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},
}

a slideshare on OpenAIRE, Infrastructure for Open Science, Zenodo and openDOAR. A map of repositories.




LOCATE A REPOSITORY Deposit once! via OpenAIRE
https://www.openaire.eu/participate/deposit/idrepos

https://www.slideshare.net/OpenAIRE_eu/openaire-einfrastructure-for-open-science






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

Monday, March 6, 2017

installing Python 3 on Mac OS X >sierra


Installing Python 3 on Mac OS X
The latest version of Mac OS X, Sierra, comes with Python 2.7 out of the box.
->Terminal ->python
Python 2.7.10 (default, Jul 30 2016, 19:40:32) 

[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin

You do not need to install or configure anything else to use Python 2. These instructions document the installation of Python 3.

The version of Python that ships with OS X is great for learning but it’s not good for development. The version shipped with OS X may be out of date from the official current Python release, which is considered the stable production version.
http://docs.python-guide.org/en/latest/starting/install3/osx/#install3-osx


Upload a PDF and publish with many metadata to ZENODO. JSON template.



For a long introduction see
http://stephane-mottin.blogspot.fr/2017/01/zenodo-github-research-data-repository.html
see also the posts with the tag "zenodo"

Here we will focus on the process and on the metadata.

4 methods
  • manual
  • python or cURL
  • tools

manual via upload user interface

Invenio and Zenodo uses the tool "json editor"
  https://github.com/jdorn/json-editor


11 fields

  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!!!)
      https://zenodo.org/dev#collapse-list16
      description String Abstract or description for deposition.
      Following HTML tags are allowed: a, p, br, blockquote, strong, b, u, i, em, ul, ol, li, sub, sup, div, strike.
    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
    witch appear on the bottom of the page
  9. journal
  10. c
  11. Book
    1. Publisher
    2. Place
    3. ISBN
    4. Book Title
    5. Page (of this book)

METADATA


schema JSON ZENODO

description Abstract or description for deposition. 

Following HTML tags are allowed: 
a, p, br, blockquote, strong, b, u, i, em, ul, ol, li, sub, sup, div, strike.

<ul>
  <li>prem</li>
  <li>second</li>
  <li>thrird</li>
</ul>

En outre attention à ce que votre texte ne contienne pas de ' ou de " comme  d'avantage ;)

code GitHub

code analyse metadata

python or cURL

Create a new deposition resource with cURL

http://developers.zenodo.org/?shell#list
curl -i -H "Content-Type: application/json" -X POST
     --data '{"metadata": {"title": "My first upload", "upload_type": "poster", "description": "This is my first upload", "creators": [{"name": "Doe, John", "affiliation": "Zenodo"}]}}' /api/deposit/depositions/?access_token=ACCESS_TOKEN


other example:
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/

curl  is  a  tool  to transfer data from or to a server, using one of the supported protocols
       (DICT, FILE, FTP, FTPS, GOPHER, HTTP, HTTPS, IMAP, IMAPS, LDAP,  LDAPS,  POP3,  POP3S,  RTMP, RTSP,  SCP,  SFTP,  SMB, SMBS, SMTP, SMTPS, TELNET and TFTP).
The command is designed to work without user interaction.

Create a new deposition resource with python

It's easier to publish with python:
http://developers.zenodo.org/?python#quickstart-upload
This short guide will give a quick overview of how to upload and publish on Zenodo, and will be using Python together with the Requests package.

more info

http://zenodo.readthedocs.io/en/latest/api/records.html
http://zenodo.readthedocs.io/en/latest/api/deposit.html

Testing

We provide a sandbox environment where you can test your API integration during development. The sandbox environment is available at http://sandbox.zenodo.org.

Please note that the sandbox environment can be cleaned at anytime. Also, the sandbox environment will issue test DOIs using the 10.5072 prefix instead of Zenodo’s normal prefix (10.5281).


Tools Zenodio

Zenodo I/O
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.

The zenodio.metadata sub package provides a Python representation of Zenodo metadata (but not File or Zenodo deposition metadata).

https://github.com/lsst-sqre/zenodio/tree/metadata_api
http://zenodio.lsst.io/en/latest/
https://jira.lsstcorp.org/browse/DM-4852

Python template

zenodo JSON format
example for a book section (in french).

see the details of each field

see how to use at

see the page of this record:

