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Open Access - Science topic

Explore the latest questions and answers in Open Access, and find Open Access experts.
Questions related to Open Access
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Our journal is Congo Research Papers. We are a peer review and open access journal. We would like to know if we can be indexed.
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Dear researchers. If we want to publish a paper in a hybrid-type journal and choose the non-open access option (for subscribers only), is it literally free, or is there still a possibility of paying a less charge than APC in their open access option? How can we identify it?
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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.
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Dear friends, I am looking for indexed journals to publish a review paper on shifting cultivation with an emphasis on the northeast region of India. Would you kindly suggest journals where I can submit my paper? A journal that charges for only for making the paper open access would be even better. Thank you in advance.
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I would consider:
- Environmental Research
- Journal of Forest Research
- Forest Policy and Economics
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I am interested in sharing preprints for externally funded projects to provide open access and am wondering about the impact on the peer review process. Specifically, at what point should preprints be posted? Do preprints impact the peer review process (potential reviewers unable to complete a "blind review")? Can copyright issues arise (potentially self plagiarism as the work is previously published)? Thank you for any insight into the preprint process.
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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.
  • Your manuscript may be copied and then published by others before you can do that. This stealing of your paper might be happening. So, you must wait until the paper is accepted and then published by that journal. Then, upload that research item on any platform you wish.
  • A journal may have automated plagiarism software to check the paper before admitting it to the reviewing process. There are chances that your paper can get a rejection at any point. Thus, to avoid this problem. Publish the preprint after you got the paper as "ACCEPTED".
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.
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Dear researchers
In my subject, I work on the characterization of the Moroccan marine microbiota by metagenomics under the discipline of microbial ecology.
During the sampling, we could not have all the in situ measurements of the Physico-chemical parameters of the studied microbiome. That's why we had recourse to the extraction of spatial data from the NASA website to complete.
my question is: do we have the right to combine our own data with those of a database to analyze them? ethical and copyright aspects. since these data are submitted to the public with open access.
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If it is open access I see no reason not to use it. It is however essential that you should properly cite them.
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I recently discovered that many open access advocates are publishing their work on open access in paid journals. Is it justified or fair enough that a researcher working on open access and advocating its immediate application across the globe is publishing their own open access research in pay-walled journals? What is your opinion in this regard?
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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.
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Dear colleagues,
We are preparing a paper on climate change and migration, and have some budget earmarked for open access fees. However, the money needs to be spent in this calendar year. The journal we wanted to submit to can only send an invoice after the article has been accepted. And it usually takes a while before the reviews are in and the revision done. Hence my question: Does anyone know a suitable journal (topic-wise and with good impact) that allows paying open access fee before an article is accepted? Or does anybody have other advice that can be of use here?
Thank you and best wishes
Kees
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Springer has several options
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Dear researchers
In my subject, I work on the characterization of the Moroccan marine microbiota by metagenomics under the discipline of microbial ecology.
During the sampling, we could not have all the in situ measurements of the Physico-chemical parameters of the studied microbiome. That's why we had recourse to the extraction of spatial data from the NASA website to complete.
my question is: do we have the right to combine our own data with those of a database to analyze them? ethical and copyright aspects. since these data are submitted to the public with open access.
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Samir Ranjan Panda , Man Kit Cheung , Phil Geis thank you very muche for your answers :)
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Could some one help me and share the word two column template for the applied eenrgy journal open access
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Wiley Open Access Journal Charges. Check out the attachment.
My question is why do they have categories in open access as well?
1) Gold Open Access
2) Green Open Access
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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)
Hope this clarifies the matter.
Best regards.
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Respected RG members,
I'm interested in free-to-publish and open-access journals. It would be great if there any Scopus indexed journals.
Thank you for your answers
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Hi!
I work with antimicrobial photodynamic therapy. I am considering Open Access journals to publish my next manuscript and I wonder if JoF is a good Journal.
