Science hubs & hub Sciences: DOI

Showing posts with label DOI. Show all posts

Wednesday, May 31, 2017

DOI versioning and Zenodo

We are pleased to announce the launch of DOI versioning support in Zenodo - the open research repository from OpenAIRE and CERN. This new feature enables users to update the record’s files after they have been made public and researchers to easily cite either specific versions of a record or to cite, via a top-level DOI, all the versions of a record.

DOI versioning support was one of our most requested features for Zenodo, and it has been co-developed by OpenAIRE’s Zenodo team and EUDAT’s B2SHARE team as an extension module for CERN’s Invenio digital repository platform, which powers both Zenodo and B2SHARE.

This update comes hot on the heels of the recent relaunch which made Zenodo faster, improved GitHub integration, integrated support for Horizon 2020 grant information, and enabled 50 gigabyte uploads!

Read more about the inner workings of new feature in the FAQ http://help.zenodo.org/#versioning

http://blog.zenodo.org/2017/05/30/doi-versioning-launched/

Saturday, March 18, 2017

twitter and how to tweet with an automatic iframe. Exemple of the open archive Zenodo (DOI)

You can see an example of the automatic iframe pushed by twitter in this tweet.

Summary Card

The Summary Card can be used for many kinds of web content, from blog posts and news articles, to products and restaurants. It is designed to give the reader a preview of the content before clicking through to your website.

The Tweet shows a Summary Card (photo and text).

https://dev.twitter.com/cards/types/summary

Our system recognizes when URLs are included in a tweet, and crawls your site to fetch the Card type and content.
To learn more about how our Card system works, read our Getting Started Guide.
https://dev.twitter.com/cards/getting-started

In the <head> of the HTML of the URL
you must have some METADATA.
In Zenodo, for example:
<meta name="description" content="Chapitre dans Matériaux et Joints d Etanchéité pour les Hautes Pressions édité dans la collection • Intégrations des savoirs et savoir faire • -- Collection dirigée et éditée par Stéphane MOTTIN" />
<meta name="citation_title" content="Les matériaux sidérurgiques et les hautes pressions" />
<meta name="citation_author" content="" />
<meta name="citation_doi" content="10.5281/zenodo.400482" />
<meta name="citation_keywords" content="Hautes pressions" />
<meta name="citation_keywords" content="Matériaux" />
<meta name="citation_keywords" content="Hautes pressions - Matériaux" />
<meta name="citation_keywords" content="Joints d étanchéité" />
<meta name="citation_keywords" content="Matériaux - Effets des hautes pressions" />
<meta name="citation_abstract_html_url" content="https://zenodo.org/record/400482" />
<meta name="citation_pdf_url" content="https://zenodo.org/record/400482/files/6Materiaux18_2011.pdf" />

Try the validor to see the visual of your tweet:
https://cards-dev.twitter.com/validator

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 name	Collection method	Update frequency	Notes
Twitter	Third party data provider API	Real-time feed	Demographics, support for retweets, with monitoring of suspicious activity.
Facebook	Facebook API	Daily	Public Facebook Pages and posts only, with prioritised popular Pages.
Policy documents	PDFs collected and scanned from policy sources and repositories	Daily	Scanning and text-mining policy document PDFs for references, which are looked up in CrossRef/PubMed and resolved to DOIs.
News	RSS feeds and API	Real-time feed	Manually curated news sources, with data provided via a third-party provider and RSS feeds direct.
Blogs	RSS feeds	Daily	Manually curated list, harvesting links to scholarly content.
Mendeley	Mendeley API	Daily	Reader counts is number of readers with the output in their Library. Not included in score.
Scopus	Scopus API	Real-time feed	Citation counts from peer-reviewed literature. Not included in score.
Post-publication peer reviews	PubPeer and Publons APIs	Daily	Peer review comments collected from item records and associated by unique identifier.
Reddit	Reddit API	Daily	Includes all sub-reddits. Original posts only, no comments.
Wikipedia	Wikipedia API	Real-time feed	Mentions of scholarly outputs collected from References section. English Wikipedia only.
Q&A (Stack Overflow)	Stack Overflow API	Daily	Scan for links to scholarly outputs.
F1000 Reviews	F1000 API	Daily	Scan for links to scholarly outputs.
Google+	Google+ API	Daily	Public posts only.
YouTube	YouTube API	Daily	Scan for links to scholarly outputs in video comments.
Open Syllabus	Static Import from Open Syllabus	Quarterly	Link syllabi's contents to HLOM IDs.

altmetrics blog

https://www.altmetric.com/blog/

https://www.altmetric.com/blog/tools-online-engagement/

---

Friday, March 10, 2017

DataCite services, Zenodo and MANY ORCID integration services (and impactstory)

DataCite services

Locate, identify, and cite research data with DataCite, a global provider of DOIs for research data.

https://www.datacite.org/
(less services than crossRef).

http://stephane-mottin.blogspot.fr/2017/01/datacite-inist-cern-metadata-schema.html

DOI handbook
http://www.doi.org/hb.html

In order to create new DataCite DOIs and assign them to your content, it is necessary to become a DataCite member or work with one of the current members.

