Open Access - Science topic

Dear Wolfgang R. Dick ,

Thanks for the interesting paper with examples in astronomy. Indeed, the examples mentioned are exactly the exceptions I meant. Journals that are effectively open access after an embargo period. These journals use so to speak an open access model ‘avant la lettre’. See for example: https://iopscience.iop.org/journal/1538-3873 you can scroll to the issues of the past year and only the open access papers are freely accessible. However, if you open August 2021 issue all papers are freely accessible (effectively ‘open access’).

So Muhammad Habiburrahman , if you think about a journal, you do not really know and find it is a subscription based journal you can check for example Google Scholar and see if 1-2 year old papers are freely accessible (which is normally not the case for subscription based published papers) then most likely the journal charge an APC. See for example JBC, PNAS and the examples mentioned by Wolfgang R. Dick . They can charge an APC and the logic is that only for a few years the subscription fee/license will cover the costs and the loss of revenue by making the papers freely accessible needs to be covered by an (lower) APC. But ‘normally’ (and unfortunately) papers in subscription-based journals remain behind a paywall (basically forever…) and then the logic is no APC since costs are covered by subscription fee/license.

Best regards.

Hello Mebaaibok Nonglait

I would consider:

- Environmental Research

- Journal of Forest Research

- Forest Policy and Economics

Dear honorable researchers,

Preprints are defined as an author’s version of a research manuscript prior to formal peer review at a journal, which is deposited on a public server. ResearchGate (RG) said about "Preprints" an early-stage research. On the other side, RG is not a publisher and, in turn, uploaded unpublished text is not regarded as a publication. Hence, a preprint is an author's own original or draft version of their paper before any peer review has taken place and before it is published.

Before answering this valuable question of Prof. Brittany Hott, please let me give my own opinion about preprint:

Why you let others know about your insights and methodologies before publication? You should avoid telling the other researchers about the details of anyone of your papers until it has been published and seeing your name by yourself. You may say that I am somewhat old-fashioned, but I have a different perspective for uploading any preprint anywhere before it has been published by your name. My advice is not to put your research anywhere until it is published.

Finally, for the coming future, do not upload any paper anywhere until it is published with your name. Even if it is a "preprint"! For the time being, If you had done something like that as a "preprint", for instance, I advise you to delete the preprint from any elsewhere and wait for two months before sending the paper to any journal.

If it is open access I see no reason not to use it. It is however essential that you should properly cite them.

Thanks Sir for your precious feedback. Many principles like Mathew's Effect or Pareto's Principle that were not directly related to scholarly communications, show similar results in this field as well. Recently, I applied Pareto Principle on Productivity of journals and found 20 of journals produce almost 80 of articles. These principles are helpful in understanding the knowledge domains to great extent.

Springer has several options

Samir Ranjan Panda , Man Kit Cheung , Phil Geis thank you very muche for your answers :)

Perhaps you may check this post too:

Dear Amir Khushk ,

There are basically three forms of open access:

-Open access journals. Journals dedicated to open access (can be Gold, Platinum etc.) See enclosed file for this list. APC varies and as you can see in the list some are free of costs (most of the times paid by a Society)

-Subscription-based journals but with the option for open access called hybrid journals (and this is the list you enclosed)

-Journals that are subscription-based but after a certain embargo period allow free access (Green open access)

See also: https://authorservices.wiley.com/author-resources/Journal-Authors/open-access/index.html and https://authorservices.wiley.com/author-resources/Journal-Authors/open-access/article-publication-charges.html

Hope this clarifies the matter.

Best regards.

This previous discussion will be useful for you: https://www.researchgate.net/post/Scientific_Journals_with_Open_Access_and_no_APC_free_charges_for_authors

Dear Gaurav H Tandon ,

One correction, MDPI has a general waiver police, which can be found here: https://www.mdpi.com/apc it states ”6. Discounts and waivers

MDPI is committed to supporting the transition of all research to fully open access, therefore we regularly offer APC waivers or discounts. On average, we waive approximately 25% - 27% of our content every year. Of the total APCs in a journal, we waive and offer discounts ranging from 15% in our most established journals, up to 100% in our new or humanities journals. In many social sciences and humanities journals we waive between 70% - 100% of APCs (an APC is still displayed on these journal's websites, in order to demonstrate to authors that there is a cost to publication). Even some of our well-established journals waive 30% of publishing costs each year.

Additionally members of societies affiliated to an MDPI journal benefit from a discount, as well as authors affiliated to institutions participating in our Institutional Open Access Program.

For journals in fields with low levels of funding, where authors typically do not have funds available, APCs are typically waived and cross-subsidized from fields for which more APC funding is available. For authors from low- and middle-income countries, waivers or discounts may be granted on a case-by-case basis. Applications submitted before article submission are assessed by the Managing Editor based on the quality of the research article and the authors’ ability to pay.”

Best regards.

Hello,

Our lab group has been publishing applied animal husbandry research in Translational Animal Science. It is an open access companion to the Journal of Animal Science. Our experience has been very good with Translational Animal Science so far. We have published three articles in TAS.

Kind regards,

Kurt

I would recommend your use a journal search and put the criteria you. want (e.g., sort by review time, etc.)

check here:

Green, Gold, Diamond, Black – what does it all mean?

There’s a lot of jargon surrounding Open Access publication, and as with all jargon it can confuse and obfuscate. Here is a simple glossary:

To the best of my knowledge, there is no open-access database suitable for this purpose. I always prefer the ORACLE database.

There are lots of confusing answers above, some incorrect, some incomplete.

1. If a paper (or anything) is published under a Creative Commons license, ANYONE can freely use the material as long as the terms of the license are followed. For example CC-BY-NC-ND allows noncommercial use of the material without changes as long as the source and original authors are fully acknowledged.

CC-BY allows any use, including commercial, of the source material in original or modified form as long as the source and original authors are fully acknowledged and cited, and any modifications clearly explained.

