Information Extraction

GIANT 2019, Reference Parsing, Deep Citation Parsing, Dataset, Cover

GIANT: The 1-Billion Annotated Synthetic Bibliographic-Reference-String Dataset for Deep Citation Parsing [pre-print]

This is the pre-print of: Mark Grennan, Martin Schibel, Andrew Collins, and Joeran Beel. “GIANT: The 1-Billion Annotated Synthetic Bibliographic-Reference-String Dataset for Deep Citation Parsing.” In 27th AIAI Irish Conference on Artificial Intelligence and Cognitive Science, 101–112, 2019. final Publication: http://aics2019.datascienceinstitute.ie/papers/aics_25.pdf Abstract. Extracting and parsing reference strings from research articles Read more…

By Joeran Beel, ago
The results of the comparison of 10 open-source bibliographic reference parsers

Machine Learning vs. Rules and Out-of-the-Box vs. Retrained: An Evaluation of Open-Source Bibliographic Reference and Citation Parsers

Our paper “Machine Learning vs. Rules and Out-of-the-Box vs. Retrained: An Evaluation of Open-Source Bibliographic Reference and Citation Parsers” got recently accepted and will be presented at Joint Conference on Digital Libraries 2018. Abstract: Bibliographic reference parsing refers to extracting machine-readable metadata, such as the names of the authors, the Read more…

By dominika_tkaczyk, ago
The workflow of author contributions extraction

Who Did What? Identifying Author Contributions in Biomedical Publications using Naïve Bayes

Our paper “Who Did What? Identifying Author Contributions in Biomedical Publications using Naïve Bayes” got recently accepted and will be presented at Joint Conference on Digital Libraries 2018. Abstract: Creating scientific publications is a complex process. It is composed of a number of different activities, such as designing the experiments, Read more…

By dominika_tkaczyk, ago
Google Scholar

Update for Docear’s “Google Scholar Parser” Library to Fetch Metadata for PDF files

Update 2018-07-31: We updated the Dropbox Link Google Scholar recently changed its layout, and as a consequence, Docear couldn’t fetch metadata anymore from Google Scholar for PDF files. Fortunately, one of our users (“Silberzwiebel”) adjusted Docear’s Google Scholar Parser, and now everything works as usual. However, we have not yet integrated Read more…

By Joeran Beel, ago

Howto: Import references from webpages (e.g. PubMed, IEEE, ACM, …)

Compared to several other reference managers, Docear lacks a feature to directly import references from the Web. For instance, if you visit the detail page of a research article on a publisher’s website, you might wish to directly import the bibliographic data of that article to Docear. Many publishers offer export options for reference managers such as Endnote, RefWorks, or Zotero. So, how do you do it with Docear?

Fortunately, Docear uses the BibTeX format to store references. BibTeX is a de-facto standard for references that is supported by almost any publisher and any reference manager. So, read on to learn how to import bibliographic data from web-pages in two steps!

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By Joeran Beel, ago

Docear 1.1 stable released with strongly improved PDF metadata extraction

Finally, after releasing the alpha and beta, today we release Docear 1.1 stable. If you have tried already one of the previous versions, there is not much news. Otherwise, read on.

Thanks to all the generous donors, our student Christoph could work on an improved PDF metadata retrieval for Docear. The new Docear 1.1 is able to extract the title of a PDF and fetch metadata from Google Scholar for that title. To do so, select a PDF in your mind-map and chose “Create or Update reference”, …

… and the following new dialog appears. The dialog shows the file name of your PDF file, and the extracted title. In the background, the extracted title is sent to Google Scholar and metadata for the first two search results are shown in the dialog.  If the title was extracted incorrectly, you can manually correct it. You may also chose to use the PDF’s file name for the search. For instance, when you named your PDF already according to the title, select the radio button with the file name, and the file name is sent as search query to Google Scholar (you may also manually correct the file name before it’s sent to Google Scholar). Of course, all other options you already know are still available, such as creating a blank entry, or importing the XMP data of PDFs. Btw. Docear remembers your choice, i.e. when you select to create a blank entry, the option will be pre-selected when open that dialog the next time. It might happen, that your IP will be blocked by Google Scholar when you use the service too frequently. If this happens, a captcha should appear, and after solving it, you should be able to proceed. We did not yet test this thoroughly. Please let us know your experiences.