Through the web interface or the API of the DataCite Metadata Store you will be able to submit a name, a metadata description following the DataCite Metadata Schema and at least one URL of the object to create a DOI. Once created, information about a DOI is available through our different services search, event data, OAI-PMH and others).

The DataCite Metadata Store is a service for data publishers to mint DOIs and register associated metadata. The service requires organisations to first register for an account with a DataCite member.
https://mds.datacite.org/

http://schema.datacite.org/

status of the services
http://status.datacite.org/

https://blog.datacite.org/

Services of DataCite profiles

DataCite Profiles integrates DataCite services from a user’s perspective and provides tools for personal use. In particular, it is a key piece of integration with ORCID, where researchers can connect their profiles and automatically update their ORCID record when any of their works contain a DOI.

https://profiles.datacite.org/
example
https://profiles.datacite.org/users/0000-0002-7088-4353
0000-0002-7088-4353 is my ORCID Id.

You can get

your ORCID Token
your API Key
(if you want to use the ORCID API).

In your profile, you can select how to connect:

You can also follow ORCID claims.
For example: "You have 5 successful claims, 0 notification claims, 0 queued claims and 0 failed claims"

You are also linked to Impactstory
Impactstory is an open-source website that helps researchers explore and share the the online impact of their research.
https://impactstory.org/u/0000-0002-7088-4353
0000-0002-7088-4353 is my ORCID id.

You must authorize impactstory.org to link with your ORCID.
You must also connect impactstory.org with your twitter.
In impactstory, Zenodo from ORCID are "datasets".

Zenodo and DataCite METADATA

If you use ZENODO, an Open Archive with DataCite DOI, DataCite services are interesting.

Zenodo gives a DataCite DOI and an export to a clean datacite METADATA (XML DataCite 3.1).

http://stephane-mottin.blogspot.fr/2017/03/zenodo-export-functions-very-good-for.html

(see also my posts on this blog with the tag "zenodo")

Zenodo DataCite and Orcid

If you use ZENODO and your ORCID Id then you have some services:

https://profiles.datacite.org/users/me

You must allow Zenodo to "Get your ORCID iD".

You must allow DataCite to allow ORCID "Add works"

But only 5 METADATA are automatically sent to ORCID by DataCite.

Title,
Year,
Description (the full field of Zenodo),
Contributor (the field 'creator' of Zenodo = authors),
DOI

You can add metadata in ORCID...
Change type 'Work category' and 'Work type'.
Then Source is changed from 'zenodo' to 'Stéphane MOTTIN'

In impactstory, Zenodo links (from ORCID) are considered as "datasets" with only 4 METADATA

Title,
Year,
Contributor (the field 'creator' of Zenodo = authors),
DOI

ORCID

You can see the list of ORCID "trusted organization"
at https://orcid.org/account
DataCite can 'add works'.

For other ORCID Search & link wizards:
http://support.orcid.org/knowledgebase/articles/188278-link-works-to-your-orcid-record-from-another-syste

for example

The Crossref Metadata Search integration allows you to search and add works by title or DOI. Once you have authorized the connection and are logged into ORCID, Crossref search results will also include a button to add works to your ORCID record.
http://search.crossref.org/
The DataCite integration allows you to find your research datasets, images, and other works. Recommended for locating works other than articles and works that can be found by DOI.
The ISNI2ORCID integration allows you to link your ORCID and ISNI records and can be used to import books associated with your ISNI. Recommended for adding books.
http://isni2orcid.labs.orcid-eu.org/
Use this tool to link your ResearcherID account and works from it to your ORCID record, and to send biographical and works information between ORCID and ResearcherID.
http://wokinfo.com/researcherid/integration/
Use this wizard to import works associated with your Scopus Author ID; see Manage My [Scopus] Author Profile for more information. Recommended for adding multiple published articles to your ORCID record.
https://www.elsevier.com/solutions/scopus/support/authorprofile

Thursday, March 2, 2017

Zenodo and example of structured PDF (signet)

Example of a structured PDF:
https://zenodo.org/record/34187#.WLiNZt_NzdQ
https://doi.org/10.5281/zenodo.34187

https://zenodo.org/badge/DOI/10.5281/zenodo.34187.svg

Multiple authors

Highlights of the 2013 International Forum on 'Polar Data Activities in Global Data Systems'

Programme & Abstracts (PDF)
Selected Papers Published in Data Science Journal (PDF)

Wednesday, March 1, 2017

medra (multilingual European Registration Agency), crossRef and DOI

mEDRA is a DOI Registration Agency (DOI RA) officially appointed by the International DOI Foundation on 1st July 2003 and provides DOI registration services to publishers, academic institutions, research centres and intermediaries in Italy, in the EU market and internationally.

mEDRA
Headquarter: C.so di Porta Romana, 108 - 20122 Milano
Società a responsabilità limitata iscritta presso l'ufficio del registro delle imprese di Milano.
C.F. - P.IVA e REG.IMPR.:04547330961 - R.E.A. 1756009
CAP. SOC. 40000 € I.V.