You do not need any special permission for this:

2. If material (eg a figure) is copyright-protected, you need permission from the copyright holder (usually the publisher, not the authors). Permission is easy to get! To obtain this, you click the "Rights and permissions" link at the published article and the rest is self-explanatory. As long as it is a moderate amount of material, it does not cost anything.

Please note that in either of the two cases 1 or 2 above, you do not have to ask the authors' permission - unless this is required by the copyright holder (the publisher) in case 2.

3. If you modify a copyright-protected figure or redraw it from an original does not matter, copyright still applies and you still need permission.

4. In all cases you must of course fully reference the source and state that you have permission. The figure caption should read "From Ref. X. (c) Elsevier [for example], used with permission" or "From Ref. X, used under Creative Commons CC-BY license."

Dear George Hood

Thanks for your suggestion. It seems like I can mimic my experimental setup in this software.

Regards,

Siddhi Vinayak Pandey

DSE-SOT, PDEU-Gandhinagar, India.

You are most welcome dear

Prof. Parisa Ghasemiyeh

Wish you the best always.

Dear Abderrazzaq Kharroubi ,

Look the link, maybe useful.

Regards,

Shafagat

Yes, There are some journals of Springer unpaid and open access, please visit or contact helpline of the springer

Hello, feel free to try Slovo a slovesnost: http://sas.ujc.cas.cz/?lang=en. It is even indexed in WoS.

It's companion with high Impact Factor and indexing in Pubmed and Scopus should be your priority anytime you want to publish.

Dear Zeynep Ciğeroğlu , learning the theoretical background of DFT and its implementation in Gaussian can require years depending on the level of depth you may want to reach. Gaussian is a somewhat old-fashioned but very flexible and solid software (at least in the linux/unix/macOS versions). There are many tutorials available, and a very good source of information is the book “Exploring Chemistry with Electronic Structure Methods”, distributed by Gaussian (https://gaussian.com/expchem3/). This notwithstanding I believe - at least based on my experience - that the most useful way one can learn at the proper level is to be paralleled by a more skilled research group. So, I suggest a scientific collaboration, at least at the beginning of this new activity.

Zhang Qixia ,

You can use any LCA databases like Athena etc.

There are many academic platforms that are offering such facilities...

Dear Md. Imtiaz Kamrul

An open-access journal will charge a publication fee and a journal not charging any fee can not be open access. Following are the SCI journals that do not charge any publication fee.

Journal of Electromagnetic Waves and Applications (https://www.tandfonline.com/toc/tewa20/current)

Wireless personal communication, (https://www.springer.com/journal/11277)

Wireless Networks (https://www.springer.com/journal/11276)

Dear Dr Diana Nagpal,

I suggest you these journals:

* Journal of Electronic Testing-Theory and Applications (Springer journal).

* Future Generation Computer Systems (Elsevier journal).

* Turkish Journal of Electrical Engineering & Computer Sciences.

* The Journal of Supercomputing (Springer journal).

Best wishes,

Sabri

Maybe these research will be useful:

Dear Preeti Oza . Yes in the case the situation becomes dangerous because of Covid .

Hello Samar Elkhalifa

My advice is that some fields even the best journals do not have such a high impact factor. Yes, if it is possible then definitely try for that but if not possible, I am safe knowing that other serious researchers in my field (including potential employers) will know what are the so-called good journals in my field and will recognise that. Journals are also labelled as Q1 - top 25% or Q2 - 25-50% and so on. That, again, I expect will be good for me, even if the journals I publish in do not have a very high IF.

See also these discussions:

Dear John Hoaglund ,

Indeed, for subscription-based journals it is officially not allowed to share public full-text versions of your publications (although some have an embargo period and after that you can, and some allow pre-print versions). However, it is completely legal to provide someone a (hard)copy of your paper, even when it is normally subjected to copyright issues. See for example: https://www.elsevier.com/about/policies/copyright

“Authors can use their articles, in full or in part, for a wide range of scholarly, non-commercial purposes as outlined below:

•Use by an author in the author’s classroom teaching (including distribution of copies, paper or electronic)

•Distribution of copies (including through e-mail) to known research colleagues for their personal use (but not for Commercial Use) ….”

I am old enough as well 😉 to remember that you received 50 or so Offprints, at the time it was quite common to send the author a brief letter requesting a hard copy. Basically, nowadays such requests go by e-mail, and you can send a pdf which you receive as author (most of the times).

Beside the ‘legal’ arguments there are more practical reasons why this is normal practice:

-The publisher is unable to track what you send to/exchange with another (interested) researcher

-In the same way that ‘in the old days’ you could copy a paper (you found in the library), who check what you are doing with it?

-Exchanging info on a one-to-one base is fundamentally different than making a paper freely accessible to everyone on a platform like RG

Yes, it is ridiculous that papers that are more than 20 years old are still subjected to all sorts of copyright rules (even patents of multi-million-dollar investments have a limit protection timeframe) but requests for those interested in your work can be ‘rewarded’.

Best regards.

Thank you dear Dr. Mônica Chaves for the inputs.

You may check it:

Artificial Intelligence An International Journal - Elsevier

Definitely not all indices together, also it depends upon required scale and resolution and temporal capacity.

It's good to download multispectral images to process the required indices.

Product indices available at MODIS, ASTER and other sources.

I hope you understand it.

Thanks

Dear Matthias, I wish you to try surviving in the poorer country, where fundind the APC is not so easy as yours.

Very interesting answers from our colleagues.

Dear Dr. Singh,

You will need to contact the Publisher and Editor at AWS with your request. Include the manuscript details and the Figure numbers that you are looking to reuse in your email. It's a relatively straightforward process.

You can see how I have referenced Welding Journal papers in my own review paper:

Hope this helps.

Regards,

Shehryar

Hello Shruti Sengupta

I think this is a complicated question. I did a quick search and found the IF to be even higher (1) than the figure you quoted. That means that journal is cited a lot, if that's useful to you. But, as we know, and has been discussed in other parts of this platform, IF is not the only factor to consider. There are many other metrics used.

