# How to Open up? (Digital) Libraries at the Service of (Digital) Scholars

Laurent Romary

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## To cite this version:

Laurent Romary. How to Open up? (Digital) Libraries at the Service of (Digital) Scholars. Fiesole Collection Development Retreat, Apr 2017, Villeneuve d'Ascq, France. hal-01513674

HAL Id: hal-01513674

https://inria.hal.science/hal-01513674

Submitted on 25 Apr 2017

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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# How to Open up?
## (Digital) Libraries at the Service of
## (Digital) Scholars

Laurent Romary

Inria - team ALMAnaCH
Upside - down

* Libraries as scientific content openers
  - Forgetting the old duties...

* A pragmatic view based on a national and institutional experience
  - Policies and infrastructures

* It's the digital turn, stupid!
  - Identifying the role and limits of technologies
# A paradigm change

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Provides
content

<figure><img src="image_4.png" /></figure>

Publishes
content

Consumes
content

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Publishes
content

<figure><img src="image_6.png" /></figure>
# A paradigm change

Once upon a time...

* Collection development

* Budget management

* Cataloguing

... and warehousing

A tough history

* Serial crisis

* Big deals

* Green and gold OA

Diving in the (cold waters of a) new world

* Coordinating scholarly publication management

* Digital content management
  - licencing, persistent identifiers, access statistics

* Drafts, reports, publication, theses, and data

...no management of physical content

... nor of open access (it's in the genes)

High-Low → low stewardship?

* Research and learning material
A FAVOURABLE CONTEXT
# Inria — a research organisation with a vision

4,400

People

(60 % paid by Inria)

8

Research Centers
in France

41

International
conferences

66

Scientific
publications

4,450

180

Project teams

250

Active patents

1,000 Doctoral students

100 Post-Doctoral

300 R&D engineers

3,500

Scientists

A BUDGET OF

€ 265M

Inria
INVENTEURS DU MONDE NUMÉRIQUE

## Vision for a scientific information policy

* Maximising the dissemination of our scientific assets (visibility and swift dissemination of knowledge), for a reasonable price

* Constitution of a reliable and sovereign institutional corpus (documentation, preservation, access), with clear public governance principles

* Contribution to shaping the scientific communication landscape in terms of editorial processes and usage made of scientific productions
# Inria scientific information policy in concrete terms

* Setting up priorities

– Printed material as disposable goods

– Deposit mandate on scientific publications

– Rejecting hybrid open access

– Engaging in developing new publication models

* Consequences

– Less collection development on the basis of our acquisitions (national consortia, national licences)

– More collection development as part of the digital curation activities
Two additional contextual elements

* A strong political support

- State: *loi pour une république numérique*

* Published in September 2016

* Two articles on *open access* and *text and data mining*

- Higher education and research

* A wide network of institutions favouring the use of publication repositories

* A technical infrastructure

- Centred on a national service Unit: CCSD

* CNRS, Inria, Université de Lyon

- Development of a comprehensive scientific information management platform
The infrastructure at our service

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# HAL – a multi-purpose publication repository

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# Going beyond the limitations of pdf

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Cow (structured data)

Hamburger
(unstructured data)

“Converting PDF to XML is a bit like converting hamburgers into cows. You may be best off printing it and then scanning the result through a decent OCR package.”

Michael Kay (http://lists.xml.org/archives/xml-dev/200607/msg00509.html)

Inspired from: Duncan Hull
# Structuring content

* GROBID: information extraction from PDF documents

* Meta-data: title, authors, affiliations, abstracts

* Bibliographical references (with crossref consolidation)

* Standards-based representation

* TEI (Text Encoding Initiative) as a reference format

* State of the art performance(CRF models)

* Cf. M. Lipinski, et al., 2013

* Used at EPO/ResearchGate/Mendeley/CERN/NASA

* Integrated in HAL

* Automatic meta-data extraction for author's deposit
# Sciencesconf- a conference management tool