At mEDRA we want to make things easy for everyone, therefore mEDRA system can be used by small and big organisations, for commercial and open access publications, with or without having technical skills. Moreover, mEDRA team is available to support customers individually and speaks Italian, English, French and German.

mEDRA also collaborates with Crossref to allow DOIs registered with mEDRA to be deposited on Crossref platform.

DOI Bracket	Annual Fee	DOIs included	Price per unit for exceeding DOIs
0	180	30 DOIs included	4.50
1	350	75 DOIs included	3.80
2	600	170 DOIs included	2.70
3	900	350 DOIs included	2.00
4	1,350	650 DOIs included	1.60
5	2,000	1,300 DOIs included	1.10

Note:
• The access to DOI registration service through mEDRA is subject to advanced payment of an Annual Fee (plus – for the new contracts – the payment for the months of the current year)
• The DOIs included in the Annual Fee have to be registered within the December 31 of every year.
• In case of a number of registrations exceeding the quantity included in the annual fee, a price per unit,
connected to the chosen bracket, is required. Once the sum of the initial DOI Bracket plus the extra DOIs reaches the fee of the next DOI bracket, customer will be upgraded to the next upwards DOI Bracket without extra cost than the amount of difference of bracket.
• Extra DOIs will be invoiced at the end of the annual contract (31/12 of every year).
• In case of termination of the contract, the Registrant has to pay € 0,1 for each registered Doi for the maintenance service.
• At the end of the first year after the termination of the contract, mEDRA will use the registered metadata in order to guarantee DOI Service.

Schema

ONIX for DOI metadata schema defines the XML format of the message requested by mEDRA system to register DOIs, showing the list of metadata concerning the object to be identified.

According to the ONIX for DOI metadata schema, you can register DOIs on Monographs, Monographic Chapters, Serial Articles, Serial Titles and Serial Issues.

The XML schema is encoded according to ONIX syntax. ONIX (Online Information Exchange) is the most authoritative standard communication format for content industry, created and regularly updated by EDItEUR, the international group coordinating the development of the standards for electronic commerce in book and serials industries.

ONIX for DOI metadata schema, jointly developed by mEDRA and EDItEUR in collaboration with Nielsen Book Data (the DOI Registration Agency for UK) has been formally endorsed by EDItEUR as the official ONIX format for DOI registration and it has newly been adopted by OPOCE, the Office for Official Publications of the European Communities.

The latest issue of ONIX for DOI metadata schema, version 2.0., is now available. The new release is fully backwards compatible with the previous one (1.1), but thanks to the inclusion of new metadata elements it allows a richer description of publications and, for Italian customers only, the deposit of the citations list to join CrossRef services via mEDRA.

http://www.medra.org/en/schema.htm

METADATA for DOI

http://www.medra.org/en/metadata_td.htm

tools

A few utilities addressed to the IT staff of your company:
Automatic upload of XML file for DOI registration
Download a Java program performing the automatic upload of the XLM file via HTTPS POST to the mEDRA registration service
http://www.medra.org/en/utilities.htm

une introduction aux DOI par cleo

Métadonnées enregistrées pour un DOI

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
sur la revue :

Nom complet et nom court
ISSN électronique
l’URL de la revue

sur l’article :

date au format jour/mois/année
l’URL de l’article
langue du l’article
le titre et le titre traduit
le ou les auteurs et leur rôle (collaborateur, etc.)

sur le livre :

langue
auteur
titre
sous-titre
date de publication papier (=annee edition)
date de publication électronique
isbn print
isbn electronique
editeur
url

sur le chapitre (déclaré avec son livre) :

Titre
sous-titre
auteur
pagination
url

sur le dépositaire :

son nom
son contact

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.
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.
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.

Que sont les DOI ? À quoi servent-ils ?

Définition

Métadonnées enregistrées pour un DOI

Les DOI sur Revues.org

Les DOI sur OpenEdition Books

Comment utiliser les DOI ?

Signaler une ressource

Retrouver une ressource

DOI, e-ISSN et e-ISBN : redondance ou complémentarité ?

Comment acquérir des DOI ?

Quelques liens de référence sur les DOI

Présentations des DOI (en)

Les sites de référence (en)

http://maisondesrevues.org/253

Thursday, February 23, 2017

ResearchGate generate free DOI for unpublished work

What type of research can I generate a DOI for?

DOIs can be generated for most of your unpublished work. However, publications of type Article, Book, Chapter, Patent, Cover Page, Poster , Code and Conference Paper are considered to have been published elsewhere, and therefore DOIs cannot be generated for these publication types. You can also add an existing DOI issued by your publisher to any of your research.
Note: Once a ResearchGate DOI has been generated, the research cannot be edited. Instead, you should remove the research completely, re-upload it with the edits and then generate a new DOI.

How do I generate a DOI for my research?

If a publication you’ve already added to your profile doesn’t have a DOI and isn't one of those types mentioned above, you can generate one by following these steps:

Go to your profile and click the Timeline tab
Select the publication you would like to generate a DOI for by clicking on its title
On the right-hand side, click on the blue arrow and select Generate a DOI (if this is not visible, then your publication is one one the types listed above; generating a DOI for these types is not possible)
Review the details of your publication to ensure they are correct
Click Generate a DOI.

