Pubmed Parser

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)

Journal (string)

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%.

Skills: Perl, Python, XML

See more: pubmed api, pubmed sql, pubmed xml download, affiliation parser, pubmed central python, python pubmed abstract, biopython pubmed, pubmed xml, css, html, python, web scraping, django, xml, web development

About the Employer:
( 0 reviews ) Wiesbaden, Germany

Project ID: #18447437

Awarded to:


hi there I have 10 years experience in Python and web development. I did lots of projects in web world, develop in most web technologies. 8 years developing Django sites and services. I did lots of projects in scra More

€300 EUR in 14 days
(52 Reviews)

16 freelancers are bidding on average €206 for this job


Hello, I'd be glad to develop the pubmed scrapper for you using python. Looking forward to chat with you soon for more details. Best regards,

€258 EUR in 3 days
(130 Reviews)

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.

€200 EUR in 2 days
(375 Reviews)

Hi, I'm interested to develop a Perl parser for you. can you please send some sample Pubmed XML query Thanks

€222 EUR in 3 days
(53 Reviews)

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.

€250 EUR in 3 days
(22 Reviews)

Hi Nice to meet you. I'm python expert and my last project on is also python scraping task. My past works: Youtube comment scrapping Real estate property list to csv Job-site content to csv And sc More

€150 EUR in 3 days
(27 Reviews)
€164 EUR in 3 days
(15 Reviews)

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.

€222 EUR in 3 days
(13 Reviews)

Hello! I'm ready to make your project with Python +Scrapy framework. This is the most suitable solution for your requirements. Scrapy allows to handle large amounts of data, it easily stores data to csv, etc. Would you More

€200 EUR in 5 days
(13 Reviews)

I have been in this field for more than 7 years. i have experience in C#,php,Perl,wordpress,Html,postgress ,Ubuntu,Crontab,Web Services, Rest Api, Zend ,YIi,Mysql. Relevant Skills and Experience so i am right can More

€244 EUR in 3 days
(5 Reviews)
€94 EUR in 3 days
(8 Reviews)

Hello, I like solving complicated problems and making the things easier for the other people. In order to achieve this, I have more than 18 years of experience as a IT professional. I have an extraordinary abil More

€250 EUR in 3 days
(2 Reviews)

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

€111 EUR in 3 days
(0 Reviews)

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.

€111 EUR in 3 days
(0 Reviews)

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

€250 EUR in 15 days
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€277 EUR in 1 day
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