https://scholia.toolforge.org/chemical/Q25112485

https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q23

https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q22

https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q21

https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q20

https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q19

https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q15

https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q2

Confidence level: https://kg-ipclimatec-reports.wikibase.cloud/wiki/Item:Q2

Open Source has been an early driver of Open Science, going back to the late nineties. Why is it not included?

Do these capture research literature from countries outside the South well? What effect does that have on the conclusions regarding Open Science policies outside the North?

How does this relate to hybrid journals often charging more APC then full CC-BY journals?

How did you ensure you captured policies from South America and Asia? Your search uses English-literature oriented search solutions? How did you make sure these do not introduce a bias against Open Science policies in the South?

Many relative or absolute? DOAJ statistics can be cited here.

How does your method distinguish between risks resulting from the Open Science ideology and resulting from how people implement/do Open Science? Since the "creative" use of terms like Open Science (e.g. by Elsevier and other publishers) and Open Access (by basically everyone), the threats of implementations can be huge, but so is the variation. The abstract, however, does not seem to distinguish between them, giving the impression that these threats are 1. unique to Open Science, 2. intrinsic to Open Science. Neither of these are supported by this study, I think.

New compared to what? How does your method compare with that "what"?

Studies that look into the changes in risks of doing Open Science compared to doing Closed Science is very much welcome to me.

I note that the study looks into literature selectively, with keywords around open topics (with the exception of a few like "justice" and "FAIR data" which are about closed science too). I find it hard to see how this corpus allows you to draw conclusions on threats resulting from doing Open Science if you do not compare this to the threats of doing Closed Science. Are the threats new? How did they change? Are they bigger or smaller then with Closed Science. Can you clarify?

FAIR data is not Open Data. Including articles about FAIR data pulls in a lot of articles about closed/proprietary data.

Can you clarify what you mean with Open Access here? What definition are you using? Does this include the use of "Open Access" by publishers, which does not always include the rights to modify and redistribute the science?

Please clarify what you mean with Open/FAIR Data. Is this Open AND FAIR Data, or Open OR FAIR Data? Because FAIR Data and Open Data are different concepts, it sounds important to me to clarify this.

"WikiPathways"

"OmnipathR"

Missing "Zenodo" as venue (publisher/"journal")

"Reactome"

KEGG

"g:Profiler"

"g:Profiler"

"through the web, we have wrapped"

"gprofiler2 R package version 0.1.9"

"Here, we demonstrate"

"easily"

"The alternative is"

"comprises experimental data "

"can be defined"

"in the g:Profiler database"

"all data sources"

Redundant, already clear from the "While..."

"from WormBase"

"knowledge bases"

-> "g:Profiler, enabling"

See also this paper: https://doi.org/10.1162/DINT_A_00035

To me, this sounds like the "release soon, release often" paradigm introduced in 1999 in https://en.wikipedia.org/wiki/The_Cathedral_and_the_Bazaar

By not setting a clear scope of the types of software these rules are about, this opening sentence is overasking. It also ignores the various reasons why a existing functionality is reimplemented (different programming language, learning the algorithms in enough details, inappropriate license, etc), tho, arguable, these are examples of "substantial novelty".

citation welcome

citation welcome

citation welcome

Scholia: https://tools.wmflabs.org/scholia/chemical/Q66480924

Scholia: https://tools.wmflabs.org/scholia/chemical/Q66363675

The source is available at https://bitbucket.org/djoumbou/biotransformer/

See https://tools.wmflabs.org/scholia/chemical/Q63086047

An 2015 analysis can be found here: https://scholarlykitchen.sspnet.org/2015/08/26/do-most-oa-journals-not-charge-an-apc-sort-of-it-depends/

The correct code is:

var results = rdf.sparqlRemote( "http://rdf.farmbio.uu.se/chembl/sparql", "SELECT DISTINCT ?predicate WHERE { [] ?predicate [] }" )

The correct code is:

rdf.importRDFa( data, "http://egonw.github.com/" )

The correct code is:

rdf.importURL( data, “http://rdf.openmolecules.net/?InChI=1/CH4/h1H4” )

https://tools.wmflabs.org/scholia/chemical/Q7076680

https://tools.wmflabs.org/scholia/chemical/Q408865

It would be good to explicitly mention the transparency here, so that everyone understands the content of that transformative agreement (as required by cOAlition S elsewhere).