To generate a DOI for unpublished work you haven't yet added to your profile you will first need to add the publication. Here's how:

Go to your profile and click Add your publications
Select the type of publication
Click Select file
Upload your file (required)
Click Continue
Verify your publication details and select Generate a DOI (if this is not visible, then your publication is one one the types listed above; generating a DOI for these types is not possible)
Click Finish to confirm your changes.

Your work will now be assigned a DOI, making it easy for researchers to find and cite it.

https://explore.researchgate.net/display/support/Generating+a+DOI

Wednesday, February 15, 2017

Tous les DOI n'offrent pas des services identiques. Le cas de Zenodo et DOI Datacite qui n'est pas un DOI crossRef. Zotero.

Introduction

CrossRef est une structure (consortium Editeur)
qui gère la redirection URL (base d’URL mise à jour) et de metadonnées biblio, la base et les services et la structure de ses serveurs.
Un des services a des fonctions de bibliométrie (qui a cité tel article).

On ne peut que l'interroger via des API js.
Ainsi Zotero peut interroger crossRef via un DOI.

Si on essaie dans Zenodo d'importer avec DOI-zenodo, il y a une erreur d'importation de Zotero car ce n'est pas crossref...

Datacite est fait pour assigner des DOI à des données, des datasets (voir la fin de ce post) alors que CrossRef est pensé pour des publications.

En outre Zotero importe bien certains champs sauf les auteurs via l'import Zenodo ou "embedded metadata!!!
En fait dans le head de la page HTML de Zenodo, les champs <meta> auteur sont vides:
<meta name="citation_author" content="">
d'où l'erreur.

Par contre on a le résumé ce que ne donne pas crossref.
Il faut donc fusionner les deux.

Les DOI

Un post de 2014
http://iphylo.blogspot.fr/2014/05/dois-are-not-enough.html
Ce qui a motivé la conversation a été l'article suivant:

Emery, Carlo et al (1899). Formiche di Madagascar raccolte dal Sig. A. Mocquerys nei pressi della Baia di Antongil (1897-1898).. Bullettino della Società Entomologica Italiana: 31 (1899) pp. 263-290. 10.5281/zenodo.9785 http://dx.doi.org/10.5281/zenodo.9785

Tous les Doi ne sont pas égaux

Les DOI de Zenodo sont attribués par DataCite et les DataCite DOIs n’ont pas toutes les fonctionnalités que CrossRef prévoit pour leur DOI.

CrossRef fournit certains services clés, l’un des plus importants est la possibilité de lier les biblio. Compte tenu du domaine des références bibliographiques, CrossRef dispose d’outils qui peuvent trouver si elle a un DOI (p. ex., http://search.crossref.org). Vous bénéficiez de ce service chaque fois que vous lisez un article et voir la section biblio citée ornée de doi. Les éditeurs peuvent ainsi convertir et structurer des citations avec des liens et outils de CrossRef. Cette fonction repose sur les CrossRef métadonnées. Lorsque les éditeurs envoient leurs métadonnées d'article lors de l’inscription de leur DOI, ils soutiennent généralement la listes des ouvrages cités (et le DOI). Cela signifie que CrossRef bâtit une base de données de référence, que vous pouvez voir si vous visitez la page web pour un article et un lien « cité par ».

Il y a des services supplémentaires. Étant donné que CrossRef a une haute qualité bibliographique de métadonnées pour les objets, alors si vous avez un DOI "crossRef" il n'est plus nécessaire de saisir les ref biblio d’un document. Un logiciel bibliographique comme Mendeley et Zotero peut prendre un DOI et les récupérer. Si un DOI ne parvient pas à résoudre ce service, vous pouvez contacter le Support de CrossRef. Viennent ensuite les nouveaux services tels que FundRef et de perspective, qui fournissent des informations sur qui a financé, et quel texte et les droits d’exploration de données disponibles pour un document.

Pourquoi utiliser un DOI ?

La justification de l’utilisation de DOI pour des articles est qu’ils puissent être identifiés sans ambiguïté, qui à son tour signifie que nous pouvons construire un réseau solide de référence. Mais cela nécessite des infrastructures, et c’est ce que CrossRef fournit grâce à des outils comme référence DOI. D'autres organismes d’enregistrement de DOI ne font pas cela, et CrossRef n’est pas au courant d’autres DOI, donc mettre, disons, un DOI DataCite (tels que ceux utilisés par les Zenodo) sur un article n’atteint pas l’objectif principal d’un DOI (embarquation dans le graphique de référence de la littérature académique).

Donc, je considère que mettre un DOI Zenodo est une opportunité gâchée. S’un article n’a pas un DOI CrossRef, il effectivement invisible. Toute la littérature académique devrait obtenir un DOI de première classe.

