Showing posts with label bibliometrics. Show all posts
Showing posts with label bibliometrics. Show all posts

Thursday, July 20, 2017

articles on Open access in Physics Today May 2017. Quantity of all scientific articles = 3 millions articles/year (2020)


The state of open access by Charles Day 

Physics Today 70, 5, 8 (2017); doi: http://dx.doi.org/10.1063/PT.3.3535
On page 24 (see below) you’ll find David Kramer’s in-depth report on the current state of open-access publishing. Open access and its place in the landscape of academic journals have changed since November 2012, when Physics Today last covered the topic. Besides authors, publishers, and policy makers, other actors are now on the open-access stage, among them charitable foundations, scholarly collaboration networks, and, yes, pirates who post unauthorized copies of papers on Russian servers.
My attitude toward open access is conflicted. On the one hand, I agree that the fruits of publicly funded research should be freely available, especially to scientists in poor countries and to scientists employed by companies and colleges that can’t afford journal subscriptions. On the other hand, I’m well aware that Physics Today is funded in part by the profits that AIP’s publishing subsidiary makes from selling subscriptions to its 19 journals. If Physics Today had to rely solely on advertising and subscription revenue, it would have to shrink and change format.
Regardless of where you, I, or anyone else stands on open access, there are forces in play that are hard for publishers to resist. One of those forces arises from the nature of the principal end product of scholarly research, a paper that’s usually in the form of a PDF. The P in PDF stands for portable, which is what PDFs all too easily are. For Physics Today’s August 2009 issue, I wrote a feature article about iron-based superconductors, which had been discovered just two years earlier. Google Scholar lists 16 unauthorized PDFs of the article, 13 of which are on Chinese websites. (I couldn’t find the article on Sci-Hub, the pirate website founded by a Kazakhstani grad student.)
Portability isn’t the only disrupting force at play. University library budgets have not kept up with inflation or with the growth in the number of the world’s scientists and their output. The cash crunch is forcing librarians to scrutinize journals based on price and usage. Subscriptions to those that don’t meet increasingly stringent criteria are not renewed.
Despite those trends, some aspects of scholarly publishing remain the same. It’s just as hard now as it was in the 19th century to conceive of an experiment or theory that is both original and significant enough to be worth publishing in a scientific journal. Reviewing your peers’ papers before publication continues to be an unpaid yet valuable duty. And a paper’s final version of record still needs to be archived, online if not in bound volumes on library shelves.
When I ask physicists and other scientists how they choose where to publish their work, I tend to get the same answers. Scientists want their papers to be read, so they publish in journals that their peers read. A physicist told me once that he regretted publishing in the prestigious Proceedings of the Royal Society because his fellow fluid dynamicists didn’t read that journal. Physics of Fluids, he mused, would have been a better choice.
Some physicists tell me that if they have a hot result, they’ll go for a journal with a high impact factor, such as Physical Review Letters, Nature, or Science. But in the digital age, as George Lozano, Vincent Larivière, and Yves Gingras discovered in an extensive bibliometric study, the correlation between a journal’s impact factor and a paper’s citations is weakening.1
One of the findings in David’s report in this issue is that open-access papers in the physical sciences currently make up just 10–12% of the total. That modest proportion likely reflects the continuing appeal and reputation of traditional journals. But as any marketing guru will tell you, appeal and reputation are intangible components of a brand. The contest for the best papers in physics will likely be won by the publishers who nurture those intangibles, regardless of access model.

REFERENCES

1. G. A. Lozano, V. Larivière, Y. Gingras, J. Am. Soc. Inf. Sci. Tec. 63, 2140 (2012). https://doi.org/10.1002/asi.22731

Steady, strong growth is expected for open-access journals

Publishing models continue evolving to accommodate government mandates. Meanwhile, publishers look to cope with article-sharing sites that affect their business.
David Kramer
Physics Today 70, 5, 24 (2017); doi: http://dx.doi.org/10.1063/PT.3.3550


In the more than 15 years since the advent of open-access (OA) journals, scientific publishers who once viewed them as an existential threat are now operating their own. But despite double-digit growth in OA, scientific societies and commercial publishers alike agree that the vast bulk of their publications will remain wedded to the traditional subscription model for the foreseeable future.
“Open access is much less of a contentious issue now,” says H. Frederick Dylla, retired executive director of the American Institute of Physics, which publishes Physics Today. “It’s happening. It’s a business model.” Of more concern to publishers today is the illicit posting of papers on article-sharing services. By some estimates, such as a 2014 report prepared for the European Commission, more than half of the scientific literature from 2007 to 2012 was accessible for free online. But it’s unclear how much of that content consists of papers that infringe on publishers’ copyrights because they are freely accessible despite licenses that are supposed to keep them behind paywalls.

Academic libraries face rising subscription costs for an ever-growing number of journals. Some libraries also underwrite researchers’ costs for publishing in open-access journals.

Broadly speaking, scientific publishing follows two models. Traditionally, most journals obtain their revenues from institutional subscribers, mainly universities. Outside those licenses, the journal content is located behind an online paywall. So-called gold OA journals provide their entire content for free online immediately upon publication. Their revenues are provided from fees, known as article processing charges, paid by the article authors or their institutional funders.
A second category, known as green OA, consists of nongold OA articles that are freely available in one of the following forms: An article may be made available prior to publication as a preprint. A manuscript version may be provided by the publisher so authors can post it to their websites and institutional archives at the time it is accepted for publication. Or it can be released in its final published form, known as the version of record, after a specified period, most often one year after publication (this is sometimes referred to as delayed gold OA). Most scientific papers today are or will become available in some fashion as green OA.
The extent of fully OA publishing, like that of journal publishing overall, is hard to measure. About 800 of the 11 000 or so journals included in Journal Citation Reports, the Clarivate Analytics (formerly Thomson Reuters) service that calculates the widely used journal impact factors, are gold OA. Of the 21 500 journals tracked by Scopus, an abstract and citation database, around 3500 are gold OA titles. But less exclusive indexes, such as the Directory of Open Access Journals, count more than 9300 journals published in 129 countries. Estimates of the total scientific journal population—subscription and OA—range from a low of 33 000 to a high of 60 000, depending in part on where the line is drawn between scholarly and trade journals.
The International Association of Scientific, Technical, and Medical Publishers, whose 120 members publish two-thirds of all STM journal articles, estimated annual revenues for English-language STM journal publishing at $10 billion in 2015, up from $8 billion in 2009. Delta Think, a scholarly publishing consulting firm, valued the fully OA journal market last year at $374 million, and for 2017 it forecasts growth of 12%, roughly twice the rate of growth in the overall journal market. “Going forward, we think that the open-access market will continue to grow at about 10% to 15% through 2020,” says Delta Think’s Dan Pollock.

