1,750 Matching Annotations
  1. Aug 2017
    1. Over the past 25 years the pace of progress in neuroscience research has been extraordinary, with advances in both understanding and technology. We might expect that this would stimulate improved understanding and treatment of mental health problems, yet in general this has not been the case. In fact, our standard treatment approaches have barely changed in decades, and still fail many people suffering from mental distress.

      Lack of translation of neuroscience advances to clinical care in mental illness.

    1. ut the non-profit, scholar-run nature of its governance is, arguably, the crucial move.

      See Neylon et al's principles of open infrastructures for the need for community governance. If these are followed, then I'm not sure whether it matters whether an entity is commercial or not. Because their system would be free to fork if they aren't responsive to the community.

    2. A publishing ecosystem centered on scholarly values – rather than 30 per cent, Elsevier-style profit margins – is within reach. For that to happen, we have to throw our weight behind the non-profits, before it’s too late.

      Agreed.

    3. Both groups have committed themselves to “fair” open access principles, which, among other things, “strongly recommend” that journal owners be “fully” non-profit. “A for-profit company accountable only to shareholders”, the statement pointedly stresses, “is not compatible” with these principles.

      I'm not sure that this is entirely true, but the companies have to be accountable to the scholarly community first, and their shareholders second. That's why we've been trying to articulate core principles that any system should adhere to: scholarlycommons.org

    4. The first set of challenges, around sustainable funding for a non-profit infrastructure, has a viable answer: the key is to redirect the billions – even a fraction of those billions – that libraries currently spend on subscriptions to the new, scholar-run platforms. These dollars are crucial, too, to underwrite an OA future for the university presses and scholarly societies.
    5. Perhaps the steepest obstruction is our own well-earned cynicism. The university, with its audit culture and industry “partnerships”, is already so entangled with corporate values that its “non-profit” status strikes many of us as hollow. What difference does it make, by extension, to bring scholarly publishing back into the fold, when the “fold” itself is shot through with market thinking?

      Fighting for the heart and soul of scholarly communications.

    1. Open source – All software required to run the infrastructure should be available under an open source license. This does not include other software that may be involved with running the organisation. Open data (within constraints of privacy laws) – For an infrastructure to be forked it will be necessary to replicate all relevant data. The CC0 waiver is best practice in making data legally available. Privacy and data protection laws will limit the extent to which this is possible. Available data (within constraints of privacy laws) – It is not enough that the data be made “open” if there is not a practical way to actually obtain it. Underlying data should be made easily available via periodic data dumps. Patent non-assertion – The organisation should commit to a patent non-assertion covenant. The organisation may obtain patents to protect its own operations, but not use them to prevent the community from replicating the infrastructure.

      Essential characteristics of open infrastructures

    1. The other partner in big data’s odd couple is the chaotic nihilist. She’s abandoned any hope of properly tagging the world, and relies on machines to find the most relevant or appropriate information. Her kind are the machine-learning data scientists who are convinced that given enough data and the right algorithm, the best results will bubble to the top.

      Funny that my brain remembered this as "data nihilist"

    2. So we now use the country itself, as its own map, and I assure you it does nearly as well.”

      I love this quote too.

    3. One camp—made up of semantic idealists who fetishize taxonomies—is to tag and organize it all. Once we’ve marked everything and how it relates to everything else, they hope, the world will be reasonable and understandable.

      Love this quote

    4. This is the article I've been looking for! I thought I had filed it in Mendeley, but I had uploaded it to FORCE11. Talk about filing... But it encapsulates what I've always said: Man or Machine: both.

    1. We propose that, in order to be cited as a data author, a person must have made substantial contributions to the original acquisition, quality control, and curation of the data, be accountable for all aspects of the accuracy and integrity of the data provided, and ensure that the available data set follows FAIR Guiding Principles, which instruct that the data and metadata meet criteria of findability, accessibility, interoperability, and reusability

      Definition of what constitutes authorship; does not preclude other forms of contributions

    2. data author

      I disagreed with this before I attended the workshop that discussed this proposal, but have now come to support it. It broadens out the concept of authorship to these other types of digital works.

    3. A meaningful and standardized designation for persons who contribute the data that are used in a peer-reviewed publication must reflect two points: first, the significance of the contribution to the scholarship, whether as part of a primary or secondary analysis; and second, the independence of the data generator from analyses performed by data users that lead to a subsequent publication when the resulting article does not derive from a collaboration.

      Data credit and data blame

    1. A strong version of moral rights even gives the author the right to retract a work from publication and to enjoin any further publication or duplication.

      But not in the scholarly commons, although I think we did recognize that this was a problem. But the persistence requirement of FAIR says they cannot remove all traces of the work.

    2. Authors also have the right to not be attributed if they no longer wish to be associated with the work.

      Interesting, to Dan's point. But does the Commons allow this?

    3. Box 1. Layers of Copyrights in Databases

      Very useful information about copyrights and data

    4. Academic researchers and their offices of sponsored projects should carefully review drafts of sponsored research agreements and clinical trial agreements to ensure they do not inappropriately restrict a researcher’s right to disseminate the results of the scientific research they have conducted. A researcher should ensure that the agreements do not permit commercial sponsors to revise, delete, or suppress information generated by the researcher. The terms and timing of disclosing research results that are trade secrets should be incorporated into the sponsored research agreements, not negotiated at the time of publication

      Things to keep in mind when negotiating a research agreement.

