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Author Topic: Open Access Scientific Databases  (Read 580 times)
Zanthius
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Open Access Scientific Databases
« on: March 18, 2018, 10:35:53 am »

« Last Edit: March 18, 2018, 05:37:34 pm by Zanthius » Logged
Death 999
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Re: Open Access Scientific Databases
« Reply #1 on: March 18, 2018, 04:15:45 pm »

Who's paying for the databases, and for editing at the journals?
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Zanthius
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Re: Open Access Scientific Databases
« Reply #2 on: March 18, 2018, 04:31:00 pm »

Who's paying for the databases, and for editing at the journals?

Who is paying for Linux? I guess the databases can be open source, and lots of the work with incorporating data from journals into databases can be done with machine learning algorithms today.

Sure, the editors at the journals should be payed, but I doubt they receive most of the money here anyhow, and what about the researchers that wrote the articles in the first place? They aren't payed at all, and in many cases the editors barely need to make any corrections, and in many journals they don't necessarily see errors. At least I often find errors in many journals.

BTW, a shared license for 1 user at a university, cost approximately 12 000 USD/Year just for SciFinder, and the universities usually need access to multiple shared users in multiple similar databases with similar prices. Regarding access to Elsevier:

Quote
In 2015 Finnish research organizations paid a total of 27 million euros in subscription fees. Over one third of the total costs went to the Elsevier.

https://en.wikipedia.org/wiki/Elsevier#Boycotts

Finland is a reasonably rich western European country, so if they are struggling with this there, imagine what the situation must be like in poor countries.

Do you think it is reasonable to have a system which makes it more or less impossible for people to do cutting edge research in poor countries?
« Last Edit: March 18, 2018, 05:19:10 pm by Zanthius » Logged
Zanthius
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Re: Open Access Scientific Databases
« Reply #3 on: March 18, 2018, 07:20:50 pm »

I am also adding this:



I have now published it at: http://www.archania.org/governance/#Linux_and_open_access_to_scientific_journals_and_databases
« Last Edit: March 18, 2018, 11:23:40 pm by Zanthius » Logged
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Re: Open Access Scientific Databases
« Reply #4 on: March 19, 2018, 02:00:28 pm »

Need a new machine, will likely test Linux on the old one, once the data has been migrated. Thanks for the advice ("Cinnamon").

Plenty of universities tried Linux.
The crux is and remains that the hardware systems are so diverse, that testing all hardware where the stuff needs to run is impossible for the university administrators.

On top of that, many institutes at universities are very independent from the central procurement, and do therefore not follow the same guidelines.

And many software needed to run the experiments are often provided Windows-only.

I know I ran my studies on three machines, 2 windows (one running windows only software from the attached test machine supplier), one Linux.
We had most issues with the Linux machine.
All kind of upgrade issues,.... New hardware -> not functioning or somehow causing problems with the older necessary hardware parts, new hardware sometimes required updates for the kernel, which older hardware elements could not be upgraded to (old testing equipment, no new drivers available).
With windows, the core remained. The whole system just remained functional. No matter what we did install/uninstall/changed in the settings/...

That was 15 years ago.
Linux got much better in that regard, but back then our institute decided to remain windows only for the time being. (So we got new hardware, and migrated the lab machine equipment to the new wondows computer.)
A new try today would likely work out much better than back then.
But I fear the basic thought which caused us to elect windows remains.
If MS ever changes their licensing fees, so that you have to pay annually or similar, then the equation will change (too much money spent on software licenses anyway, money is better spent on the equipment), until then, we have a warm heart for Linux, but Windows remains the cheaper option for many institutes.


Regarding publications: in the Netherlands and in Germany, Elsevier and the like now give huge discounts to the universities still publishing via their scientific magazines.
The universities found it unfair, that they provided the studies to be published, some publisher made money, and the universities had to subscribe and pay to get their own studies...

The bigger scientific publications still pay to double-check the content of the publications, and this costs a lot of money.
"Free publication servers" are taking a hold too (especially for public-money funded researches), but the publications there remain "unconfirmed", and thus are not as desireable for publications and citing.



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Zanthius
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Re: Open Access Scientific Databases
« Reply #5 on: March 19, 2018, 02:48:07 pm »

All kind of upgrade issues,.... New hardware -> not functioning or somehow causing problems with the older necessary hardware parts, new hardware sometimes required updates for the kernel, which older hardware elements could not be upgraded to (old testing equipment, no new drivers available).

This is why I changed from Linux Mint to Manjaro/Arch Linux a while ago. With my Manjaro-Cinnamon combination, I get updates immediately when a new kernel is released, and it is super easy to upgrade:





The newest kernels are often compatible with most of the newest hardware. They are at 4.15.11 now, so I am a little bit behind, but not a lot: www.kernel.org

I have been using Linux for at least 15 years now, and I would say that it is much better now than back then. I have also experimented with different distributions and desktop environments recently, and I definitely like the Manjaro-Cinnamon combination best.