Not all DOIs are equal

As Geoffrey Bilder notes in his post DOIs unambiguously and persistently identify published, trustworthy, citable online scholarly literature. Right?
...some have adopted a cargo-cult practice of seeing the mere presence of a DOI on a publication as a putative sign of “citability” or “authority.”
There is a danger that we fall into the trap of thinking that all we need to do is slap a DOI on a paper and all the good things that we associate with DOIs will magically happen. This isn't the case. Not all DOIs are the same. Zenodo DOIs are proved by DataCite, and DataCite DOis don't have all the features that CrossRef provides for their DOIs.

CrossRef provides some key services, one of the most important is discoverability. Given a bibliographic references, CrossRef has tools that can find whether it has a DOI (e.g., http://search.crossref.org). I use this a lot to map taxonomic papers to DOIs (by a lot I mean searching for DOIs for tens of thousands of articles). Most people don't do this, but you benefit from this service every time you read an article and see the literature cited section decorated with DOIs. Publishers use CrossRef's tools to convert citations from dumb strings to useful links. This feature we come to expect from any modern article relies on CrossRef have definitive metadata for lots (millions) or articles, all of which have DOIs. When publishers submit article metadata when registering their DOIs, they usually submit lists of literature cited (and the DOIs). This means that CrossRef is building a citation database, which you can see if you visit the web page for an article and see a "cited by" link.

Then there are additional services. Given that CrossRef has high quality bibliographic metadata for articles, if you have a DOI there is no need to type in the details of a paper. Most bibliographic software such as Mendeley and Zotero can take a DOI and flesh out those details for you. If a DOI fails to resolve, you can contact CrossRef Support and have somebody investigate. Then there are the new services such as FundRef and Prospect, which provide information on who funded a paper, and what text and data mining rights are available for a paper.

Datacite, crossref, ORCID

The scholarly communications sector has built and adopted a series of openidentifier and metadata infrastructure systems to great success. Content identifiers (through Crossref and DataCite) and contributor identifiers (through ORCID) have become foundational infrastructure to the industry. But there still seems to be one piece of the infrastructure that is missing. There is as yet no open, stakeholder-governedinfrastructure for organizationidentifiers and associated metadata. In order to understand this gap, Crossref, DataCite and ORCID have been collaborating to.
The easiest way for Crossref members to participate in this is to cite data using DataCite DOIs and to include them in the references within the metadata deposit. These data citations are automatically detected. Alternatively and/or additionally, Crossref members can deposit data citations (regardless of identifier) as a relation type in the metadata. Data & software citations from both methods are freely propagated. This blog post also describes how to retrieve the links collected between publication and data & software.
Do you want to see if a Crossref DOI (typically assigned to publications) refers to DataCite DOIs (typically assigned to data)?
Here you go: http://api.labs.crossref.org/graph/doi/10.4319/lo.1997.42.1.0001
Conversely, do you want to see if a DataCite DOI refers to Crossref DOIs?
Voilà: http://api.labs.crossref.org/graph/doi/10.1594/pangaea.185321
Background “How can we effectively integrate data into the scholarly record?” This is the question that has, for the past few years, generated an unprecedented amount of handwringing on the part researchers, librarians, funders and publishers.
https://www.crossref.org/categories/datacite/

Tuesday, February 14, 2017

format file 2 import into HAL (XML TEI) ZENODO (JSON) via API. Converter, serialization, Metadata from marc, marcXML; YAML...

Une introduction en français sur les formats:
http://sametmax.com/yaml-xml-json-csv-ini-quest-ce-que-cest-et-a-quoi-ca-sert/

JSON
http://stephane-mottin.blogspot.fr/2017/01/datacite-inist-cern-metadata-schema.html
Implementations below are written in different languages:
http://json-schema.org/implementations.html
https://github.com/jdorn/json-editor

XML
http://stephane-mottin.blogspot.fr/2017/01/moissonnage-oai-pm-structure-ead-puis.html

converters CSV-XML CSV-JSON XML-JSON

zenodo/zenodo/modules/deposit/jsonschemas/deposits/records/record-v1.0.0.json

(863 lines)

"description": "Describe information needed for deposit module.",

"title": "Zenodo Deposit Schema v1.0.0",

"required": [

"_deposit"

zenodo/zenodo/modules/deposit/jsonschemas/deposits/records/legacyrecord.json

(432 lines)

"$schema": "http://json-schema.org/draft-04/schema#",

"additionalProperties": false,

"description": "Describe information needed for deposit module.",

"id": "http://zenodo.org/schemas/deposits/records/legacyjson.json",

"properties": {

"$schema": {

"type": "string"

example of a chapter book

https://zenodo.org/record/259721#.WIkL1GrNzdR

example of an export via the JSON button

https://zenodo.org/record/259721/export/json#.WIkMNWrNzdQ

(not exactly the same of the initial JSON)

API Documentation for developers:

https://zenodo.cern.ch/dev

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

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

JSON Schema zenodo and invenio

zenodo is based on invenio.
Invenio uses JSON Schema to describe formats of managed entities such as records.