MANDATES AND ARCHIVES

The growth of OA is largely driven by dozens of governments around the globe that have mandated free access to the results of publicly funded research. In most cases, including in the US, those mandates require grantees to make their papers free after a one-year embargo. The same applies in the UK, where the government also sets aside funding to pay for gold OA. The European Union requires grantees of its €80 billion Horizon 2020 program to provide free access within six months of publication (see Physics Today, March 2014, page 26).
In the US, the major federal research-funding agencies have chosen several public repositories for their sponsored research. The largest, PubMed Central (PMC), has been operated by the National Institutes of Health since 2000. In addition to NIH-funded research, PMC has been designated by NASA, NIST, the Environmental Protection Agency, the Department of Homeland Security, and other, smaller funding agencies to house their research results.
The Department of Energy, NSF, US Geological Survey, Department of Defense, Smithsonian Institution, and Department of Agriculture have chosen to link their individual repositories to the Clearinghouse for the Open Research of the United States (CHORUS) database, established by a consortium of journal publishers. As of 30 March 2017, the CHORUS repository held 327 000 articles, of which 74 000, just under 25%, were post-embargo and freely accessible.
Unlike PMC, where articles are deposited in their entirety, CHORUS directs users to the participating publishers’ websites. The distinction is important for publishers, who want to attract traffic.
In response to public mandates, the majority of subscription journals now offer the option for authors to pay an article processing charge to make their articles immediately OA. That so-called hybrid model currently accounts for about 4% of published papers (see the figure on page 26). But at some future theoretical tipping point, says Ken Heideman, publications director at the American Meteorological Society (AMS), the amount of free content could outweigh the subscription-only articles and force publishers to lower their subscription rates. “If you think of the whole of your content as a piece of cheese, pretty soon the hole gets bigger and it’s Swiss cheese,” he says.


Numbers of scientific articles published in fully open-access (gold) journals 
and of fully open-access articles in subscription journals (hybrid) 
are increasing at a faster rate than are numbers of articles in subscription-only journals. 
Nearly all articles ultimately become freely available 
in some form (green open access), 
often after an embargo period. (Data provided by Elsevier.)

Some nonprofit research funders, notably the Bill & Melinda Gates Foundation and the Max Planck Society, now require gold OA publication of their sponsored research. Some organizations also may permit publication in hybrid journals.

Some nonprofit research funders, notably the Bill & Melinda Gates Foundation and the Max Planck Society, now require gold OA publication of their sponsored research. Some organizations also may permit publication in hybrid journals.

THE ECONOMICS

It’s clear that the subscription model remains more lucrative. Journal publishers receive, on average, about $5000 per article from subscriptions, according to industry consultant Joseph Esposito in the Scholarly Kitchen blog in December 2016. But article processing charges for OA journals generally are only $1000–$1500 per article.
While they contain as much as 18% of all journal content, gold OA journals and gold articles in hybrids produce just 3–6% of all publishing revenues. A smaller proportion of articles in the physical sciences, some 10–12%, are published in OA journals, Pollock says. The disparities between content and revenue probably reflect the fact that OA is still a relatively young market, with publishers discounting article processing charges, he says.
Two of the 11 AMS journals, including the flagship Bulletin of the American Meteorological Society, are gold OA. Heideman says physical sciences have been “dragged along” to OA by the biomedical community. “We certainly agree that open access is a good thing within the limits of our business model. But it isn’t one size fits all. We’ll continue to do it incrementally.”
AMS decided a year ago to make all content of its nine subscription journals freely available after a one-year embargo, regardless of funding source. It was felt to be unfair to authors not subject to mandates to have their work remain stuck behind a paywall.
But Heideman regards the finite embargo period as an experiment, and its financial impact on AMS is uncertain. “We’re banking on the fact that libraries are still going to see the value in subscribing to our content rather than waiting for a full year to get it free. We feel confident, but there are no guarantees,” he says. “So far we haven’t seen anything that would alarm.”
With more than 200 gold OA journal titles, Elsevier is second to Springer Nature in the number of fully OA journals published. All but 200 of Elsevier’s 2300 subscription journals are hybrid, and roughly 20 000 of the 420 000 articles published in Elsevier journals last year were gold OA. Elsevier policy and communications director Gemma Hersh sees gold OA continuing to grow alongside subscription. In addition, she says, “we’re doing a lot of work with institutions in the US and globally to make green open access more effective and workable.”
Nature Research, a component of Springer Nature and the parent company of Nature and its related journals, declined an interview request. However, a spokesperson said in a statement that the company offers more than 70 journals with OA options, from the multidisciplinary Nature Communications to highly specialized titles such as the 25 Nature partner journals, which are published in association with academic institutions, philanthropies, and membership organizations.
Nature Research believes the subscription model is the best way to provide sustainable and widespread access to journals with low article-acceptance rates, the spokesperson said.
OA is a particular challenge for highly selective journals such as Science and Nature, which publish fewer than 10% of submissions and thus have a considerably higher cost per article published. Jeremy Berg, editor-in-chief of Science, says, “A substantial part of your costs relates to processing, peer reviewing, and so on, for papers you end up not accepting.” A 2013 report in Nature put that magazine’s per-article cost at $30 000 to $40 000. For both flagship publications, advertising and income from other journals offset those high costs. Berg says there have been discussions about adopting hybrid models for Science and the four other Science-branded journals (a fifth, Science Advances, is fully OA).
PLOS, founded by former NIH director Harold Varmus and other prominent scientists in 2001 as one of the original all-OA publishers, in 2007 created PLOS One, a multidisciplinary online platform. As of 30 March, PLOS One had published nearly 18 000 physics articles. Its “megajournal” model differs from nearly every other journal in that research need not be novel, although it still must be sound and is peer reviewed.
After peaking at 31 500 in 2013, annual submissions to PLOS One fell to 22 000 last year. The decline came as other publishers started up copycats such as Nature Research’s Scientific Reports. Some observers, including Phil Davis, a publishing consultant, have questioned PLOS’s continued viability should PLOS One continue to shrink. And David Knutson, PLOS communications manager, acknowledges that PLOS One accounts for the “lion’s share” of parent company revenues, which help to offset costs of PLOS’s four biomedical journals. But Knutson says that the company remains in strong financial shape and that PLOS One today is “at the point where it’s healthy and sustainable.” PLOS’s reported net assets were steady at $30 million from 2014 to 2015.
PLOS considers itself an advocacy organization, and Knutson notes that former CEO Peter Jerram once asserted that should it be put out of business by other OA publishers, it will have accomplished its mission.
Davis is concerned that the Trump administration’s proposed cuts to research could cause a falloff in demand for OA publishing, since authors will have less funding to pay article processing charges. Some university libraries offer support for researchers to pay for publication, even as they claim to have insufficient funds to afford subscriptions to thousands of journals. “Should they be spending $3000 on buying access to a really excellent collection of journals or pay for one paper to be published?” Davis asks.

