PubChem_SDQ_LitSearch
Search PubChem for PubMed, Patent, Springer Nature, Thieme, and Wiley Literature associated with a CID
% Vincent F. Scalfani, Serena C. Ralph, Ali Al Alshaikh, and Jason E. Bara
% The University of Alabama
% Tested with MATLAB R2020a, running Ubuntu 18.04 on March 30, 2020.
% N.B. PubChem SDQ is used internally by PubChem webpages and is still being rapidly developed.
Define the PubChem API and SDQ agent base URL
% PubChem API
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/';
% PubChem SDQ agent
sdq = 'https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?outfmt=json&query=';
% set a longer web options timeout and json output
options = weboptions('Timeout', 60, 'ContentType','json');
% Retrieve and display PNG Image of 1-Butyl-3-methylimidazolium chloride;
% CID 2734161
CID_query = '2734161';
CID_query_url = [api CID_query '/PNG'];
[CID_img,map] = imread(CID_query_url);
imshow(CID_img,map);
Replace the above CID value (CID) with a different CID number to customize
Explore Total Literature and Data Counts
% Retrieve total count of associated literature references
litCountQ_url = [sdq '{"hide":"*","collection":"*","where":{"ands":{"cid":"' CID_query '"}}}'];
litCountQ = webread(litCountQ_url, options);
% display all available collections
collections = cell(1,length(litCountQ.SDQOutputSet)); % preallocate
for k = 1:length(litCountQ.SDQOutputSet)
collections{k} = litCountQ.SDQOutputSet{k, 1}.collection;
end
collections = collections'
% Display total literature counts of selected collections:
% pubmed, patent, springernature, thiemechemistry, and wiley
litCountQ_pubmed = litCountQ.SDQOutputSet{7,1}.totalCount;
litCountQ_patent = litCountQ.SDQOutputSet{4,1}.totalCount;
litCountQ_springernature = litCountQ.SDQOutputSet{15,1}.totalCount;
litCountQ_thieme = litCountQ.SDQOutputSet{13,1}.totalCount;
litCountQ_wiley = litCountQ.SDQOutputSet{14,1}.totalCount;
fprintf(['litCountQ_pubmed = %d \nlitCountQ_patent = %d \nlitCountQ_springernature = %d' ...
'\nlitCountQ_thieme = %d \nlitCountQ_wiley = %d'] ,...
litCountQ_pubmed, litCountQ_patent, litCountQ_springernature, litCountQ_thieme, litCountQ_wiley)
If interested in different collections:
- Determine the collection you are interested in (e.g., 'clinicaltrials') from the litCountQ.SDQOutputSet structure
- Then, record the row number the collection appears in (18 for 'clinicaltrials')
- Next, use this number to index into the litCountQ.SDQOutputSet
- For example, litCountQ.SDQOutputSet{18,1}.totalCount
Explore Categories of the Literature Data
% Retrieve 1 associated literature reference from each selected collection to look at
% JSON field data
% pubmed
litQpubmed1_url = [sdq '{"select":"*","collection":"pubmed","where":{"ands":{"cid":"' CID_query '"}},' ...
'"start":1,"limit":1}'];
litQpubmed1 = webread(litQpubmed1_url, options);
disp(litQpubmed1.SDQOutputSet.rows)
% patent
litQpatent1_url = [sdq '{"select":"*","collection":"patent","where":{"ands":{"cid":"' CID_query '"}},' ...
'"start":1,"limit":1}'];
litQpatent1 = webread(litQpatent1_url, options);
disp(litQpatent1.SDQOutputSet.rows)
% springernature
litQspringernature1_url = [sdq '{"select":"*","collection":"springernature","where":{"ands":{"cid":"' CID_query '"}},' ...
'"start":1,"limit":1}'];
litQspringernature1 = webread(litQspringernature1_url, options);
disp(litQspringernature1.SDQOutputSet.rows)
% thiemechemistry
litQthieme1_url = [sdq '{"select":"*","collection":"thiemechemistry","where":{"ands":{"cid":"' CID_query '"}},' ...
'"start":1,"limit":1}'];
litQthieme1 = webread(litQthieme1_url, options);
disp(litQthieme1.SDQOutputSet.rows)
% wiley
litQpwiley1_url = [sdq '{"select":"*","collection":"wiley","where":{"ands":{"cid":"' CID_query '"}},' ...
'"start":1,"limit":1}'];
litQwiley1 = webread(litQpwiley1_url, options);
disp(litQwiley1.SDQOutputSet.rows)
In each collection there are multiple unique searchable fields that we can use to perform literature searching. Some examples are presented below for how to combine the fields with keywords. Please note that this is still an experimental method. The limit was set at 10 for demo purposes.
Search PubMed Collection
% Search pubchem pubmed collection for
% referencess containing meshheadings "Imidazoles" and meshsubheadings "chemical synthesis"
% (associated with CID_query)
litQpubmedF = [sdq '{"select":"*","collection":"pubmed","where":{"ands":{"cid":"' CID_query '",' ...