Based on JSON Schema, we can generate forms permitting users and curators to enter records. There are two use cases: (1) deposition by end users such as physicists; (2) editing by power users such as curators and librarians.
This talk will show work-in-progress for both these scenarios. We can discuss pros/cons of using available tools such as JSON Editor:
https://indico.cern.ch/event/407109/
Invenio uses https://github.com/jdorn/json-editor

interesting slides

good/bad performances of "JSON Editor"
BibEdit

http://slides.com/neumann/json-based-record-editing#/
Ref.
https://github.com/inveniosoftware/invenio/issues/2854

export from catalogue SUDOC (and Brise-ES)

http://stephane-mottin.blogspot.com/2017/01/importance-du-catalogage-librairie.html
http://stephane-mottin.blogspot.fr/2012/06/catalogage-sudoc-abes-unimarc-des.html
http://stephane-mottin.blogspot.fr/2011/10/sudoc-export-et-interoperabilite.html

Somes codes XML JSON

generate code.json / zenodo.json metadata files for github? (comments @2014)
Seems like it would be a straight-forward exercise to serialize some json-ld from an R DESCRIPTION file (and potentially other sources) to provide more metadata to zenodo (and potentially other sites if this becomes a more standard schema). Not sure if this package is the right home for it.
Ref. https://github.com/ropensci/zenodo/issues/3

Minimal metadata schemas for science software and code, in JSON and XML

1/
Matthew B. Jones, Carl Boettiger, Abby Cabunoc Mayes, Arfon Smith, Peter Slaughter, Kyle Niemeyer, Yolanda Gil, Martin Fenner, Krzysztof Nowak, Mark Hahnel, Luke Coy, Alice Allen, Mercè Crosas, Ashley Sands, Neil Chue Hong, Patricia Cruse, Dan Katz, Carole Goble. 2016. CodeMeta: an exchange schema for software metadata. KNB Data Repository. doi:10.5063/schema/codemeta-1.0
https://raw.githubusercontent.com/codemeta/codemeta/1.0/codemeta.jsonld
https://github.com/codemeta/codemeta/blob/master/codemeta.jsonld
(193 lines)

CodeMeta contributors are creating a minimal metadata schema for science software and code, in JSON and XML. The goal of CodeMeta is to create a concept vocabulary that can be used to standardize the exchange of software metadata across repositories and organizations.
CodeMeta started by comparing the software metadata used across multiple repositories, which resulted in the CodeMeta Metadata Crosswalk.
https://github.com/codemeta/codemeta/blob/master/crosswalk.csv

That crosswalk was then used to generate a set of software metadata concepts, which were arranged into a JSON-LD context for serialization (see codemeta.jsonld, or an example CodeMeta document).

This is an extension of the work done by @arfon, @hubgit, @kaythaney and others on Code as a Research Object / fidgit. Code as a research object is a Mozilla Science Lab (@MozillaScience) project working with community members to explore how we can better integrate code and scientific software into the scholarly workflow. Out of this came fidgit - a proof of concept integration between Github and figshare, providing a Digital Object Identifier (DOI) for the code which allows for persistent reference linking.

With codemeta, we want to formalize the schema used to map between the different services (Github, figshare, Zenodo) to help others plug into existing systems. Having a standard software metadata interoperability schema will allow other data archivers and libraries join in. This will help keep science on the web shareable and interoperable!
https://github.com/codemeta/codemeta

json-LD
http://www.arfon.org/json-ld-for-software-discovery-reuse-and-credit
http://json-ld.org/

2/
This repository contains the software implementation for our paper A Novel Approach to Higgs Coupling Measurements (Cranmer, Kreiss, Lopez-Val, Plehn), arXiv:1401.0080 [hep-ph]. It contains tools to apply the discussed methods to new models and contains a Makefile to recreate the plots in the paper.
https://github.com/lnielsen/decouple/blob/master/.zenodo.json

Serializer Serialization

https://en.wikipedia.org/wiki/Serialization

The Serializer component is meant to be used to turn objects into a specific format (XML, JSON, YAML, ...) and the other way around.

php framework
http://symfony.com/doc/current/components/serializer.html
http://www.django-rest-framework.org/api-guide/serializers/

Serializers allow complex data such as querysets and model instances to be converted to native Python datatypes that can then be easily rendered into JSON, XML or other content types. Serializers also provide deserialization, allowing parsed data to be converted back into complex types, after first validating the incoming data.

https://en.wikipedia.org/wiki/Comparison_of_data_serialization_formats

brief history

In the late 1990s, a push to provide an alternative to the standard serialization protocols started: XML was used to produce a human readable text-based encoding. Such an encoding can be useful for persistent objects that may be read and understood by humans, or communicated to other systems regardless of programming language. It has the disadvantage of losing the more compact, byte-stream-based encoding, but by this point larger storage and transmission capacities made file size less of a concern than in the early days of computing. Binary XML had been proposed as a compromise which was not readable by plain-text editors, but was more compact than regular XML. In the 2000s, XML was often used for asynchronous transfer of structured data between client and server in Ajax web applications.

JSON is a more lightweight plain-text alternative to XML which is also commonly used for client-server communication in web applications. JSON is based on JavaScript syntax, but is supported in other programming languages as well.