Personally, I would not be able to afford the amount of the fees that they charge so publishing in that journal would never be an option for me.

The following discussions deal with the question of how to find a suitable journal:

Hi,

The gray literature are reports, pre prints, and a lot of other informal materials. The publication process of gray literature is often faster than in formal journals, and therefore, it is preferred when authors would like to establish authorship to a discovery or an original paper of some sort. Gray literature receives citations, in many cases, so it is visible to the scientific community. Publishing in a formal journal, though, is considered more valuable for academic promotion, since, the paper goes through reviewers judgements. Comparing the two publication routes resembles comparing the formal and informal education.

This question has been discussed several times before without any solution:

See also these discussions on funding of APC:

Research works in itself time consuming an full of hurdles. It need money to directly or indirectly. Really it is painful to pay extra to share your knowledge.

Please, try:

Dear Cenk Çalışkan ,

Norbert Tihanyi one little warning, if you look whether a particular journal is mentioned in the Beall’s list you should not only check the journal title in the stand-alone journal list (https://beallslist.net/standalone-journals/) but also the publisher behind it (if any). In this case the publisher is not mentioned in the Beall’s list (https://beallslist.net/). Anis Hamza I suppose you mean ISSN number, this journal with ISSN 1547-5816 and/or E-ISSN:1553-166X is mentioned in Scopus (https://www.scopus.com/sources.uri?zone=TopNavBar&origin=searchbasic) and Clarivate’s Master journal list (https://mjl.clarivate.com/home).

Back to your question, it is somewhat diffuse. There are signs that you are dealing with a questionable organization:

-Contact info renders in Google a nice residence but does not seem to correspond to an office and I quote “The American Institute of Mathematical Sciences is an international organization for the advancement and dissemination of mathematical and applied sciences.” https://www.aimsciences.org/common_news/column/aboutaims

-Both websites https://www.aimsciences.org/and http://www.aimspress.com/ function more or less okay but not flawless

-The journal “Journal of Industrial & Management Optimization (JIMO)“ is somewhat vague about the APC. It positions itself as hybrid (with an APC of 1800 USD), but all papers I checked can be read as open access (although not all have a CC etc. license). It mentions something like open access for free when an agreement is signed with your institution but how much this cost is unclear

-No problem by itself but the majority of authors are from China, makes you wonder about American Institute…

-Editing is well…sober

On the other hand it looks like and I quote “AIMS is a science organization with two independent operations: AIMS Press (www.aimspress.com) and the American Institute of Mathematical Sciences (AIMS) (www.aimsciences.org ).” AIMS Press is focused on Open Access journals while the journals published by AIMS (www.aimsciences.org) are/used to be subscription-based journals. Pretty much like Springer has there BioMed Central (BMC) journal portfolio and Bentham has their Bentham Open division.

Facts are:

-AIMS ( www.aimsciences.org ), more than 20 of their journals are indexed in SCIE and indexed in Scopus as well (under the publisher’s name: American Institute of Mathematical Sciences)

-AIMS Press (www.aimspress.com ), four journals are indexed in SCIE and thus have an impact factor and 14 journals are indexed in Clarivate’s ESCI. 7 journals are indexed in Scopus.

-AIMS Press, 20 of their journals are a member of DOAJ

-Journal of Industrial & Management Optimization (JIMO) https://www.aimsciences.org/journal/1547-5816 is indexed in Clarivate’s SCIE (impact factor 1.801, see enclosed file for latest JCR Report) and Scopus indexed CiteScore 1.8 https://www.scopus.com/sourceid/12900154727.

-For the papers I checked the time between received and accepted varies between 6 and 9 months and an additional 3-4 months before publication (it is well… not fast but not unusual)

So, overall, I think that the publisher has quite some credibility and it might be worthwhile to consider.

Best regards.

Google scholar is (just) a search engine dedicated to scholarly/academic article, however, it is not an indexing criteria/authority. It can index any journal type regardless if the articles are peer-reviewed or quality of article or journal as a whole.

Dear Mohammad Razib Hossain this is certainly a good question of broad general interest. However, I fully agree with Vadim S. Gorshkov in that the statement "Generally open access journals have high impact factors" is questionable. At least in our discipline, chemistry, the most renowned journals with the highest impact factors are subscription-based journals which have no "article processing charges (APCs)". We published ca. 95% of all our 400+ research articles and review articles in such free journals. There were times where I was even paid a small honorarium for a review article...

As for MDPI journals, we published ca. 4-5 papers in 3 of their journals and my personal experience with the review and publication process was generally quite good. However, their APCs are often exceptionally high, and nowadays I regard MDPI as a "money printing machine". What I also don't like with MDPI that they are often "chasing" you with "personal invitations" and countless "special issues". Thus my personal advice would be to go for free journals which often have higher impact factors.

Good luck with your own publications and best wishes, Frank Edelmann

Hello

The goods ones are in Scopus or Web of Science

Best regards

Open access is just a financing model - the author pay the publisher, not the subscribers to the journals. There is no connection to quality. many high-ranking journals are open access. However, there are also predatory journals with mostly open access and low quality. But predatory and open access are not the same. Very often people mix the two terms.

Here are some of my replies from several previous discussions:

There is no direct connection between the subscription business model of a journal and publication fees. Whether there is a publication fee or not depends on the finance model of the journal in general. Some journals have low costs and sells well or get donations, so they may publish without fees for authors.

The publication of scientific articles always costs money (paying the staff of the publisher, servers, printing costs, taxes, ...). Most of the large scientific journals are being published on the basis of subcriptions by libraries, at least partially. Other parts of their financial models are APCs (Article Processing Charges) and payments for downloading articles. The question is, who raises this money - the readers, the authors or third institutions; at least not the publishers, who are private enterprises and have to work economically. To demand financing from the publishers is unrealistic. Today there are not enough paying subscribers, so that the authors, sponsors or readers have to pay.

