What software can be utilized to extract data from scientific publications?

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In which Sector It is more common to look, analyze Bar Charts from someone else papers?

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i have some problem with chtMultiRegionSimpleFoam

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What degree of missing data in a particular case/participant results in Expectation-Maximisation no longer working?

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Alessandro Veneri

The only useful tools I know are :

- http://digitizer.sourceforge.net/

- http://www.esuli.it/software/toxy/

Irene B. Teich

Not for data but for knowledge I use "WisARD" of AIQ.go Enterprises. If I find something, I get the data by copy/paste and add the source in EXCEL.

Aren't there plattforms to share raw data? One is https://www.opensciencedatacloud.org/

Maxime Harnois

Inkscape for 2D and Blender for 3D pictures.

Blender for animations

For instance: https://www.youtube.com/watch?v=RasemoYzsFA

Paolo Messina

If you are looking to extract bar charts here is another interesting link :

http://pdfextractoronline.com/bar-charts-to-excel/#!

Meléndez-González Claudio

Datathief is another option and is free. You should copy the graph from pdf file and save as a jpg (for example with "Paint" from Windows). Later, open the image.jpg with Data Theft and extract the data. Is very useful to extract data for effect size calculation for meta-analysis:

Fatima Kies

Dear All

Thank you for this precious information.

Kind Regards

Fatima

Emad Kamil Hussein

Dear Colleagues,

I think the following link is helpful

http://pdfreducer.orpalis.com/

Regards, Emad

Osmar Antonio Bonzanini

Dear @Emad,

Thank you for sharing!

You are welcome Dr. Osmar, I have useful collection contain all facilities related to PDF as a free website and ready for sharing.

Emad

Álvaro Gómez-González

In my case 99% of the times the link Paolo originally suggested is not able to recognize tables in the papers I work with.

There are many options available so I would recommend to test yourself which one is the best:

If there are a lot of tables, save the pdf as an Excel workbook in your acrobat reader. Then, copy-paste the tables you are interested in. If you are only interested in one table, select it, right-click and export as xls. Personally, it's the one I use after trying several. It's quick and easy although it has got problems, mainly with headers, so you usually have to revise it and iron out for minor changes. It works the same if you were interested in other formats.

Online converters: (quick and easy), (works well but you have to receive an email to download the document).

Offline (free software tools): Bytescout PDF Multitool , Tabula

In my experience, all these options are quicker than the usual copy-paste (even using "Text Import Wizard" or "Paste special"). I consider formatting the table in Word the most time-consuming option.

Hope it helps!

Abhay Suresh Zambare

Please see this video, it explains

How to extract data from plot: extract data from graph image to excel (WebPlotDigitizer tutorial)

https://www.youtube.com/watch?v=8EEGyk9hG-8

Paula De Waal

Hi, if i can be of some help here: for mac users, just use the program called Automator (it comes with your mac, in the folder named applications). It's a 2 step process, no configuration necessary, transforms pdf in text.

If you need to create a dataset, instead, extracting also tables, you will need to use ad hoc programs such as Rapidminer which can create datasets from collections of documents (it is free for students).

Another guest for R-users: https://www.biorxiv.org/content/early/2018/01/15/247775

Origin Software can be used for this . Please see the video !

How to extract data from Graph in Origin Software https://www.youtube.com/watch?v=MJiAWVM0TXQ