http://www.indepth-network.org/

http://alpha.lshtm.ac.uk/

well said

diversity of needs & goals

important for reuse and reusability, among other things

useful overview

encouraging optimism

this should be "A"

efficiency

They have a website as well: https://www.iddo.org/

incentives

Lots of hits for CDISC at the site of the Search Results Pharmaceuticals and Medical Devices Agency in Japan, e.g. https://www.pmda.go.jp/english/review-services/reviews/advanced-efforts/0007.html

more details via https://www.fda.gov/drugs/developmentapprovalprocess/formssubmissionrequirements/electronicsubmissions/ucm248635.htm

Some reference would have been nice here as well. Website is https://www.cdisc.org/

tools and standards again

Important points

facilitating reuse

seems wrong here

reuse

prestige

yes, the benefits of tools and standards are much more apparent when they go together

A reference would have been nice here. I found http://www.wwarn.org/tools-resources/toolkit/analyse/parasite-clearance-estimator-pce as a starting point.

Where? Not in the WWARN_Papers.ris file.

research affecting policy

incentives

change of course by readjusting goals

Not sure the abbreviations were necessary here, given that they are rarely used in the text, and there is enough space in the table, which might be more easily parsable without them.

Any info on the extent to which these patient populations overlap across those studies? I had the same question for the "135,000 individual patients" mentioned in the abstract, but understood that such detail would not fit into an abstract, so did not comment there.

that's natural for many databases at the beginning of their existence

but not for ever; some temporal component would be valuable here

one of the original goals

incentives

diversity of perspectives again

sad

An actual number may have been more useful here. In other words, did only 1 not say it? Or some only said it indirectly?

well-captured diversity of perspectives

important to get those voices heard here as well

That's a slowed-down version of the speed argument from above.

Now not available any more. Public versioning would have been helpful.

And even those three pages use non-standard terms, which requires more lawyers to assess the compatibility of these terms with those of any other database one might wish to combine with WWARN data.

https://dhsprogram.com/

Kudos for being explicit about this. Visa issues affect research in multiple ways, and in cases like these, the information about even the existence of the problem is largely hidden.

i.e. 22

The thumbnail preview of the table is irritating in that it suggests there are only three content rows in the table, when there are several times as many.

Neither from the WWARN_Papers.ris nor from the rest of the paper, I could infer which these 18 "core" publications were, which would help in understanding the reserch presented here.

further down, the number 78 is given, and it's not entirely clear to me whether the number should be the same in both places.

proprietary_documents_coded.tab lists 69 files

That COREQ file is very useful for human consumption, but it would be useful if it were machine actionable as well, which would allow, for instance, to discover it more easily when searching for studies involving, say, native Thai speakers, or NVivo 11.3.2. Just saying - I understand this is beyond the scope of the current paper, but I'm involved in efforts to make data management plans machine actionable, which means dealing with these same issues.

As an aside, the COREQ file states (at the very bottom):

For reasons of length, the paper reports only the major themes.

I don't know of restrictions in Wellcome Open Research in terms of article length, and in the paper's introduction, the authors had stated

here we focus on findings we believe to be of greatest interest to researchers who share data, or are contemplating doing so.

which seems a more valid reason to leave out some minor themes.

Kudos for listing the identifier. I googled that, which brought me to http://researchsupport.admin.ox.ac.uk/governance/ethics/committees/oxtrec , and under "Approved studies 2016", I found the entry

593-16 Elizabeth Pisani What makes data sharing work? WWARN case study Minimal Risk N/A 16/5/16

which is way more transparent than most ethics statements in published papers.

Also kudos to the Central University Research Ethics Committee (CUREC) for the decision highlighted under the "Approved studies 2016" headline:

It was agreed by CUREC in early 2016 that, in the interest of transparency, OxTREC should make publicly available a list of studies that it has approved. The list below sets out those studies that have been approved by OxTREC since January 2016.

It might well have been better to get each of these documents their own unique identifier rather than bundling them all together under this DOI.

It would be great if software were cited according to the Software Citation Principles: https://doi.org/10.7717/peerj-cs.86 .

Again, the forms are included in Study_protocol.docx , which is probably worth mentioning.

kudos for multilinguality

kudos for citing (rather than just mentioning) the dataset and especially for including the consent forms (they are in Study_protocol.docx)

Is that available somewhere? That curation effort - if shared - could well form the basis of reuse. For an example, see https://github.com/Daniel-Mietchen/ideas/issues/491 .