PHYSICISTS’ VIEWS

Physics-related papers have routinely been shared on the arXiv website since the 1990s. Those preprints typically are posted prior to the peer-review and editing processes that are performed by publishers. University of Maryland physicist Daniel Lathrop says posting to arXiv “satisfies our intent to have open access,” and he notes that the preprint includes both figures and the basic conclusions. “It’s not clear to me why you need open access in the refereed journal as long as it’s the common practice” to post on arXiv, he says.
Still, Lathrop acknowledges that some fellow authors, particularly younger ones, feel strongly about OA, and their views will be considered in deciding where to submit a paper. But a more important consideration, particularly for young researchers, is the reputation and impact factor of the journal.
David Helfand, a Columbia University astrophysicist, sees OA as largely irrelevant to all but “the few people who are ideologically committed to it, who believe it’s just right,” and to those whose sponsors require publishing in OA journals. Helfand, a past president of the American Astronomical Society, says free public access to AAS’s journal content is available through US public libraries. “The number of times this has been used in the past few years can probably be counted on your fingers,” he says.
In AAS’s publishing model, two-thirds of revenues are from article processing charges, with the remainder derived from subscriptions. Should funding for US science drop, Helfand worries that astronomers may submit their work to Monthly Notices of the Royal Astronomical Society, which has no author charges but costs institutions more than $14 000 a year.
“I don’t think if AAS went gold it would change very much, because 98% of the papers are publicly available the day they are accepted, or several weeks before that” in arXiv, he says. A larger problem for public access, he thinks, is scientists’ failure to write in “actual understandable English.”
Helfand’s and Lathrop’s views are supported by author surveys. In a 2015 Nature Publishing survey of its authors, 18 000 respondents ranked an OA option 14th on a list of 17 factors driving the choice of where they submit articles.
Paul Hardaker, chief executive of the UK’s Institute of Physics, which publishes more than six dozen journals, says its 2015 author survey also placed OA well down the list of considerations. “There is quite clearly a small community of strong advocates for open access, but it’s not reflected in the response we’ve had from the broader community.”
However, some view OA as an imperative. Daniel Kammen, a physicist at the University of California, Berkeley, is editor-in-chief of the decade-old OA journal Environmental Research Letters. Kammen says it is “absolutely the case” that all academic research should be open access, whether its funding comes from public or private sources. “The primary mission of a researcher is to be in some sense H. L. Mencken’s public intellectual,” he says, which requires that both the paper and the underlying data be openly accessible. OA, he says, needs to rapidly get research results out “in a world where research is competing with tweets and Instagram and all these rapid things.”

A CITATION ADVANTAGE?

A long-standing debate has surrounded whether research will be cited more frequently in other scientific articles if it is openly available. Several studies have identified a citation advantage for such research articles. The OA advocacy organization Scholarly Publishing and Academic Resources Coalition (SPARC) maintains a scorecard of 70 citation studies, 46 of which find an advantage for OA articles. Seventeen others find no advantage, and 7 are inconclusive.
One of the more recent reviews, released in August 2016 by Science-Metrix and 1science, finds a 50% citation advantage for OA articles compared with subscription ones that aren’t subsequently made open through green OA options. But a September 2016 report by Hersh and coauthor Andrew Plume claims that and other studies’ methodologies are flawed, principally because of selection bias caused by a lack of randomization and control. Authors could be choosing OA journals for their most important research, for example, or researchers from elite institutions may be authoring a disproportionate share of OA articles.
By some accounts, a 2011 review by Davis is the sole randomized and controlled study to date. He concludes that while OA articles received significantly more downloads and reached a broader audience in the first year, they were cited no more frequently, nor any earlier, than subscription-access articles over the three-year study period.

BEYOND OPEN ACCESS

Publishers are trying to accommodate demand for OA while maintaining the subscription model. Last October, Springer Nature launched a content-sharing initiative to encourage “reasonable” free sharing with nonsubscribers by authors of articles in the publisher’s 2300 journals, including Nature titles. Immediately upon publication, authors are provided shareable links to their papers, which can be viewed but not downloaded. The links can be posted anywhere, including the author’s website, article-sharing sites known as scholarly collaboration networks (SCNs), and social media. Notably, an earlier year-long pilot version of the shared links program involving 50 journals resulted in no loss of institutional sales for the subscription-based journals.
Dylla sees figuring out how to deal with the SCNs as the new challenge for publishers. SCNs help scientists collaborate at all stages of their research and raise the visibility of their results, says Hersh of Elsevier, which owns Mendeley, the third largest SCN. Smaller SCNs have been around for decades. But the two largest—Berlin-based ResearchGate claims 10 million members and San Francisco-based Academia.edu boasts 50 million academic users—were founded in 2008 and are funded by venture capital.
Many articles shared on SCNs have been posted contrary to licensing agreements, intentionally or not. “They have a mixture of proper and improper content,” says Dylla. Publishers seem to have reached a consensus to allow articles to be shared privately among collaborators, he says, in the same way that authors would mail reprints of articles to colleagues in the pre-electronic era. But there is a limit to how broadly a paper can be shared, and the particular version that can be shared, without jeopardizing the publishers’ ability to solicit, review, produce, and archive the content, he notes.
The International Association of STM Publishers has developed voluntary principles for article sharing and operates a website, How Can I Share It, to inform researchers about which versions of articles they can properly share. “The aim is not in any way to shut down collaborations but to make sure the ecosystem works effectively,” says Hersh.
To counter unauthorized content sharing, Dylla says publishers should strive to make content accessible with one-click convenience, akin to accessing movies on Netflix. “If you’ve got a single password, it doesn’t matter if you’re on a phone, iPad, or desktop, you can get to it and it comes right back to where you left off,” he says. “Try that with journals.” The music industry too, he adds, managed to avoid extinction from rampant piracy by working with Pandora, YouTube, and other providers to share revenues.
 

Ref.

© 2017 American Institute of Physics.

Tuesday, May 23, 2017

comparison figshare versus zenodo






Zenodo

see my posts (tag zenodo)

HTML of figshare

9 fields (input)


HTML


Three levels of services

  1. general features for FREE accounts
  2. services for publishers
    1. figshare Viewer
    2. visualize any format of supplemental and digital files within your articles
  3. services for institutions
    1. Curation workflows
    2. manage the curation of files to be made public, control quotas and administer rights
https://figshare.com/features

 additional custom METADATA

Public files hosted on figshare are issued with Digital Object Identifiers (DOIs) via DataCite through the California Digital Library. In order to meet with DataCite metadata requirements, figshare requires users to add the following information before making files public and citable: Title, author list (ordered), categories (set ontology), tags (free text) and a description with as much context as needed to interpret the files. Users can also add links to external sources.

