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bio2rdf/bio2rdf-scripts
Inquiry about using bio2rdf to parse drugbank

Hi, I m currently trying to parse drugbank and convert it to RDF using bio2rdf. I followed the developers guide in the Wiki to set up the environment and ran runparser.php but it gave me an error: Fatal ...
  • yq-leo
  • 1
  • Opened 
    on Apr 5, 2022
  • #480

bio2rdf/bio2rdf-scripts
Link to v3 release notes broken

https://download.bio2rdf.org/release/3/release.html -- 404
  • MattBrauer
  • 1
  • Opened 
    on Apr 6, 2021
  • #477

bio2rdf/bio2rdf-scripts
dataset hyperlink not functional???

https://github.com/bio2rdf/bio2rdf-scripts/wiki#wiki-body:~:text=35%20datasets Error 404 when clicked on 35 Datasets
  • csrajath
  • 1
  • Opened 
    on Mar 1, 2021
  • #476

bio2rdf/bio2rdf-scripts
How can I parse the Drugbank.nq.gz?

I have generated the rdf file named Drugban.nq.gz by running the code ,but I do not know how to parse it,can you give me some advice.Thank you.
  • DuZhenzhen399
  • 2
  • Opened 
    on Jul 3, 2020
  • #465

bio2rdf/bio2rdf-scripts
Drugbank drug-target interactions

Interesting work!But some links are invalid,such as drugbank.xml.zip in folder drugbank ,I did not find it.Please check it.Thank you so much.
help wanted
  • DuZhenzhen399
  • 4
  • Opened 
    on Jun 30, 2020
  • #461

bio2rdf/bio2rdf-scripts
WikiPathways license in datasets documentation is outdated

Current license is CC0
  • Chris-Evelo
  • 1
  • Opened 
    on Aug 20, 2019
  • #458

bio2rdf/bio2rdf-scripts
Malformed Links

By running this query: select distinct * where { http://bio2rdf.org/pharmgkb:PA128394620 ?p ?o} Several malformed URIs can be retrieved, e.g., http://bio2rdf.org/omim:611868
  • mevs
  • 1
  • Opened 
    on Jul 16, 2018
  • #457

bio2rdf/bio2rdf-scripts
XML parse error for clinicaltrials

Fatal error: Uncaught Error: Call to a member function asXML() on null in C:\bio2rdf-scripts\clinicaltrials\clinicaltrials.php:367
bug
  • micheldumontier
  • 1
  • Opened 
    on Jan 23, 2018
  • #455

bio2rdf/bio2rdf-scripts
backslash characters in clinicaltrials

Hi everyone, I was trying to extend the ClinicalTrials.gov bio2rdf conversion script (see https://github.com/jvsoest/bio2rdf-scripts/commit/ce09d8386f71f8a6c7b18f78ee0699e53133de23), and test it before ...
  • micheldumontier
  • 4
  • Opened 
    on May 12, 2017
  • #453

bio2rdf/bio2rdf-scripts
drugbank: protein group problem

When the target is a protein_group, then only identifier for the first member of the group is returned. for instance a target id for olanzapine is BE0004872, which is a protein group containing 3 members, ...
bug
  • micheldumontier
  • Opened 
    on Mar 15, 2017
  • #452
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