Somewhere near here, it would be good to mention that the list of historic records included in the analysis is available as proprietary_documents_coded.tab from the data supplement.

https://wellcome.ac.uk/what-we-do/our-work/public-health-research-data-forum

what about the vectors?

and still is, I presume

Since they do have a website, might as well mention it: http://www.wwarn.org/

That's not a strong foundation to rest on - sharing data does not mean that reuse will occur. For some data, no reuse will occur within a given time frame, while for other data, reuse may well occur even when the way it was shared did not make reuse easy.

The point here should rather be that sharing data with reuse in mind (e.g. following the FAIR principles) can facilitate reuse, and such reuse can contribute to "speeding up discoveries". When speed is a concern, the timeliness of sharing should also be considered.

This should be "WWARN".

computational fluid dynamics https://www.wikidata.org/wiki/Q815820

This took about 15 min (leading to HTML for 609 papers).

I used

norma --project zika-20161116 -i fulltext.xml -o scholarly.html --transform nlm2html

This took about 5min (for 666 papers).

Typo

Another example:

getpapers -q zika -o zika-20161116 -x info: Searching using eupmc API warn: We had to retry the last request 2 times. info: Found 683 open access results Retrieving results [==============================] 100% (eta 0.0s) info: Done collecting results info: Saving result metadata info: Full EUPMC result metadata written to eupmc_results.json info: Individual EUPMC result metadata records written info: Extracting fulltext HTML URL list (may not be available for all articles) info: Fulltext HTML URL list written to eupmc_fulltext_html_urls.txt warn: Article with pmcid "PMC4931661" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5038420" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5038412" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4998506" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4800905" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4800906" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4998507" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4773937" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5058489" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4344295" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5018718" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4773938" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5054515" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4928527" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4991975" was not Open Access (therefore no XML) warn: Article with pmcid "PMC3854913" was not Open Access (therefore no XML) warn: Article with pmcid "PMC3019486" was not Open Access (therefore no XML) info: Got XML URLs for 666 out of 683 results info: Downloading fulltext XML files Downloading files [==============================] 100% (666/666) [45.6s elapsed, eta 0.0] info: All downloads succeeded!

When I ran this, I got

-bash: getpapers: command not found

even though I had just installed getpapers successfully as per the getpapers section above.

Re-running

npm install --global getpapers

fixed this.

Should be consistent to norma above.

i.e. something like

export PATH=$PATH:~/contentmine/bin

This should be linked. I found two .zip files: https://github.com/ContentMine/norma/releases/download/v0.2.26/norma-0.1-SNAPSHOT-bin.zip and https://github.com/ContentMine/norma/archive/v0.2.26.zip . Since this is under the norma heading and referred to as binary release, I assume I should go for the former of these two.

link to explanation

again, some link to an explanation would be useful

Consistent spelling makes it easier to find one's way around.

This worked for me, though it required to restart the terminal.

Would be useful to have some description of what Node is and does and what role it plays in getpapers.

Would be useful if this linked to some description of getpapers

The policy does not mention metadata, but it should, and metadata should basically be shared on an ongoing basis rather than just at the end of the project.

Why not require these to go into a repository as above?

Below comes the requirement for the Full Data Package to be deposited in a repository with long-term archiving, so perhaps clarify here that, for some projects, the package has to be additionally maintained locally for at least seven years.

Perhaps worth thinking about scenarios where that repository might disappear before those seven years (or even after) and to put these thoughts into some sort of guideline that could be referenced here.

Why not the final progress report as well?

at the latest

The policy could encourage these components to be identified in a machine-actionable manner, as outlined in http://www.slideshare.net/StephanieSimms/making-dmps-actionable-and-public

and ethical review/ approval

Probably worth to explicitly mention that the plan should be updated as the project moves forward, and be maintained with a complete version history.

Here, the timing should be indicated in some way. For instance, the data sharing plan should be produced "in Month 1" or "by Month 3" of the project at the latest.

Good move.

It's not really analyzable if not shared with the protocols and code that produced it. I see why you'd want to make a distinction to the Full Data Package, so I suggest to use a different qualifier word for the data set.

Entity names (e.g. for species, proteins, drugs) could all be communicated more effectively if they were linked to a controlled vocabulary with persistent identifiers.

The actual core of the project. As is all too common, it is buried here in the supplement, when it should be in the center of attention.

Not a great format for sharing information.

A caption with a bit more detail would be more helpful to the reader to decide whether to download the file.

As mentioned in comments above, I think this article would have benefited from the supporting information being integrated into the main body.

Would have liked to see this discussed a bit.

Some of them can be found in the forums, e.g. at http://www.worldcommunitygrid.org/forums/wcg/listthreads?forum=720 .