Institutional clients can define additional custom metadata when implementing figshare.
https://support.figshare.com/support/solutions/articles/6000079087-metadata-and-dois

Profile: All about your profile page

https://support.figshare.com/support/solutions/articles/6000088096-profile-all-about-your-profile-page

Example of a publisher 

https://plos.figshare.com/

Other programmatic tools (in GitHub)

https://github.com/search?utf8=%E2%9C%93&q=figshare


comparison of 2 open archives: figshare zenodo


Zenodo

see my posts (tag zenodo)

HTML of figshare

9 fields (input)


HTML


Three levels of services

  1. general features for FREE accounts
  2. services for publishers
    1. figshare Viewer
    2. visualize any format of supplemental and digital files within your articles
  3. services for institutions
    1. Curation workflows
    2. manage the curation of files to be made public, control quotas and administer rights
https://figshare.com/features

Additional custom METADATA

Public files hosted on figshare are issued with Digital Object Identifiers (DOIs) via DataCite through the California Digital Library. In order to meet with DataCite metadata requirements, figshare requires users to add the following information before making files public and citable: Title, author list (ordered), categories (set ontology), tags (free text) and a description with as much context as needed to interpret the files. Users can also add links to external sources.

Institutional clients can define additional custom metadata when implementing figshare.
https://support.figshare.com/support/solutions/articles/6000079087-metadata-and-dois

Profile: All about your profile page

https://support.figshare.com/support/solutions/articles/6000088096-profile-all-about-your-profile-page

Example of a publisher 

https://plos.figshare.com/

Other programmatic tools (in GitHub)

https://github.com/search?utf8=%E2%9C%93&q=figshare

Tuesday, March 14, 2017

Altmetrics and free tools

If you click , you will get details:




In scholarly and scientific publishing, altmetrics are non-traditional metrics proposed as an alternative to more traditional citation impact metrics, such as impact factor and h-index.
https://en.wikipedia.org/wiki/Altmetrics

free tools

https://www.altmetric.com/products/free-tools/

Altmetric Bookmarklet

The Altmetric bookmarklet enables you to instantly see Altmetric data for any published research output with a DOI.

It’s quick, free and easy to install in just 3 simple steps.



The Bookmarklet only works on PubMed, arXiv or pages containing a DOI
It only supports publishers who embed Google Scholar friendly citation metadata on their pages by default, though we’re adding support for others. You can hurry along support for a particular journal by asking @altmetric for it on Twitter

Institutional Repository badges

We offer free embeddable badges for repositories within academic institutions. They can be installed with just a few lines of code, and you can choose the style of badge you’d like to display. Users will be able to click on the badge to view the full details page for each research output.

examples:
-> HAL
-> Zenodo

Explorer for Academic Librarians

We offer free individual access to the Altmetric Explorer for Publishers for academic librarians based within universities. This version of the Explorer can be used to browse and filter all of the research outputs in the Altmetric database, but does not include any institutional views, functionality or reporting. Please email us to request an account.
https://www.altmetric.com/products/explorer-for-publishers/

Real-time updates

Our attention data is collated and updated in real time – meaning you start to get feedback on your publications almost as soon as they’re made available online.

Email alerts

Set up daily, weekly or monthly email alerts to receive regular updates on the attention surrounding content you care about, delivered straight to your inbox.

Powerful search & filtering

Browse all articles in the database, or filter by specific journals, publishers, or time last mentioned. Enter unique identifiers (including DOIs, ISBNs, PubMed IDs, arXiv IDs and Handles) to track specific items. Alternatively, search for individual outputs using keywords.

Export data

All of the data in the Explorer can be exported via Excel or an API to be used in other internal reporting or dashboards.

Badges for Individual Researchers

Individual researchers can embed our badges for free too! It’s a great way to add context to your personal website or online CV, and can help demonstrate the reach of your work to visitors.

Once embedded you can click on the badge to view the full details page for each research output.
https://www.altmetric.com/about-our-data/altmetric-details-page/

Showcase the influence of your work
https://www.altmetric.com/products/free-tools/free-badges-for-researchers/

Step 1

Choose the badge style you want to display, and then grab the embed code from our site and add it to the html of your page.
http://api.altmetric.com/embeds.html

https://www.altmetric.com/products/altmetric-badges/

Step 2

Let us know you’ve done it (mailto support@altmetric.com)! This way we can unlock the details pages to make sure everyone can see all of the original mentions of your work (otherwise they’ll just see the first 4 most recent ones from each source).

Identify the most effective channels:
https://www.altmetric.com/audience/researchers/

API for research

http://api.altmetric.com/

We’re happy to provide free access to the Altmetric API for academic research purposes. Please see the API page for information about the different levels of API access we offer.

If you’d like to request a key or have any questions about how the API works and the data you’re gathering, please email us.

t's free to use this API to fetch basic alt-metrics information about articles & datasets and to use that information in your own apps and mashups - just give altmetric.com attribution somewhere.

However, if you'd like to download the data in bulk, perform more complex queries, remove the rate limits and see more detailed data about articles then you'll need a commercial license (if you'd like to let us know about your use case you can reach us at info@altmetric.com).

If you'd like to use the data in an academic research project then let us know and we can grant you a free license for non-commercial use.

Want to see some examples of what's possible? Check out our API gallery.
https://www.altmetric.com/products/altmetric-api/

Sources

https://help.altmetric.com/support/solutions/articles/6000060968-what-data-sources-does-altmetric-track-

The table below describes the process for collecting data, update frequency and any additional details across all of our sources.

Source nameCollection methodUpdate frequencyNotes
Twitter                                           Third party data provider APIReal-time feedDemographics, support for retweets, with monitoring of suspicious activity.
FacebookFacebook APIDailyPublic Facebook Pages and posts only, with prioritised popular Pages.
Policy documentsPDFs collected and scanned from policy sources and repositoriesDailyScanning and text-mining policy document PDFs for references, which are looked up in CrossRef/PubMed and resolved to DOIs.
NewsRSS feeds and APIReal-time feedManually curated news sources, with data provided via a third-party provider and RSS feeds direct.
BlogsRSS feedsDailyManually curated list, harvesting links to scholarly content.
MendeleyMendeley APIDailyReader counts is number of readers with the output in their Library. Not included in score.
ScopusScopus APIReal-time feedCitation counts from peer-reviewed literature. Not included in score.
Post-publication peer reviewsPubPeer and Publons APIsDailyPeer review comments collected from item records and associated by unique identifier.
RedditReddit APIDailyIncludes all sub-reddits. Original posts only, no comments. 
WikipediaWikipedia APIReal-time feedMentions of scholarly outputs collected from References section. English Wikipedia only.
Q&A (Stack Overflow)Stack Overflow APIDailyScan for links to scholarly outputs.
F1000 ReviewsF1000 APIDailyScan for links to scholarly outputs.
Google+Google+ APIDailyPublic posts only.
YouTubeYouTube APIDailyScan for links to scholarly outputs in video comments.
 Open Syllabus Static Import from Open SyllabusQuarterly Link syllabi's contents to HLOM IDs. 

altmetrics blog

Horizon 2020 -the Work Programme 2017



Horizon 2020 is an €80 billion fund for research from the European Commission.

http://ec.europa.eu/research/horizon2020/pdf/press/fact_sheet_on_horizon2020_budget.pdf

A recent statement from Carlos Moedas, European Commissioner for Research, Science and Innovation told us that “as of the Work Programme 2017, the current Open Research Data Pilot will be extended to cover all thematic areas of Horizon 2020, making open research data the default setting. This move will boost competitiveness by accelerating innovation and collaboration, improving transparency, and avoiding duplication of efforts.”

