WikiPathways linkouts - Githubissues

bridgedb / datasources

Repository with the BridgeDb data source.

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WikiPathways linkouts #2

Closed fehrhart closed 3 years ago

fehrhart commented 4 years ago

Tested the gene/product linkouts on Wikipathways

[x] Affymetrix - log in required - is that intended, shall we keep that?
[x] Agilent, Illumina - not a link, just a number - is that intended?
[x] Ensembl - patch bridgedb/BridgeDb#146 and bridgedb/BridgeDb#147
[x] UCSC genome browser - does not work - action required
[x] UniGene - does not work - action required
[x] WikiGenes - connection timeout - check again and then decide

egonw commented 3 years ago

"Agilent, Illumina - not a link, just a number - is that intended?" - There is indeed no URL pattern, so intended.

egonw commented 3 years ago

"Affymetrix - log in required - is that intended, shall we keep that?" - Yes, let's do that. Generally, if there is no clear reason to remove it, it's saver to keep it, because someone may actually use it (e.g. someone with a login).

egonw commented 3 years ago

WikiGenes fixed by https://github.com/bridgedb/datasources/commit/2530dbb0dfb52d59602ee9b99e55e18717bba4d3

egonw commented 3 years ago

UniGene no longer exists: https://web.archive.org/web/20210425074853/https://ncbiinsights.ncbi.nlm.nih.gov/tag/unigene/

egonw commented 3 years ago

@mkutmon, @Chris-Evelo, what do you know about the UCSC genome browser link? How is/was this used?

Chris-Evelo commented 3 years ago

Not sure this answers your question. But traditionally the UCSC genome browser is one of the 3 most used browsers for the human genome, next to ENSEMBL and NCBI. I haven't looked at it in a while, but traditionally it had some tracks for things like variants not easily available from other browsers. I suppose the three converged, but many people get used to a specific browser.

egonw commented 3 years ago

Not sure this answers your question. But traditionally the UCSC genome browser is one of the 3 most used browsers for the human genome, next to ENSEMBL and NCBI. I haven't looked at it in a while, but traditionally it had some tracks for things like variants not easily available from other browsers. I suppose the three converged, but many people get used to a specific browser.

Okay, then we need to figure out what the currently working URL pattern is.

egonw commented 3 years ago

Remaining issue continued here: https://github.com/bridgedb/datasources/issues/17