I appreciate your help.
All the best!
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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.
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Could you share your experiences publishing in open access journals in animal science and animal husbandry sector, which are your favorite, and why?
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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
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Dear All,
I want to know the fastest publishing journals especially from submission to the notification of acceptance in the electrical engineering field in the certified Scopus list and not be fully open access.
I am grateful in advance.
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I would recommend your use a journal search and put the criteria you. want (e.g., sort by review time, etc.)
check here:
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What's the frequent license chosen by you all for publication if allowed to choose? Rationale?
CC- BY
CC-BY- NC
CC-BY-NC-ND
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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:
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  • Nowadays, there are many databases available in the different subject domains. Some of them are Multidisciplinary, and some of them are subject specifics. It plays a significant role in the academic and in R & D. In this way, I wanted to know about the Open access databases available for Agriculture Science Subjects.
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To the best of my knowledge, there is no open-access database suitable for this purpose. I always prefer the ORACLE database.
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I am writing a review paper. In my paper, can I use figures from "open access" journals/articles etc provided I cite them properly? (i.e. without have to go for requesting permission for using). Also, is there any way to obtain permission to use already published figures without incurring cost?
Thank you in advance for your answer.
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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."
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Please list Zero Author Publication Fee charging journals in pharmacology subject which are indexed in Pubmed or Scopus or Science Index or Medline or Central Science Citation Index, or Science Citation Index, or Expanded Embase, Scopus, Directory of Open Access Journals (DoAJ)
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I need to simulate Lenticular Lenses to observe their behavior in presence of light. So can anyone suggest some open-access software for this observation?
#optics #simulation #ray
Regards,
Siddhi Vinayak Pandey
DSE-SOT, PDEU - Gandhinagar, India
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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.
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Dear Colleagues,
Is it necessary to get permission for reuse of figures that are published in "open access journals"?
Best regards,
Parisa
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You are most welcome dear
Wish you the best always.
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Hello,
Is there any point clouds dataset for railway asset classification? Or are some network's weights pre-trained on such a dataset? to date, there are no datasets available in open access for this purpose.
Thank you.
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Look the link, maybe useful.
Regards,
Shafagat
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The journal should be related to agricultural science.
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Yes, There are some journals of Springer unpaid and open access, please visit or contact helpline of the springer
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Could you kindly share some free open access scopus indexed journals Q3 and Q4 , please?
Research areas: Applied linguistics, psychology, and language issues
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Hello, feel free to try Slovo a slovesnost: http://sas.ujc.cas.cz/?lang=en. It is even indexed in WoS.
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Note: Both journals are Elsevier and Scopus Index, although, the open-access is new, free for now (No APC) and it's a companion journal to high IF journal
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It's companion with high Impact Factor and indexing in Pubmed and Scopus should be your priority anytime you want to publish.
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I would like to add the density function theory to the adsorption study. Those who work on this issue recommend Gaussian software about it. However, I have no knowledge about this. Is there any online open-access course on this subject ? Also, is there anyone who can help me with this software? Could it also be colloborate? Thanks in advance.
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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.
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Where can the researchers aquire the open-access dataset of datacenter energy comsumption?
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You can use any LCA databases like Athena etc.
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Dear all,
I am looking for positive and negative mood induction through short films (preferably an open access database?). Meta-analysis recommends that short films are the most effective method of positive and negative mood induction. Does anyone please have some short films to share, preferable in German or with no words.
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There are many academic platforms that are offering such facilities...
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Could you please recommend a good Q1/Q2/Q3 journal in the Electromagnetic/Antenna/Wireless communication field that does not charge publication fees?
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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)
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I have written a comprehensive survey and I wish to communicate it to SCI journal but most of the journals are open access. Kindly suggest some journals.
That would be really helpful..!!
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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
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What are the most important enabling technologies for Industry 4.0?
Can you provide links to open access papers that provide a quality survey on the topic?