    5. For example, if a researcher collaborates with a pharmaceutical company, the researcher may be contractually bound to suppress the release of research data until the sponsor has developed a patentable product.

      Commercial partnerships

    6. so long as the information has been subject to reasonable measures to keep it secret.

      Certainly a barrier to data publishing!

    7. First, the source of all intellectual property rights is national law. Certain international treaties harmonize intellectual property owners’ rights but leave the users’ rights to vary by country. Second, certain countries have added protection beyond what the treaties require. Specifically, the members of the European Union, candidate countries in Eastern Europe, Mexico [2], and South Korea have created a specialized database right that applies to certain databases created or maintained within their borders. These laws regulate uses of these databases only within their borders.

      Important to recognize that national laws may interfere with free exchange of data.

    8. legal uncertainty interferes with the productive reuse of research data.

      Good quote.

    1. Researchersareusuallyexpectedtoobtaininformedconsentforpeopletoparticipateinresearchandforuseoftheinformationcollected.Wherepossible,consentshouldalsotakeintoaccountanyfutureusesofdata,suchasthesharing,preservationandlong-termuseofresearchdata.Ataminimum,consentformsshouldnotprecludedatasharing,suchasbypromisingtodestroydataunnecessarily

      Recommendations about informed consent.

    2. Researchdata—evensensitiveandconfidentialdata—canbesharedethicallyandlegallyifresearcherspayattention,fromthebeginningofresearch,tothreeimportantaspects:•whengaininginformedconsent,includeprovisionfordatasharing•whereneeded,protectpeople’sidentitiesbyanonymisingdata•considercontrollingaccesstodata

      Prepare ahead if you are collecting sensitive information.

  2. dvnweb-vm1.hmdc.harvard.edu dvnweb-vm1.hmdc.harvard.edu
    1. Can the data be digitized?

      We need to give an action here: data should be digitized.

    1. The “state” of a research object is comprised of the external, objectively determinable characteristics of the object. This includes records of claims made about the object, metadata, statements of validation processes the object has undergone, etc.

      But isn't it also the object itself?

    2. he “standing” of a research object is the position, status, or reputation of an object.
    3. At the core, we have a fundamental issue of what “counts”, and what counts will clearly depend on the community doing the counting. This is the central social and political issue on which disagreements on the status of preprints are based. We will never agree on a universal definition because communities naturally value different things

      In our discussions of the scholarly commons, we left out "credit and reward" for precisely this reason.

    4. But they all illustrate the same central point. There exists no universal standard of when an output is considered as part of the formal scholarly record. Rather, it is determined by particular groups in particular contexts

      Good quote for the Scholarly Commons section on credit as well

    5. On the origin of nonequivalent states: How we can talk about preprints [version 1; referees: 2 approved]

      Relevant for "Don't publish, release!"

    1. Adjusted Reelin-positive cell densities were also reduced in CA4 areas of subjects with bipolar disorder (ANOVA, P < 0.001)

      Cells immunopositive for reelin are reduced in CA4 hippocampal subfield

    2. Significant reductions were observed in Reelin-positive adjusted cell densities in the dentate molecular layer (ANOVA, P < 0.001), CA4 area (ANOVA, P < 0.001), total hippocampal area (ANOVA, P < 0.038) and in Reelin-positive cell counts in CA4 (ANOVA, P < 0.042) of schizophrenics vs controls.

      Cells immunopositive for reelin are reduced in several hippocampal subfields

    1. For many, the elephant in the acquisition will be open access. While bepress leaders have been vocal in support of open access, a review of the Digital Commons marketing this week emphasizes its ability to “Expand reach and visibility for the full spectrum of faculty work” rather than on transforming scholarly communications. It is interesting to reflect on apparent institutional objectives and priorities even before Elsevier’s acquisition.

      Indeed

    2. But, over time this portfolio will become more seamless for customers and end users and it is on a strong path strategically. Digital Science — a sibling company to SpringerNature — is the only competitor demonstrating an interest in building a similar kind of portfolio, but although it is bundling products together for sales purposes (for example, at Carnegie Mellon), it seems to be less focused on integrating discrete products onto a common infrastructure and for a seamless user experience.

      Elsevier has put its finger on the next great need: seamless experience. But it shouldn't be one platform.

    1. Immunohistochemistry

      I don't see any mention of a negative control or a positive control. I am always a little suspicious of antigen retrieval methods without them

    2. These receptors are known as cannabinoid receptors (CBs), and along with their endogenous ligands, the endocannabinoids (ECs), and the enzymes responsible for their synthesis and degradation, constitute the endocannabinoid system [6, 7].

      Definition of endocannabinoids

    1. Peer review’s role in the scientific community has never been static. Its form and purpose have been shaped and reshaped according to what scientists needed from the practice—whether it was credibility for a scientific society, improvements in the scientific literature, or assurances to public funders that their money was being spent responsibly. If scientists are to tranform peer review’s future, they must consider what purpose they want it to serve—and whether that purpose can indeed be fulfilled by reports from two or more referees.

      Great conclusion. Peer review can make articles better; it makes them clearer and catches mistakes and omissions. But should it be the gate keeper? I think not. Our public service as referees should be for the former and should be done on open archives. If a journal then wishes to commission additional review for inclusion in their journal, they are welcome to. But they should pay their reviewers for their time as professional consultants.

