Broken Links

[arpaddanos]

The following links should be updated or removed from https://dgidb.org/browse/sources

1. NCIt
   https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=

possible replacement:
https://ncithesaurus.nci.nih.gov/ncitbrowser/

2. RxNorm
   https://rxnav.nlm.nih.gov/REST/rxcui/rxcui/allrelated.xml

possible replacement:
https://lhncbc.nlm.nih.gov/RxNav/

3. CKB-CORE
   https://ckb.genomenon.org/gene/show?geneId=

possible replacement:
none found

4. GuideToPharmacology [appears 2x]
   https://www.guidetopharmacology.org/DATA/

possible replacement:
https://www.guidetopharmacology.org/

5. CarisMolecularIntelligence
   https://www.carislifesciences.com/products-and-services/molecular-profiling/profiling-technologies/

possible replacement:
https://www.carislifesciences.com/

6. GO
   https://amigo.geneontology.org/amigo/gene_product/UniProtKB:

possible replacement:
https://amigo.geneontology.org/amigo

[jsstevenson]

I think this is referring to links on the Browse Sources page

It looks like some of those URLs are being rendered based on the source prefix URLs (i.e., they're supposed to be concatenated with record IDs to link to specific records on the source website). This is the base_url column in the DB. It should be using the site_url column. I bet the client is just grabbing the wrong URL.

• I'm pretty sure we don't even use the base_url column anymore, maybe we should either remove it, or start using it again? My recollection is that we make decisions about generating URLs from xrefs fully within the client code, we don't need to refer to the backend.

[jsstevenson]

For reference, this is what we have under the site_url column

         source_db_name          |                                              site_url                                               
---------------------------------+-----------------------------------------------------------------------------------------------------
 Drugs@FDA                       | https://www.accessdata.fda.gov/scripts/cder/daf/
 NCI                             | https://wiki.nci.nih.gov/display/cageneindex
 CarisMolecularIntelligence      | http://www.carismolecularintelligence.com/
 BaderLab                        | http://baderlab.org/Data/RoadsNotTaken
 CancerCommons                   | http://www.cancercommons.org/
 CGI                             | https://www.cancergenomeinterpreter.org/
 FDA                             | https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling
 FoundationOneGenes              | http://www.foundationone.com/
 OncoKB                          | http://www.oncokb.org/
 Oncomine                        | https://www.thermofisher.com/us/en/home.html
 Pharos                          | https://pharos.nih.gov/
 Ensembl                         | https://ensembl.org
 PharmGKB                        | http://www.pharmgkb.org/
 HingoraniCasas                  | http://stm.sciencemag.org/content/9/383/eaag1166
 MyCancerGenome                  | http://www.mycancergenome.org/
 RussLampel                      | http://www.ncbi.nlm.nih.gov/pubmed/16376820/
 TALC                            | https://www.ncbi.nlm.nih.gov/pubmed/24377743
 GO                              | http://www.geneontology.org/
 ChEMBL                          | https://www.ebi.ac.uk/chembl/
 DTC                             | https://drugtargetcommons.fimm.fi/
 HemOnc                          | https://hemonc.org
 ClearityFoundationBiomarkers    | https://www.clearityfoundation.org/healthcare-pros/drugs-and-biomarkers.aspx
 COSMIC                          | https://cancer.sanger.ac.uk/cosmic
 ClearityFoundationClinicalTrial | https://www.clearityfoundation.org/form/findtrials.aspx
 HopkinsGroom                    | http://www.ncbi.nlm.nih.gov/pubmed/12209152/
 dGene                           | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067980
 DoCM                            | http://docm.info/
 GuideToPharmacology             | http://www.guidetopharmacology.org/
 HumanProteinAtlas               | https://www.proteinatlas.org/
 IDG                             | https://druggablegenome.net/
 NCBI                            | https://www.ncbi.nlm.nih.gov/gene/
 CIViC                           | https://www.civicdb.org
 TdgClinicalTrial                | http://www.ncbi.nlm.nih.gov/pubmed/24016212
 MyCancerGenomeClinicalTrial     | http://www.mycancergenome.org/
 Tempus                          | https://www.tempus.com/
 TTD                             | http://bidd.nus.edu.sg/group/cjttd/
 MskImpact                       | https://www.mskcc.org/msk-impact
 TEND                            | http://www.ncbi.nlm.nih.gov/pubmed/21804595/
 DrugBank                        | https://go.drugbank.com/
 Wikidata                        | https://www.wikidata.org/
 RxNorm                          | https://www.nlm.nih.gov/research/umls/rxnorm/overview.html
 ChemIDplus                      | https://chem.nlm.nih.gov/chemidplus/
 NCIt                            | https://ncithesaurus.nci.nih.gov/ncitbrowser/pages/home.jsf
 CKB-CORE                        | https://ckb.genomenon.org
 HGNC                            | https://www.genenames.org

[github-actions]

Closed by #562.