sparql endpoint down

[Matt Karikomi]

Hi,

The sparql endpoint (mentioned in the documentation here) is down.

Is there an alternate endpoin?

Thanks,

Matt

[Gary Bader]

Hi Matt - sorry about this. Keeping this up requires us to upgrade the Virtuoso server version and maintain the service with current data. Unfortunately this is not something we’ve been able to accomplish given our current funding and staffing levels, as we are focusing on keeping the main Pathway Commons website working and updated.

In the meantime, users could load the data themselves into their own database instance to run their own SPARQL queries.

If this changes, we would bring it back up.

Best,
Gary

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[Matt Karikomi]

Hi Gary,

Thanks for the followup.

I've used the local hosting strategy before and it works great!

But I previously used a sparql query to basically export an RDF image from pathwaycommons.org.
Do you have any guidance on how to get the RDF from exported from the current web interface?

Best,

Matt

[Matt Karikomi]

Whoops, nm I just found the link (sorry it's been a couple years!):

https://www.pathwaycommons.org/archives/PC2/v11/

On Tuesday, January 31, 2023 at 9:53:44 AM UTC-8 gary.ba...@gmail.com wrote:

[Gary Bader]

Great. https://www.pathwaycommons.org/archives/PC2/v12/ is the latest.

Best,
Gary

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[Matt Karikomi]

Hi Gary,

I previously used the RDF import wizard on onotext/graphdb to import the pc11 .owl files and host them locally, but that feature is paywalled now.

I'm trying to use Virtuoso but getting weird errors following the documentation on importing RDF (.owl) files.

Do you guys happen to have the bulk loading script you previously used to load the PathwayCommons12.All.BIOPAX.owl.gz into Virtuoso?

Thanks,

Matt

[Gary Bader]

Hi Matt - here is the info we currently have about this in our internal documentation. We haven’t tested it with the latest virtuoso versions. Hope it helps.

To update the BioPAX model, e.g., replace PC10 with PC11 version, do

sudo isql-vt
SQL> sparql clear graph <http://pathwaycommons.org>;
... takes 30-50 min ...
Done. -- 3000000 msec.
SQL> quit;

Next, upload new BioPAX RDF/XML model, e.g, PathwayCommons11.All.BIOPAX.owl.gz to

/datb/rdf/pc2/

and read the document (https://vos.openlinksw.com/owiki/wiki/VOS/VirtBulkRDFLoader) that details how large RDF data set files can be bulk loaded into Virtuoso (select statements below are to check status):

sudo isql-vt
SQL> ld_dir ('/datb/rdf/pc2', '*.rdf.gz', 'http://pathwaycommons.org');
SQL> select * from DB.DBA.load_list;
SQL> rdf_loader_run();
... takes time ...
SQL> rdf_loader_stop();
SQL> select * from DB.DBA.LOAD_LIST where ll_error IS NOT NULL;
SQL> quit;

After data is loaded successfully (takes more than an hour), refresh and re-index the db:

isql-vt
SQL> RDF_OBJ_FT_RULE_ADD (null, null, 'All');
SQL> VT_INC_INDEX_DB_DBA_RDF_OBJ ();
SQL> urilbl_ac_init_db();
SQL> s_rank();
SQL> quit;

Finally, define "bp:" (http://www.biopax.org/release/biopax-level3.owl#) and "pc12:" (http://pathwaycommons.org/pc12/) namespace (depends on PC data version) prefixes using the Virtuoso Conductor, LinkedData UI (or isql-vt).

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[Matt Karikomi]

Awesome, thank you!

[Gary Bader]

Let us know how it goes!  We could update our documentation to include this information.

Thanks,

Gary

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[Matt Karikomi]

Hi Gary,

I've create a public github repo with a docker-compose script that automates bulk RDF loading (pc v12), self hosting, and VAD plugin installation on Virtuoso 7.

 
Feel free to check out the documentation and please let me know of suggested improvements!

Best,

Matt

[Gary Bader]

Thanks Matt! We’ll check it out and let you know if we have any comments.

Gary

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