Building a tool to sync articles annotations across different copies of the same article

wrote a blog February 9th, 2018 he named Preserving comments from PubMed central about PubMed announced discontinuation of PubMed comments because it wasn´t used enough (only 6.000 articles of the 28 millions had gotten comments).

In the blog  Jon Udell tell how they did build a tool to extract comments from an article and then being able to sync it across different copies of it at journal websites, PubMed and PubMedCentral. I hope this development will go on and will also get to the repositories.

You can browse here the comments they did extract from PubMed, they are all filtered by PubMedCommonsArchive tag which they added to every annotation when they did import it. They also tagged each comment with unique PMID of related document.  And now everyone can browse and search all comments by using a PMID tag.


At the end of the blog Jon Udell say :

“In our strong opinion, all article feedback, commenting, review or other collaboration systems should as quickly as possible adopt W3C standards for web annotation, so that we can begin to move towards an integrated and open framework for engagement across scientific and scholarly literature.”


DOAJ launches the DOAJ Best Practice Guide

Screenshot 2018-01-31 16.02.33

DOAJ has made a guide (web resource) that provides selection criteria, resources and tools for the identification of reputable open access journals to support researchers, publishers and librarians in their search of best practice and transparency standards.

It will also collect discussions about open access to publications and its development.

I did send my Scopus information to ORCID

When I was making my profile page with Impactstory they could not find any publications associated with my ORCID. Then I got information about that I could send Scopus my details and my publication list to ORCID. It is done throught the tool Scopus ORCID importer wizard.

I also did make a tutorial about how to give Scopus permission to read your ORCID record. Scopus needs a permission to find authors profiles in Scopus and send the author Scopus ID to ORCID.

A screenshot from Scopus about how to send Scopus Author details and publication list to ORCID

Unpaywall. Getting fulltext scholarly articles

I do recommend to all that want to read scholarly paper to get Add-ons, named Unpaywall for their Firefox or Chrome browser. made by Impactstory.

It is an add-on that will show green OA logo on articles that are available as fulltext (grey if they can´t find it). They say the green tab is on 65-85% of all scholarly articles. It is fast, free and legal and do allow us to skip the paywall. It is powered by a database of millions of author-uploaded PDF´s.

It is a nonprofit project to make science more open and reusable online. Impactstory is getting grants from the National Science Foundation and the Alfred P. Sloan Foundation.

Memo in Atlas.ti

I did find two very useful articles about how to use Memo in the program Atlas.ti.

Susanne Friese. 2009. Working Effectively With Memos In ATLAS.ti. Atlas.ti Library. Sótt af

Susanne Friese. 2008. Methodological Tips On The Use Of Memos. ATLAS.ti Library. Sótt af

Screenshot 2017-05-02 23.26.14

Picture 1: Screenshot from Susanne Friese article name Methodological Tips on the use of Memos.

Susanne Friesesays that the Memos overall purpose is best served if they are meaningfully structured and organized.

She suggests that if I have an ideoa about a text passage I should not use Memo. Rather I should create a quotation and insert my thoughts there in the comment field for the quote.

She tells me to identify my central research questions, to create a memo for each individual research question. And if the questions are more comprehensive they should be broken down into subtopics. Each Memo for the Research Questions could f.ex. start on RQ#: Title. I can then see them in alphabetical order. The Memos I want at top I use * (a star) in front of the title. See picture 2 from Susanne Friese sample project.

Screenshot 2017-05-02 23.35.25Picture 2: Screenshot from the Memo Manager in Susanne Friese sample project. It is from the year 2008 in the Window invironment.

I decided to use her sample to put up my Memo in my Atlas.ti (in the MacOS environment / year 2017). It looks quite different so it took me some time to figure out how to do it.

I did open the Memo Manager and started  making a new memo by clicking the + (plus) in the upper left corner. Then a new Memo was created in the main window, where I did rename it as can be seen in picture 3.

Screenshot 2017-05-02 23.50.53Picture 3: New Memo created and renamed.

Then I did repeat this process until all my Memos were putted up. I still need to make some Literature memos and putted a star in front of those I want at top. See picture 4.

Screenshot 2017-05-02 23.26.55Picture 4: The Memos I did make.

As can be seen from Susanne sample then she was able to say which type here memos were. In MacOS grouped are used. I opened therefore the Memo Group Manager. There I did click on + (the plus in the upper left corner) and made my Memo groups. I used the ones Susanne suggested and also some the Atlas.ti Manual did suggest. In the windows at the bottom I did put my Memos into the right groups. See picture 5.

Screenshot 2017-05-02 23.32.45Picture 5: The Group Managers with the groups I did make and my grouped memos. Here is a sample of the Research Questions (RQ#) which I grouped as Analysis.

Now when I open the Memo Manager I can see the Memo Groups in the left column. I can choose there to see the memos of all groups or I can choose which group to see the memos of. See Picture 6.

Screenshot 2017-05-02 23.34.12Picture 6. A Screenshot of my Memo Manager in my MacOS.