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:

DOIprefix/acronymofjournal.volumeno.issueno.articleviewno

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

journaldomain/index.php/journalaccronym/article/view/articleviewno

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.

 

 

 

 

 

Malware Intrusion

We know that there is no ideally secure server. I witnessed many times that hosting companies and their employees sometimes suffer from a lack of resources, equipment and skilled people that should take care on security of servers.  One of them tried to convince me that permission for folders in public_html should be 777. (If you are new to web applications and setting up your system for open access publishing please find on the internet information about permissions on your server. Majority of hosting companies with shared hosting accounts by default set that folders do have permissions set to 755 and files to 644.  Those people who want to compromise your server usually inject code that is planned to exploit vulnerabilities and use your server for some, usually illegal, operations as on image below.  When you in the process of choosing application, hosting company and person who will administer server the security should be top priority issue.

example of intrusion codeThere are various methods how to do that. Example on presented here was part of one larger file that was present on one server used to publish scientific journals.  Sometimes, servers are safe but applications installed are very vulnerable.  Strong competition and financial urges force developers to issue product as soon as they can without proper testing. I came across several times that some pieces of software are written for very obsolete and insecure versions of PHP which poses additional risks for security of site. On the other side, various additions of custom code that is not tested can make system insecure.

Such incidents can endanger your reputation and trust of authors, readers, reviewers and librarians that would like to visit your site often. Above all, sometimes some drivers, firmware, operating systems are vulnerable and you as user of one account cannot do anything to prevent that. That is job of people in hosting company and manufacturers of hardware with vulnerable software to fix vulnerable parts of software. Nevertheless, this should not discourage your from publishing open access.  Constructive and proactive caution is always necessary and welcome.

 

Once, I received call from one association that is publisher of one scientific journal. They informed me that some strange code appeared on their site and I used various malware testing tools and my result was like on image below. I found soon that server was infected so called db.php infection.  Since malware was successfully uploaded on server, it GET requests and it infects every javascript files (.js) with javascript malware code.encoded intrusion  I decoded strings displayed on page and I found IP address of server that is infected and which is used for distribution of malware and which redirects users to other sites. Since such code was all over the site it was very hard to read pages and visitors were prevented from using open access content.

I reported editorial board of the journal on my findings and we informed hosting company and domain registrar of domains used to spread malware asking them to check issue and undertake necessary measures to stop abuse of our and possibly other sites infected by that malware.

The process was rather tense, stressful and painful for editorial board and all people concerned.  The hosting company that hosted server with domain used for spreading malware informed us that they will take care on the case. 

We used other tools to block IPs that are detected as attackers. We have had that day more than 290 attacks from computers from Panama and more than 150 attacks from computers from Ukraine. We restored our site by using fresh backups and reinstallation of web applications we use.  Our hosting company upgraded PHP version that was obsolete, unsupported and insecure at  the time.

 

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.

 

Accessibility and Open Access

I have experienced many times that people avoid implementation of accessibility guidelines.  Some governments and individuals dedicated a lot of time and effort to develop legal, technological and educational regulations and incentives for implementation of accessibility guidelines.

Software packages such as OJS and ATutor implement accessibility guidelines.  But, accessibility is not just another set of technical specifications that we have to learn on top of all our duties. It is continuous process because social interaction is ever evolving and inherent to the humans.  Dedicating effort to accessibility is sign of your willingness to respect other participants in the learning process having easier access to open access publications. Thus, OA is not something that should be narrowly understood as a practice that is focused only on helping researchers to gain more citations and increase scores for professional and career advancement.

Ask your students, colleagues, NGOs of persons with disabilities to assist you in testing and adjusting your content so the persons with disabilities can easier access and use the content you publish on line.  By doing so, you will attract a number of individuals who will support your effort and give you precious suggestions how to attract more readers. There are numerous resources on the web that can help you to understand that disability is not exclusively linked to clinical and traumatic experience. Commitment to disability issues is profoundly important for all of us. Disability can affect anyone in various contexts. So, Open Access should be ready for use and interaction with as much as possible users.