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## Services

* Online conference management tool

* Abstracts, full paper, peer review, conference program, registration

## Technologies

* Modular services

* Unique authentication system

* Connection to HAL authorities

* Upload to HAL

## Library support

* Supervises the creation of a conference instance

* Create conference series

* Moderates the integration of the papers as a collection in HAL
# épisciences – an overlay journal
platform

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# AureHAL – authorities management

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## Services

* General purpose authorities

* Authors

* Organisations

* Journals

* National and EU projects

## Technologies

* Connection to external databases

* ORCID, IdRef, VIAF, etc.

* Integration in the French organisational framework

* APIs

* Standardised export formats (TEI, again)

## Library support

* Curates the creation and de-duplication of authorities

* Confronts with external data bases (e.g. EU projects)
AN ENABLING INFRASTRUCTURE
FOR ADDITIONAL SERVICES
# 1. Setting up an institutional digital library

* IFIP - International Federation for Information Processing

- One of the major scholarly society in Information & Communications

- Organized in technical committees and working groups

* Objective: setting up a sustainable digital library

- All volumes publishes as IFIP conferences

- Visibility, trust, technical facilities

* Publication agreement with Springer

- Systematic publication in the AICT, LNBIP and LNCS series

- 3-year embargo before free online dissemination

- Provision of meta-data (XML Springer) and author post-review manuscripts (PDF)

* Note: XML Springer formats often contains full-text

* For Inria: an experiment in ingesting and aggregating legacy collections
# IFIP DL - architecture

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AuréHAL
# IFIP: technical setting

* Standardized ingestion workflow

* Towards a unified TEI-based format for
scholarly papers

— Cf. EU Peer project (massive ingestion of
preprints)

— Istex, OpenEdition, HAL, EPO

— More flexible and extensible than JATS (e.g. full
text)
# IFIP: editorial management

* The central role of library staff

- Quality check: format, content

- Collection management: conference series and volumes, technical committees, working groups, etc.

- Maintenance of authorities in AureHAL: authors, affiliations

- Approximate affiliations and duplicates

- Creation and maintenance of XML schemas and XSLT style sheets

* Next step: introducing more automation

- Objective: limiting boring, repetitive tasks

- Automatic quality check

- Entity matching
# The entity-matching problem

JACQUES NEVEU ET LES MODÈLES PROBABILISTES DE
RÉSEAUX

PHILIPPE

Dans cette brève
dans le domaine des
sonnels en tant
aussi, bien sûr
mathématicien

**Motivation.** Let us
avant tout de s
formatique est

**Inria Sophia-Antipolis:** Prof
Philippe Robert, PUPH at CMRR
CHU Nice Hospital, COBTek

**Inria Paris:** Philippe Robert
Research Director -
Responsable RAP team

nt using different sensors

Sophia Antipolis, France

CMRR Plateforme patient CHU, Nice, France

National Cheng Kung University, Taiwan

EA CoBTek Université de Nice Sophia-Antipolis, France

National Cheng Kung University Hospital, Taiwan

* Corresponding author (francois.bremond@inria.fr)

**Purpose:** Older people population is expected to grow dramatically over the next 20 years (including Alzheimer's patients), while the number of people able to provide care will decrease. We present the development of medical and information and communication technologies to support the diagnosis and evaluation of dementia progress in early stage Alzheimer disease (AD) patients. **Method:** We compare video and accelerometers activity assessment for the estimation of older people performance in instrumental activities of daily living (IADL) and physical tests in
# Mapping

The mapping is a set of domain specific wrappers transforming the input/output from/to the internal data model.

The internal data model is composed of:

- entities

- attributes

- relations

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# HAL authors

**Local attributes:** surname, last name, title, email, etc

Comparison using distances depending upon the type of
the attribute:

e. g. Person Name is computed using Dice Sorensen,
Cosine similarity and Jaro Winkler.