Regarding publications: in the Netherlands and in Germany, Elsevier and the like now give huge discounts to the universities still publishing via their scientific magazines.

Maybe they give discounts to huge universities in rich countries, which are in a strong position to bargain with them. I doubt they give a lot of discount to small universities, and universities in poor countries.

« Last Edit: March 19, 2018, 03:26:17 pm by Zanthius » Logged
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Re: Open Access Scientific Databases
« Reply #6 on: March 19, 2018, 03:46:30 pm »

Regarding publications: in the Netherlands and in Germany, Elsevier and the like now give huge discounts to the universities still publishing via their scientific magazines.

Maybe they give discounts to huge universities in rich countries, which are in a strong position to bargain with them. I doubt they give a lot of discount to small universities, and universities in poor countries.
But then, the universities in the big countries are the ones who publish the most in the scientific publications.
That was the leverage to enforce a deduction in subscription fees.
(Otherwise the German universities would've left the "old" system and would publish via their own online publication system.
I find the latter still a good idea, and I hope they'll implement it anyway sometime soon.)
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Zanthius
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Re: Open Access Scientific Databases
« Reply #7 on: March 19, 2018, 05:29:40 pm »

But then, the universities in the big countries are the ones who publish the most in the scientific publications.

Sure, but how are universities with less bargain power ever going to get better, if they don't even have access to relevant scientific publications and databases?
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Zanthius
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Re: Open Access Scientific Databases
« Reply #8 on: June 06, 2018, 03:22:40 pm »



https://www.archania.org/research/#Academic_research_articles_should_be_rated

For academic articles that aren't about chemical reactions, we can just put the "abstract" instead. I am going to put all the references from my website into a database where people can rate them, and write comments. I will also put lots of chemical reactions into the database, and make it open so that people can add new articles or reactions.
« Last Edit: June 07, 2018, 07:24:26 am by Zanthius » Logged
Zanthius
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Re: Open Access Scientific Databases
« Reply #9 on: June 11, 2018, 10:52:10 pm »

Okay.... here is the beta version of my database with rated chemical reactions:

https://www.archania.org/research/reactions/?name=&year=&type=&sortby=name

I am thinking that chemists tend to be reasonably smart people, so I want chemists to come to my website. And if I put a lot of chemical reactions into the database, chemists from all over the world might be lured to my website when they search for chemical reactions in google. Seems like it could be a quite good tractor beam generator.

If I made a similar database with mathematical theorems, I might be able to lure mathematicians from all over the world to my website....
« Last Edit: June 11, 2018, 11:09:49 pm by Zanthius » Logged
Zanthius
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Re: Open Access Scientific Databases
« Reply #10 on: June 18, 2018, 07:25:11 pm »

I have now added 80 chemical reactions, and you can write comments and rate anyone of them anonymously without any account.

The reactions can also be sorted according to how they are rated: https://www.archania.org/research/reactions/
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Re: Open Access Scientific Databases
« Reply #11 on: July 24, 2018, 10:25:09 pm »

Google has started indexing the reactions on my webpage now: https://www.google.com/search?q=site:archania.org/research/reactions&source=lnms&tbm=isch

I would like to make it so that people can draw chemical motifs, and search for reactions fitting the motifs. Unfortunately, this seems to be a bit beyond my skills as a programmer. Sad

They have it like that in the 10 000 USD per year per user database called SciFinder. If my database also got something like that, it could become a serious free competitor to super expensive databases like SciFinder and Reaxys.
« Last Edit: July 24, 2018, 10:48:05 pm by Zanthius » Logged
CommanderShepard
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Re: Open Access Scientific Databases
« Reply #12 on: July 24, 2018, 10:49:32 pm »

Universities can also have their own public databases, just look at how popular Cornell's ArXiv is, which you can also find here https://arxiv.org/
« Last Edit: July 24, 2018, 10:56:30 pm by CommanderShepard » Logged
Zanthius
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Re: Open Access Scientific Databases
« Reply #13 on: July 29, 2018, 10:58:14 am »

Universities can also have their own public databases, just look at how popular Cornell's ArXiv is, which you can also find here https://arxiv.org/

Yes. I have written a bit more about why universities should publish in open access journals today:



https://www.archania.org/research/#Universities_should_use_Linux_and_publish_in_open_access_journals

Also... if you think open access journals don't provide as much quality control as expensive closed access journals, I have also written about how all researchers should be allowed to rate scientific articles, similarly to how you might rate a movie on imdb.com.

Anyhow, I see that the problem with closed access publishing is particularly prevalent with chemistry:



https://peerj.com/articles/4375/
« Last Edit: July 29, 2018, 06:57:18 pm by Zanthius » Logged
Zanthius
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ratedreactions.com
« Reply #14 on: August 02, 2018, 04:41:08 pm »

I bought a separate domain for the database with rated chemical reactions. I might hire people to work for me to make this database better.

https://www.ratedreactions.com/
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