125 Matching Annotations
  1. Jul 2021
    1. resultsTOPIC

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

    2. ScopusandWeb of Science

      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?

    3. APC-based OA hence risks stratifications

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

    4. has been driven by richer, global North nations

      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?

    5. but many OA journals

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

    6. Key threatsinclude

      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.

    7. new risks of bias and exclusion

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

    8. above all by Open Science advocates

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

    9. Methods

      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?

    10. R "FAIR Data"

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

    11. Open Access

      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?

    12. Open/FAIR Data

      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.



  2. Aug 2020
    1. Wikipathways


    2. Omnipathr


    3. 2020.

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

    4. reactome


    5. kegg


    6. g:profiler


    7. g:profiler


    8. through the web we have wrapped

      "through the web, we have wrapped"

    9. gprofiler2 R package

      "gprofiler2 R package version 0.1.9"

    10. Here we demonstrate

      "Here, we demonstrate"

    11. quickly


    12. Alternative option is

      "The alternative is"

    13. comprises data from experiment

      "comprises experimental data "

    14. can be made

      "can be defined"

    15. in g:Profiler database

      "in the g:Profiler database"

    16. all the data sources

      "all data sources"

    17. unlike the others,

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

    18. from the WormBase

      "from WormBase"

    19. knowledge-bases

      "knowledge bases"

    20. g:Profiler enabling

      -> "g:Profiler, enabling"

  3. Jun 2020
  4. Sep 2019
    1. exposing potential users to a prototype

      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

    2. Unless you are a pioneer, and few of us are, the problem you are working on is likely addressed by existing tools.

      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".

    3. As a result, scientific software is often poorly documented, non-intuitive, non-robust with regards to input data and parameters, and hard to install.

      citation welcome

    4. a substantial fraction of these tools are probably abandonware; i.e., these are no longer actively developed or supported in spite of their potential value to the scientific community.

      citation welcome

    5. Unfortunately, efforts in scientific software development are constrained by limited funding, time, and rapid turnover of group members.

      citation welcome

  5. Aug 2019
  6. May 2019
  7. Apr 2019
  8. Mar 2019
  9. Feb 2019
    1. var results = rdf.sparqlRemote( "", http://rdf.farmbio.uu.se/chembl/sparql "SELECT DISTINCT ?predicate WHERE { [] ?predicate [] }" )

      The correct code is:

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

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

      The correct code is:

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

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

      The correct code is:

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

  10. Jan 2019
    1. transformativeagreement

      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).

    2. CC BY license

      "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.

    3. Author's Accepted Manuscript

      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.

    4. hybrid Open Acces

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

    5. subscription journals

      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.

    6. re-use for any purpose

      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)?

    7. default

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

    8. San Francisco Declaration on Research Assessment

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

    9. does not favour any specific business model

      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.

    10. all scholarly publications

      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.

    11. young scholars have opportunities to excel and advance their careers

      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.

    12. definitiveshift towards newmodelsof academic publishing

      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.

    1. The Funders will monitor compliance and sanction non-compliance.

      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.

    2. open archives and repositories

      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.

    3. all types of scholarly publications

      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.

    4. notably to ensure transparency

      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.

    5. When

      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.

    6. The ‘hybrid’ model of publishing is not compliant with the above principles;

      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.

    7. acknowledged that all scientists should be able to publish their work Open Access even if their institutions have limited means

      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).

    8. Open Access publication

      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.

    9. the Funders will, in a coordinated way, provide incentives to establish and support

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

    10. will ensure jointly the establishment of robust criteria and requirements

      This is postponing important guidance without setting clear starting points.

    11. Berlin Declaration
    12. preferably

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

    13. open 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)
    14. Authors retain copyright

      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.

    1. An Open Letter from Researchers

      "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.

    2. far-reaching consequences

      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.

    3. We support open access

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

    4. improbable

      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).

    5. surely

      Based on what data, evidence?

    6. cOAlition S grantees vs. the rest of the world

      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?

    7. pre-prints

      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.

    8. Green OA

      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?

    9. cheaper solutions

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

    10. hybrid journals

      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.

    11. the copyright model (CC-BY) demanded by Plan S

      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).

    12. serious violation

      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.

    13. quickly result in lower international ranking and standing of individual cOAlition S researchers

      More ad metum, in terrorem, ad baculum.

    14. Plan S has (probably) a much larger negative effect on chemistry than on some other fields.

      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.

    15. coupled to perverse financial incentives: Stimulate accepting as many papers as possible - regardless of their quality - and keep increasing the already high APCs in more selective journals.

      Non sequitur

    16. we won’t even be able to legally read

      See below: not true.

    17. too risky for science in general


    18. unfair for the scientists involved

      Ad misericordiam

    19. with its strong focus on the Gold OA publication model, in which researchers pay high APCs for each publication

      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.)

    20. if they are not allowed to publish in journals that are important for their career progression

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

    21. if Plan S succeeds in splitting the global research system

      Ad metum, in terrorem, ad baculum

    22. move to another country

      Ad metum, in terrorem, ad baculum

    23. Students in our universities are already starting to wonder if it is wise to do a PhD in a cOAlition S country

      ad passiones

    24. Germany and Switzerland already indicated

      Unspecified totum pro parte.

    25. Fully banning even more society journals

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

    26. legal access to most RSC journals

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

  11. Nov 2018
  12. Sep 2018
  13. Jun 2018
  14. May 2018
  15. Apr 2018
  16. Feb 2018
  17. May 2017
  18. metabmaster.jcbwndsr.com metabmaster.jcbwndsr.com
    1. alternative carbon sources are used

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

    2. little

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

    3. external sources

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

    4. are not highly limited


    5. Low

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

    6. signalling molecules

      Such as?

    7. fatty acids

      Give "Fatty acids" in the pathway an ID.

    8. nutrients

      Was it possible to make this a green action too?

    9. Nature Reviews Cancer.

      add the DOI

  19. Apr 2017
  20. Dec 2016
    1. 1234

      But that's a gene identifier...

    2. Nucleic Acids Res

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