Change of DOI and Associated URL

The Digital Object Identifier is special service introduced with aim to advance indexing, searching, publishing and distribution of publications. It is accepted by the International Organization for Standardization as ISO26324 .

DOI services and registration are provided by the International DOI Foundation (IDF) which is a not-for-profit membership organization.  IDF is governance and management body for the federation of Registration Agencies providing DOI services and registration.  Detailed information about DOI system is published on the site of IDFResources about DOI including video materials are free to download on the site of IDF so those interested to learn more about DOI can check materials and clarify their dilemmas about use and management of DOIs.

One of very important features of DOI is that it is unique and that metadata associated with it can be updated if necessary. Option to update metadata is very important since DOI once registered can be updated so it can easily accommodate all changes related to that digital object (article, issue of journal, book, conference proceedings, supplementary files etc.) that can take place in reality.

Let me describe one situation that I have had recently in work with one editorial board which may in similar form occur in the process of development of any scientific journal or publishing of any publication.  In our case, the editorial board due to changes of partner organizations, establishment of NGO that will support some journals and some technical reasons had to change servers and domains pointing to those servers. In addition, they publish their journals in three installations of the Open Journal Systems that had three domains and two DOI prefixes.  They moved those installations on new servers and they use three installations of Open Journal Systems now on two domains  (URLs) and DOIS created using two DOI prefixes.

Due to flexibility of options to manage DOI numbers in the Open Journal Systems editors can create efficient and easy to use pattern to create DOI numbers or create custom DOI for each article or other digital object they publish.

DOI options in OJS

The editorial board I work with decided that DOI number for each article of their scientific journal should be created like this:


Such a DOI number will have associated the URL that is created by the following principle:


Thus, it is easy to associate each article DOI to unique URL. That URL will point to the page with metadata of article and downloadable article. If URL change there will be change only in the part of URL “journaldomain”. The rest will remain the same.  That enables editorial board and system administrator to update easily any change of URL.

Well, that is fine. But, how to accomplish that task without programming skills?  And, we do not have funds to buy software to accomplish that.  Thus, solution will be to use free software in a way that programming skills are not needed.  Imagine that editor is expert in veterinary medicine for sheep and goats. Very important for local village population. The most probably, editor did not receive any training in PHP, SQL, JavaScript.  So, we have to manage this issue without programming skills.

We will use the following software:

phpMyAdmin that is free and usually preinstalled on server

LibreOffice – advanced office suite with spreadsheet, text writing, presentation and drawing capabilities

Geany – text editor (You can use Notepad ++ or other similar text editor)

Download LibreOffice and Geany on your computer and you are powered with powerful software without proprietary licensing limiting your work.

Firstly, we need to export table from the database in which we can find DOI numbers and after that sort out those DOIs and associate proper URLs to them. Your hosting company will give you link to phpMyAdmin. It is usually part of your cpanel. You will find it in section Databases like on image below:

phpmyadmin icon

When you click on icon phpMyAdmin it will direct you to the screen that display on the left side a list of databases. Click on proper database and phpMyAdmin will direct you to the screen with a list of tables and you will see that there is table called submission_settings like on image below.

submission settings

When you click on that table the system will prompt you with the following screen:

rows in database table

In some cases you will see that such a table consists of 2500 or more rows. You can select how many rows you will see and export data in page by page.  Image above shows that we selected 25 rows, that we are on the page one, we checked all of them. Since table submission_settings contains a lot of rows please feel free to choose that you see 250 or 500 rows. We have to click on Export that you see on the right side below the rows.  When we click on Export the system will direct us to the page that will perform export in desired format. In our case we will choose OpenDocumentSpreadsheet  format as on image below by clicking on little drop down arrow right from the format of export file.

selecting format of export

We have to click on Go button.  So far, we are only clicking, no programming skills required.  After we click on Go button we will be prompted with the screen that will offer us to open file with LibreOfficeCalc which we installed previously on our computer.

selecting LibreOfficeCalc


When you click on OK button your computer will open rows that you exported and it will look like on image below:

LibreOffice opened rows

Well, although this looks abstract please notice that we still stick with clicking. But, now some logic we have to apply, not programming skills.  We have to filter out DOI numbers we need and copy them in a separate file. Click on menu Data/More Filters, Standard Filter and you will be prompted with the following screen that will handle what to do with data in columns.  In our case we know that in Column C should be value as displayed on image below and that in Column D should be value that contains your DOI prefix that you have got from CrossRef or other authority that can provide DOI services.