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Should premier institutions open up their doors to open access education?
In the wake of Covid 19 since last two years, we have seen a complete paradigm shift in the teaching learning methodology.
Do you think that now as most of the teaching learning is happening online, the premier universities and colleges open up their programmes for the larger audience and wider student base?
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Dear Preeti Oza . Yes in the case the situation becomes dangerous because of Covid .
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I don't know if this was already asked or not, but I thought I'd give it a try. How do you guarantee your research reaches more audience? What if it is not a generic topic that has similar previous applications? How do citations work (Other than keyword-ing and finding similar topics online and in journals)? What constitutes a great work if the audience of the paper(s) is only a handful of people? Does it have to be one of the very well-known journals to get highly cited (from your experience)?
Please share.
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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.
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Dear Researchers
I have completed two manuscripts on SARS-CoV-2. Unfortunately, I do not have any grant or any other source of funds that can pay the APC. In this circumstance, I want to submit my manuscript to those journals which are free but open access. Can you recommend that?
Thank you all in advance.
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I am constantly barraged with requests to upload "my" published manuscripts to this site, as well as individual messages from members here for the same. It is usually wrong to oblige because the journal has the copyright, even for manuscripts that are over 20 years old. Don't get me wrong here, I'm an advocate for the open journal movement so that "non- affiliated" scientists with no affordable access to journals can have access to academia and continue to work as professional scientists, rather than Starbuck baristas while illegitimate (non-peer-reviewed) information reigns for free on the internet. BUT, we're not there yet. For my own promotional purposes, I would like nothing more than to fulfil these requests for my publications. It was a rude awakening to discover that I don't even have the legal right to send pdf's to colleagues through email. I'm old enough to remember the "50 complimentary pre-prints" that you were allowed give or snail mail to colleagues, but not much has changed: there's a paywall for every one of my papers. Until those go away, I cannot / will not upload papers here.
Let's broaden the discussion for open access journals to include the major "name brand" journals in each field, rather than having to take chances with the new upstart "open access" journals.
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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.
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Dear Researchers in evidence synthesis,
We are mostly dependent on Google Scholar, PubMed, and Cochrane only for our search to cater and include the studies. How much of the total health sciences records are covered by these engines? What are the others available open access? Can we add ClinicalTrials.gov as an engine?
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Thank you dear Dr. Mônica Chaves for the inputs.
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Is there any AI-related (mainly NLP, Computer Vision, Reinforcement Learning based) journal where I can submit short papers? It should be non-open access.
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You may check it:
Artificial Intelligence An International Journal - Elsevier
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Hello everyone,
I would like to download spectral data for satellite images. Please is there available source for obtaining the datasets easily such as NDVI, EVI, WI, SAVI,......etc, without downloading the images and processing?.
Thanks in advance
Regards,
Ahmed
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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
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After 1 January 2020 scientific publications on the results from research funded by public grants provided by national and European research councils and funding bodies, must be published in compliant Open Access Journals or on compliant Open Access Platforms. https://www.scienceeurope.org/wp-content/uploads/2018/09/Plan_S.pdf
What is your opinion?
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Dear Matthias, I wish you to try surviving in the poorer country, where fundind the APC is not so easy as yours.
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Trying to make a list of non för profit journals. I mean journals with no APC. Do you know any?
My list so far
- International journal of health policy and management @IJHPM
- Global health, sience and practice @GHSPJournal
- Nordic journal of migration research @njmr_journal
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Very interesting answers from our colleagues.
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I am writing a review paper and I want to use a figure from the paper published in AWS. AWS articles can be accessed without any subscription means it is a kind of open access. In addition, there is no such link "using RightsLink" "Get rights and content" available on the main page of the publisher. I have already requested the authors for the permission. What should I do now?
Do I need permission if my figure/figures are taken from Open Access articles?
Please share your experience.
