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Glycolysis Similarity Among Humans, Chimps, and Salmon

Michael Hale
Posted 8 years ago
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POSTED BY: Michael Hale
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Let's wrap this post up with a simple, interesting exercise using the KEGG database. Let's see how similar the DNA and protein amino acid sequences used for glycolysis (a fundamental process in all organisms) are among humans, chimps, and something really different like salmon.

This is really cool! Thanks so much for taking the time to share your work. It may be a "simple" exercise to you but as a total beginner it's awesome to see what you can achieve with Wolfram.

POSTED BY: Evelyn Alnwickson

Michael,

This looks quite interesting, but I am stymied early on in the import.

In[1]:= human = Import["http://rest.kegg.jp/get/hsa00010/kgml", "XML"][[2, 3]]; 

XML`Parser`XMLGet::prserr: 
   MalformedURLException: The URL used an unsupported protocol at Line: 2
     Character: 73 in /tmp/m00000184221/kgml.

Import::fmterr: Cannot import data as XML format.

Part::partd: Part specification $Failed[[2,3]] is longer than depth of object.

Any idea what might be amiss?
POSTED BY: Daniel Lichtblau
Michael Hale
Michael Hale
Posted 8 years ago

Strange. I just copied the exact line you provided into a fresh kernel. I'm using 11.3 on Win 10. Are you using an internal build?
POSTED BY: Michael Hale

No, I am using the shipping version of 11.3, but on Linux. A mystery.
POSTED BY: Daniel Lichtblau

Dear Daniel,

same as you, but on OSX.

Cheers,

Marco

Update: It is still processing, but this appears to work:

human = Import["http://rest.kegg.jp/get/hsa00010/kgml", "XML", "ReadDTD" -> False][[2, 3]];
POSTED BY: Marco Thiel
Michael Hale
Michael Hale
Posted 8 years ago

Hm. I did have to use "ReadDTD" -> False when getting XML from the NCBI API, but not the KEGG API. Like in the following to get a list of all of the NCBI databases.

Import["https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi", \
"XML", "ReadDTD" -> False]

But it did provide a more helpful error message than what Daniel was getting.
POSTED BY: Michael Hale
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