DOI filter

After that you will see table with DOI numbers exported from that number of rows. You can copy those numbers in a separate spreadsheet and repeat this process until you come to the last row of submission_settings table. It can sometimes have 4500 or more rows, but if you follow this procedure and choose let say 500 rows on the first step you will finish that easily.

After you copy all those DOI numbers and put them in one column you will have all DOI numbers.  If you follow pattern that we mentioned above you will easily generate URLs and put all those URLs in second column.  You can write URLs in software Geany which we mentioned  and put them neatly one below each other. We can copy that and paste in the second column in your spreadsheet. After you finish that you can send that file to support in CrossRef and they will manage for you deposits so the proper file will be easily associated with proper URL.  So, we accomplished task only by clicking and at the end applying some logic. Well, it is needed sometimes.







Intuition is better than manual?

In more than 25 years of working with software I have passed through various stages of using software. I was struggling with bad books, close to empty help files. I stumbled upon parts of interface, guessing what is logic behind, why workflow for some operations and procedures is not obvious. I could not do even simple things since books were scarce and expensive.

Translators who translated manuals and various technical books often invented new terminology and sometimes used awkward sentences in order to translate quite technical text on language which does not have those words in vocabulary. Some linguists were horrified with new intrusion of foreign languages and often coined their own  terms based on a lack of knowledge about technology concerned, misinterpretation of concepts and meaning.

Writing style was often very modest at least. There were no typographic differences between narrative text and command lines, illustrations too general and not representing the process described in paragraph.  Instructions were written in a way that can understand only those who already know that software. Those who did not know to use that software were mostly lost.  Procedures were not described concisely, some steps missing and above all, some examples were not workable.

On the other side, we have to be honest and confess that at the time, despite the fact that more than 20 years passed after wider using of operating systems and the development of software,  the software technology was at the beginning of introduction to the wider user population.  The code for Apollo mission was written by hand. Image bellow taken from Wikipedia shows Margaret Hamilton next to a stack of code she and her team wrote for the Apollo Mission computers.

software developer with books with code

The development of software and its maintenance was rather a hard way with a number of difficulties.

I strongly recommend those interested in history of software development to read article”No Silver Bullet – Essence and Accident in Software Engineering” by Fred Brooks in 1986.  Very interesting Wikipedia article states that: “Brooks distinguishes between two different types of complexity: accidental complexity and essential complexity. Accidental complexity relates to problems which engineers create and can fix; for example, the details of writing and optimizing assembly code or the delays caused by batch processing. Essential complexity is caused by the problem to be solved, and nothing can remove it; if users want a program to do 30 different things, then those 30 things are essential and the program must do those 30 different things. ”  Many scientists, software developers and businessmen noted that software grow faster in size and complexity than are invented methods to handle such complexities.  Some software companies initiated marketing slogan that their software is “intuitive and user friendly” which proved to be just marketing slogan far from truth.
All of that sometimes created great confusion . I felt like some botanist looking for magic flower in the middle of jungle.  I felt I was stuck in the middle of rainforest with gigantic trees, huge bushes, my skin crisscrossed with scratches and covered up with blood stains. It looked like I wanted to fit a square peg to a round hole. Enormous insects around me and snarling of hungry beasts was frightening. How did I get here?  How to get out from this?

In addition, increasingly complex software was often not well developed  and crashed frequently which caused even more confusion.  It was sometimes fun, but sometimes I have had embarrassing experience. A number of hours wasted, loss of data, broken hard disk.  I asked myself: What I have done wrong?  Is all of that really so sensitive that pressing wrong key on keyboard can toast my computer?  Who will use this stuff if it is so easy to ruin all I have done?

