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OHDSI / MedlineXmlToDatabase

A command line Java application for parsing MEDLINE XML files and inserting the data into a relational database
Apache License 2.0
19 stars 11 forks source link

Annual postgres version of the database #3

Open vojtechhuser opened 7 years ago

vojtechhuser commented 7 years ago

This is a great tool. NLM changed their terms since 2017 and the Medline downloads are public (no need to send signed DUA any more)

This would allow to provide a postgres instance in the cloud of the output of this program (or a back up file only; cheaper option).

This may make this package (work) more accessible to a larger set of users.

schuemie commented 7 years ago

That is an awesome idea!

I apologize in advance for any issues. The tool hasn't been thoroughly tested. But I do know of 3 people (including myself) that eventually got it working, so there is hope ;-)

vojtechhuser commented 7 years ago

Here are the terms ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/README.txt

the key part is (see bold) General Terms and Conditions:

-Users of the data agree to: --acknowledge NLM as the source of the data in a clear and conspicuous manner, --properly use registration and/or trademark symbols when referring to NLM products, and --not indicate or imply that NLM has endorsed its products/services/applications.

-Users who republish or redistribute the data (services, products or raw data) agree to: --maintain the most current version of all distributed data, or --make known in a clear and conspicuous manner that the products/services/applications do not reflect the most current/accurate data available from NLM.

vojtechhuser commented 7 years ago

I have a postgres 15.8G backup file that has the data until end of 2016. Now the question is where to put it and test it with one other person. (I used postgres custom backup)