PubChem_SDQ_Bibliometrics
Count references in PubChem associated with a CID (e.g., from PubMed, Patent, Springer Nature, Thieme, and Wiley Collections)
% 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.
% 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/';
% PubChem SDQ agent
sdq = 'https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?outfmt=json&query=';
% set a longer web options timeout
% this prevents a MATLAB timeout if the server is slow to respond.
options_api = weboptions('Timeout', 30);
options_sdq = weboptions('Timeout', 60,'ContentType','json');
% Retrieve and display a PNG image of 1-Butyl-3-methyl-imidazolium; CID 2734162
CID_SS_query = '2734162';
Replace the above CID value (CID_SS_query) with a different CID number to customize.
CID_url = [api 'cid/' CID_SS_query '/PNG'];
[CID_img,map] = imread(CID_url);
imshow(CID_img,map)
Perform a Similarity Search
% Search for chemical structures by Similarity Search (SS),
% (2D Tanimoto threshold 95% to 1-Butyl-3-methyl-imidazolium; CID 2734162)
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
SS_url = [api 'fastsimilarity_2d/cid/' CID_SS_query '/cids/JSON?Threshold=95'];
SS_CIDs = webread(SS_url,options_api);
SS_CIDs = num2cell(SS_CIDs.IdentifierList.CID)
In the above SS_url value, you can adjust to the desired Tanimoto threshold (e.g., 90)
% set a CID limit to 25 max
number_SS_CIDs = length(SS_CIDs)
number_SS_CIDs = 249
A limit of 25 was added as an initial testing safety for time consideration. This limit can be increased.
if number_SS_CIDs > 25
SS_CIDs = SS_CIDs(1:25)
else
disp('Number of SS_CIDs not changed')
end
Retrieve Isomeric SMILES for CIDs, Number of Substances, and Literature
% setup a for loop that processes each CID one-by-one.
for j = 1:length(SS_CIDs)
CID = SS_CIDs{j};
% define api call
api = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/';
% define api call for isomeric SMILES
CID_IsoSMILES_url = [api 'cid/' num2str(CID) '/property/IsomericSMILES/TXT'];
% retrieve isomeric SMILES
try
CID_IsoSMILES = webread(CID_IsoSMILES_url,options_api);
catch ME
CID_IsoSMILES = 'not found'
end
n = 0.5;
pause(n)
% add isomeric SMILES data to SS_CIDs data array
% j increases by 1 on each iteration, so the first CID Isomeric SMILES
% gets added to {1,2}, the second to {2,2}, third to {3,2}, etc.
SS_CIDs{j,2} = CID_IsoSMILES;
% define sdq call to retrieve count data
sdq = 'https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?outfmt=json&query=';
litCountQ_url = [sdq '{"hide":"*","collection":"*","where":{"ands":{"cid":"' num2str(CID) '"}}}'];
try
litCountQ = webread(litCountQ_url, options_sdq);
catch ME
litCountQ = 'not found'
end
n = 1;
pause(n)
% add selected collection count data to SS_CIDs data array
% here the column index values on the left (e.g., {j,3})
% represent where the data will be stored (column 3), and the values
% on the right (e.g., litCountQ.SDQOutputSet{2,1}), is an index value (2),
% to retrieve the substance count data from the litCountQ.SDQOutputSet
% structure array.
% substance
SS_CIDs{j,3} = litCountQ.SDQOutputSet{2,1}.totalCount;
% add the associated collection row value as a manual validation check
SS_CIDs{j,4} = litCountQ.SDQOutputSet{2,1}.collection;
% patent
SS_CIDs{j,5} = litCountQ.SDQOutputSet{4,1}.totalCount;
SS_CIDs{j,6} = litCountQ.SDQOutputSet{4,1}.collection;
% pubmed
SS_CIDs{j,7} = litCountQ.SDQOutputSet{7,1}.totalCount;
SS_CIDs{j,8} = litCountQ.SDQOutputSet{7,1}.collection;
% thiemechemistry
SS_CIDs{j,9} = litCountQ.SDQOutputSet{13,1}.totalCount;
SS_CIDs{j,10} = litCountQ.SDQOutputSet{13,1}.collection;
% springernature
SS_CIDs{j,11} = litCountQ.SDQOutputSet{15,1}.totalCount;
SS_CIDs{j,12} = litCountQ.SDQOutputSet{15,1}.collection;
% wiley
SS_CIDs{j,13} = litCountQ.SDQOutputSet{14,1}.totalCount;
SS_CIDs{j,14} = litCountQ.SDQOutputSet{14,1}.collection;
end
For adding custom bibliometric data counts:
% 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'
- 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
- Add the new bibliometric data count into the for loop above.
Validate Extracted Counts and Fields
% convert cell array to string and remove leading and trailing white space
SS_CIDs_string = strtrim(string(SS_CIDs));
% convert to table and verify expected counts match extracted collection
% e.g., in the patent_lab column all rows should be 'patent'
SSq_bibtable_validate = array2table(SS_CIDs_string, 'VariableNames',{'CID','Isomeric_SMILES','num_substances',...
'substances_lab','num_patent','patent_lab','num_pubmed','pubmed_lab','num_thiemechemistry',...
'thiemechemistry_lab','num_springernature','springernature_lab','num_wiley','wiley_lab'})
Compile Bibliometric Data into a Table
% select only the numerical count data to export
SSq_bibtable = SSq_bibtable_validate(:, {'Isomeric_SMILES' 'CID' 'num_substances' 'num_patent' 'num_pubmed'...
'num_thiemechemistry' 'num_springernature' 'num_wiley'})
% export data as tabbed text file
% prompt user to select folder for data export
save_folder = uigetdir;
% change directory to selected folder
cd(save_folder)
writetable(SSq_bibtable,'MATLAB_SDQ_Bibliometrics_results.txt','Delimiter','tab')