At the same time, business companies followed old devastating principles that everything should become commodity and they invested less in the development of supporting documentation.  They rather established support service that is not neither cheap nor efficient.  The free software movement gave to everyone free access to code being protected by GNU/GPL license which granted everyone right to develop, modify, distribute and document software as they like. That was promising framework and social, legal and technological basis for more responsible development and use of software.  At the same time users of many software packages experienced a lack of support, partly documented manuals, a variety of undocumented features, and sometimes unhelpful, arrogant and cynical support guys.

Even when manuals were written properly they were often very large and nicely illustrated books.  Too small number of people have had enough time to read them. I strongly believe that those who have had enough time for studying such manuals benefited a lot.

But, use of software manual is not based only on existence of sufficiently illustrated and written books.  Since I am more than 10 years involved in open access movement I strongly believe(d) that people from academia would use software manuals in a more systematic and principled way. But, my experience is very different.

There may be different reasons for that:

  • not sufficient time for reading detailed manuals
  • scientists and various scholars develop their own software for some purpose so they know it
  • software is developed for special purpose and it will not be used by wider audience
  • manuals and support are expensive or nonexistent
  • scholars and scientists are tired of reading and exhausting tedious work at academia so any additional obligation to read is rather avoided
  • some scholars and scientists display various psychological traits when being confronted with new scientific areas including software
  • some scholars and scientists have (un)diagnosed dyslexia, discalculia or other neurological conditions on a (sub)clinical level which prevents them from detailed reading of manuals, following procedures, remembering various relationships and hierarchies in managing various contexts managed by proper use of software features
  • some scholars and scientists for various reasons are print disabled and they do need assistive technologies to help them to learn to efficiently to use software

I am sure that there may be other reasons too.  But, those who write software and support scientists especially in the field of open access use of software should observe the following  principles:

  • written manuals should be written and tailored to the needs of some institution/library/journal
  • manuals should present procedures with examples from real use of software in a given context according to the version of software the is in production use by the users
  • manuals should describe each step in procedure or workflow and present screenshot that user see on the screen
  • manuals should be written in an accessible format
  • manuals should be enriched with infographics and other illustrations intended to present information in a brief and clear way.  They  can improve learning process by utilizing graphics to enhance the user’s ability to understand structures, workflows and procedures
  • manuals should offer links with screencasts that will show to the users how some tasks can be accomplished
  • software features that are invented with aim to improve workflow of users should be documented with examples of the real scenarios and contexts for a given group of users (i.e. journal, institute, faculty, library)
  • manuals, infographics and screencasts should be licensed with soem acceptable Creative Commons or GNU Free Documentation License

Well, one can say that it is not easy to do. But, software as manuals are a significant part of social interaction of various types of users (in the context of open access there may be readers, authors, reviewers, editors, librarians, lawyers, students, businessmen, policy makers). That is not commodity in a box. The manuals and software are part of ongoing incremental build model due to very dynamic development of various standards and services associated with academic publishing. Contemporary  software platforms require developers and users to take pace of the development of the internet, academic publishing, various technological, cultural, social, legal and scientific challenges and developments.  Consequently, when some editorial board or institution plans to deploy some software platform for academic and scientific publishing it is needed to plan continuous development, testing, support, documentation development and distribution.

GDPR Compliance

I have experienced several times that various companies purchased databases of e-mail addresses and other information about persons who may be potential customers of their commodities. Those companies used that information to send them their mail campaigns. Sometimes they receive information about clients that are retired, young, athletes or sorted according to various criteria. Many people asked themselves how they do now that I am retired recently or that I my kids just enrolled in secondary school. Many people felt embarrassed and confused after they realized that their privacy is not protected and that their private information is distributed to third parties without their consent.

Search engines often allowed anyone to easily find information about people that are registered in any on line system.

