Re: Importing into Mathematica from URL (PubMed)
- To: mathgroup at smc.vnet.net
- Subject: [mg117626] Re: Importing into Mathematica from URL (PubMed)
- From: "Hans Michel" <hmichel at cox.net>
- Date: Tue, 29 Mar 2011 06:49:21 -0500 (EST)
I don't know the field but the problem you are experiencing has nothing to do with mathematica or one site providing better data than another. This just returned the FASTA text amino acid sequence: Import["http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=o n&log$=seqview&db=protein&dopt=fasta&val=3336842&extrafeat=0&maxplex=1", "Text"] Or Import["http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=o n&log$=seqview&db=protein&dopt=fasta&val=3336842&extrafeat=0&maxplex=1", "FASTA"] for straight to "FASTA" format import. This returned the GenPept full format Import["http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=o n&log$=seqview&db=protein&dopt=gpwithparts&val=3336842&extrafeat=0&maxplex=1 ", "Text"] This site needs to run in a browser, what you see in the browser seems to be code that is generated through javascript. Mathematica only imports the raw sources not not the final source when viewed through a web browser with javascript engine on. If you view your original site through a web browser " http://www.ncbi.nlm.nih.gov/protein/CAA76847.1"; the "Send to:" link and drop down image will give you the opportunity to save what you are viewing to file. I just copied the representative URL from the save to file result. This did not involve mathematica in any way. You may also get this in xml format if you play around with the URL viewr.fcgi? query strings $Version "7.0 for Microsoft Windows (32-bit) (February 18, 2009)" Hans -----Original Message----- From: Thomas Dowling [mailto:thomasgdowling at gmail.com] Sent: Thursday, March 24, 2011 6:27 AM To: mathgroup at smc.vnet.net Subject: [mg117626] [mg117594] Importing into Mathematica from URL (PubMed) Hello, Does anyone know how to import a protein sequence from the PubMed database into Mathematica, or can anyone advise me as to where I am going wrong in the following approach? 1. As an example, I'd like to import the data for BSA (bovine serum albumin) from the following site: http://www.ncbi.nlm.nih.gov/protein/CAA76847.1 I wish to import all meaningful data from this page, but the bit I am particularly interested in is the amino acid sequence (in one-leter code) which is right at the end (between ORIGIN and //): ORIGIN 1 mkwvtfisll llfssaysrg vfrrdthkse iahrfkdlge ehfkglvlia fsqylqqcpf 61 dehvklvnel tefaktcvad eshagceksl htlfgdelck vaslretygd madccekqep 121 ernecflshk ddspdlpklk pdpntlcdef kadekkfwgk ylyeiarrhp yfyapellyy 181 ankyngvfqe ccqaedkgac llpkietmre kvltssarqr lrcasiqkfg eralkawsva 241 rlsqkfpkae fvevtklvtd ltkvhkecch gdllecaddr adlakyicdn qdtissklke 301 ccdkplleks hciaevekda ipenlpplta dfaedkdvck nyqeakdafl gsflyeysrr 361 hpeyavsvll rlakeyeatl eeccakddph acystvfdkl khlvdepqnl ikqncdqfek 421 lgeygfqnal ivrytrkvpq vstptlvevs rslgkvgtrc ctkpesermp ctedylslil 481 nrlcvlhekt pvsekvtkcc teslvnrrpc fsaltpdety vpkafdeklf tfhadictlp 541 dtekqikkqt alvellkhkp kateeqlktv menfvafvdk ccaaddkeac favegpklvv 601 stqtala // 2. Import["http://www.ncbi.nlm.nih.gov/protein/CAA76847.1","Elements";] gives the following {Data,FullData,Hyperlinks,Images,ImageURLs,Plaintext,Source,Title,XMLObject} However, Import["http://www.ncbi.nlm.nih.gov/protein/CAA76847.1","Data";]; only gives what looks like a load of rubbish, and there is NO SEQUENCE 3. Trying in FASTA format (which is supported by Mathematica) Import["http://www.ncbi.nlm.nih.gov/protein/3336842?report=fasta ","Elements"] gives {Data,FullData,Hyperlinks,Images,ImageURLs,Plaintext,Source,Title,XMLObject} but Import["http://www.ncbi.nlm.nih.gov/protein/3336842?report=fasta","Data";] also gives only rubbish. (Changing the Element to FullData or Plaintext has no effect) 4. NO SUCH PROBLEMS OCCUR with Uniprot (Swiss-Prot). Import["http://www.uniprot.org/uniprot/P02769","Elements";] Import["http://www.uniprot.org/uniprot/P02769","Data";] (Note that the sequence is now imported) Or, BEST, using the FASTA format and importing from this site Flatten@Characters@StringReplace[Import[" http://www.uniprot.org/uniprot/P02769.fasta";, "Plaintext"] , Whitespace-> ""]//Short giving {M,K,W,V,T,F,I,S,<<592>>,S,T,Q,T,A,L,A} which is where I'd like to get to. So my question is the following: What is so unusual about the PubMed site, and what am I doing wrong in the approach I am taking? It would be a great advantage to me to be able to import from PubMed in the manner shown above for Uniport. Thanks for your help Tom Dowling