The real question is who can finance the publication. Since there are not enough subscribers for the many journals and the authors often cannot cover the costs, sponsors must be sought. Publication costs must be taken into account as early as the research planning stage.

For developing countries the question is how these additional costs for publication of the results can be raised. There is no such thing as "free" publication, in all cases someone has to pay the costs.

The problem of financing scientific publications is as old as science is. When you read, e.g., an extended biography of Johannes Kepler (beginning of 17th century), you will learn about his problems when seaking financial support for printing his works. "Open access and free of charge" does not mean that it is free of costs. In this case, an institution is paying the costs of staff, server maintainance, printing, etc. To "create a platform in which we control our science and make it completely free of access", there has to be an international organization which will organize and finance it. You will need a staff similar to privat publishers. Where will its finances come from? Those who are familiar with international organizations like UN know the difficulties of organizing large projects on an international level. If you wish a single platform for all sciences, the difficulties will be tremendous. It is possible to publish free and open-access journals at the level of institutes and societies, but each of them is for a narrow field. Although I agree that a "free" and open access platform for all sciences would be a nice thing, I do not see ways to realize it.

Publishers are privat enterprises, so they have to pay their staff, pay for their offices, for all hardware, for software, for advertisement, pay taxes, etc. Large publishers with high-ranking journals are mostly stock companies or similar and therefore they also have to pay dividends to stockholders. However, as for all companies it is nearly impossible to get details of their business model.

Publication fees are mainly there to cover the publisher's costs, fully or partially. The profit comes from the sale of printed or online journals by subscription and the sale of individual articles as PDF files.

Extreme costs for publishing are also a consequence of the monopolization. The tendency to publish only in "high-impact" journals is another reason for monopolization. This tendency is a consequence of the "fixation on bibliometric indicators" by the actors in science governance - see demand No. 3 of the petition "Stop Tracking Science" (https://www.researchgate.net/post/Petition_Stop_Tracking_Science).

Publishing is a private business. Therefore, when you ask whether high costs for open access are ethical or not you may also ask whether profits of billions of dollars by private companies like Google, Amazon, etc. and by their private owners are ethical in general. Indeed, the profit rates of some large publishers are extremely high. One of the reasons is the run for high-impact journals and the monopolization which follows from this preference. Although there are many small publishers, the free market does not really work. Another negative side of the impact-factor fetish are manipulation, fraud and other scientific misconduct.

I do not agree at all with the way some publishers do business. However, this is a free market as any other business. There is no worldwide conspiracy by publishers to suck scientists dry. If there is so much money to be made here, why aren't there more big publishers? Of course, there is also monopolization, as everywhere in the economy. But there are also many small publishers and small journals. The problem also lies with the scientists themselves. The greed for high-impact journals leads to the situation that some journals hardly need to fear competition. The whole problem is very complex, and there is no point in portraying publishers as the bogeymen. It requires concrete proposals for improvement. - One of the problems is also that more and more is published and less and less is read. Libraries are no longer able to acquire all the books and journals. As a result, sales figures are falling, so publishers have to raise prices. A vicious circle. More than 50 years ago, Polish philosopher and science fiction writer Stanislaw Lem satirically envisioned a future in which scientists get paid if they don't publish anything. As soon as they publish something, they get a pay cut.

Hi

Unfortunately, one of these is not an open-access paper, but I think these articles may help you. Regards

I can find only two. Use this link:

https://app.dimensions.ai/discover/publication?search_mode=content&search_text=s-box%20construction&search_type=kws&search_field=text_search&or_facet_year=2022

Dear Linas Balciauskas thank you for your kind response and new question ("but it really matters if review process takes a year, and then you get rejection without any reviews?"). Yes, such a case is certainly a reason to worry, but it shows that the editor / journal / publisher are not doing their job professionally. I think that this varies very much with the different disciplines. In our field of research, chemistry, I did not experience such a case in over 40 years. In my personal experience the editors of all renowned journals are excellent chemists themselves. They are carefully selected by the publishers based on their scientific performance and leading skills. The same is true for the vast majority of reviewers who are selected based on their areas of expertise. Apparently in chemistry we as researchers are lucky that the publishing and reviewing process is largely fair and fact-based.

Patents are all about making information available - the whole idea behind them is to give an inventor exclusive rights in exchange for disclosing how the invention works. So "access" to the information is not a problem, rather, it's the whole point.

Few inventors or small businesses can afford to patent an invention all around the world, and entrepreneurs in the smaller countries are often free to make and sell products that are patented in, say, the US, Europe, Japan, and China. That's good for the local economy, and it's not exactly a "threat" to the inventor -- although it can reduce the potential to earn profits in those countries. Inventors have to make a business decision on where they intend to market the product, and how much they should invest in patent protection in those countries.

Journals are not needed anymore, this is an old concept.

Dear Evan Flynn ,

Consider this as a hard lesson. Unfortunately for you they were transparent about the (way too high) APC (https://norcaloa.com/PYBT/guidelines-to-author). Provided that you want to go for the official way and since you already send your manuscript you don’t have that many options if you want NOT to publish:

-1. Pay the withdrawal fee

If you accept the fact that they will publish your accepted manuscript you can opt. for:

-2. Pay but ask for substantial waiver (50% or more)

-3. Or pay nothing. Two things can happen: they will publish anyway (since they need content) or they will keep your paper for an unknown period

It depends on how much you value the work you’ve put into this paper: if it is high valuable to you go for option 1 (but make sure you have an official withdrawal statement) or if it is not that extremely important you might go for option 2 or 3.

Best regards.

Dear H. A. Kumara Swamy ,

Unfortunately your question remains unanswered. As you rightfully so indicated both journals are so-called hybrid-journals, meaning they have an open access option but if you don’t opt for that it remains behind a paywall as subscription-based.