Sometimes journal editors while entering archives of previous issues of their journals, articles and information about authors in web applications such as OJS are faced with repetitious work of entering information about some authors.  Some of them asked developers to develop plugin which will enable that will enable them to have drop down list of users so they can easily select user and insert it in list of authors of some scientific article. They did not have any intention of making public that list or to use that feature anywhere except in administration panel of their web applications. But, their benevolent intention can in some contexts produce unpleasant consequences for some authors.  Thus, it is needed that privacy is protected by design not just by possible honest intentions of people who use data about other people.

Numerous complaints in previous years motivated legislators in the EU to pass by very strict rule that will protect data about people. The EU adopted General Data Protection Regulation.

“The EU General Data Protection Regulation (GDPR) replaces the Data Protection Directive 95/46/EC and was designed to harmonize data privacy laws across Europe, to protect and empower all EU citizens data privacy and to reshape the way organizations across the region approach data privacy.”  It will have very strong impact on entities within EU and those which store and use information of the citizens of the countries that are the EU members. The EU General Data Protection Regulation (GDPR)  was approved by the EU Parliament on April 14, 2016 and enforcement day is May 25, 2018.  Organizations in non-compliance can face heavy fines.  It is important to read part on extra-territorial applicability which reads:

“Arguably the biggest change to the regulatory landscape of data privacy comes with the extended jurisdiction of the GDPR, as it applies to all companies processing the personal data of data subjects residing in the Union, regardless of the company’s location. Previously, territorial applicability of the directive was ambiguous and referred to data process ‘in context of an establishment’. This topic has arisen in a number of high profile court cases. GPDR makes its applicability very clear – it will apply to the processing of personal data by controllers and processors in the EU, regardless of whether the processing takes place in the EU or not. The GDPR will also apply to the processing of personal data of data subjects in the EU by a controller or processor not established in the EU, where the activities relate to: offering goods or services to EU citizens (irrespective of whether payment is required) and the monitoring of behaviour that takes place within the EU. Non-Eu businesses processing the data of EU citizens will also have to appoint a representative in the EU. ”

There is still time to be prepared and in order to do so properly please read the text of adopted text of The EU General Data Protection Regulation (GDPR).


Spellcheck-Scientific Texts

The Open Journal Systems users use embedded TinyMce editor to enter various information during publishing their articles in journals.  Some users may need for various reasons spellcheck in order to make sure that texts they enter are spelled correctly.  TinyMce developers  developed one very simple spellchecker plugin that is not configured by default in the Open Journal Systems. There is free version and Spell Checker Pro version. TinyMce developers stated on the web page for Spell Checker pro that: A TinyMCE Enterprise subscription includes the ability to download and install a spell check as-you-type feature for the editor.

If you are editor, editorial board member or administrator of the site of your journal various payment schemes for spellchecking might not be affordable.

For general purpose texts you can use spellcheck capability of your browser.

But, if you need free, easy to install TinyMce spellchecker capable to spellcheck medical, scientific and legal terms you can consider using Nanospell spellchecker.  The developers of Nanospell stated on their site  that: It is perfect for secure applications and websites where user experience counts:

  • Guaranteed dictionary availability across all browsers, including medical, scientific and legal words.
  • Never sends your secure data to any remote servers: everything is done locally.
  • Works in older browsers which do not have spellchecking capabilities of their own.
  • No popup Ads

I supported some members of editorial boards to install it and configure properly in their Open Journal Systems installations. That is very easy and straightforward process which should not last more than 5 minutes and its icon should appear in toolbar of TinyMce editor in your Open Journal Systems installation.  It is easy to install its dictionaries which can meet your editorial and authoring needs.  However, please be aware of their licensing policy.



History of Science Communication

Journal of Science Communication published in their special issue (Issue 03, 2017) articles on history of science communication.

Authors from various countries wrote articles and essays about history of science communication in thier respective countries.  Readers can learn about history of science communication in Japan, Australia, New Zealand, Spain, United Knigdom, Estonia, Mexico, South Africa.

Authors of editorial emphasized that: “The papers published in this issue are organized in three groups, though with diffuse boundaries: geography, media, and discipline. The first group contains works that deal descriptively and critically with the development of PCST actions and either general or specific public policies for this area in specific countries. A second set of papers examines aspects of building science communication on TV or in print media. The third group of papers presents and discusses important PCST cases in specific areas of science or technology at various historical moments.”