"a CC-BY" license OR "the CC-BY license"? The use of a/the sounds relevant here, where the former suggests various versions of the CC-BY are allowed, but then that needs clear definition.

I disagree with this. Only the VoR should be acceptable. Otherwise we end up in a situation where we have to track which version is which, which sounds very expensive. Worse, current publishers and repositories are not mature enough to handle this level of complexity.

This needs a more clear definition: "journals that do not publish all articles under an open license".

This may need clarification. A CC-BY journal based on subscription is a possible business model that now seems discouraged, which contradicts the earlier point of not wanting to limit business models.

Does this imply reuse, modify, redistribute?

Second, does this specifically allow commercial use and making derivatives, to clauses that CC license can be complemented with (but other open licenses too)?

When can Funders deviate from this default? Is there a transparent process for that?

cOAlition S needs to be better here: strong enforcement of DORA is essential.

I disagree with this statement: by requiring a specific open license, you do steer possible business models. Of course, just requiring open licenses generally limits the number of business models: after all, it rules out making business by exploiting IP (paywall model), but that is assumed as logical here, I believe.

This is more ambitious then the specific goals set by (and for) The Netherlands. Setting high goals is a common pattern in our competitive western culture and expected. The current "middle ground" is a half-baked hybrid system, and not even that in all cases.

This is indeed currently not the situation: establishing yourself as researcher is now requiring support from senior researchers and rich universities, even if this effect is small, it is noticable.

I think this is important. The current situation is weird and inhibits the dissemination of knowledge. This is a fairly new situation, as copyright law has changed a lot in the past 50 years. We find ourselves in a situation where text and data mining is not generally allowed (UK seems to be an exception), where papers of more than 100 years still paywalled behind a copyright wall, and information in journal articles are not available in FAIR ways.

The word "transparent" is missing here. It must also be clarified how much room Funders have, or whether there will be jointly established of robust criteria.

Here too, it must be clarified what cOAlition means with "open". Does the cOAition agree on the three open science principles? Principle 8 should be extended to capture retaining copyright too.

This must be refined and is too limited at this moment. I understand where the bias towards journal publications come from, but even within that section there is a lot of diversity.

It is not uncommon that national deals are hidden behind non-disclosure agreements (NDAs), so FOI-requests has broken up this practice. The NDAs allowed publisher to ask different sums to different parties, taking advantage of the monopolies they have (there is only one supplier of Nature, of Cell, etc). Principle 6 attemps, as I read it, to ensure a more open, free market, according to western standards.

To me, this has been a key word: it sketches a situation where APC can be zero. It also indicates puts limits on the APC.

I need to refresh my facts here, but "hybrid" journals did not exist 20 years ago. I believe they have been introduced as an intermediate solution to ensure a migration to full open access journals. Adoption varies and publishers may not have the same reasons as others. One huge problem in The Netherlands is that national package deals often exclude coverage of full OA journals and only cover paywalled and hybrid journals, reversing the effort of a migration to open access.

This is a general research problem and is not new. Where the cost of research is, is slowly changing. Where it currently is by getting access to old knowledge (paywalled journals), it now moves to the production side. There, the cost of publishing an article must be minimized, but still small compared to other overhead researchers pay universities (rooms, IT, library, etc).

The wording is not optimal: it is confounded with a lot of emotion. What I believe the cOAlition should have said here is that the cost of knowledge dissemination should not be covered by individual researchers. Subscription costs are nowadays commonly covered at the university level (many researchers do still have personal subscriptions too). In The Netherlands covering cost of knowledge dissemination with Open Access journals is generally handled at a national level already.

It will be critical that the Funders push for open innovation and open licensing of these new platforms, to ensure inclusiveness of existing publishers.

This is postponing important guidance without setting clear starting points.

This is a 2003 document, see https://en.wikipedia.org/wiki/Berlin_Declaration_on_Open_Access_to_Knowledge_in_the_Sciences_and_Humanities

If the three rights would be explicitly mentioned, there would be no need to shortlist a particular license.

An open license ensures three rights for the reader:

1. reuse (e.g. extraction knowledge, reuse figures)
2. modify (e.g. fix typos or reformat)
3. redistribute (e.g. share with students)

Traditionally, publisher requested copyright, because it made their work easier (legally less risky). With open licenses, this risk was taken away and there is no need anymore for giving away your copyright to publishers.