JSON


data = {'metadata':{'upload_type': 'publication','publication_type': 'section','title': 'Introduction au dimensionnement', 'creators': [{'name': 'Pádua, Agílio'}],'partof_pages':'17-25','contributors': [{'name': 'Boissinot, Patrick ', 'type': 'DataCollector'},{'name': 'Langlois, Patrick ', 'type': 'DataCollector'},{'name': 'Pádua, Agílio', 'type': 'DataCollector'},{'name':'Lelièvre, Gérard', 'affiliation': 'CNRS', 'type': 'Editor'},{'name':'Mottin, Stéphane', 'affiliation': 'CNRS', 'type': 'Editor', 'orcid': '0000-0002-7088-4353'},{'name':'Mottin, Stéphane', 'affiliation': 'CNRS', 'type': 'RightsHolder', 'orcid': '0000-0002-7088-4353'}],'notes': ' licence CC-BY-NC-ND; Ce volume est une 3ième édition. Collection -- Intégrations des savoirs et savoir faire-- dirigée par Stéphane MOTTIN; http://www.sudoc.fr/155436619 (voir SUDOC pour trouver cet ouvrage en bibliothèque); ce PDF contient des metadata bibliographiques directement utilisables par exemple par Jabref (logiciel open source pour bibTeX). Ce PDF est structuré.','partof_title': 'Matériaux et joints d étanchéité pour les hautes pressions','publication_date': '2011-04-15','description': ' <b>  Sommaire de ce volume 18 de la Collection Intégrations des savoirs et savoir faire </b> <ul> <li>Préface / Dominique Leguillon</li><li>P. 13; Introduction générale / Patrick Boissinot, Patrick Langlois, Agílio A.H. Pádua</li><li>P. 17; Introduction au dimensionnement / Agílio A.H. Pádua; <br /> 1 Définition du problème; 2 Dimensionnement; 3 Obturateurs; 4 Conclusion</li><li>P. 27; Frettage et autofrettage / Patrick Langlois;<br /> 1 Considérations préliminaires au frettage; 2 Frettage d une enceinte bibloc; 3 Frettage d une enceinte multibloc; 4 Formulation de l autofrettage; 5 Modes de réalisation de l autofrettage; 6 Conclusion</li><li>P. 51; Méthodes d éléments finis en calcul de structures élastiques / Joël Frelat;<br /> 1 Introduction; 2 Rappel de la formule théorique; 3 Formulation variationnelle; 4 Formulation numérique; 5 Etapes d une mise en oeuvre pratique; 6 Conclusion Extension aux problèmes non linéaires</li><li>P. 61; Les matériaux sidérurgiques et les hautes pressions / Jean-Paul Dichtel; <br /> 1 Caractérisation mécanique des aciers; 2 Métallurgie des aciers et superalliages; 3 Commentaires : la Directive Européenne Appareils à Pression</li><li>P. 73; Les métaux non ferreux Alliage cuivre-béryllium et titane / Jean-Pierre Petitet; <br /> 1 Introduction; 2 Le cuivre-béryllium; 3 Le titane</li><li>P. 81; Les Carbures cémentés WC-Co / Emmanuel Pauty;<br />  1 Les procédés de fabrication; 2 Les propriétés des carbures cémentés; 3 Conclusions</li><li>P. 95; Choix et usinage des carbures de tungstène / Jacques Calzas;<br />  1 Choix des carbures de tungstène; 2 Usinage du carbure de tungstène</li><li>P. 107; Céramiques et matériaux pour l optique / Jean-Claude Chervin;<br />  1 Céramiques; 2 Matériaux pour l optique</li><li>P. 137; Types de joints et de montage / Roger Argoud et Jacques Roux;<br />  1 Introduction; 2 Généralités; 3 Joints à basse pression; 4 Joints cône sur cône; 5 Joints Bridgman Champignon; 6 Joints annulaires auto-serrés; 7 Joints coniques d Amagat; 8 Autres joints; 9 Conclusion</li><li>P. 157; Joints hautes pressions pour la compression de gros volumes solides / Sylvie Le Floch;<br />  1 Joints solides utilisés dans les différents types d enceintes hautes pressions; 2 Matières premières des joints; 3 Assemblages HP-HT</li><li>P. 169; Le matériel standard / Jean-Pierre Petitet;<br />  1 Tubes, conduites et raccords; 2 Les vannes; 3 Quelques types d enceintes commercialisées; 4 Les générateurs de pression; 5 Le matériel moins standard</li><li>P. 183; Assemblages haute pression / Gérard Hamel;<br />  1 Montage des raccords de pressions; 2 Montage de quelques passages électriques; 3 Les passages de thermocouple; 4 Les passages optiques, montage des fenêtres; 5 Montage des joints et des obturateurs sur une cellule haute pression</li><li>P. 193; Usinage / Jean-Pierre Michel;<br />  1 Introduction; 2 Les joints de faible épaisseur; 3 Les bagues anti-extrusion à 45; 4 Les joints à 45; 5 Les joints  double Bridgman ; 6 Les joints plats en élastomères; 7 Les joints en indium (étanchéité en hélium et azote liquide; 8 Joints métal-métal type Lens ring; 9 Les passages du courant; 10 Usinage de matériaux exotiques</li><li>P. 207; Les règles de sécurité / Patrick Boissinot;<br />  1 Dangers présentés par les appareils à pression; 2 Appareils à pression rencontrés dans les laboratoires et facteurs de risques; 3 Principes généraux de prévention et réglementation; 4 Moyens de protection; 5 Conclusion</li> </ul> ','keywords': ['Hautes pressions - Matériaux', 'Joints d étanchéité', 'Matériaux - Effets des hautes pressions'],'imprint_isbn': '2862723304','subjects': [{'term': ' Physical sciences ', 'identifier': ' http://id.loc.gov/authorities/subjects/sh89005705.html ', 'scheme': 'url'}],'related_identifiers': [{'relation': 'isCitedBy', 'identifier': 'http://www.sudoc.fr/078023866'}, {'relation': 'isCitedBy', 'identifier': 'https://hal.archives-ouvertes.fr/INTEGRATIONS/page/materiaux-et-joints-etancheite-pour-les-hautes-pressions'}],'communities': [{'identifier':'integrations'}],'access_right': 'open','license': 'cc-by-nc-4.0', 'imprint_publisher': 'MRCT-CNRS','imprint_place': 'Meudon, France',}}