    2. We often speak of refereeing as something that has been a stable and unchanging part of science ever since the age of Isaac Newton, but peer review’s story is both shorter and more complex than we often assume. It is also littered with criticism. As early as 1845, the scientific referee was described as “full of envy, hatred, malice, and all uncharitableness.”33. A. Csiszar, Nature 532, 306 (2016). https://doi.org/10.1038/532306a Complaints about reviewer uselessness and bias, in other words, are hardly new.
    3. In 2014 Michael Eisen, a cofounder of the publisher Public Library of Science (PLOS), told the Wall Street Journal that scientists and nonscientists need to discard the notion “that peer review of any kind at any journal means that a work of science is correct. What it means is that a few (1–4) people read it over and didn’t see any major problems.”11

      Purpose of peer review, and a counter to a columnist who implied it was suspect because editors sent it to "a few friends". Will dig that reference out at some point.

    4. However, Stever insisted that referees must remain anonymous to ensure their candor

      Single blind peer review

    5. The study was published in a document called the Project Hindsight report, whose findings caused some legislators and commentators to begin questioning scientific spending more broadly.

      Interesting. That's not the narrative that we've been led to believe, where things were "always better when I started in science"...*

    6. The term “peer review” first began to appear in the scientific press in the 1960s. Interestingly, the term does not seem to have originated at journals. Instead, “peer review” was originally used to describe review committees at grant organizations—most often NIH—and in the medical community.

      Origin of the term peer review

    7. The story of external refereeing at grant organizations is similar to the story for journal refereeing. Private grant organizations such as the Rockefeller Foundation generally left funding decisions in the hands of trusted middle managers long after World War I.77. R. Kohler, Partners in Science: Foundations and Natural Scientists, 1900–1945, U. Chicago Press (1991), p. 68. Grant organizations associated with governments or scientific societies were more likely to use external refereeing, although the practice was by no means universal.

      History and origins of peer review of grants

    8. o staunch a flood of “veritable sewage thrown into the pure stream of science,” as physiologist and Member of Parliament Michael Foster put it
    9. The referee reports came to be seen as confidential documents for the internal use of the society. For many years, they were not made available to the authors of accepted or rejected papers.

      Interesting!

    10. A handful of reports did appear in Proceedings, but by the mid 1830s that practice had ceased. Instead, the society decided that referee opinions were mainly useful for helping it avoid printing anything embarrassing in its publications.

      Oops. Retreat from open.

    11. Proceedings of the Royal Society of London, thereby fulfilling the dual purpose of fostering rich scientific discussions and providing material for the new publication.3

      So again, the idea that we wanted to facilitate not close off discussion of papers.

    12. Oldenburg would simply print what interested him and what he thought might be of value to his readers, including not only experimental papers but secondhand accounts of others’ experiments, discussions of recent books, and even his own personal correspondence.

      So Oldenburg was the first editor, not the first purveyor of peer review.

    13. In crediting Oldenburg with the invention of peer review, Zuckerman and Merton implied that peer review’s form and function had changed little since the 17th century.

      Misinformation about the origins of peer review

    14. But 80 years later, peer review is an expected and established part of publishing for scientists and scholars in almost every academic discipline. How did this process become so ingrained in scientific life?

      Origins of peer review

    15. had sent you our manuscript for publication and had not authorized you to show it to specialists before it is printed. I see no reason to address the—in any case erroneous—comments of your anonymous expert. On the basis of this incident I prefer to publish the paper elsewhere.

      Einstein's reaction to blind peer review

    1. Finally, it was important that the data host/provider is not necessarily a participant in making their data interoperable—rather, the interoperability solution should be capable of adapting existing data with or without the source provider’s participation. This ensures that the interoperability objectives can be pursued for projects with limited resourcing, that ‘abandoned’ datasets may still participate in the interoperability framework, but most importantly, that those with the needs and the resources should adopt the responsibility for making their data-of-interest interoperable, even if it is not owned by them.

      Wise, but it's hard to make things completely FAIR without the cooperation of the data producer.

    2. All of these Service-oriented projects enjoyed success within the community that adopted their approach; however, the size of these adopting communities have, to date, been quite limited and are in some cases highly domain-specific

      Polite way of saying that they weren't really used

    3. While APIs allow mechanized access to the data holdings of a special-purpose repository, each repository has its own API, thus requiring specialized software to be created for each cross-repository query.

      Important distinction that isn't always appreciated.

    1. a) Review and assess the project in the medium in which it was created. Permalink for this paragraph 0 b) Recognize the intrinsically collaborative nature of digital projects. Permalink for this paragraph 0 c) Consult specialists in relevant disciplines regarding the various components of the project.

      Criteria for evaluating digital works

    1. Institutions and departments should develop written guidelines so that faculty members who create, study, and teach with digital objects; engage in collaborative work; or use technology for pedagogy can be adequately and fairly evaluated and rewarded.

      But where are these guidelines? Does anyone have any examples?

    1. I hate the narrative of the Semantic Web because the focus has been on the wrong set of things for a long time. That community, who I have been consciously distancing myself from for a few years now, is schizophrenic in its direction. Precious time is spent in groups discussing how we can query all this Big Data that is sure to be published via RDF instead of figuring out a way of making it easy to publish that data on the Web by leveraging common practices in use today. Too much time is spent assuming a future that’s not going to unfold in the way that we expect it to. That’s not to say that TURTLE, SPARQL, and Quad stores don’t have their place, but I always struggle to point to a typical startup that has decided to base their product line on that technology (versus ones that choose MongoDB and JSON on a regular basis). I like JSON-LD because it’s based on technology that most web developers use today. It helps people solve interesting distributed problems without buying into any grand vision. It helps you get to the “adjacent possible” instead of having to wait for a mirage to solidify.