The precision of our metadata tool depends on two factors, A) the precision of the title extraction and B) the coverage of Google Scholar. According to a recent experiment, title extraction of our tool is around 70%. However, the final result very much depends on the format of your research articles. In my research field (i.e. recommender systems), I would say that our tool extracts the title correctly for about 90% of the articles in my personal library. In addition, almost all articles that are relevant for my research are indexed by Google Scholar (i would estimate, more than 90%). This means, for around 80% of my PDFs the correct metadata is retrieved fully automatically. Given that I provide the title manually, for even more than 90% the metadata may be retrieved. Please let us know your experience (and your research field). (more…)

By Joeran Beel, ago

Docear 1.1 Beta Released: New PDF Metadata Extraction, Better Zotero and Mendeley BibTeX support, and Bug Fixes

If you have tested the Preview of Docear 1.1 you may already know about some of Docear’s new features. With your feedback and the mind maps, log files and BibTeX files you shared with us, these features have matured. We are proud to introduce the first (and hopefully only) Beta release of Docear 1.1.

The new key features of Docear 1.1

Improved metadata retrieval

Thanks to your donations, our student Christoph greatly enhanced Docear’s PDF metadata retrieval. For us, it works really great, and with Docear 1.1 Beta the last bugs have been fixed. Btw. if you like what Christoph did, and if you are using LibreOffice, or OpenOffice, please also read our call for donation to develop an add-on for these two text processing tools.
Image

Improved support for Zotero / Mendeley BibTeX files

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By Joeran Beel, ago

Preview of Docear 1.1 with PDF Metadata Retrieval from Google Scholar

Thanks to all the generous donors, our student Christoph could work on an improved PDF metadata retrieval for Docear, and today it’s time to present the first preview. The new Docear 1.1 (preview) is able to extract the title of a PDF and fetch appropriate metadata from Google Scholar. Whenever you select a PDF in your mind-map and chose “Create or Update reference”, the following new dialog appears.

The dialog shows the file name of your PDF file, and the extracted title. In the background, the extracted title is sent to Google Scholar and metadata for the first three search results are shown in the dialog.  If the title was extracted incorrectly, you can manually correct it. You may also chose to use the PDF’s file name for the search. For instance, when you named your PDF already according to the title, select the radio button with the file name, and the file name is sent as search query to Google Scholar (you may also manually correct the file name before it’s sent to Google Scholar). Of course, all other options you already know are still available, such as creating a blank entry, or importing the XMP data of PDFs. Btw. Docear remembers your choice, i.e. when you select to create a blank entry, the option will be pre-selected when open that dialog the next time. It might happen, that your IP will be blocked by Google Scholar when you use the service too frequently. If this happens, a captcha should appear, and after solving it, you should be able to proceed. We did not yet test this thoroughly. Please let us know your experiences.

The precision of our metadata tool depends on two factors, A) the precision of the title extraction and B) the coverage of Google Scholar. According to a recent experiment, title extraction of our tool is around 70%. However, the final result very much depends on the format of your research articles. In my research field (i.e. recommender systems), I would say that our tool extracts the title correctly for about 90% of the articles in my personal library. In addition, almost all articles that are relevant for my research are indexed by Google Scholar (i would estimate, more than 90%). This means, for around 80% of my PDFs the correct metadata is retrieved fully automatically. Given that I provide the title manually, for even more than 90% the metadata may be retrieved. Please let us know your experience (and your research field). (more…)

By Joeran Beel, ago

Docear Beta 7 with PDF Metadata Extraction

Beta 7 is out and has one major new feature: (semi-)automatic extraction of bibliographic metadata from PDF files.  That means, when creating a new reference, you don’t have to type everything manually but bibliographic information such as title, author, year, journal, etc. is all provided to you automatically. Here is how it works:
Do a right click on a node with a PDF and select as shown in the picture
By Joeran Beel, ago