Another alternative, YAML, is similar to JSON and includes features that make it more powerful for serialization, more "human friendly," and potentially more compact. These features include a notion of tagging data types, support for non-hierarchical data structures, the option to structure data with indentation, and multiple forms of scalar data quoting.

Many institutions, such as archives and libraries, attempt to future proof their backup archives—in particular, database dumps—by storing them in some relatively human-readable serialized format.

google gears

Le transfert de fichier texte avec l'apparition de l'internet a laissé place à des protocoles client/Serveur gérant le transfert de données sous forme de classes. Les anciens clients avaient des cookies dont la taille et l'origine étaient limités. Les objets sont l'évolution des cookies et peuvent ou non être sauvegardés dans l'espace de travail du navigateur web.

Google Gears est un plug in AJAX pour navigateur web. Il permet de façon transparente de sauvegarder des données localement dans une base de données SQLite durant une connexion internet. Ces données pourront être utilisées en mode non connecté. Il est fourni par défaut avec Google Chrome. Les services web en ligne Google Reader et Remember the Milk sont compatibles Google Gears
https://fr.wikipedia.org/wiki/S%C3%A9rialisation

Zenodo serializer

http://pythonhosted.org/zenodo/api/records.html#module-zenodo.modules.records.serializers

bibtex, marcxml, json, oai, datacite.

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

Friday, February 3, 2017

metadata, DOI and crossRef 2.0 (2017)

Intro

Metadata Search is our primary user interface for searching and filtering of our metadata. It allows users to quickly enter any term and users can search and filter on a number of elements, including ISSN, ORCIDs, funding data and more. It can be used to lookup the DOI for a reference or a partial reference or a set of references.
https://www.crossref.org/services/metadata-delivery/

In order to encourage publishers and other content producers to embed metadata into their PDFs, we have released an experimental tool called “pdfmark”, This open source tool allows you to add XMP metadata to a PDF. What’s really cool, is that if you give the tool a Crossref DOI, it will lookup the metadata in Crossref and then apply said metadata to the PDF. More detail can be found on the pdfmark page on the Crossref Labs site. The usual weasels words and excuses about “experiments” apply.
dec 2009
https://www.crossref.org/blog/add-crossref-metadata-to-pdfs-using-xmp/

Using Crossref metadata to enable auditing of conformance to funder mandates: A Guide for publishers
Funders are increasingly setting mandates around publications that result from research they have funded. The mandates include specifications about licenses, embargoes, and notifications of publication acceptance and/or publication. This poses logistical problems for all the parties involved. Funders will need a way to track outputs from thousands of publishers. Publishers will need a standard and efficient way to demonstrate conformance to the mandates. All the stakeholders in the process (funders, publishers, institutions and researchers) will span disciplines, institutions, geographies and jurisdictions. Crossref was setup specifically to deal with these sorts of multiple bilateral relationships.

Crossref has extended its metadata schemas and Application Programming Interfaces (APIs) to enable funding agencies, institutions and publishers to use Crossref as a metadata source that can be used to track research that is subject to these mandates and to ensure that said research is being disseminated according to the requirements of the mandates.

https://data.crossref.org/schemas/

Ref.
https://github.com/CrossRef/rest-api-doc/blob/master/funder_kpi_metadata_best_practice.md

60 ref in
https://www.crossref.org/categories/metadata/

Get ready for Crossmark 2.0

Publishers can upgrade to the new and improved Crossmark 2.0 including a mobile-friendly pop-up box and new button. We will provide a new snippet of code for your landing pages, and we’ll support version v1.5 until March 2017.
We recently revealed a new look for the Crossmark box, bringing it up-to-date in design and offering extra space for more metadata. The new box pulls all of a publication’s Crossmark metadata into the same space, so readers no longer have to click between tabs.
Linked Clinical Trials and author names (including ORCID iDs) now have their own sections alongside funding information and licenses.

https://www.crossref.org/blog/get-ready-for-crossmark-2.0/

https://www.crossref.org/blog/crossref-to-auto-update-orcid-records/

This is a summary of the technical and production steps that a publisher will need to follow to participate in CrossMark.
Sign up

Drop an email to crossmark_info@crossref.org to let us know that you want to get started with CrossMark. CrossMark fees are activated when you start to deposit, and are US$0.20 for current content, $0.02 for back file (older than two years)

CrossMark metadata should be deposited as part of a regular CrossRef DOI deposit, but can also be deposited as stand-alone data to help publishers populate their backfiles.