This means that as of January 1st 2017, all funded proposals will need to make all of the data and digital research outputs they generate openly available.


---
Ref.
https://figshare.com/blog/The_European_Commission_Mandates_Open_Data_From_January_1st_2017/234

Thursday, March 9, 2017

Mendeley Elsevier 2.x , publication and data (DOI per dataset)

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

see an open alternative: zotero
(see my posts with the tag "zotero").

https://en.wikipedia.org/wiki/Mendeley
Mendeley was purchased by the Elsevier publishing company in 2013. The sale led to debate on scientific networks and in the media interested in Open Access, and upset members of the scientific community who felt that the program's acquisition by publishing giant Elsevier, known for implementing restrictive publishing practices, the high prices of their journals, and publicly supporting the SOPA bill, was antithetical to the open sharing model of Mendeley. David Dobbs, in The New Yorker, suggested Elsevier's reasons for buying Mendeley could have been to acquire its user data and/or to "destroy or coopt an open-science icon that threatens its business model."

Web library

connect to https://www.mendeley.com
 and https://www.mendeley.com/library/

2 GB Personal Space
100 MB Shared Space


links with bibliometrics tools of Elsevier



data mendeley

Make your research data citable
DOIs and versioning following Force11 guidelines
Your published research data will include a Force11 compliant citation so that other researchers can effortlessly cite your research. We will also provide a unique DOI for each version of your dataset, so that your dataset's citation will always be valid.

Mendeley Data assigns a provisional DOI to draft datasets. The issuing of a permanent DOI for Mendeley Data submitted datasets is carried out by the British Library via DataCite. It is used to make a document/reference uniquely identifiable from any other document/reference when your article is published and made available electronically. The DOI for a document remains fixed over the lifetime of the document.

https://data.mendeley.com/

with many choices of licenses.

mendeley extension

chrome firefox safari IE

chrome

https://chrome.google.com/webstore/detail/mendeley-importer/dagcmkpagjlhakfdhnbomgmjdpkdklff?hl=en
Save references to Mendeley from Chrome easily! Mendeley is a free, easy-to-use tool to help you collect, organise, cite and share…
Save references to Mendeley from Chrome easily!

Mendeley is a free, easy-to-use tool to help you collect, organise, cite and share your research sources.

With the Mendeley Web Importer extension, you are able to easily save references and PDF files into your personal library with a single click. You’ll need to have a Mendeley account already set up in order to use the Mendeley Web Importer. Creating a Mendeley account takes just a couple of minutes.

To use the new Mendeley Web Importer for Chrome, you just need to be viewing an article or a list of references in the browser. This can mean that you’re looking at an actual PDF file, an article entry in an online catalog, or even a list of search results. The Mendeley Web Importer extension will scan the page for metadata, and provide you with a list of the results it finds.

Click on the red Mendeley button next to the address bar in Chrome to import the content you are currently viewing. Depending on the number of results the Importer finds, you’ll be provided with a list of different items, or specific details of a single item. You can then review the details, and even make manual corrections within the Importer itself, before choosing to add the references to your personal Mendeley library.

Version: 2.0.0
Updated: March 2, 2017

Desktop Application 

Use the Desktop Application to save your documents offline and cite your references in Microsoft Word or LibreOffice
https://www.mendeley.com/download-mendeley-desktop/

version 1.17
download Mac OSX.dmg = 92Mo  ->300Mo

Support

What is the mapping between .bib files and Mendeley?

Wednesday, March 8, 2017

Comparing Repository Types. The dark side of open access in Google and Google Scholar.


An article

Title

Comparing Repository Types: Challenges and Barriers for Subject-Based Repositories, Research Repositories, National Repository Systems and Institutional Repositories in Serving Scholarly Communication

Year

2010

Authors

Laurent Romary INRIA and Humboldt Universität zu Berlin, Germany
Chris Armbruster Max Planck Society, Germany

Abstract

After two decades of repository development, some conclusions may be drawn as to which type of repository and what kind of service best supports digital scholarly communication. In this regard, four types of publication repository may be distinguished, namely the subject-based repository, research repository, national repository system, and institutional repository. Two important shifts in the role of repositories may be noted and in regard to content, a well-defined and high quality corpus is essential. This implies that repository services are likely to be most successful when constructed with the user and reader in mind. With regard to service, high value to specific scholarly communities is essential. This implies that repositories are likely to be most useful to scholars when they offer dedicated services supporting the production of new knowledge. Along these lines, challenges and barriers to repository development may be identified in three key dimensions, i.e., identification and deposit of content, access and use of services, and preservation of content and sustainability of service. An indicative comparison of challenges and barriers in some major world regions is offered.

http://www.igi-global.com/gateway/article/48203
http://dl.acm.org/citation.cfm?id=2436650
ACM association Computer Machinery
The ACM Digital Library is a research, discovery and networking platform containing:

  • The Full-Text Collection of all ACM publications, including journals, conference proceedings, technical magazines, newsletters and books.
  • A collection of curated and hosted full-text publications from select publishers.
  • The ACM Guide to Computing Literature, a comprehensive bibliographic database focused exclusively on the field of computing.
  • A richly interlinked set of connections among authors, works, institutions, and specialized communities.

http://dl.acm.org/

Cited by

Kristin R. Eschenfelder , Kalpana Shankar , Rachel Williams , Allison Lanham , Dorothea Salo , Mei Zhang,
What are we talking about when we talk about sustainability of digital archives, repositories and libraries?
Proceedings of the 79th ASIS&T Annual Meeting: Creating Knowledge, Enhancing Lives through Information & Technology, p.1-6, October 14-18, 2016, Copenhagen, Denmark
http://dl.acm.org/citation.cfm?id=3017595&CFID=736601247&CFTOKEN=53449726

Enrique Orduña-Malea , Emilio Delgado López-Cózar,
The dark side of open access in Google and Google Scholar: the case of Latin-American repositories, 
Scientometrics, v.102 n.1, p.829-846, January 2015
http://dl.acm.org/citation.cfm?id=2716369&CFID=736601247&CFTOKEN=53449726

Abstract

Since repositories are a key tool in making scholarly knowledge open access (OA), determining their web presence and visibility on the Web (both are proxies of web impact) is essential, particularly in Google (search engine par excellence) and Google Scholar (a tool increasingly used by researchers to search for academic information). The few studies conducted so far have been limited to very specific geographic areas (USA), which makes it necessary to find out what is happening in other regions that are not part of mainstream academia, and where repositories play a decisive role in the visibility of scholarly production. The main objective of this study is to ascertain the web presence and visibility of Latin American repositories in Google and Google Scholar through the application of page count and web mention indicators respectively. For a sample of 137 repositories, the results indicate that the indexing ratio is low in Google, and virtually nonexistent in Google Scholar; they also indicate a complete lack of correspondence between the repository records and the data produced by these two search tools. These results are mainly attributable to limitations arising from the use of description schemas that are incompatible with Google Scholar (repository design) and the reliability of web mention indicators (search engines). We conclude that neither Google nor Google Scholar accurately represent the actual size of OA content published by Latin American repositories; this may indicate a non-indexed, hidden side to OA, which could be limiting the dissemination and consumption of OA scholarly literature.