      I love this paragraph!

    2. and continue the narrative that the Semantic Web community creates esoteric solutions to non-problems

      That is pretty funny

  3. Jul 2017
    1. Machine readable is not synonymous with digitally accessible. A digitally accessible document may be online, making it easier for humans to access via computers, but its content is much harder to extract, transform and process via computer programming logic if it is not in machine-readable format.

      Good distinction to make

    1. spzYDf(3R) TI 58Rx
    2. Partial loss-of-func- tion alleles cause the preferential loss of ventral structures and the expansion of remaining lateral and dorsal struc- tures (Figure 1 c) (Anderson and Niisslein-Volhard, 1988). These loss-of-function mutations in spz produce the same phenotypes as maternal effect mutations in the 10 other genes of the dorsal group.

      This paper has been curated by Flybase.

    1. However, a surprising number of studies show that the biological systems of animals living in standard laboratory housing are abnormal. To make animal studies more relevant to human health, research animals should live in the wild or be able to roam free in captive environments that offer a natural range of both positive and negative experiences.

      Plus, we should use behaviors that are natural to the animal, rather than what makes sense to humans.

    1. Female rats are generally considered less territorial than males, but their behavior changes once they become mothers (also known as 'dams') and they can become aggressive towards potentially dangerous intruders, even if this will also place the dam in danger (Bosch, 2013).

      Grendel's mother

    2. While the neural mechanisms that give rise to different defensive responses are relatively well understood, the vast majority of studies reported to date have been based solely on experiments on male subjects.

      Good example of where sex bias in animal research has led to a gaping hole and a real missed opportunity in understanding aggression.

    1. This is a page note.

    2. This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community;

      This paper is an interesting way to measure tool uptake in a community.

    3. red and blue nodes form distinct communities with only a few ties between them, suggesting the methods used by authors of the red publications could have low social validation.

      Interesting perhaps for the resource co-mention work. Disconnected communities.

    4. Thequantitativemethodsintroducedherefindthathigh-throughputtoxicologymethodsarespreadthroughoutalargeandwell-connectedresearchcommunity,whichsuggestshighsocialvalidation

      Metric for "social validation" that perhaps can be used to measure whether a standard has been "adopted by the community>

    1. Most proposals (148) were for a new study and publication, with confirmation of original studies’ results (3) being quite uncommon.

      This is a very important statistic to quote, because people always assume the negative use case, i.e., "weaponizing data". I think that does happen, but the more we can gather the statistics, the better we are able to address it.

    1. Journal policies, peer review, and editorial practices would need to evolve to include data authorship.

      Roadmap for scholarly publishers to support data citation.

    2. “d-index”

      Jeff Grethe proposed this several years ago.

    3. The instructions for the academic narrative, such as in the current NIH biosketch,7 should be modified to allow the inclusion of publications that cite data authorship, indicating the number of citations for each contribution and an explanation of its significance.

      Or at least the top 5 citations if there are a lot of them.

    4. We propose that, in order to be cited as a data author, a person must have made substantial contributions to the original acquisition, quality control, and curation of the data, be accountable for all aspects of the accuracy and integrity of the data provided, and ensure that the available data set follows FAIR Guiding Principles, which instruct that the data and metadata meet criteria of findability, accessibility, interoperability, and reusability.

      Possibly: Who do I need to talk to to understand the data if I have a problem and if I detect a problem, who will take responsibility? as criteria.

    1. In recognition of the growing importance of publishing data, publishers are providing specilized journals, e.g., Scientific Data, published by Springer-Nature, or a specialized article type called a data paper, specifically for publishing well curated and described data sets.

      Update with the information from Honor et al.

    2. Documentation and management of data

      Should point to ReproNIM tools

    1. Another issue for future consideration is standards for landing pages. The DOI specification does not impose requirements or standards for landing pages, and this is appropriate to its scope. In practice, landing pages vary in their quality and usefulness, and it will fast become an issue that needs to be addressed.

      See the recommendations put forth by the FORCE11 repository metadata working group, Fenner et al., 2016

    1. BRAC intends to work to make the plants profitable, but it will be difficult to pull the plug on this operation even if profitability is never achieved.

      Here is where business would cut bait, as it is not the appropriate business for Bangladesh.

    2. the corporation has been able to cover its operating costs for the venture fund and to make new investments

      How was it able to have investments with grant fundiong?

    3. The most likely direct payers are government agencies and corporations that have a vested interest in an intended beneficiary group or in the enterprise’s mission.

      For annotation, this would be the publishers?

    4. The challenge is to find a financial structure that reinforces the organization’s mission, uses scarce resources efficiently, is responsive to changes, and is practically achievable.

      That's all!

    5. And she is far from unique. Social workers, curators, educators, doctors, nurses, artists, scientists, and other professionals who staff nonprofits may balk when they are expected to adapt more to businesslike methods of operation.

      Guess I just don't fit in either place. Does speak to the need to create a 3rd way.

    6. some nonprofit managers still bristle at the use of business language

      As we just found out today in our conference call.

    7. Many nonprofits simply do not have the business-specific organizational skills, managerial capacity, and credibility to succeed in commercial markets. And building new organizational capabilities can be costly and difficult. Hiring people with business skills and market focus is not enough. An organization must be receptive to and supportive of new activities; it also must be able to integrate the skills and values of the new staff. Many MBAs who go to work in nonprofit organizations find themselves ostracized by their colleagues.

