There are several tools out there, but none meeting quite the requirements.
I need a scripting tool to extract information from Pubmed Queries (XML).
The tool should be written in Python or if need be in PERL.
It should be able to handle data with more than 100.000 entries.
The required result is a csv-table or txt-table with the following fields:
Article key (int)
Year of Publication (string: YYYY-MM-DD)
Number of authors (int)
Author last name (string)
Author first name (string)
Author affiliation (string)
Author email (string)
Position of Author in List (int)
First Author position (boolean)
Last Author position (boolean)
The article key is a variable which is unique to the article. DOI or PID may be used for this. The table has to be sorted by author and article. That means that every combination of author and article key is unique within the table!
For every article of the list, the table gets an entry for every author with additional data.
The script has to be fault tolerant to entries with no available entries. The estimated complete data entries is around 20%.
16 freelancers are bidding on average €206 for this job
I can provide you Python script that will execute Pubmed query, parse XML and save it as CSV output. I can complete it in less than two days for just €200. All I need to start is a sample query you want to execute.
Hello. As a python expert, I think I can make a scripting tool wonderfully. Please provide me a detailed info and please let me know your deadline and budget. Thanks.
Hi there, I am interested in the project. I can develop the solution in Python, and it can easily handle the data volume you have mentioned without any problem.
Hi, I am a certified python programmer. I will provide you the script file in python which will extract the said information and provide you the excel sheet. Thanks, Niraj
Hi, I'll be writing the script in Python 3, and it'll write output to a CSV file. If I do get the project, I hope you will be available for queries to help me make the script better suited to your needs.
Hi, I have 7 years of experience in perl. I can do it as per requirement. can you please provide sample XML input and sample output for the corresponding input? thanks