One volunteer describes his motivation for contributing in this video: https://www.youtube.com/watch?v=rqEvcFm7pP8

Collaboration. Reminds me of

What if everyone in the world were in your lab – a ‘hive mind’ of sorts, but composed of countless creative intellects rather than mindless worker ants, and one in which resources, reagents and effort could be shared, along with ideas, in a manner not dictated by institutional and geographical constraints?

from https://doi.org/10.1242/dmm.003285

Those machine learning models are not explained in the supplementary files, but some examples of their use in drug discovery are available here in PLOS NTD, e.g. via http://dx.doi.org/10.1371/journal.pntd.0003878 .

Citing these three supplementary files all in a row here does not help the reader in finding what information they are referenced for.

Another argument for data sharing.

This declaration of intent fits well with a similar statement made by numerous funders and publishers in February: http://www.wellcome.ac.uk/About-us/Policy/Spotlight-issues/Data-sharing/Public-health-emergencies/index.htm .

Would be good to see the data management plan for OpenZika.

Why only upon request and not in a more general way?

This has actually started to happen - watch out for "Results" tabs on that page.

I don't think that's the right word here; if the computer is dormant, it consumes less energy, and if it is dormant a lot, it may be available for a longer period of time for its primary purpose, which may not require permanent on-time.

Nice example of reuse.

This table too would have been more useful here in the main text than in the supplement.

Figures could be more reusable if they were shared as SVG rather than in bitmap formats.

My bias: I have been running the OpenZika software on my machine since May.

Here, it would have been nice to have a synthesis of the insights gained from those 18 structures in terms of (accelerating) Zika virus drug discovery.

Again, relegating this to the supplement is not helpful.

Different ways of sharing along the research cycle. We need more of that.

I could not highlight the CrossMark symbol but when I clicked it, I got "Document is current".

These could do with links to a controlled vocabulary with persistent identifiers.

The ancient practice of abbreviating author names could well do with an update.

Mentioning the version (4.0, as per the link) would be useful here.

This is my first attempt at using Hypothes.is for a journal club.

I am reading the article with a focus on aspects of data sharing and scholarly communication around Zika virus.

Is relegating these references into that additional file really useful?

Shouldn't this be "we"?

The article type "From Innovation to Application" is described at http://journals.plos.org/plosntds/s/other-article-types#loc-from-innovation-to-application :

These short articles (1,000 words, 10 references) discuss new technologies, such as drugs, vaccines, and diagnostics, relevant to NTDs. Authors are asked to take an objective and critical view, and they should include a box that lists up to 3 advantages and 3 disadvantages of the new technology. We will ask for a second box or table depending on what kind of tool is described (for example, if the tool is a new diagnostic tool, we will ask for a table that gives the sensitivity and specificity of the new tool compared with the existing gold standard). Authors with competing interests related to the technology (e.g., financial ties) will not be allowed to write for this section. We encourage all authors to include a display item (a figure, photo, or illustration).

This number 4 seems to appear out of nowhere. Either drop it or make it more obvious what its role is supposed to be. If properly engineered, persistent identifiers for these pages could be a lightweight tool to introduce the concept of open PIDs, as per https://hypothes.is/a/1Ta8dmkGEeaVvnsT43LJqA .

Somewhere on the page, there should be a license statement for it.

Linking and attribution is good, but the license should be mentioned as well.

sentence incomplete: add "it.".

It's good to have so many comments (and please keep them coming), but they are not necessariy efficient to handle that way.

Many comments address multiple passages or elements of the draft, but where a mapping between comments and text passages is possible, I propose that we use annotations like https://hyp.is/AVQW11OTH9ZO4OKSlvBo/wiki.surfnet.nl/display/OSCFA/Amsterdam+Call+for+Action+on+Open+Science to do that mapping.

As per https://via.hypothes.is/https://wiki.surfnet.nl/display/OSCFA/Amsterdam+Call+for+Action+on+Open+Science?focusedCommentId=54701361#comment-54701361 , add the idea of improving the things that are listed here.

It's a pity that users from outside the SURF institutional network are forced to be anonymous here.

If TDM is limited to non-commercial and/or academic use, then addressing societal challenges basically excludes contributions from outside the non-commercial and/ or academic realm, i.e. from large parts of society.

Delete "preferably". Limiting the scope of text mining to exclude societal and commercial purposes limits the usefulness to enterprises (especially SMEs that cannot mine on their own) as well as to society. These limitations have ramifications in terms of limiting the research questions that researchers can and will pursue.

This statement is more generally applicable than just to TDM. Besides, "Encourage" is too weak a word here, and from a societal perspective, it would be far better if researchers were to retain their copyright (where it applies), but make their copyrightable works available under open licenses that allow publishers to publish the works, and others to use and reuse it.

Delete, as per the comment above on the same word.

Not sure what you mean here - this tweet of yours is anchored to my preceding one (i.e. https://twitter.com/EvoMRI/status/657026077664137218 ).

Very original, inspiring title