Regards
Dr. Jaivindra
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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
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I have been asked to submit a paper on a special issue of Genes- MDPI. The impact factor of the journal is showing to be 3.4 but I saw conflicting articles about the MDPI journals being a predatory one. Though the editor of the issue is a reputed person in the field, I am bit confused about the journal in general. What are your thoughts?
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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.
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Gray literature vs. scientific literature
-What are the advantages and disadvantages of gray literature compared to scientific literature.
-What are the repositories that you know about gray literature.
-What is the importance of gray literature for developing countries
Gray literature is "materials and research produced by organizations outside of the traditional commercial or academic publishing and distribution channels. Common gray literature publication types include reports (annual, research, technical, project, etc.), working papers, government documents, white papers and evaluations"
Scientific literature "comprises scholarly publications that report original empirical and theoretical work in the natural and social sciences. Within an academic field, scientific literature is often referred to as the literature. Academic publishing is the process of contributing the results of one's research into the literature, which often requires a peer-review process".
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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.
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In my opinion, An article-processing charge (APC), also known as a publication fee poses an obstacle for Academic Studies. Because the most important making-known activity of your research and its importance, results etc is turning it into a publication and publishing it in a good journal. But if you do not have funding or enough money to cover the APC charge (which is really high sometimes) an article that is already submitted, already accepted can wait even more than 2 years for publication without open access. This should not be like that if scientific works really matter in this world. Additionally, it's really sad to see even publish an article in a good journal turn into a business.
On the other hand, the journal is making an agreement with authors about in case if they share full-version in any academic platform to make it available for other authors they can not publish an article in any other open-access journal for the upcoming 2 years.
I have an article about #femaleimmigrantenterprenurship that got accepted nearly 2 years ago and I and co-authors are still waiting for the publication because it's not open-access due to APC. This is just unfair and damages the scientific works. if you have such an experience too and what you think about it please do not hesitate to raise a voice, it's vital importance.
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This question has been discussed several times before without any solution:
See also these discussions on funding of APC:
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I have recently published an article in a Taylor & Francis journal. The journal asked me to pay more than 3000USD to make the article open access and post on RG and other platforms. I was shocked by that demand. The article is currently under a paywall and people cannot access it unless I share the PDF with them. As far as I know, this is a common practice by Taylor & Francis, Elsevier, Sage, Wiley, Emerald, and so on.
I would love to hear what the RG community thinks about this type of practice.
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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.
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For the purpose of an analysis of the effects of COVID-19 in Sub-Saharan Africa, I would like to know if it is possible to get data such as: number of daily tests, number of confirmed cases, number of hospitalizations, number of recoveries, number of deaths, measures taken by the government, etc. Thanks.
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Journal of Industrial & Management Optimization (JIMO) is an open access journal. You pay a substantial amount to publish a paper. When you go to the website of its publisher, American Institute of Mathematical Sciences (AIMS Press), it seems that it is not really based in the United States. I am not sure if it is a legitimate professional organization or if it is a predatory publisher. They have a large number of open access journals. On the other hand, their handling of papers is terrible: extremely slow and low-tech, which is not typical for predatory journals. It may take 13 months to get an editorial rejection, for instance. Furthermore, they don't have an online submission system with user profiles on it, you just submit the paper on a website, and they give you a URL to check your paper's status, which makes your submission open to anyone who has the URL. It has an impact factor of 1.3, which makes me puzzled. Any comments on this organization and the journal will be appreciated.
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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.
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A journal has accepted my paper which has multiple indexing including google scholar and is open access. But it ain't scopus indexed. Does that make the journal less desirable or credible?
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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.
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Why do the journals (mostly energy related) under MDPI do not considerably have high impact factors despite of their open access tags?