References

1
Albanese, A. R. 2009. Institutional Repositories: Thinking Beyond the Box. Library Journal. Retrieved from http://www.libraryjournal.com/
 
2
Armbruster, C. 2008. Access, Usage and Citation Metrics: What Function for Digital Libraries and Repositories in Research Evaluation? Online Currents, 225, 168-180. Retrieved from http://ssrn.com/author=434782
 
3
Bailey, C. W. 2008. Open Access Bibliography. Retrieved from http://www.digital-scholarship.com/
 
4
Bailey, C. W. 2009. Scholarly Electronic Publishing Bibliography. Retrieved from http://www.digital-scholarship.com/
 
5
Bailey, C. W. 2010. Institutional Repositories Bibliography. Retrieved from http://www.digital-scholarship.com/
 
6
Basefsky, S. 2009. The End of Institutional Repositories and the Beginning of Social Academic Research Service: An Enhanced Role for Libraries. Law and technology resources for legal professionals. Retrieved from http://www.llrx.com/authors/1133
 
7
Kennan, M. A., & Kingsley, D. A. 2009. The State of the Nation: A Snapshot of Australian Institutional Repositories. First Monday, 142. Retrieved from http://firstmonday.org
 
8
Laurent Romary , Chris Armbruster, Beyond Institutional Repositories, International Journal of Digital Library Systems, v.1 n.1, p.44-61, January 2010  [doi>10.4018/jdls.2010102703]
 
9
Salo, D. 2008. Innkeeper at the Roach Motel. Library Trends, 572. Retrieved from http://muse.jhu.edu/journals/library_trends/v057/57.2.salo.html.
 
10
Vernooy-Gerritsen, M., Pronk, G., & van der Graaf, M. 2009. Three Perspectives on the Evolving Infrastructure of Institutional Research Repositories in Europe. Ariadne, 59, ¿¿¿. Retrieved from http://www.ariadne.ac.uk/issue59/vernooy-gerritsen-et-al/.
 
11
Wellcome Library. 2008. The Year in Review. Wellcome Collection, 13. Retrieved from http://library.wellcome.ac.uk/assets/wtx055651.pdf



BibTeX


@article{Romary:2010:CRT:2436646.2436650,
 author = {Romary, Laurent and Armbruster, Chris},
 title = {Comparing Repository Types: Challenges and Barriers for Subject-Based Repositories, Research Repositories, National Repository Systems and Institutional Repositories in Serving Scholarly Communication},
 journal = {Int. J. Digit. Library Syst.},
 issue_date = {October 2010},
 volume = {1},
 number = {4},
 month = oct,
 year = {2010},
 issn = {1947-9077},
 pages = {61--73},
 numpages = {13},
 url = {http://dx.doi.org/10.4018/jdls.2010100104},
 doi = {10.4018/jdls.2010100104},
 acmid = {2436650},
 publisher = {IGI Global},
 address = {Hershey, PA, USA},
 keywords = {Deposit Mandate, Institutional Repository, National Repository System, Repository Infrastructure, Research Repository, Scholarly Communication, Subject-Based Repository},
}

ZENODO Feature request: bibliometrics, statistics of page views and downloads. Datacite statistics.



Zenodo is very useful and the new release adds a lot of improved functionality. One feature I think is still missing are download statistics for each deposit. The altmetrics integration is nice, but I suspect a lot more people download an item than blog or tweet about it. So download statistics would provide very welcome, more fine-grained information and it wouldn't even take an external provider to collect the data. The French repository HAL does this very nicely (even distinguishing between page views and downloads). I personally would prefer those statistics to be public, but if this raises concerns, maybe an opt-out / opt-in solution is necessary.
In order to enhance Zenodo and monitor traffic,
non-personal information such as IP addresses
and cookies may be tracked and retained, and log files may be shared
https://zenodo.org/policies

Datacite

datacite statistics are only for DATA centers
Try this example:
https://search.datacite.org/ui?q=*&fq=has_metadata%3Atrue&fq=is_active%3Atrue&fq=prefix%3A%2210.5281%22&

GitHub

https://github.com/zenodo/zenodo/issues/915

Thursday, March 2, 2017

Wednesday, March 1, 2017

une introduction aux DOI par cleo



Métadonnées enregistrées pour un DOI

  1. Un DOI unique est attribué à chaque ressource et ne sera pas réutilisé. Il est établi en enregistrant des métadonnées liées à la ressource numérique
  2. sur la revue :
    1. Nom complet et nom court
    2. ISSN électronique
    3. l’URL de la revue
  3. sur l’article :
    1. date au format jour/mois/année
    2. l’URL de l’article
    3. langue du l’article
    4. le titre et le titre traduit
    5. le ou les auteurs et leur rôle (collaborateur, etc.)
  4. sur le livre :
    1. langue
    2. auteur
    3. titre
    4. sous-titre
    5. date de publication papier (=annee edition)
    6. date de publication électronique
    7. isbn print
    8. isbn electronique
    9. editeur
    10. url

  5. sur le chapitre (déclaré avec son livre) :
    1. Titre 
    2. sous-titre
    3. auteur
    4. pagination
    5. url
  6. sur le dépositaire :
    1. son nom
    2. son contact
  7. En conséquence, les DOI lient les métadonnées de la revue, du livre, celles du document ( article, chapitre…) et l’emplacement web de la ressource. Ils permettent de faciliter le fonctionnement des bases de données ainsi que les logiciels de gestion bibliographique, mais également de suivre une ressource dans le monde numérique.
  8. Le corollaire de ce système est la génération d’un code permanent même en cas de déplacement de la ressource. Il est important de garantir la pérennité de la ressource pour intégrer ces bases et donc d’éviter les doublons, et les suppressions de documents.
  9. Comme les URL, les DOI sont des codes structurés qui débutent par le code de l’organisation responsable de la diffusion de la ressource, puis l’identifiant du document.


http://maisondesrevues.org/253

Thursday, February 23, 2017

List of Researcher Services (a paper in Journal of Library Administration 2016)



Author/Researcher Identification

—these services provide some necessary infrastructure that may be used in the other two categories, such as unique identifiers and name disambiguation

Academic and Professional Networking

—most succinctly described as “social networking for academics,” these services focus on connecting users based on research interest, affiliation, geography, or other variables.