I strongly recommend all readers of this blog to read those articles and follow study in this are since this will help authors, editors, reviewers, system administrators to collaborate efficiently and make informed choices that put forward advancement of science communication in theory and everyday practice.

Licensing – Open Access

In my work with editorial boards of scholarly journals I found often that they support idea of open access in general. But, it is not clear always that licensing itself from the legal point of view may be quite complex.  Heads of scientific libraries and editorial boards sometimes discuss for long time issues related to licensing issues.  Sometimes that takes too much time since their lawyers sometimes say:  “That license gives you framework for implementation of open access ideas, but in our legislation it will be hard to make defense at the court. ” Well, it might be quite useful to have close cooperation with lawyers, NGOs and other people involved in the development of legislative efforts and translate Creative Commons license and do necessary steps so it can be accepted and accepted in legislation in your country.

In some countries people register their work in national copyright agencies, but absence of registration does not imply absence of protection and copyright.

One of successful and viable licensing practices is to choose appropriate Creative Commons licenses for article, data set, images or other article components.  Scientists who would publish source code of software used and created in research may use free software licenses. Please note that license does not relate to the content on images, video in terms of privacy and other potential legal issues.  For example, video showing a woman doing breast self-exam can be from the point of video authoring protected by Creative Commons. But if video shows face of the woman showed in video recording her privacy is violated if she had not given clear consent for that previously.

Editorial boards and librarians should often visit the website of EIFL.  They made very useful Handbook on Copyright and Related Issues for Libraries.  Those who would like to learn more on use of Creative Commons and what users can do with Creative Commons licenses please visit page with information on webinar related to that topic.  Knowledge acquired from those resources can help you to be more efficient, productive and safe in your publishing efforts. Your administrator can insert appropriate licensing information in published content.

The Open Journal Systems can insert licensing information in the article metadata  automatically and save your effort and time.


Admins, Authors and Editors: An Important Relationship

laptop with headphones

Many times, I have experienced situations where people try to draw
lines between authors, editors, and system administrators. True, they
do have very different roles. But they should understand each other
beyond awareness of their role differences. Technically speaking,
system administrators do not care whether an author makes spelling
mistakes or not. Editors do care about spelling and grammar errors,
but they do not know much about server infrastructure.

If we really want to be productive, then we have to go beyond
polarized communication. Working together, authors, editors, and
technical people can create articles with clarity, cohesion,
concision, and precision. The more they understand the basics of
communication, the faster and smoother the process of creating a
quality document is.

I came across a very interesting book that will be helpful to authors
and editors, and will make life easier for system administrators too.

Roy Jensen, M.Sc., Ph.D., is a chemistry instructor and author of
Communicating Science and Exploring Chemistry. It is Communicating
Science that I recommend to authors here so they can acquire skills
that will help them to convey messages efficiently. His book is an
introductory communication guide that provides learners with a
foundation for writing, reviewing, and presenting technical
information to academic and public audiences.

His site, Rogue Publishing, contains useful information on these and
other topics.

The system messed up everything! Please correct.

The secretary of one association that is publisher of four journals asked me to install the Open Journal Systems and to train their staff member to upload articles.
I have installed OJS on their local machine since they were not clear about hosting they would like to use. I met their staff member and showed how to enter data in the forms for metadata, how to create journal, sections, users and other details.
He looked quite confident and confirmed my instructions using phrases: I will do that easily.  I will manage that somehow.
After a couple of days their secretary called me and said that the Open Journal Systems messed up all information entered.