      Always comes down to people.

    8. Of course, changing a mission in order to ensure the survival of a worthwhile organization may be justifiable.

      What other choice do they have?

    9. Like the proverbial tail wagging the dog, new sources of revenue can pull an organization away from its original social mission.

      Important to consider.

    10. They are no longer deciding where their grant dollars will go solely on the merits of the programs they will fund but on the value they will derive from the relationship with a particular nonprofit.

      That is an interesting take, and does suggest that grant funding does not come without strings.

  4. Jun 2017
    1. In a sense, it is not any one publisher’s fault that the scientific world seems to bend to the industry’s gravitational pull. When governments including those of China and Mexico offer financial bonuses for publishing in high-impact journals, they are not responding to a demand by any specific publisher, but following the rewards of an enormously complex system that has to accommodate the utopian ideals of science with the commercial goals of the publishers that dominate it. (“We scientists have not given a lot of thought to the water we’re swimming in,” Neal Young told me.)

      Publishers are selling us what we are willing to buy. I don't blame them for becoming rich on our stupidity.

    2. We look at the numbers [of scientists who trust their results to Elsevier] and that suggests we are doing a good job.”

      Corporate speak. I doubt once a journal is established, scientists know who publishes it.

    3. On 5 November 1991, Maxwell was found drowned off his yacht in the Canary Islands.

      I remember this, but I didn't realize his importance to the current mess of scientific publishing.

    4. Between 1975 and 1985, the average price of a journal doubled. The New York Times reported that in 1984 it cost $2,500 to subscribe to the journal Brain Research; in 1988, it cost more than $5,000.

      I had often thought that science went off the rails in the 1980's, but had no evidence to back it up. But this article certainly does suggest that things set in motion in the 1970's began to have their impact in the 1980's.

    5. “Academics are incentivised to produce research that caters to these demands,” said the biologist and Nobel laureate Sydney Brenner in a 2014 interview, calling the system “corrupt.”
    6. and, breaking with the idea that journals were passive instruments to communicate science, he rejected far more papers than he published

      So PLoS One was not revolutionary at all. It was a course correction.

    7. was a journal started by Massachusetts Institute of Technology (MIT) to showcase the newly ascendant field of molecular biology. It was edited a young biologist named Ben Lewin, who approached his work with an intense, almost literary bent.

      So again, the publishers get the blame, but the scientists actually were willing parties.

    8. In the mid-1970s, though, publishers began to meddle with the practice of science itself, starting down a path that would lock scientists’ careers into the publishing system, and impose the business’s own standards on the direction of research. One journal became the symbol of this transformation.

      Tell me more!

    9. “He realised early on that the scientists were vitally important. He would do whatever they wanted. It drove the rest of the staff crazy,”

      This attitude persists I think.

    10. publishers were seen as a necessary partner in the advancement of science

      Great business strategy

    11. Suleski, who ran Pergamon’s Japanese office in the 1970s, told me that the Japanese scientific societies, desperate to get their work published in English, gave Maxwell the rights to their members’ results for free.

      This really is an astonishing story. The man was a genius, regardless that it was a bad model for science, at least in the long run.

    12. He always said we don’t compete on sales, we compete on authors,” Albert Henderson, a former deputy director at Pergamon, told me. “We would attend conferences specifically looking to recruit editors for new journals.” There are tales of parties on the roof of the Athens Hilton, of gifts of Concorde flights, of scientists being put on a chartered boat tour of the Greek islands to plan their new journal.

      All is vanity...

    13. After the war, government emerged for the first time as the major patron of scientific endeavour, not just in the military, but through newly created agencies such as the US National Science Foundation, and the rapidly expanding university system.

      Origins of government funding of science

    14. And no one was more transformative and ingenious than Robert Maxwell, who turned scientific journals into a spectacular money-making machine that bankrolled his rise in British society. Maxwell would go on to become an MP, a press baron who challenged Rupert Murdoch, and one of the most notorious figures in British life. But his true importance was far larger than most of us realise. Improbable as it might sound, few people in the last century have done more to shape the way science is conducted today than Maxwell.

      Interesting. I did not know this.

    15. The long, slow, nearly directionless work pursued by some of the most influential scientists of the 20th century is no longer a viable career option. Under today’s system, the father of genetic sequencing, Fred Sanger, who published very little in the two decades between his 1958 and 1980 Nobel prizes, may well have found himself out of a job.

      Very sad.

    16. Journals prize new and spectacular results

      But this is not the publisher, it is the editor, who is a scientist.

    17. “bizarre” “triple-pay” system,

      Great quote.

    18. cientists create work under their own direction – funded largely by governments – and give it to publishers for free; the publisher pays scientific editors who judge whether the work is worth publishing and check its grammar, but the bulk of the editorial burden – checking the scientific validity and evaluating the experiments, a process known as peer review – is done by working scientists on a volunteer basis. The publishers then sell the product back to government-funded institutional and university libraries, to be read by scientists – who, in a collective sense, created the product in the first place.

      Whenever I explain this to someone outside of academia, they think we are insane. And we are!

    19. It was a 36% margin – higher than Apple, Google, or Amazon posted that year.

      Nice to have this figure in print. It is often quoted but I've meant to track it down.