'"meshheadings":"Imidazoles", "meshsubheadings":"chemical synthesis"}},"start":1,"limit":10}'];
options = weboptions('Timeout', 60, 'ContentType','json');
litQpubmedF = webread(litQpubmedF, options);
% Display results: pmid, articletitle, articlejourname, articleauth, pubmed link
for k = 1:length(litQpubmedF.SDQOutputSet.rows)
pmid = litQpubmedF.SDQOutputSet.rows{k,1}.pmid
articletitle = litQpubmedF.SDQOutputSet.rows{k,1}.articletitle
articleauth = litQpubmedF.SDQOutputSet.rows{k,1}.articleauth
articlejourname = litQpubmedF.SDQOutputSet.rows{k,1}.articlejourname
citation = litQpubmedF.SDQOutputSet.rows{k,1}.citation
pubmed_root = 'https://www.ncbi.nlm.nih.gov/pubmed/?term=';
pmid = num2str(pmid);
pubmed_link = [pubmed_root pmid];
fprintf('<a href = " %s ">%s</a>\n', pubmed_link, pubmed_link)
disp(' ')
end
pmid = 24307868
pmid = 20582335
pmid = 30760673
pmid = 31121813
pmid = 16917949
pmid = 19384978
pmid = 21742316
pmid = 21809450
pmid = 21989309
pmid = 23694706
Search Patent Collection
% Search pubchem patent collection for patents with "imidazolium" in the abstract and "preparation" in the title
% (associated with CID_query)
litQpatentF = [sdq '{"select":"*","collection":"patent","where":{"ands":{"cid":"' CID_query '",' ...
'"patentabstract":"imidazolium", "patenttitle":"preparation"}},"start":1,"limit":10}'];
options = weboptions('Timeout', 60, 'ContentType','json');
litQpatentF = webread(litQpatentF, options);
% Display results: patentID, patenttitle, patentinventor, and patenturl
for k = 1:length(litQpatentF.SDQOutputSet.rows)
patentID = litQpatentF.SDQOutputSet.rows{k,1}.patentid
patenttitle = litQpatentF.SDQOutputSet.rows{k,1}.patenttitle
patentdate = litQpatentF.SDQOutputSet.rows{k,1}.patentdate
patentinventor = litQpatentF.SDQOutputSet.rows{k,1}.patentinventor
patenturl = litQpatentF.SDQOutputSet.rows{k,1}.patenturl;
fprintf('<a href = " %s ">%s</a>', patenturl, patenturl)
disp(' ')
end
Search Springer Nature
% Search springer nature collection for "imidazolium" in the title and publication year 2019
% (associated with CID_query)
litQspringernatureF = [sdq '{"select":"*","collection":"springernature","where":{"ands":{"cid":"' CID_query '",' ...
'"articletitle":"imidazolium", "articlepubdate":"2019"}},"start":1,"limit":10}'];
options = weboptions('Timeout', 60, 'ContentType','json');
litQspringernatureF = webread(litQspringernatureF, options);
% Display results
for k = 1:length(litQspringernatureF.SDQOutputSet.rows)
extID = litQspringernatureF.SDQOutputSet.rows{k,1}.extid
articletitle = litQspringernatureF.SDQOutputSet.rows{k,1}.articletitle
articlejournalname = litQspringernatureF.SDQOutputSet.rows{k,1}.articlejourname
articlepubdate = litQspringernatureF.SDQOutputSet.rows{k,1}.articlepubdate
articleurl = litQspringernatureF.SDQOutputSet.rows{k,1}.url;
fprintf('<a href = " %s ">%s</a>', articleurl, articleurl)
disp(' ')
end
Retrieve Thieme and Wiley Chemistry References
% Retrieve all Thieme and Wiley Chemistry References associated with our
% CID query (since both are < 10 results)
% (associated with CID_query)
% Thieme
litQthiemeF = [sdq '{"select":"*","collection":"thiemechemistry","where":{"ands":{"cid":"' CID_query '"}},' ...
'"start":1,"limit":10}'];
options = weboptions('Timeout', 60, 'ContentType','json');
litQthiemeF = webread(litQthiemeF, options);
% Display results
for k = 1:length(litQthiemeF.SDQOutputSet.rows)
extID = litQthiemeF.SDQOutputSet.rows(k).extid
articletitle = litQthiemeF.SDQOutputSet.rows(k).articletitle
articlejournalname = litQthiemeF.SDQOutputSet.rows(k).articlejourname
articlepubdate = litQthiemeF.SDQOutputSet.rows(k).articlepubdate
articleurl = litQthiemeF.SDQOutputSet.rows(k).url;
fprintf('<a href = " %s ">%s</a>', articleurl, articleurl)
disp(' ')
end
% Wiley
litQwileyF = [sdq '{"select":"*","collection":"wiley","where":{"ands":{"cid":"' CID_query '"}},' ...
'"start":1,"limit":10}'];
options = weboptions('Timeout', 60, 'ContentType','json');
litQwileyF = webread(litQwileyF, options);
% Display results
for k = 1:length(litQwileyF.SDQOutputSet.rows)
extID = litQwileyF.SDQOutputSet.rows(k).extid
articletitle = litQwileyF.SDQOutputSet.rows(k).articletitle
articlejournalname = litQwileyF.SDQOutputSet.rows(k).articlejourname
articlepubdate = litQwileyF.SDQOutputSet.rows(k).articlepubdate
articleurl = litQwileyF.SDQOutputSet.rows(k).url;
fprintf('<a href = " %s ">%s</a>', articleurl, articleurl)
disp(' ')
end