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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
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Are the credentials of Open Access and non-Open Access journals equal (provided that the impact factor and .... the parameters of the two journals are exactly the same)
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The goods ones are in Scopus or Web of Science
Best regards
Ph.D. Ingrid Del Valle García Carreño
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I have been interested in research since the beginning of my university life. My first research paper was accepted in an open access journal (Q3, Scopus indexed) when I was a last year student. Since then I have published 4 journal papers (all are open access journals, scopus indexed, between Q2-Q3, cite scores > 3).
But, now-a-days, I have often heard that the value/quality of open access journal is low. However, there are plenty of open access journals that are scopus indexed as well as in Q1 - Q4 with good cite scores. My question is : " Are open access journals really low in quality?. If so, why? If no, what would be the justification?
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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.
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Reputed journals like Nature, Scientific Reports, PlosOne, BMC series few Springer, Elsevier Journals are all charging hefty amounts from authors just to put their reseach open access,
Its only a pdf to be put online
Mo printing charges
No formatting charges
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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.
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Hello everyone, I am interested in patent strategy cases for Amazon sellers - reports, articles with open access, etc. The copyright strategies are interesting as well, but not case studies regarding trademarks.
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I am looking for research articles that either discuss or propose the design of a critical component of image encryption algorithms and their implementations, specifically s-boxes. Can you provide links to 2022 open access articles on S-box construction?
Here is one such example:
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Peer-reviewed (refereed or scholarly) journals - Articles are authored by specialists and vetted by numerous other experts in the subject before being published in the journal to assure the quality of the article. (The paper has a better chance of being scientifically sound, reaching reasonable findings, and so on.)
Because they have gone through the most rigorous review process, articles from scientific, peer-reviewed, academic, and refereed publications are more reputable than those from popular or trade journals ('magazines'). They also have the highest number of references or citations.
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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.
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Do you think that the free access to information resources in countries that do not have deterrent laws may pose a risk to the intellectual property rights of the researchers themselves?
Why? And why not?
Do you think that the free access to information resources in countries that do not have deterrent laws may pose a risk to the intellectual property rights of the researchers themselves?Why? And why notDo you think that free access to information sources poses a threat to the intellectual property rights of researchers themselves?
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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.
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It is the link of a beneficial Q&A page with more than 320 answer by RG colleagues.
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Journals are not needed anymore, this is an old concept.
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Hello
I have been contacted about publishing with this journal . But it seems a bit strange to me . I know it’s open access but it was also hard to find papers online from it. Can you help ?
Thanks
Evan
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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.
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My research articles are published in Scopus indexed journals which are not an open access, but in my Scopus profile it is showing that the articles are open access. Can anybody please tell me the reason and can it be corrected?
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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.
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Nowadays, there is a trend to change most journals towards completely open access.
Is open access an advantage or disadvantage for a published article and its author?
Does this harm the value of the published article and its author?
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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:
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What is the best open access journal for a pediatric nutrition manuscript...?
Any past experience?
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Journals for pediatric nutrition
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
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I want to publish an article related to groundwater analysis using geospatial techniques. Can anyone suggest me to find out suitable open access journal that does not have any article processing charges.
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Thank you all for your valuable information. It will help me a lot.
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I have designed and modeled a wastewater treatment plant recently. I want to publish my work in an open-access journal. I found many journals which accepts original, experimental research work. Can anyone share a me a journal which accepts these types of paper and does fast peer-review process. Thank you.
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Journal of Mining and Geotechnical Engineering
This journal isn't indexed in Scopus/WoS, so publication is free of charge
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has anyone already deal with lambert academic publishing before ? what is their reputation ? do you thing it is a good choice to deal with this publisher ?
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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.
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Hi guys,
I am looking for suggestions/recommendations from the research community regarding public databases that are most commonly used by researchers in their analysis.
Just like GEO, GTex, TCGA, Gnomad, TopMed etc, even databases from other countries besides US.
#genomics #publicdata #genomicdatabases #databases #datamining #TCGA #HCA #GTEX #GEO #ARRAYEXPRESS
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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*
  • Université de Bretagne Occidentale, Brest, France
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."
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