    1. t’s noteworthy that 174 of the 177 proposals submitted did not involve reanalysis of original results or disproving of the findings of the original analyses; the bulk of the proposals were for new research. Thus, sponsors’ fears regarding making these data available have not been realized.

      Good statistic to have

  5. May 2017
    1. Our results, when compared with the careful and detailed stereological work of Napper and Harvey (Harvey and Napper, 1988, 1991;Napper and Harvey, 1988a,b), suggest that a large fraction, up to ∼85%, of parallel fiber synapses did not generate electrical responses that we could detect. Although this estimate may be reduced somewhat if we attempt to take into account cases in which axons did not traverse or reach the Purkinje cell dendritic tree, we still obtain a worst case of ∼80% undetectable connections.

      That's very surprising.

    1. When I copy files in a repository, it should be clear for all to see that these files were created by me, and not someone else.

      I still maintain that attribution is a core priniple (now it is a rule) of the commons.

    2. Those wishing to offer new approaches to the allocation of names, to ensuring availability or other value-added services could do so – without any kind of contract. The only prerequisite would be compliance with the protocols of the relevant decentralised system.

      Very similar to a principle of the commons (that got cut out but will be brought back as a rule if I have my way!): a publisher is any entity that makes objects available according to the principles of the commons.

    3. As shown above, content-addressable objects are suitable for ensuring that the same object is obtained each time.

      And yet GitHub repositories are so difficult to understand and often very messy. Does point to the critical "knowledge worker" layer envisioned in the commons that curate and provide other services on top of the basic objects.

    4. The mere allocation of a persistent name does not ensure the long-term accessibility of objects. This is also the case for a P2P file system such as IPFS. After all, a file will only be accessible if at least one copy of the file is available on a computer connected to the network.

      Always the weak link, which is why institutions are still required in the scholarly commons.

    5. all payment transactions are irreversible and clearly documented for all to see.

      Transparent provenance.

    6. under its own name

      Stable entities within the commons.

    1. You commit to actively maximizing links with other Crossref members by linking out from the references in your journal articles, (using DOIs retrieved from Crossref), and where possible from other content types too.

      I didn't realize this.

    2. You must have your DOIs resolve to a page containing complete bibliographic information for the content with a link to—or information about—getting the full text of the content.

      Same with data citation principles, but am wondering whether FAIR specifies this. Doesn't seem to.

    3. You commit to updating URLs associated with all registered content, redepositing metadata if your content moves.

      Contract with CrossRef

    4. You commit to maintaining and updating your metadata and DOIs for the long term. DOIs are designed to be persistent in order to preserve the citation record, so should never be deleted.

      Contract with CrossRef

    1. So a PID is necessary, but not sufficient.

      Note that in the Data Citation Principles, we recommend that the PID resolve to a landing page and not to the data set itself. Need to bring this up with Tim and Martin.

    2. That said, the default for maximal FAIRness should be that the data themselves are made available under well-defined conditions for reuse by others (panel E).

      level 2 in the commons decision trees

    3. for instance, those published as obscure and unstable links to supplemental data in narrative articles, not even (as a set) having a proper, machine-resolvable, Persistent, Unique Identifier (PID) which renders both the data elements themselves, as well as their metadata, non-machine-readable.

      Another good phrase: obscure and unstable links to supplemental data.

    4. Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud

      This is a good article that gives some additional explanations of FAIR.

    5. The FAIR principles, although inspired by Open Science, explicitly and deliberately do not address moral and ethical issues pertaining to the openness of data

      Which is why the Commons explicitly includes Open as the first principle. It is exactly to address the moral and ethical issues.

    6. RDF plus proper ontologies are very effective for the purpose of interoperability and information-sharing, particularly at the level of metadata; however, any other format may also be used in a FAIR context, including size-efficient formats aimed at high performance analytics applications. Data (or portions of data) should only be exposed using FAIR formats if this clearly increases their findability, accessibility, or reusability.

      Yeah! At last a recognition that RDF is not the answer to everything!

    7. They describe characteristics and aspirations for systems and services to support the creation of valuable research outputs that could then be rigorously evaluated and extensively reused, with appropriate credit, to the benefit of both creator and user.

      I like that: characteristis and aspirations.

    8. n addition, there is a need for set of community-acceptable ‘rules of engagement’, that define how the resources within that community will/should function and promulgate themselves.

      What we are up to at the Scholarly Commons

    9. Common to all these is the idea of building infrastructure based on rich metadata for the resources in the research environment, that support their optimal re-use.

      Good quote to use

    10. Internet of FAIR Data and Services

      Need to look this up.

    11. The UniProt example is spot-on, but there are also emerging indications that the original meanings of findable, accessible, interoperable, and reusable sometimes may be stretched; even, in some cases, in order to avoid change or improvement

      Well, that would not be a good thing.

    12. The G20 went further in the 2016 Hangzhou summit by endorsing the FAIR Principles by name [8].

      Yay for FORCE11

    13. how the FAIR principles should manifest in reality was largely open to interpretation.

      As it should have been.

    1. One is that a researcher or company could stop caring about a particular tool for various reasons and thus not be interested in updating its permanent identifier.

      Again, it is a social contract not magic!

    2. Until now, maintaining the availability of scientific contributions has been decentralized, mature and effective, utilizing methods developed over centuries to archive the books and journals in which they were communicated.

      Good quote.

    3. The availability of a web page is most dependent on the time it is published and the top-level domain names.

      Good support for tying scholarly content to institutions rather than the raw web.