"Researchers" refers here to the people who signed this letter, not researchers in general. Unfortunately, some media have picked it up that Plan S is bad to researchers in general.

That is the intention: one consequence cOAlition S likes to achieve is general, global, irrevokable access the scholarly knowledge. I quite agree that the plan is ambitious. Maybe too risky, but we cannot conclude that if we ignore the current observed risky consequences of the current model. The current wording suggests it introduces new risks and particularly risks that are bigger than the current problems. The current letter, however, does not compare the sketched risks to the current situations, leaving the reader with the impression that Plan S makes it worse than it is now.

The letter would have benefited from what the authors define as "open access".

Unquantified and leaving out to mention the scholarly societies that actually made the transition already. Arguing that not every research domain is the same, would support the notion that there already is a research divide (see below).

Based on what data, evidence?

This assumes there is no separation at this moment. However, there are currently many separations in publishing: not all fields have equal change to get published in the same journals, not all fields pay the same for access to literature, not every university has access to all literature. There already is a divide. The real question should be: will this divide grow or shrink?

While I welcome pre-prints, they are not a replacement for deposition (archival) of the final version of an article ("Version of Record", VoR). Current pre-print servers do not guarantee an open license, many journals do not allow deposition of the VoR, etc. Pre-prints are currently not an proper alternative.

Green OA is a fuzzy term without a clear definition. Clarification welcome. For example, do they authors guarantee here compatability with the principles of Open Science?

There is a lot of focus on cost, but for me the core rights matter (reuse, modify, redistribute).

A historical note: 20 years ago hybrid journals did not exist. In at least NL they were seen and part of national deals as a temporary intermediate solution, towards full Open Access journals.

CC-BY is not a copyright model: it's a license that gives rights to users. That's the whole idea of Open Science. While the original principles spoke about CC-BY or equivalent licenses (giving the same principal rights: reuse, modify, redistribute), practically, not many alternative are available. ND violates one of the three core rights, and NC has issues in itself (e.g. not being legally well-defined).

Even in Germany this discussion is ongoing and not decided. It also leaves undiscussed that in some countries the IP of research is with the employer, and not the researcher. These aspects should have been discussed.

More ad metum, in terrorem, ad baculum.

Undiscussed is who is to blame here. The "too risky" title suggests Plan S. It is not discussed, however, what role and ethical responsibilities the societies themselves have.

Non sequitur

See below: not true.

Unfounded.

Ad misericordiam

APC should not be the goal. In The Netherlands there has been a longer running effort to make deals with publishers, removing the APC. Check the deals the VSNU makes on behalf of researchers. (BTW, these have been biased to paywalled journals, disfavoring journals which traditionally encourage Open Science.)

I do not understand this argument. To me, the actual research should be important to the career, not in which journal it was published.

Ad metum, in terrorem, ad baculum

Ad metum, in terrorem, ad baculum

ad passiones

Unspecified totum pro parte.

This follows the assumption that journals are now banned (not true).

That is a inaccurate statement: nothing in the past six months has forbidden researchers to get (buy) access to these journals.

The link is broken, but you can find more info on my homepage: http://egonw.github.io/

https://orcid.org/0000-0002-4322-6179

meer?

http://bioportal.bioontology.org/ontologies/ENM/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_51050

http://bioportal.bioontology.org/ontologies/ENM/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_707

https://tools.wmflabs.org/scholia/chemical/Q53818335

https://www.wikidata.org/wiki/Q43507062

https://www.wikidata.org/wiki/Q183453

https://www.wikidata.org/wiki/Q2354337

Link is broken.

Missing period at the end of the sentence.

Impossible to see what is highlighted with this click...

Mmm... the arrow does not reflect this is not happening...

you could add a cancer cell outer membrane, making it more clear the origin...

Typo?

Add a number, to stress it's the first of four...

Such as?

Give "Fatty acids" in the pathway an ID.

Was it possible to make this a green action too?

add the DOI

https://www.wikidata.org/wiki/Q143252

https://www.wikidata.org/wiki/Q418348

GenX is said to be this compound: https://www.wikidata.org/wiki/Q29388239 (provencen in that page).

But that's a gene identifier...

Mmm... it seems the 2016 paper is not listed here yet...