Record the DOI in HTML metadata

The publisher should ensure that the DOI is embedded in the HTML metadata for all content to which CrossMark buttons are being applied as follows:

<meta name=”dc.identifier” content=”doi:10.5555/12345678” />

http://crossmarksupport.crossref.org/technical-implementation-guidelines/

DOI

Over 20,000 DOI name prefixes within the DOI System
Over 5 billion DOI resolutions per year

Relation to other schemes

Strong focus on interoperability and on working with existing and new schemes; technical, syntactic, and semantic interoperability

http://www.doi.org/factsheets/DOIKeyFacts.html

Thursday, February 2, 2017

semi-automatiser des liens DOI d'une liste de référence bibliographique dans adobe InDesign

Voici une procédure semi-automatique

copier la bibliographie d'un article mis en forme dans InDesign
Une référence par ligne.
Si elles sont numérotées, nettoyer avec un éditeur
Par exemple MS word : remplacer ^p ^?^?^?^? par ^p
coller dans le metamoteur CrossRef
http://search.crossref.org/references
Match references to DOIs using Crossref Metadata Search fuzzy matching
Paste references into the box below, making sure that there is one reference on each line. You may copy and paste the references section of an article but must adjust the references to one-per-line. This tool does not understand reference numbering.
hélas suivant la mise en forme des références (erreurs, pas de titre (i.e. que auteurs et journal) et le "fuzzy" moteur, les liens DOI des références proposés ne sont pas bons.
Il faut donc les vérifier. même avec un "Match score" assez bon.. Puis copier le lien qui est OK, hélas, un par un...
Coller le lien en dessous de la référence dans InDesign
Deux possibilités

si les liens DOI sont simples comme "http://dx.doi.org/10.1137/0720033"
les coller puis
les sélectionner tous
et faire menu "texte" puis "hyperlien..." puis "convertir les URL en hyperliens"
si des liens sont du style "http://dx.doi.org/10.1016/0045-7949(92)90306-k"
la conversion en hyperlien n'est pas bonne.
Il faut sélectionner le lien puis y faire clic droit,
puis "objet interactif" puis "nouvelle cible d'hyperlien".

Rem. ne pas oublier de créer un style de caractère avant par exemple "DOI" en mettant couleur bleu et surligné.

Plus

https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md

Thursday, January 26, 2017

JSTOR, open access and DOI

We are pleased to announce a new program to make Open Access monographs available on the JSTOR platform. An initial set of titles is available from four outstanding publishers: University of California Press, University of Michigan Press, UCL Press, and Cornell University Press. We expect to add several hundred more Open Access titles over the next year.

The ebooks, which reflect JSTOR’s high standards for quality content, are freely available for anyone in the world to use. Each ebook carries one of six Creative Commons licenses determined by the publisher. The titles are easy to use, with no DRM restrictions and no limits on chapter PDF downloads or printing. Users will not need to register or log in to JSTOR. Librarians can receive free MARC records and activate the titles in discovery services.

This initiative furthers JSTOR's mission to expand access to knowledge and education while lowering costs, and joins other efforts to maximize access including the Early Journal Content program, the Register and Read program, and the African Access Initiative. We look forward to sharing what we learn with the scholarly community.

October 25, 2016
http://about.jstor.org/news/open-access-ebooks-now-available-jstor

http://about.jstor.org/open-access?cid=dsp_j_oabooks_10_2016&utm_source=jstor&utm_medium=display&utm_campaign=books_ad_dec2015&cid=dsp_booksad_Oct2016

https://en.wikipedia.org/wiki/JSTOR
---

http://about.jstor.org/publishers-faq

How will JSTOR work with CrossRef?
JSTOR has joined CrossRef and paid membership dues. JSTOR plans to register DOIs for all articles in the archive that have not previously been registered. This will enable users of the CrossRef system to link to hundreds of years worth of articles in the arts, humanities, sciences, and social sciences.

Are there any fees for having JSTOR register DOIs for our articles?
JSTOR covers all the fees associated with registering DOIs on behalf of our participating publishers in the archive collections.

Will JSTOR register DOIs with Cross Ref for all content types?
No. JSTOR will only register DOIs for full length articles and book reviews. This is the content most likely to be cited in other publications and therefore the target of links. JSTOR may decide to include other materials (news items, editorials, etc.) in the future.

---

DOI's are managed by Crossref.org. For each DOI, Crossref's database has a redirect to the current location of that digital object, and the owners can move things around and update the Crossref database as needed. When you follow a link to http://dx.doi.org/doi..., the crossref servers redirect this request to the current location of that paper. As mentioned in another answer you can lookup an article in the crossref.org database to see whether or not it has a DOI.

Recent articles have typically been assigned a DOI by the publisher, and most publishers put the DOI on the title page of the paper so it's easy to find that way.

Older articles were originally published without a DOI, but the publisher may have assigned one after the fact. If the publisher has not already assigned a DOI, then JSTOR may have assigned a DOI to the article that will point to the copy of the article in the JSTOR database. This is a service offered to publishers by JSTOR, but not all publishers use it. Thus not all articles in JSTOR have DOI's.

It appears that the article you linked to has not been assigned a DOI by either its original publisher or JSTOR and thus has no DOI. I can't find the article in the crossref database. The "stable URL" that you linked to is probably the best way to link to the article.

http://academia.stackexchange.com/questions/42233/how-to-find-doi-for-article-in-jstor
---

An example of a free article

http://www.jstor.org/stable/10.1086/674336

For example, in JSTOR
search "biophotonics"
you will get only one article:

'Biophotonics' is inside the text of this article.
If you download the pdf, you will get a pdf (you copy/paste text).

If you click, you will see this infos
and the DOI of jstor

Three "sheets"

Pages