Those claiming that these are open access journals, have a look here:

International Journal of Applied and Computational Mathematics: https://www.springer.com/journal/40819

Heat transfer: https://onlinelibrary.wiley.com/page/journal/15231496/homepage/forauthors.htmlI quote “Authors who choose to publish using open access will be charged a fee. A list of Article Publication Charges for Wiley journals is available here.”

Those who claim that nevertheless your papers are open access are wrong as well, just have a look here on RG:

Analysis of Entropy Generation and Energy Transport of Cu-Water Nanoliquid in a Tilted Vertical Porous Annulus

Thermal effects of nonuniform heating in a nanofluid-filled annulus: Buoyant transport versus entropy generation

So, my conclusion is Scopus made a mistake in both cases. They are quite recent so it might be corrected. Personally, I would not bother, just be pleased with two fine papers.

Best regards.

Open access is a chance that an article will be read by scientists more frequently and get more attention. I do not see any harm. A few people may think that only predatory journals are open access, but this view is obviously not true. There is a good summary of the pros and cons od open access at https://www.openaccess.nl/en/what-is-open-access/pros-and-cons.

See also these previous RG discussions:

One of the problems of open-access journals (and open-access papers in subscription-based journals) may be the higher APCs, which may prevent scientists in developing countries from publishing in such journals and may lead to a discrimination. This has been discussed here and in several other previous discussions:

One of the problem of open-access journals (and open-access papers in subscription-based journals) are the high APCs. This is discussed here and in several other previous discussions:

1.Journal of Pediatric Gastroenterology and Nutrition

2.Maternal and Pediatric Nutrition Peer Reviewed Journals

3.Maternal & Child Nutrition - Wiley Online Library

4.International Journal of Child Health and Nutrition

5.Pediatric Nutrition Research Guide: Nutrition Journals

6.Open Access Nutrition Research

Thank you all for your valuable information. It will help me a lot.

Journal of Mining and Geotechnical Engineering

This journal isn't indexed in Scopus/WoS, so publication is free of charge

I think 'Lambert Academic Publishing (LAP)' is one of the vanity publishers. Do not fall into the trap. I mean do not publish your thesis or book via this publisher, it may bring trouble in your future scientific career.

Mamta Giri ,

Congratulations for your selection of a very important ResearchGate discussion thread question, which has in recent years been generating a great deal of controversy along with lateral and longitudinal expansion from the public into the private domain.

The following article appeared in 2018 and it gives a good overview of some of the relevant issues involved in big data sharing of genomic data:

"OPINION article

Front. Public Health, 28 November 2018 | https://doi.org/10.3389/fpubh.2018.00334

Big Data Sharing: A Crucial Democratic Issue for Genomic Medicine

📷Benjamin Derbez*

Introduction

Big data are often viewed as responsible for major upheavals in many aspects of contemporary life (1) and in the health sector in particular (2). For instance, in medicine, big data are perceived as one of the major drivers of genomic medicine (3). Indeed, rapid genomic data collection on a large scale, made possible by the use of high-throughput sequencing technologies, has made the production of new medical knowledge possible. This knowledge has helped to improve disease prevention, risk prediction, individualized care, and patient involvement (4, 5). One of the conditions of such progress, however, is the need to create databases large enough to enable successful comparative analyses (6). While some initiatives seeking to share different national databases have been launched at the international level (7), the sharing of data between public institutions and private organizations remains a critical question.

Drawing on the example of databases of variants in breast and ovarian cancer predisposition BRCA 1–2 genes, we will show that genomic data is a techno-scientific democracy issue worth discussing. In this case, the recent evolution of patenting legislation has led to a shift from gene sequencing to the clinical interpretation of its results as the key activity of oncogenetics (8). Database access, which is necessary to estimate the risks associated with sequenced genetic variants, has become a critical issue, especially for private firms wishing to break into the market. In this context, the partial privatization of public databases, such as that of the French consortium that will be discussed later, is proof that there is a growing movement of public-private hybridization of these infrastructures. This shift, accentuated by the developments of high-throughput sequencing and genomic medicine, needs to be accompanied by reflection about the public health system user information contributing to the constitution of these databases.

Patenting genes

The controversy that shook the world of genetic cancer for years is well known. Indeed, the American company Myriad Genetics filed a patent application claiming BRCA1, BRCA2, and genetic methods of diagnosing a predisposition for breast and ovarian cancer (9, 10). Thanks to the legal ownership of these genes which had been designed as biotechnologies, the start-up from Salt Lake City sought to have a global monopoly on the hereditary breast cancer market, which was expected to experience robust growth. In the face of this offensive, institutional resistance (bringing together hospitals, ministries, associations, etc.) arose in the early 2000s in Europe and then in the United States (11). This resistance has often been interpreted as paradigmatic of the opposition between an “open science,” regulated by peers respecting the law of priority, and a “proprietary science,” regulated by the market, and respecting intellectual property (12). There was thus concern that the production of public knowledge would decline because of the legal appropriation of genes by private organizations (13).

An analysis of the British case, however, helps to get a more balanced view of this dichotomy. Indeed, (14–16) has shown that patents are perceived as legal weapons by private organizations as well as by public scientific, medical, and social institutions. Moreover, actors from private and public groups cannot be radically distinguished insofar as each defines the other in a complex network of negotiated interrelationships. In line with the studies undertaken on the role of patents in management science between academic circles and the business world (17, 18), Parthasarathy calls attention to how the NHS and Myriad reached an agreement in the early 2000s, making it possible to connect the “moral order” of the former, based on the principle of equal access to healthcare for all citizens, to the freedom of consumers valued by the latter. Among the negotiated items, it appears clearly that the issue of the transfer of data from Myriad to the NHS was essential and intended to add onto the public BRCA mutation databases. Beyond the issue of monopoly over the gene sequence through the patenting of genes or methods, this example clearly shows that the ownership of data is of crucial importance to both groups. With high-throughput sequencing technology, it has become a major issue.

