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.”


A guide about how to publish journal articles

Interesting post from Editage Insights with a step-by-step guide to creating a journal publication schedule. It was first posted in 2013 but refreshed January 30, 2018. I recommend reading it. The url is

How to cite a journal article using APA style –

editage Insights made this nice APA style cheat sheet about how to cite a journal article using APA style.

Screenshot 2018-02-04 20.38.44

See the pdf:

And here is the url to the website where it is interactive, You need to sign up with editage Insights if you want to download it from this site. I think it is worth it thought, now I do get a lot of nice stuff sent from them to my email.

National and Unversity Library of Iceland have signed the open access 2020 statement

I was glad to see that the National and University Library of Iceland did sign November 9, 2017, the open access 2020 express of interest in the large-scale implementation of open access to scholarly journals

The text following is from that website:

With this statement, we express our interest in establishing an international initiative for the OA transformation of scholarly journals, and we agree upon the following key aspects:

  • We aim to transform a majority of today’s scholarly journals from subscription to OA publishing in accordance with community-specific publication preferences. At the same time, we continue to support new and improved forms of OA publishing.
  • We will pursue this transformation process by converting resources currently spent on journal subscriptions into funds to support sustainable OA business models. Accordingly, we intend to re-organize the underlying cash flows, to establish transparency with regard to costs and potential savings, and to adopt mechanisms to avoid undue publication barriers.
  • We invite all parties involved in scholarly publishing, in particular universities, research institutions, funders, libraries, and publishers to collaborate on a swift and efficient transition for the benefit of scholarship and society at large.

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.

How to read and comprehend scientific research articles

Here is a good tutorial from the University of Minnesota libraries about how to read, take effective notes and find the main points in scientific resarch articles.


key findings in the tutorial

How to read a scientific article

Skim for key findings

The structure of most scientific articles

  1. Abstract
  2. Introduction
  3. methods
  4. Results
  5. Discussion

The most effective order to read an article

  1. Abstract
  2. Discussion
  3. Introduction
  4. Results
  5. Methods

Is the article interesting and relevant enough to my research assignment?

The Abstract

  1. Purpose of the study (why)
  2. Methodology (how)
  3. Results (what they found)
  4. Conclusion (what it means)

Is this article worth reading or should I move into another one

The Discussion

  1. Clearly answers the question posed in the introduction
  2. Explains how the results upport the conclusion

Do I understand and believe the author´s claims?


  1. Stimulate interest
  2. Put the article in larger context

General -> Specific -> Focused Question the authoer is asking.

Authors describe previous work and how their work relates to it.

Why did the reasearchers do this study?

Does the research question match up with the conclusions read int he discussion?

The Results

  1. What the authors found
  2. Key data, often in figures or tables

Is the data collected appropriate to answer the research question?

Does the data support the conclusions?


The Methods

  1. What experiments were done
  2. Can be difficult to read dut to technical language and details

How to find the main points of an article

Key places to look

  1. Title
  2. Abstracts
  3. Keywords
  4. Figure and table titles
  5. First and last sentences of the Introduction

Within the articles the authors main point

  1. “We hypothesize that …”
  2. “We propose…”
  3. “We introduce…”


How to take effective notes

Effective note-taking will save you time and help you clarify your thoughts.

Creating a standard template for taking notes will  help you organize your research

Enable you to make quick comparisions, and will save you time rereading articles

Screenshot 2018-01-30 17.42.34


This text and screenshots are from the tutorial from the University of Minnesota libraries,

Copyright information of the webpage of the Bureau of Labor Statistics USA

I really like the copyright, The Bureau of Labor Statistics (BLS) in USA, has on their material on the website. Everything with public domain (except on material when it is not possible). It means peopla are free to use their material without specific permission. Although they ask people using it to cite the Bureau of Labor Statistics.

Screenshot from the webpage of The Bureau of Labor Statistics in USA about copyright of their materials