Friday, March 3, 2017

pdf balisé signet structuré avec sommaire dynamique. InDesign, word, acrobat, LibreOffice, OpenOffice. Convert equation OMML mathML.





Un exemple de PDF structuré généré avec Word 2016 sous windows 

Le balisage (tag en anglais) à plusieurs avantages :

  • cela permet au document PDF de s’adapter à n’importe quelle taille d’écran, y compris sur les périphériques mobiles. C’est donc indispensable pour diffuser des eBooks favorisant au mieux l’expérience utilisateur.
  • cela rend le fichier PDF accessible aux handicapés (visuels ou moteurs) : la structure logique du texte étant balisée par des marqueurs spécifiques, les logiciels d’assistance à la lecture ou de synthèse vocale n’ont aucune difficulté pour en restituer fidèlement le contenu.
  • cela permet aux moteurs de recherche d’accéder à un texte correctement référencé.


Depuis InDesign ou LibreOffice c’est un jeu d’enfant, il suffit de cocher la case adéquate.
On peut aussi créer des PDF balisé depuis les logiciels de Microsoft Office, sous réserve d’utiliser Acrobat PDFMaker lors de la conversion en PDF (sur Windows uniquement).

Que faire quand on ne peut pas utiliser les logiciels cités ci-dessus, ou bien si on doit utiliser de « vieux » documents PDF dont on n’a plus les originaux ?

À ma connaissance actuellement Acrobat est le seul logiciel qui puisse s’acquitter de cette tâche (depuis la version 9 cette opération peut s’effectuer automatiquement). Mais il ne faut en attendre de miracles, selon la complexité du document il y aura plus ou moins de retouches manuelles à faire.
http://www.pdf-accessible.com/

http://abracadabrapdf.net/ressource...cation/creer-signets-automatiquement-acrobat/

Ref. http://abracadabrapdf.net/le-pdf-parfait/balisage-et-accessibilite/

InDesign

https://helpx.adobe.com/fr/indesign/using/structuring-pdfs.html#adding_structure_to_pdfs

https://helpx.adobe.com/fr/indesign/using/dynamic-pdf-documents.html

Word Mac, LibreOffice, OpenOffice

Créer un PDF balisé avec Word pour Mac pas possible même avec word 2016 (http://stephane-mottin.blogspot.fr/2017/02/pdf-interpreter-converter-word-to-pdf.html).
Avec save PDF c'est OK mais pour que pour des petits fichiers. De plus il faut que les équations soient en format OMML.
http://stephane-mottin.blogspot.fr/2017/01/exporter-fichier-format-equation-word.html

Le processus le plus fluide et complet serait d'utiliser LibreOffice, même si c'est juste pour la conversion en PDF, parce-que ça éviterait l'étape avec Acrobat Pro (LibreOffice génère aussi les Signets et sommaire).
https://forums.macg.co/threads/acrobat-xi-creation-dun-pdf-balise-a-partir-dun-doc-word.1262385/

LibreOffice (15.4.3; version début 2017) a des problèmes de conversion des notes de bas de page (avec des équations) en ouvrant en .doc ou .docx. Ouvrir en .docx (et converti) pose moins de problème.
On a des problèmes avec les équations réalisées avec l'ancien éditeur d'équation (mathtype) et un peu moins  en OMML (les raçines posent problèmes).
Les équations non OMML sont transformées en image par LibreOffice alors que celles en OMML restent en format équation. Si on clique sur celle-ci dans LibreOffice on peut éditer l'équation.
http://stephane-mottin.blogspot.fr/2017/01/exporter-fichier-format-equation-word.html

La génération en pdf balisé et sans perte de compression pour les images est OK.


OpenOffice (4.1.3; fin 2016) n'affiche pas les équations si on ouvre le fichier en .docx. Si on ouvre en .doc les équation sont à 50% OK mais nous avons d'autres problèmes avec dans le texte des caractères "bizarres"  (les insertions "symboles"). Les notes de bas de page sont OK.

Thursday, March 2, 2017