Next generation sequencing

Two major developments placed the issue of the sharing of BRCA databases at the center of the debate from the 2010s. The first, naturally, was the full or partial decline in the patents claimed by Myriad Genetics around the world (19, 20). Indeed, this decline opened up the sequencing market to new private actors (GeneDx, Invitae, Pathway Genomics, Counsyl, etc.) and allowed public laboratories to carry out their activities. The second development was the progressive introduction of high-throughput DNA sequencing technology which began in the mid-2000s. The use of these “next generation” devices reinforced laboratories' analytical capacities. It is now possible to analyse within a few hours, and at the same time, several genes (panels) of several individuals, or even the complete genome of an individual at a much lower cost-100 dollars is regularly mentioned, compared to the 3 billion dollars spent in the framework of the Human Genome Project 20 years ago (21). All these developments have led stakeholders to focus on the issue of the classification of the genetic variants in BRCA genes.

A genetic variant from a sequenced individual can only acquire the status of “mutation,” i.e., the status of “pathogenic” variant, if it is clearly linked to a history of illness, either directly (in the individual or in their family) or indirectly (in a family affected by cancer and found to have the same variant). According to the current classification in genetics, the clinical significance of these variants may vary: they can be pathogenic, probably pathogenic, of unknown significance, benign, or probably benign. As (22) have pointed out, distinguishing between these categories is a major “interpretive dilemma” for geneticists. The classification of a variant in a given category depends on available data concerning the frequency of the link associating it with a specific disease. In the absence of data, the clinical significance of the variant is deemed unknown—a Variant of Unknown Significance (VUS)—until it is identified in other individuals with similar phenotypic characteristics. The importance of new DNA sequencing technologies thus lies in their ability to increase genetic databases more quickly in order to reduce the at times dramatic clinical uncertainty associated with diagnosed genetic anomalies (23). The sharing of information among geneticists, thanks to databases fed on an international scale, is a central issue1. This sharing of information, however, is now problematic.

Genomic databases

For several years now, science and technology studies have been stressing that physical infrastructure plays a central role in the production of knowledge (24–27). In this area, the study of genetic databases serves as a model (28–31). Indeed, the first molecular biology databases were launched by different public institutions around the world in the early 1980s [(32): 75]. With the spread of the Internet and the Human Genome Project in the 1990s, they quickly developed as a form of support for new open “communication regimes” between scientists, likely to encourage the emergence of new knowledge (33). However, an analysis of the construction of this information infrastructure shows that the modes of data publishing remain a major source of tension between different actors.

This tension has been highlighted by Bruno Strasser, for instance, in his study on the development of the comprehensive GenBank sequence database (32). This historian of life sciences argues that tensions linked to the different conceptions of data ownership arose from the outset of the project. Participants engaged in a “moral economy of natural history,” i.e., in a “system of values that places emphasis on the exchange of scientific knowledge” inherited from the naturalists of the eighteenth century, considered that the sequences published in scientific journals should be freely accessible data. Other participants, advocates of a “moral economy of experimentation” which has garnered momentum among molecular biologists, view sequences as the products of scientific activity and as the property of their authors. According to Strasser, GenBank embodies a form of hybridization of these two value systems. It appears that those who conceived it succeeded in taking advantage of the “ambiguity” of the very notion of “data,” owing to the fact that what seems “literally given” is at the same time “the result of an organized action” (34): 248). In the context of the Human Genome Project, this ambiguity has manifested itself in the emergence of information control modes which involve a complex interplay of revelation and concealment (35). Nowadays, as seen previously, in addition to the tensions inherent in the moral economies of science, other tensions associated with the political economy of knowledge resulting from the growing role played by private firms in the production of knowledge emerged from the early 1990s (36, 37). Beyond the question of the patentability of living organisms, it is now the question of sharing that is in front of the debate, like the case of BRCA1 and BRCA2 genes clearly shows it.

Data sharing

In the present case, i.e., the focus on BRCA1 and BRCA2 genes, there is no unique and comprehensive database of BRCA variants accessible to all professionals around the world. On the contrary, different databases developed by consortia of multinational public institutions or private organizations exist, but their access is generally limited. This is the case of the database developed by Myriad Genetics throughout the period the patents were under discussion. Although this is the largest database in the world, Myriad Genetics has exclusive access to it. This has given the company a major competitive asset in the BRCA testing market insofar as the database offers a solid basis on which to interpret results. According to genetics professionals, the main issue is not the sequencing itself. Rather, what matters most is the interpretation of the results intended to give clinical significance. This has turned out to be the most costly activity, both in terms of the recruitment of highly qualified personnel and for the development, maintenance, and access to huge databases that list the known variants of specific genes. Certain professionals estimate that there is a 1 to 10 ratio with regards to the cost of complete genome sequencing and its interpretation. In this context, ownership and the opening up of genetic variants databases emerges as a crucial issue.

From this context, the example of the future of the UMD BRCA base—Universal Mutation Database-BRCA—speaks volumes. Developed in the 1990s by a public consortium of French geneticists, it was considered to be one of the most important global databases until 2015. Driven by two major players in genetic testing in the United States [Quest Diagnosis and Laboratory Corporation of America (LabCorp)], the database was partially privatized in 2015. These two companies purchased the right to obtain access to data in exchange for funding the database. While the French sought to finance over the short- and medium-term an activity that had become too costly for public finances to sustain, the Americans' objective was to quickly be able to compete with Myriad Genetics by improving the quality of their analyses. The question that arises, then, is: How will this be handled over the long term? Will the French geneticists at the origin of the database still be able to access it? Will French patients still benefit from the knowledge generated thanks to the data they provided? What justifies this privatization if we consider the donations made by patients who agreed to have their data kept in this database? Similar questions had already been raised by the NHS during its negotiations with Myriad in the early 2000s, when the issue of the privatization of access to BRCA testing for British citizens arose (16). Questions revolving around access (currently and in the future) to genetic databases thus remain relevant.

