 3.8 years ago by enricoferrero570
Answer: Reactome pathway names from IDs?
3
3.8 years ago by
United States
James W. MacDonald51k wrote:

Yes, it's kept up to date. For any annotation package, there is the SQLite database that actually contains all the data, and then a thin package wrapper that allows people to query the database without having to know any SQL. This particular package is generated in collaboration between Willem Ligtenberg and Bioconductor. He generates some of the tables in the SQLite DB, then sends it to us, and we put in the rest. So that part gets updated every six months, and it's really the only important part.

To generate the package we then take the package from the last release, dump out the database, and put the new one in there, increment the version number, and build. So everything except the SQLite database is old, having been originally generated back in 2010. This includes the part you show above - if you go to that website, there isn't even a sql.gz file in there! Probably hasn't been one for years.

Probably more than you wanted to know, but hope it helps.

ADD COMMENTlink written 3.8 years ago by James W. MacDonald51k
1

Thank you James for answering this.
Indeed, every six months we update the reactome.db package.
Once there were some issues when Reactome changed their database dumps, but we updated our end, and everything is functioning fine again.

ADD REPLYlink written 3.8 years ago by willem.ligtenberg150

Thanks both!
May I suggest to update the docs by removing that misleading statement?
Cheers,

ADD REPLYlink written 3.8 years ago by enricoferrero570
1

sure, and done! :)

ADD REPLYlink written 3.8 years ago by willem.ligtenberg150

Hi Willem,

Please note that I didn't use the package you sent me for this last annotation build. I just took the SQLite DB and put it into the package from the last release, because there was something wrong with the code in the package you sent me. In other words, after I updated the SQLite DB with our data, and then did a build and check, it failed. So I downloaded a source version of reactome.db from last release, extracted it, put the SQLite DB into that package, bumped the version and then built/checked. That did work.

So if you are updating the docs in whatever package shell you used, don't bother. Instead, get the source version of the current release package and update that instead. Then when you send to Val (next time), she should be able to use what you send directly.

Does that make sense?

Jim

ADD REPLYlink written 3.8 years ago by James W. MacDonald51k

yes it does. :)

ADD REPLYlink written 3.8 years ago by willem.ligtenberg150
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