    4. A cross disciplinary study of link decay and the effectiveness of mitigation techniques

      Tried to add to Mendeley, but it kept pulling up an article with a similar subject, but it was not the same article.

    1. A 2013 study in BMC Bioinformatics looked at the lifespan of links in the scientific literature — a place where link persistence is crucial to public knowledge. The scholars, Jason Hennessey and Steven Xijin Ge of South Dakota State University, analyzed nearly 15,000 links in abstracts from Thomson Reuters’ Web of Science citation index. They found that the median lifespan of Web pages was 9.3 years, and just 62% were archived. Even the websites of major corporations that should know better — including Adobe, IBM, and Intel — can be littered with broken links.

      Link rot statistic

    1. Crossref enables a common linking contract among its participants.

      Persistent identifiers are not just technology; they are a contract.

    1. We propose to consider the following 'levels' for FAIRports, or actually Data Objects contained in them (in other words, one FAIRport could contain Data Objects with Different 'levels of FAIRness) (see figure). Level 1: Each Data Object has a PID and intrinsic FAIR metadata (in essence 'static') Level 2: Each Data Object has 'user defined' (and updated) metadata to give rich provenance in FAIR format of the data, what happened to it, what it has been used for, can be used for etc., which could also be seen as rich FAIR annotations Level 3. The Data Elements themselves in the Data Objects are 'technically' also FAIR, but not fully Open Access and not Reusable without restrictions (for instance Patient data or Proprietary data). Level 4: The metadata as well as the data elements themselves are fully FAIR and completely public, under well defined license. (Non-licensed data considered 'public' by their owner will still be excluded from integration projects by for instance Pharmaceutical companies).

      We just switched our numbering for levels of compliance for the commons, with 1 = best and 4 = least compliant. I don't know if these are used anywhere else, but we should probably be consistent. Perhaps we should switch to a non-numbering system so as to avoid confusion.

    1. If you publish, you’re a publisher We are a global community of members, large and small, who publish scholarly content in all disciplines and in many formats. We define publishing broadly; your business model is your business.

      Cross map this in the Scholarly Commons

    1. UniProt was one of the case studies presented in the original FAIR publication. What makes UniProt FAIR?

      Good figure to use for FAIR. Now available in Wiki Commons

    1. A study published in 2015 by Narod and his colleagues found a low rate of cancer death — 3.3 per cent at 20 years — among women treated for DCIS. Importantly, more aggressive therapy — lumpectomy plus radiation — didn’t improve survival over surgery alone.

      Cancer treatments are not benign either.

    2. The problem is DCIS absolutely tortures women

      I have friends who were thus tortured

    3. As many as 20 to 30 percent of women who undergo mastectomy experience post-mastectomy pain syndrome

      The surgeons don't tell you that.

    1. These findings suggest somatic mosaicism is the rule, not the exception, with every neuron potentially having a different genome than those to which it is connected.

      I'm not sure why this is a surprise. Why would anyone think that they would be identical? Does anyone think everything is nature and nothing is nurture?

    1. rejected article for submission to another journal, this will amount to some 10,000 scientist-hours over just one year.

      Not just articles, but grant applications. See The Tyranny of Formatting for my perspective.

    2. Publishing: Reformatting wastes public funds

      Need to put a number to this.

    1. Yet, the human stories behind scientific advances can teach us a lot about the miraculous ecosystem that drives biomedical progress—about the roles of serendipity and planning, of pure curiosity and practical application, of hypothesis-free and hypothesis-driven science, of individuals and teams, and of fresh perspectives and deep expertise.

      I know that it is controversial as to intellectual property regarding CRISPR, but I hope that the "origin story" is faithfully represented here, because it has important lessons.

    1. The FAIR Data Principles

      Tried to comment on the site but couldn't. Here is an update on FAIR from some of the original authors.

  6. Apr 2017
    1. Provenance of objects in the commons should be transparent and persistent

      And machine readable. I really want this statement to be in the principles, because I believe that attribution and citation are integral to scholarship. We are not attributing them just because of the reward; we are doing so because proper provenance is good scholarship.

    2. is

      are

    3. All activities and outputs that take place in in the commons remain in the commons

      I don't see how this follows from R3.

  7. dvnweb-vm1.hmdc.harvard.edu dvnweb-vm1.hmdc.harvard.edu
    1. NEED TO ELABORATE ON THIS

      We have a document that provides guidance on whether one has permissions. That is what the little question marks in the draw.io documents mean. We can leave this as a document or we can create a mini-decision tree. But if the latter, I want it to be a standalone tree that can be referenced by other trees, as permission issues are fairly generic and cover many objects.

    1. 17. <ELocationID> The purpose of the ELocationID element, defined in 2008, is to provide an electronic location for items which lack standard page numbers. The element houses Digital Object Identifiers (DOIs) or Publisher Item Identifiers (PIIs) that are provided by publishers for new citations submitted to NLM for inclusion in MEDLINE/PubMed. ELocationID may reside either in lieu of pagination or, for items with both print and electronic locations, in addition to the Pagination element. Beginning in October 2012, DOI data submitted by publishers in the PubMed-only ArticleId element is added to the ElocationID element if no other data are present. Retrospectively, DOI data in the ArticleId element were copied to the ElocationID element for citations back to 2008.

      Identifier mapping in Pub Med

    1. * How do I check if a molecule X is a nuclear receptor?

      Do I upload all the data at once or can I do it multiple times?