Conclusion

At a time when the opening up of public data has become common practice in the field of administration (38), the example of the genetics of breast cancer shows that data sharing is still a major issue in research (39). The question here is the extreme overlapping of public issues and private interests. In this case, there is a need to go beyond a simple comparison between the open regimes of data publication associated with academic institutions, and the closed regimes of the privatization of knowledge developed by business communities. Hybrid forms of database ownership such as those mentioned earlier, highlight the need to pay attention to the significance given to data sharing during the initial negotiations underpinning their establishment. Once these databases are filled by voluntary citizens who provide their DNA data, data sharing becomes a crucial issue in terms of technical democracy (40). Once again, however, citizens seem to be largely absent from the debate about the ownership and use of the genomic data stored in these databases. With increased power given to major programmes seeking to collect big data in genomics, it may be time to reflect on how citizens can be informed and involved in the decisions that will be made in this area.

At the very least, it seems necessary to provide people with information about the future of their genomic data: in which databases will the data be stored? For how long? Who will be able to use them? Can they be exploited for commercial purposes by private firms? As in the field of the Internet, database contributors should be able to oppose the reuse of their “data” for the benefit of private interests. The information challenge involves the very value of consent (41).

Author Contributions

The author confirms being the sole contributor of this work and has approved it for publication.

Funding

This opinion paper is based on a research funded by the Fonds Avenir/Masfip pour la Recherche, 2016.

Conflict of Interest Statement

The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Acknowledgments

The author would like to thanks Emmanuel Rial-Sebbag, S. de Montgolfier, Pr Dominique Stoppa-Lyonnet, Pr Eric Vilain, and Dr. Zaki El Haffaf for their help and collaboration. Thank you to Catherine Davies from UBO BTU for the translation.

Footnotes

1. ^For example: Human Gene Mutation Database (HGMD) or Online Mendelian Inheritance in Man (OMIM).

References

1. Mayer-Schönberger V, Cukier K. Big Data: A Revolution That Will Transform How We Live, Work, and Think. Boston, NY: Eamon Dolan /Mariner /Houghton Mifflin Harcourt (2013).

2. Groves P, Kayyali B, Knott D, Van Kuiken S. The Big Data Revolution in Health Care. Seattle, DC: McKinsey Quarterly (2013).

Google Scholar

3. Guttmacher AE, Collins FS. Genomic medicine – a primer. N Engl J Med. (2002) 347:1512–20. doi: 10.1056/NEJMra012240

PubMed Abstract | CrossRef Full Text | Google Scholar

4. Alyass A, Turcotte M, Meyre M. From big data analysis to personalized medicine for all: challenges and opportunities. BMC Med Genomics 8:33. doi: 10.1186/s12920-015-0108-y

PubMed Abstract | CrossRef Full Text

5. Flores M, Glusman G, Brogaard K, Price ND, Hood L. P4 medicine: how systems medicine will transform the healthcare sector and society. Personal Med. (2013) 10:565–76. doi: 10.2217/PME.13.57

PubMed Abstract | CrossRef Full Text | Google Scholar

6. He KY, Ge D, He MM. Big data analytics for genomic medicine. Int J Mol Sci. 18:412. doi: 10.3390/ijms18020412

PubMed Abstract | CrossRef Full Text

7. Scollen S, Page A, Wilson J. From the data on many, precision medicine for “one”: the case for widespread genomic data sharing. Biomed Hub (2017) 2:15. doi: 10.1159/000481682

CrossRef Full Text | Google Scholar

8. Stoppa-Lyonnet D. Tests génétiques: le défi n'est plus le séquençage mais l'interprétation. Pour Sci. (2014) 439:12–3.

Google Scholar

9. Parthasarathy S. Building Genetic Medicine. Breast Cancer, Technology, and the Comparative Politics of Health Care. Cambridge, MA: MIT Press (2017).

Google Scholar

10. Sherkow JS, Greely HT. The history of patenting genetic material. Annu Rev Genet. (2015) 49:161–82. doi: 10.1146/annurev-genet-112414-054731

PubMed Abstract | CrossRef Full Text | Google Scholar

11. Cassier M, Stoppa-Lyonnet D. L'opposition contre les brevets de myriad genetics et leur révocation totale ou partielle en Europe: Premiers enseignements. Med Sci. (2005) 21:648–62. doi: 10.1051/medsci/2005216-7658

CrossRef Full Text | Google Scholar

12. Dasgupta P, David PA. Towards a new economics of science. Res Policy (1994) 23:487–521. doi: 10.1016/0048-7333(94)01002-1

CrossRef Full Text | Google Scholar

13. Orsi F, Coriat B. Are Strong Patents beneficial to Innovative Activities - Lessons from genetic testing for breast cancer controversies. Indus Corp Change (2005) 14:1205–21. doi: 10.1093/icc/dth086

CrossRef Full Text | Google Scholar

14. Parthasarathy S. The patent is political: the consequences of patenting the BRCA genes in Britain. Community Genet. (2005) 8:235–42. doi: 10.1159/000087961

PubMed Abstract | CrossRef Full Text | Google Scholar

15. Parthasarathy S. Architectures of genetic medicine: comparing genetic testing for breast cancer in the USA and UK. Soc Stud Sci. (2005) 35:5–40. doi: 10.1177/0306312705047172

PubMed Abstract | CrossRef Full Text | Google Scholar

16. Parthasarathy S. Reconceptualizing technology transfer: the challenge of building an international system of genetic testing for breast cancer. In: Guston DH, Sarewitz D, editors. Shaping Science and Technology Policy: The Next Generation of Research. Madison, WI: University of Wisconsin Press (2006).