Reference and Citation Management

—while these tools and services include some of the functionality and features of other categories, they are distinct given their primary focus on management of citations that a researcher compiles for use within a publication or for sharing with other researchers.


Reference 

http://dx.doi.org/10.1080/01930826.2016.1146534
http://www.tandfonline.com/doi/full/10.1080/01930826.2016.1146534


Friday, February 10, 2017

INIST DOI Handle PURL ARK ePIC




Elément majeur d’une bonne pratique dans le mouvement de l’Open Science, les identifiants pérennes* jouent un rôle clé en facilitant la découverte et l’accès à long terme aux objets scientifiques issus de la recherche. Ils permettent ainsi d’identifier, référencer, partager et citer les données afin d’accroître leur visibilité.

Le DOI (Digital Object Identifier) en est un exemple. Il peut être attribué aux résultats de la recherche (données, images, vidéos…).
Une équipe dédiée au sein de l’Inist-CNRS se tient à votre disposition pour vous conseiller au plus près de vos recherches dans l’attribution de DOI à vos données (fourniture des préfixes DOI, assistance à la création et la conversion de métadonnées…). Elle vous accompagne également dans l’utilisation des différents services proposés par DataCite
https://www.datacite.org/

En savoir plus sur les identifiants pérennes
http://www.inist.fr/formations/IdentifiantsPerennes/story.html
(date de dec 2016)
Contact :datasets@inist.fr

English

/*Persistent identifiers* are an important element of good practices in
the movement of Open Science, playing a key role by facilitating the
discovery and long-term access to scientific objects that arise from
research. They allow the identification, referencing, sharing and citing
of data to increase their visibility.*

The DOI (Digital Object Identifier) is an example of persistent
identifier that can be assigned to the results of research (data,
pictures, videos etc.).
A dedicated team within Inist-CNRS is at your disposal to advise you
concerning the attribution of a DOI to your research data (supply of DOI
prefixes, help with the creation and conversion of metadata etc.). The
team also accompanies you in the use of different services proposed by
DataCite.

*To learn more about persistent identifiers

   Contact : datasets@inist.fr

Thursday, January 12, 2017

API IMPORT in Zenodo, Zenodo Github. Research data repository and open access archives. ORCID and DataCite Metadata


Zenodo is a research data repository. It was created by OpenAIRE and CERN to provide a place for researchers to deposit datasets.
https://home.cern/about/updates/2013/05/cern-and-openaireplus-launch-european-research-repository

some examples

an example of a .zip with many pdf

https://zenodo.org/record/168580#.WIeylGrNzdQ

7 blocks (see green arrows)

  1. Title
  2. author
  3. abstract
  4. acknowledgments
  5. frame with pdf or zip...
  6. Files
  7. References




DOI





many export solutions

  1. BibTeX Export
  2. Citation Style Language JSON Export
  3. DataCite XML Export
  4. Dublin Core Export
  5. JSON Export
  6. MARC21 XML Export
  7. a link to Mendeley:
    https://www.mendeley.com/sign/in/?acw=&utt=


If you select JSON for example, you will get directly in the window:


another example, communities COAR

Publications and outputs from or related to the Confederation of Open Access Repositories (COAR). Topics on open access repositories, interoperability, usage data, vocabularies, training, licenses and more.
https://zenodo.org/communities/coar

another example, an article

https://zenodo.org/communities/2249-0205/?page=1&size=20
And
google search
gives this 2nd position:

a web service

Zenodo, a CERN service, is an open dependable home for the long-tail of science, enabling researchers to share and preserve any research outputs in any size, any format and from any science.

DOI

Zenodo assigns all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. Zenodo further supports harvesting of all content via the OAI-PMH protocol.
Withdrawal of data and revocation of DOIs:
Content not considered to fall under the scope of the repository will be removed and associated DOIs issued by Zenodo revoked. Please signal promptly, ideally no later than 24 hours from upload, any suspected policy violation. Alternatively, content found to already have an external DOI will have the Zenodo DOI invalidated and the record updated to indicate the original external DOI. User access may be revoked on violation of Terms of Use.

 DOI from DataCite not CrossRef then you cannot use the crossRef's services.
http://stephane-mottin.blogspot.fr/2017/02/tous-les-doi-noffrent-pas-des-services.html

log

You can log by
  • ORCID Id/passORCID
  • GitHub username/pass
  • email/pass

Upload

What can I upload?

All research outputs from all fields of science are welcome. In the upload form you can choose between types of files: publications (book, book section, conference paper, journal article, patent, preprint, report, thesis, technical note, working paper, etc.), posters, presentations, datasets, images (figures, plots, drawings, diagrams, photos), software, videos/audio and interactive materials such as lessons. We do check every piece of content being uploaded to ensure it is research related.

Dans le champ "description" qui a un  Rich text editor, on ne peut même pas copier/coller du HTML par exemple d'un article PLOS. On ne peut même pas mettre un lien.
On peut saisir une équation en TeX sous la forme par exemple (entre {}):
x = {-b \pm \sqrt{b^2-4ac} \over 2a}

community

Zenodo allows you to create your own collection and accept or reject uploads submitted to it. Creating a space for your next workshop or project has never been easier. Plus, everything is citeable and discoverable!

Want your own community?
It's easy. Just click the button to get started.
  • Curate — accept/reject what goes in your community collection.
  • Export — your community collection is automatically exported via OAI-PMH
  • Upload — get custom upload link to send to people
We currently accept up to 50GB per dataset (you can have multiple datasets); there is no size limit on communities.

Metadata types and sources

All metadata is stored internally in MARC according to the schema defined in http://inveniosoftware.org/wiki/Project/OpenAIREplus/DevelopmentRecordMarkup.
Metadata is exported in several standard formats such as MARCXML, Dublin Core, and DataCite Metadata Schema according to OpenAIRE Guidelines.


Open source

Powered by Invenio
Zenodo is a small layer on top of Invenio http://github.com/inveniosoftware/invenio, a ​free software suite enabling you to run your own ​digital library or document repository on the web.

code:
https://github.com/zenodo/zenodo


GitHub

Zenodo has integration with GitHub to make code hosted in GitHub citable.
  • Select the repository you want to preserve, and toggle the switch below to turn on automatic preservation of your software.
  • Go to GitHub and create a release. Zenodo will automatically download a .zip-ball of each new release and register a DOI.
  • After your first release, a DOI badge that you can include in GitHub README will appear next to your repository below.

https://zenodo.org/account/settings/github/

---

Ref.

https://en.wikipedia.org/wiki/Zenodo
https://en.wikipedia.org/wiki/Category:Open-access_archives

IMPORT in zenodo

resources

Invenio

Zenodo is a small layer on top of Invenio <http://github.com/inveniosoftware/invenio>, a ​free software suite enabling you to run your own ​digital library or document repository on the web.