    2. How do I find a list of drugs that target nuclear receptors?

      Do I have to use dkNEt or can I use other tools?

    3. How do I find the list of nuclear receptor?

      Do I have to be an NIDDK funded researcher to join? Can I be a student?

    4. * So what does nuclear receptor even mean?

      Do I need to submit the dataset itself?

    1. At its core, the implementation of Agile is a very output-driven process; how much can we get out the door each quarter, twice a year, or in a sprint.

      But to judell's point, is this the correct intepretation?

    2. Huge consultancies and one-off consultants have been paid to implement a great manifesto as a repeatable process, not taking the size, stage, growth, culture, and capabilities into consideration.

      Sic semper

    1. FAIR Data 1

      We should be making the principles themselves machine readable.

    2. Best:  Is there a specialized community repository for your type of data?

      What happens if it has to go to two places? Or it should go to two places? We actually have a FAQ on this for the data citation?

    3. FAIR Data 1

      Perhaps just restrict to Findable at this point.

    4. Are your data in a repository?

      Need to rethink this. Should not start this with repositories. But if there isn't a FAIR repository, then what should you do?

    1. Choosing a commons-compliant data repository, V0.2

      Need to insert link to the FAIR Data help page

    2. Does the repository provide a machine-readable landing page?

      Need to link to the white paper from the repositories group

    1. YesNo4Does your code use code from others that is allowed to be redistributed under a permissive license?

      Formatting problem here.

    1. Is there any existing infrastructure organisation that satisfies our principles? ORCID probably comes the closest, which is not a surprise as our conversation and these principles had their genesis in the community concerns and discussions that led to its creation. The ORCID principles represented the first attempt to address the issue of community trust which have developed in our conversations since to include additional issues. Other instructive examples that provide direction include Wikimedia Foundation and CERN.
    2. Even with the best possible governance structures, critical infrastructure can still be co-opted by a subset of stakeholders or simply drift away from the needs of the community. Long term trust requires the community to believe it retains control. Here we can learn from Open Source practices. To ensure that the community can take control if necessary, the infrastructure must be “forkable.” The community could replicate the entire system if the organisation loses the support of stakeholders, despite all established checks and balances. Each crucial part then must be legally and technically capable of replication, including software systems and data.
    3. An organisation that is both well meaning and has the right expertise will still not be trusted if it does not have sustainable resources to execute its mission.
    4. If an infrastructure is successful and becomes critical to the community, we need to ensure it is not co-opted by particular interest groups. Similarly, we need to ensure that any organisation does not confuse serving itself with serving its stakeholders.
    5. Transparent operations – achieving trust in the selection of representatives to governance groups will be best achieved through transparent processes and operations in general (within the constraints of privacy laws).
    6. Stakeholder Governed – a board-governed organisation drawn from the stakeholder community builds more confidence that the organisation will take decisions driven by community consensus and consideration of different interests.
    7. Open source – All software required to run the infrastructure should be available under an open source license. This does not include other software that may be involved with running the organisation. Open data (within constraints of privacy laws) – For an infrastructure to be forked it will be necessary to replicate all relevant data. The CC0 waiver is best practice in making data legally available. Privacy and data protection laws will limit the extent to which this is possible. Available data (within constraints of privacy laws) – It is not enough that the data be made “open” if there is not a practical way to actually obtain it. Underlying data should be made easily available via periodic data dumps. Patent non-assertion – The organisation should commit to a patent non-assertion covenant. The organisation may obtain patents to protect its own operations, but not use them to prevent the community from replicating the infrastructure.

      Would be really nice to have all these principles as individual objects so that we easily cross reference them in the scholarly commons work.

    8. Trust must run strongly across each of the following areas: running the infrastructure (governance), funding it (sustainability), and preserving community ownership of it (insurance).

      Establishing trustworthiness

    9. We believe we risk repeating the mistakes of the past, where a lack of community engagement lead to a lack of community control, and the locking up of community resources.

      Was it really a lack of community engagement or more a limitation of what technologies were available at the time?

    1. Publishers should consider the types of licensing allowed under their data policy. It is recommended that data submitted to repositories with stated licensing policies should have licensing that allows for the free reuse of that data, where this does not violate protection of human subjects or other overriding subject privacy concerns.

      Not something that was mentioned in the JDDCP, but probably should have been.

    2. In addition, the reference should also include “[dataset]” within the reference citation so that it becomes easily recognizablewithin the production process. This additional tag will not be visible within the reference list of the article.

      Articles should be tagged as data set (not visible in reference list)

    3. Data citations are formal ways to ground the research findings in a manuscript, upon their supporting evidence, when that evidence consists of externally archived datasets.

      Nice definition of data citation

  8. Mar 2017
    1. We propose the creation of an international coalition whose mission is to collectively support those core data resources deemed essential to the work of life science researchers, educators, and innovators worldwide. Through this coalition, funders of the life sciences should commit to the long-term shared responsibility to sustain the open access to core data resources because of their value to the global life science community and adhere to the oversight principles outlined above.

      Recommendation for international funding for sustainability of core data resources.

    1. Slides and posters can be shared on the Biocuratio

      Test

    2. 85. Repurpos.us: A fully open and expandable drug repurposing portal

      Uses Wikidata. Website is just a prototype but available.

    3. 43. NaviCom: A web application to create interactive molecular network portraits using multi-level omics data Inna Kuperstein, Maturin Dorel, Eric Viara, Emmanuel Barillot and Andrei Zinovyev