Google Scholar

17. Huang KG, Murray FE. Does patent strategy shape the long-run supply of public knowledge: evidence from human genetics. Acad Manag J. (2009) 52:1193–221. doi: 10.5465/amj.2009.47084665

CrossRef Full Text | Google Scholar

18. Murray F. The oncomouse that roared: hybrid exchange strategies as a source of distinction at the boundary of overlapping institutions. Am J Sociol. (2010) 116:341–88. doi: 10.1086/653599

CrossRef Full Text | Google Scholar

19. Cassier M, Stoppa-Lyonnet D. Un juge fédéral et le gouvernement des États-Unis interviennent contre la brevetabilité des gènes. Med Sci. (2011) 27:662–7. doi: 10.1051/medsci/201228s204

CrossRef Full Text | Google Scholar

20. Pollack A,. Myriad Genetics Ending Patent Dispute on Breast Cancer Risk Testing, New York Times. (2015). Available online at: https://www.nytimes.com/2015/01/28/business/myriad-genetics-ending-patent-dispute-on-breast-cancer-risk-testing.html (Accessed 18/09/18)

21. Reuter. New Illumina Tech Could Usher in $100 Gene-Sequencing Era. (2017). Available online at: https://www.reuters.com/article/us-illumina-stocks/new-illumina-tech-could-usher-in-100-gene-sequencing-era-idUSKBN14U1PO (Accessed 18/09/18)

22. Timmermans S, Tietbohl C, Skaperdas E. Narrating uncertainty: variants of uncertain significance (VUS) in exome sequencing.(2016) BioSocieties 12:439–58. doi: 10.1057/s41292-016-0020-5

CrossRef Full Text | Google Scholar

23. Stivers T, Timmermans S. Negotiating the diagnostic uncertainty of genomic test results. Soc Psychol Quart. (2017) 79:199–221. doi: 10.1177/0190272516658770

CrossRef Full Text | Google Scholar

24. Star SL, Ruhleder K. Steps towards an ecology of infrastructure: design and access for large information spaces. Inform Syst Res. (1996) 7:111–34. doi: 10.1287/isre.7.1.111

CrossRef Full Text | Google Scholar

25. Star SL. The Ethnography of Infrastructure ≫. Am Behav Sci. (1999) 43:377–91. doi: 10.1177/00027649921955326

CrossRef Full Text | Google Scholar

26. Bowker G, Baker K, Millerand F, Ribes D. Towards information infrastructure studies: ways of knowing in a networked environment. In: Hunsinger J, Klastrup L, Allen M, editors. International Handbook of Internet Research Dordrecht. Dordrecht: Springer (2010). p. 97–117.

Google Scholar

27. Bowker GC, Star SL. Sorting Things Out: Classification and Its Consequences. Cambridge, MA: MIT Press (1999).

28. Brown C. The changing face of scientific discourse: analysis of genomic and proteomic database usage and acceptance. J Am Soc Inform Sci Technol. (2003) 54:926–38. doi: 10.1002/asi.10289

CrossRef Full Text | Google Scholar

29. Bowker G. Memory Practices in the Sciences. Cambridge, MA: MIT Press (2005).

30. Hine C. Databases as scientific instruments and their role in the ordering of scientific work. Soc Stud Sci. (2006) 36:269–98. doi: 10.1177/0306312706054047

CrossRef Full Text | Google Scholar

31. Dagiral E, Peerbaye A. Making knowledge in boundary infrastructures: inside and beyond a database for rare diseases. Sci Technol Stud. (2016) 29:44–61.

Google Scholar

32. Strasser B. The Experimenter's Museum: GenBank, natural history, and the moral economies of biomedicine. Isis (2011) 102:60–96. doi: 10.1086/658657

PubMed Abstract | CrossRef Full Text | Google Scholar

33. Hilgartner S. Biomolecular databases: new communication regimes for biology? Sci Commun. (1995) 17:240–63. doi: 10.1177/1075547095017002009

CrossRef Full Text | Google Scholar

34. Desrosières A. The Politics of Large Numbers. A History of Statistical Reasoning. Boston, MA: Harvard University Press (2002).

Google Scholar

35. Hilgartner S. Reordering Life: Knowledge and Control in the Genomics Revolution. Cambridge, MA: MIT Press (2017).

36. Cassier M, Gaudillière JP. Recherche, médecine et marché: la génétique du cancer du sein. Sci Soc Santé (2000) 18:29–49. doi: 10.3406/sosan.2000.1504

CrossRef Full Text | Google Scholar

37. Huang KG, Murray FE. Entrepreneurial experiments in science policy: analyzing the human genome project. Res Policy (2010) 39:567–82. doi: 10.1016/j.respol.2010.02.004

CrossRef Full Text | Google Scholar

38. Goëta S, Davies T. The daily shaping of state transparency: standards, machine-readability and the configuration of open government data policies. Sci Technol Stud. (2016) 29:10–30.

Google Scholar

39. Nature Editorial. The ups and downs of data sharing in science. pooling clinical details helps doctors to diagnose rare diseases — but more sharing is needed. Nature (2016) 534:435–6. doi: 10.1038/534435b

CrossRef Full Text | Google Scholar

40. Callon M, Lascoumes P, Barthe Y. Acting in an Uncertain World. An Essay on Technical Democracy. Boston, MA : MIT Press (2009).

Google Scholar

41. Ducournau P. The viewpoint of DNA donors on the consent procedure. New Genet Soc. (2007) 26:105–15. doi: 10.1080/14636770701218191

CrossRef Full Text | Google Scholar

Keywords: big data, genomics, BRCA, oncogenetics, database

Citation: Derbez B (2018) Big Data Sharing: A Crucial Democratic Issue for Genomic Medicine. Front. Public Health 6:334. doi: 10.3389/fpubh.2018.00334

Received: 03 July 2018; Accepted: 31 October 2018; Published: 28 November 2018.

Thomas Lefèvre, Université Paris 13, FranceEdited by:

Nicole C. Nelson, University of Wisconsin-Madison, United StatesReviewed by:

Copyright © 2018 Derbez. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Benjamin Derbez, benjamin.derbez@univ-brest.fr

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher."

This published article is also available on ResearchGate:

Source link:

Alessandro Albieri how does Lizmap compares to Leafmap, they share the same functionalities?

Why don't you try some Python pre-existing code?

Dr.Muhammad Irshad

I think you did not understand the intent of the researcher who asked the question well.

Greetings