Documentation

From MATLAB, open the MATLAB Editor by selecting File > New > Function.

Define the getpubmed function, its input arguments, and return values by typing:

function pmstruct = getpubmed(searchterm,varargin)
% GETPUBMED Search PubMed database & write results to MATLAB structure

Add code to do some basic error checking for the required input SEARCHTERM.

% Error checking for required input SEARCHTERM
if(nargin<1)
    error(message('bioinfo:getpubmed:NotEnoughInputArguments'));
end

Create variables for the two property name-value pairs, and set their default values.

% Set default settings for property name/value pairs, 
% 'NUMBEROFRECORDS' and 'DATEOFPUBLICATION'
maxnum = 50; % NUMBEROFRECORDS default is 50
pubdate = ''; % DATEOFPUBLICATION default is an empty string

Add code to parse the two property name-value pairs if provided as input.

% Parsing the property name/value pairs 
num_argin = numel(varargin);
for n = 1:2:num_argin
    arg = varargin{n};
    switch lower(arg)
        
        % If NUMBEROFRECORDS is passed, set MAXNUM
        case 'numberofrecords'
            maxnum = varargin{n+1};
        
        % If DATEOFPUBLICATION is passed, set PUBDATE
        case 'dateofpublication'
            pubdate = varargin{n+1};          
            
    end     
end

You access the PubMed database through a search URL, which submits a search term and options, and then returns the search results in a specified format. This search URL is comprised of a base URL and defined parameters. Create a variable containing the base URL of the PubMed database on the NCBI Web site.

% Create base URL for PubMed db site
baseSearchURL = 'https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search';

Create variables to contain five defined parameters that the getpubmed function will use, namely, db (database), term (search term), report (report type, such as MEDLINE^®), format (format type, such as text), and dispmax (maximum number of records to display).

% Set db parameter to pubmed
dbOpt = '&db=pubmed';

% Set term parameter to SEARCHTERM and PUBDATE 
% (Default PUBDATE is '')
termOpt = ['&term=',searchterm,'+AND+',pubdate];

% Set report parameter to medline
reportOpt = '&report=medline';

% Set format parameter to text
formatOpt = '&format=text';

% Set dispmax to MAXNUM 
% (Default MAXNUM is 50)
maxOpt = ['&dispmax=',num2str(maxnum)];

Create a variable containing the search URL from the variables created in the previous steps.

% Create search URL
searchURL = [baseSearchURL,dbOpt,termOpt,reportOpt,formatOpt,maxOpt];

Use the urlread function to submit the search URL, retrieve the search results, and return the results (as text in the MEDLINE report type) in medlineText, a character array.

medlineText = urlread(searchURL);

Use the MATLAB regexp function and regular expressions to parse and extract the information in medlineText into hits, a cell array, where each cell contains the MEDLINE-formatted text for one article. The first input is the character array to search, the second input is a search expression, which tells the regexp function to find all records that start with PMID-, while the third input, 'match', tells the regexp function to return the actual records, rather than the positions of the records.

hits = regexp(medlineText,'PMID-.*?(?=PMID|</pre>$)','match');

Instantiate the pmstruct structure returned by getpubmed to contain six fields.

pmstruct = struct('PubMedID','','PublicationDate','','Title','',...
             'Abstract','','Authors','','Citation','');

Use the MATLAB regexp function and regular expressions to loop through each article in hits and extract the PubMed ID, publication date, title, abstract, authors, and citation. Place this information in the pmstruct structure array.

for n = 1:numel(hits)
    pmstruct(n).PubMedID = regexp(hits{n},'(?<=PMID- ).*?(?=\n)','match', 'once');
    pmstruct(n).PublicationDate = regexp(hits{n},'(?<=DP  - ).*?(?=\n)','match', 'once');
    pmstruct(n).Title = regexp(hits{n},'(?<=TI  - ).*?(?=PG  -|AB  -)','match', 'once');
    pmstruct(n).Abstract = regexp(hits{n},'(?<=AB  - ).*?(?=AD  -)','match', 'once');
    pmstruct(n).Authors = regexp(hits{n},'(?<=AU  - ).*?(?=\n)','match');
    pmstruct(n).Citation = regexp(hits{n},'(?<=SO  - ).*?(?=\n)','match', 'once');
end

Select File > Save As.

When you are done, your file should look similar to the getpubmed.m file included with the Bioinformatics Toolbox software. The file is located at:

matlabroot\toolbox\bioinfo\biodemos\getpubmed.m