Invenio is a free software suite enabling you to run your own digital library or document repository on the web. The technology offered by the software covers all aspects of digital library management, from document ingestion through classification, indexing, and curation up to document dissemination. Invenio complies with standards such as the Open Archives Initiative and uses MARC 21 as its underlying bibliographic format. The flexibility and performance of Invenio make it a comprehensive solution for management of document repositories of moderate to large sizes.

Invenio has been originally developed at CERN to run the CERN document server, managing over 1,000,000 bibliographic records in high-energy physics since 2002, covering articles, books, journals, photos, videos, and more. Invenio is nowadays co-developed by an international collaboration comprising institutes such as CERN, DESY, EPFL, FNAL, SLAC and is being used by many more scientific institutions worldwide.

zenodo interface

pour un upload à la main, il y a 11 catégories de champs

  1. Upload type 
    1. Book section 
    2. ... Journal article, etc
  2. Basic Info
    1. date
    2. Title
    3. Authors (one by one)!!!
    4. Description (only text (and math formula) without link!!!)
    5. Keyword
    6. Additional notes, for example sommaire
  3. License
    1. Open
    2. CC 4.0; you must add its category
  4. Communities
    1. integrations (for example)
  5. Funding
    1. CNRS (for exemple)
  6. related/alt identif
    1. ISSN, ISBN, URL
  7. Contributors for example the dir of collection
  8. reference
  9. journal
  10. c
  11. Book
    1. Publisher
    2. Place
    3. ISBN
    4. Book Title
    5. Page (of this book)

zenodo API

The process

an example:
Similar to figshare, Zenodo can store your data and give you a DOI to make it citable.
We have started to deposit all Brain Catalogue’s data at Zenodo, and soon you should be able to cite your favourite brains in your works.
Initially, we uploaded the data manually, but that became tedious very soon. Luckily, Zenodo has a very simple to use and well documented API. In just 3 lines of code using curl you can easily deposit a data file and make it citable (Full information is available at https://zenodo.org/dev).

Before starting anything you need to obtain a token, which is a random alphanumeric string that identifies your queries. You only need to do this once. With your token safely stored (I keep it in the $token variable), data uploading takes just 3 steps:

1. Create a new deposit and obtain a deposit ID:

curl -i -H "Content-Type: application/json" -X POST --data '{"metadata":{"access_right": "open","creators": [{"affiliation": "Brain Catalogue", "name": "Toro, Roberto"}],"description": "Brain MRI","keywords": ["MRI", "Brain"],"license": "cc-by-nc-4.0", "title": "Brain MRI", "upload_type": "dataset"}}' https://zenodo.org/api/deposit/depositions/?access_token=$token |tee zenodo.json

Zenodo responds with a json file, which here I’m saving to zenodo.json. Now you can use awk to parse that file and recover the deposit id. I do that like this:
zid=$(cat zenodo.json|tr , '\n'|awk '/"id"/{printf"%i",$2}')

With your deposit ID in hand, you are ready to upload your data file

2. Upload data file:

curl -i -F name=MRI.nii.gz -F file=@/path/to/the/data/file/MRI.nii.gz https://zenodo.org/api/deposit/depositions/$zid/files?access_token=$token

The server will respond with a HTTP 100 ‘Continue’ message, and depending on the size of your file you’ll have to wait some time. Once the upload is finished you are ready to

3. Publish your dataset:

curl -i -X POST https://zenodo.org/api/deposit/depositions/$zid/actions/publish?access_token=$token

And that’s it. You can now go to Zenodo and view the web page for your data


Ref.
http://siphonophore.org/blog/2016/01/16/at-brain-catalogue-we-love-zenodo/

---
A bug in JSON object
https://github.com/zenodo/zenodo/issues/865
on the web documentation API Documentation for developers ( https://zenodo.org/dev)
Resources > Representations > Deposition metadata > subjects

the example of json object for subject is :
[{"term": "Astronomy",
"id": "http://id.loc.gov/authorities/subjects/sh85009003",
"scheme": "url"}]
but id is not supported and the json is rejected
the field must named 'identifier'

resources

http://developers.zenodo.org/ 
(Zenodo REST API documentation uses Slate. )

bof: https://zenodo.readthedocs.io/



Ref. https://indico.cern.ch/event/533421/contributions/2330179/attachments/1378438/2094268/kumasi2016-practical-exercises-rest-api.pdf

blog zenodo

http://blog.zenodo.org/
Zenodo docs have landed!
by  Krzysztof Nowak on January 23, 2017

wiki zenodo

https://github.com/zenodo/zenodo/wiki/What's-new%3F

YAML Github
Zenodio is a Python package we’re building to interact with Zenodo. For our various doc/technote/publishing projects we want to use YAML files (embedded in a Git repository, for example) to maintain deposition metadata so that the upload process itself can be automated.
The zenodio.metadata sub package provides a Python representation of Zenodo metadata (but not File or Zenodo deposition metadata).
Zenodio is a simple Python interface for getting data into and out of Zenodo, the digital archive developed by CERN. Zenodo is an awesome tool for scientists to archive the products of research, including datasets, codes, and documents. Zenodio adds a layer of mechanization to Zenodo, allowing you to grab metadata about records in a Zenodo collection, or upload new artifacts to Zenodo with a smart Python API.
We’re still designing the upload API, but metadata harvesting is ready to go.
Zenodio is built by SQuaRE for the Large Synoptic Survey Telescope.
https://github.com/lsst-sqre/zenodio/tree/metadata_api
http://zenodio.lsst.io/en/latest/
https://jira.lsstcorp.org/browse/DM-4852

Differences between ORCID and DataCite (DOI) Metadata

THOR is a 30 month project funded by the European Commission under the Horizon 2020 programme. It will establish seamless integration between articles, data, and researchers across the research lifecycle. This will create a wealth of open resources and foster a sustainable international e-infrastructure.

Differences between ORCID and DataCite Metadata
One of the first tasks for DataCite in the European Commission-funded THOR project, which started in June 2015, was to contribute to a comparison of the ORCID and DataCite metadata standards. Together with ORCID, CERN, the British Library and Dryad we looked at how contributors, organizations and artefacts - and the relations between them - are described in the respective metadata schemata, and how they are implemented in two example data repositories, Archaeology Data Service and Dryad Digital Repository. The focus of our work was on identifying major gaps. Our report was finished and made publicly available in September 2015. The key findings are on these topics:
  • Common Approach to Personal Names
  • Standardized Contributor Roles
  • Standardized Relation Types
  • Metadata for Organisations
  • Persistent Identifiers for Projects
  • Harmonization of ORCID and DataCite Metadata

https://project-thor.readme.io/docs/differences-between-orcid-and-datacite-metadata

This document identifies gaps in existing PID infrastructures, with a focus on ORCID and DataCite Metadata and links between contributors, organizations and artefacts. What prevents us from establishing interoperability and overcoming barriers between PID platforms for contributors, artefacts and organisations, and research solutions for federated attribution, claiming, publishing and direct data access? It goes on to propose strategies to overcome these gaps.:
https://zenodo.org/record/30799#.WIi5DmrNzdQ