I was confused with what they said and I came to inspect what was going on.  I noticed that some titles are written in capital letters, some are not, there is very noticeable inconsistency in typographical presentation of all information, numerous spelling mistakes, missing commas, periods.
Some references had number only associated to one reference, order was not good.
I was sure that this was not technical issue. The system cannot mess up entered information in that way.
Their staff member was looking at wrongly completed forms and he did not react much. When I asked details about entered data I realized that he entered them in that way.
I was more and more sure that he is person with dyslexia and that he was not aware on textual inconsistencies, fields in forms that are not completed, inaccurate years of journals etc.
I reported the secretary of that association on my opinion and that there is no magic software that will easily correct all mistakes in titles, subtitles, references, abstracts, numbering of references.
My suggestion was that their staff member is person with dyslexia. They expressed that they have had already some difficult misunderstandings with that person.
A couple of weeks later they said that their board is not against him. Well, it should not be against him, but it is questionable that being “for him” assumes that he can do work that is extremely hard.
From my point of view, that person should undergo medical examination and if the board decided to keep him involved in on-line publishing that is fine, but he must have personal assistant or to do some other work that is less difficult for him.
Persons with dyslexia should not be excluded, but we have to create relationship that is based on informed and scientifically supported decision making process that will make sure that there is no discrimination against that person and too great expectations.

Many people with dyslexia are never diagnosed and consequently not supported properly. When we notice that there is person in our working environment that does often spell-check errors or have had great difficulty reading texts. That person can be quite intelligent. Some important guidelines and explanations about dyslexia can be helpful to develop strategies that will not hurt a colleague with dyslexia. Even more, we can come up with solutions that can be very supportive for that person.

There are people who have had similar issues and they made a lot of effort to find solutions.  Good resource about typefaces for dyslexia is worth reading.   Some others developed special fonts that can help person with dyslexia to read better. Dr. Robert Hillier’s site offers useful information about his efforts confronting such issues.

Editors and administrators of the Open journal Systems can add information related to dyslexia in the information block for librarians, authors and readers.  Sharing of good practice cases can multiply success in treating that phenomena.

Do we have prejudices in our work?

During one weekend training program on using web platforms  one young teacher approached me and said: Thank you that you helped me yesterday to learn a lot. When I came back home I said to my husband that he can be proud to have so smart since I know to set up journals on line.  I was happy that  I became skilled after your training.  But, he was upset and he said: It is better that you cook lunch instead of setting up journals. Women are for cooking not programming.

I was shocked when I heard that story. In my work with numerous institutions I experienced many times situations in which some prejudices were so dominantly present.  Some are based on gender, background education or other basis for wrong conclusions.  Well, those prejudices were not openly expressed but it was obvious in different situations what is their predominantly situational and organizational articulation.  I will list just a few prejudices:

  1. Men are better in technology than women
  2. Scholars in exact/natural sciences are better in technologies than those who work in art and humanities
  3. All young students are better in technology than older scholars
  4. Learning of procedures of OA reviewing, editing and publishing is for system administrators
  5. Free software is marketing method for asking for money later on
  6. Scholars from developed countries are better than those from developing countries
  7. Being professor means that you do not need to learn about web platform and Open Access, since you are intellectual already

I could list more, but all of that means that there is still long way in front of us.






Communicating Science! How to do that?

I have witnessed many times that students, researches, scholars do understand some scientific concepts but for various reasons behave differently or even contrary. Some their beliefs or psychological traits are overwhelming.

That is sometimes a big issue in work of editorial boards, communication with system administrator(s), addressing authors and reviewers.

I believe that system administrators should not be focused only on technical troubleshooting.  They should use their knowledge and inform editorial boards how to use technology to foster the development of efficient ways to communicate science.   In my experience, that was not always easy since many people think that if there is information available people will necessarily change.

That did not work always, I am pretty sure.  That issue is more complex than we by inertia think.  That complexity is difficult, but also an opportunity. We are accustomed to challenges. Aren’t we?  Many people including the scientists are sometimes overwhelmed by various biases.

Some work on that and related topics may be found in publications written by Daniel Kahneman, Amos Tversky, Garry Klein.

We have to find a way how to overcome those biases and to find ways how to communicate science effectively. The National Academies Press published one very interesting public with title: Communicating Science Effectively: A Research Agenda that you can find quite interesting and providing a larger space to address that issue.

Huh, being administrator and work with scientists is not just as easy and simple as it looks like. But, it is potentially more rewarding.