PubMed and xml extraction

CorText Manager Q&A forum › Category: Data processing › PubMed and xml extraction
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Christophe Gauld asked 3 years ago

Dear Cortext member, 
Since the last version of Pubmed, it is no longer possible to extract articles in xml via the platform.
As the Pubmed format is not considered by Cortext manager (is that it?), and the other pubmed extraction formats (csv and txt) do not contain all the data, is there a way to get what was possible with the xml formerly?
Regards, 
Christophe

2 Answers
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Lionel Staff answered 3 years ago

Bonjour Christophe,

True! As PubMed has moved from xml PubMed to .nbib, and consequently does not deliver any more xml export ability, CorText Manager is not able to parse data from PubMed (see deprecate sources).

.nbib is not so far from RIS format but offers more fields (see here for more details).
You can still download the data in a nbib format and import it in Zotero, and export it in RIS. But you will loose the unsupported fields (e.g. author addresses…). See below the strategy.

We are aware of this limitation, we are working on a new parser which is supposed to be release in few month.
L

Step 1 // PubMed

  1. Build your search in PubMed.
  2. In the search results, use the checkboxes to select individual references.
  3. In the upper right side of the screen, select “Send To”. Then select “Citation manager” and then select (Selection:all files) the “Create File” button.
  4. A strong limitation is that you can only download batches of 10000 documents at a time. So, you probably will need to do several batches (divided by years, semesters and months depending on the number of documents written).
  5. Double-click the “.nbib” file saved to your Downloads folder on your computer.

Step 2 // Zotero

  1. Install Zotero (https://www.zotero.org/)
  2. Import the “.nbib” files in Zotero (See topic on Troubleshooting problems with Zotero, if you have issues downloading references). Depending on the size of your file, It could be long: take a coffee!
  3. Export the collection in RIS format

Step 3 // CorText Manager

  1. Zip the file “.ris”
  2. Upload it in CorText Manager
  3. Chose the option : “RIS (Standard) “
  4. Begin you analysis

 

Christophe Gauld replied 3 years ago

Dear Lionel,

Thank you, perfect answer and it works very well indeed.

Yours,
Christophe

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Lionel Staff answered 2 years ago

Dear Christophe,
We have developed and deployed a parser for the nbib format, used in particular by PubMed. It has been a few months, so it is not yet documented.

Don’t hesitate to use it and to give us feedback! It will be welcome.
Kind regards,
Lionel