Biorxiv

Users asking other users for import filters.
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doconnor
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Joined: Sun Nov 27, 2005 7:50 pm

Biorxiv

Post by doconnor »

Hi there,

Has anyone made an import filter for Biorxiv (http://biorxiv.org) that they would be willing to share?

Thanks!

dave

iandol
Posts: 402
Joined: Fri Jan 25, 2008 2:31 pm

Re: Biorxiv

Post by iandol »

There is a direct bookends compatible RIS output in Citation Tools, e.g. http://biorxiv.org/highwire/citation/25230/bookends — possibly there is a compatibility issue with the abstract, requiring a small edit of the RIS import filter but give it a try first.

Jon has also improved Biorxiv import directly from the Bookends browser recently.

doconnor
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Re: Biorxiv

Post by doconnor »

Thanks!

--dave

kdv
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Re: Biorxiv

Post by kdv »

I wondered if there now is a BioRXiv filter availble?
Kurt

Jon
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Re: Biorxiv

Post by Jon »

BioRxiv is a web site, there is no API and no BioRxiv-specific filter. You can search the site with Bookends Browser and import directly, or you can search in your preferred browser and use their Citation Tools to export the reference in a Bookends-compatible format (or use the bookmarklet to open Bookends Browser and import from there).

Jon
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doconnor
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Re: Biorxiv

Post by doconnor »

Resurrecting this old thread. It now seems that there is API access to Medrxiv/Biorxiv (https://www.medrxiv.org/tdm). Is the API sufficient to enable direct online searching and batch downloading of articles?

Thanks!

dave

Jon
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Re: Biorxiv

Post by Jon »

I took a cursory look, and it seems it returns the metadata if you have the DOI, but you can't search the database (e.g. looking for an author or a topic).

Bookends Browser works very well with biorXiv and gives easy access to all of it's search features, you should use that.

Jon
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doconnor
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Re: Biorxiv

Post by doconnor »

Thanks for looking into this Jon. I'm not sure the Bookends browser helps with the batch download issues. It is a great solution for single articles.

Somewhat relatedly, is there any way to force Bookends to try to download the Pubmed Central version of an article in the Pubmed online search? When batch downloading, it would be great to use advanced search to find those that are in PMC and then download from PMC. Right now, when I search from PMC the PDF import still seems to try to pull from the publisher website.

Jon
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Re: Biorxiv

Post by Jon »

I'm not sure why you say Bookends Browser won't do batch downloads. I just searched biorXiv for "CD45" and got 10 hits. I clicked on the down arrow and after a few seconds a dialog with all 10 hits was listed. I Selected All and imported 10 at once. No need to do this one at a time.

As for you question, I don't know exactly what you're doing. You're doing a direct PubMed search? A Bookends Browser search of PubMed? Or a Bookends Browser search of PubMed Central?

Jon
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doconnor
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Re: Biorxiv

Post by doconnor »

Thanks Jon,

I had the misapprehension that the browser needed to navigate to a single paper and download papers one at a time. You are right. Performing a search in Medrxiv and clicking the down arrow seems to do what is necessary.

In terms of Pubmed Central, I was searching with the 'Online Search' interface for PubMed, using 'Advanced Search'. I change the Search Subset to PubMed Central. This should yield results that are all in PubMed Central and should have accessible PDFs. Some do not, however. I just tried to do the same search in Bookends Browser from the Pubmed Central search page. Of the first 20 references, only about 10 imported a PDF along with the reference.

Thanks again.

Jon
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Re: Biorxiv

Post by Jon »

I'll take a look at that.

Jon
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Jon
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Re: Biorxiv

Post by Jon »

I expect we'll have this in the next update.

Jon
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doconnor
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Re: Biorxiv

Post by doconnor »

Coming back to this with delayed thanks - just saw that fallback to PubMed Central was added in the newest version. Seems to work great! Thanks again!

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