**Relation attributes:** co-authorship, affiliations,
popularity*, years of activity*, etc.

Relations are computed using affiliation information

Preliminary results are promising, F-1 score of 0.964
# HAL organisation

## Representation and errors are more frequent

observatoire astronomique strasbourg

Tout type de structure

Rechercher

Voir

Trier

Afficher

<table><thead><tr><td>id</td><td>name</td><td>sigle</td><td>typestruct</td><td>adresse</td><td>url</td><td>ACTIONS</td></tr></thead><tbody><tr><td>93746</td><td>Observatoire astronomique de Strasbourg</td><td>OAS</td><td>laboratory</td><td>11 Rue de l'université 67000 STRASBOURG</td><td>http://astro.u-strasbg.fr/</td><td> eyes</td></tr><tr><td>1102</td><td>Observatoire astronomique de Strasbourg</td><td>OAS</td><td>laboratory</td><td>11 Rue de l'université 67000 STRASBOURG</td><td>http://astro.u-strasbg.fr/</td><td> eyes</td></tr><tr><td>473646</td><td>CDS, Centre de Données astronomiques de Strasbourg, Observatoire astronomique de Strasbourg, France</td><td></td><td>laboratory</td><td></td><td></td><td> eyes</td></tr><tr><td>8740</td><td>CDS, Centre de Données astronomiques de Strasbourg, Observatoire astronomique de Strasbourg, France + ESO, European Southern Observatory, Garching bei Muenchen, Allemagne</td><td></td><td>laboratory</td><td></td><td></td><td> eyes</td></tr><tr><td>9182</td><td>Observatoire Astronomique de Strasbourg</td><td></td><td>laboratory</td><td></td><td></td><td> eyes</td></tr><tr><td>388886</td><td>Observatoire astronomique de Strasbourg</td><td></td><td>researchteam</td><td></td><td></td><td> eyes</td></tr><tr><td>209748</td><td>Université de Strasbourg, CNRS, Observatoire Astronomique</td><td></td><td>laboratory</td><td>Université de Strasbourg, CNRS, Observatoire Astronomique, 11 rue de l'Université, 67000 Strasbourg, France</td><td></td><td> eyes</td></tr><tr><td>13307</td><td>observatoire astronomique de strasbourg</td><td></td><td>laboratory</td><td></td><td></td><td> eyes</td></tr><tr><td>305832</td><td>observatoire astronomique de strasbourg</td><td></td><td>institution</td><td></td><td></td><td> eyes</td></tr></tbody></table>
# HAL organisation

**Local attributes:** name, address, region, country, etc

**Relation attributes:** mother-child (e.g Inria -> Inria Paris), authors affiliated, global relations*

Like for authors, relations are computed using complementary information.

Preliminary results are still too low, F-1 score of 0.345
## 2. Exploiting repository contents: AnHALytics

* Objectives

- Designing a scholarly dashboard

* Scientific profiles: publications and authors

- Experimenting various data extraction mechanisms

* Reference content from the HAL publication repositories

- Meta-data: title, periods, authors, affiliations

- Full-text: full-text indexing, conceptual search

* Technical background

- NERD and Grobid full text

* Librarians are shaping the service with developers

- Researchers, Inria management
## SOURCES

arXiv.org

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HAL
archives-ouvertes.fr

OAI-PMH

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PDF

TEI

XML

## DEDUPLICATION

## KNOWLEDGE BASE

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GRAPHDB

INDEX

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TEI

## PERSISTANCE

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mongoDB

OCR

GROBID

(N)ERD

KEYTERM

GROBID-QU

BIOGROBID

## ANNOTATEURS

ISTEX

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$

...
Making things concrete

* AnHALytics - demo Inria
Plugging additional technologies - 1

* Grobid quantities

- Identifying measured quantities in scientific documents

- Value, unit, measured entity

- Multiple search scenarios in a scholarly context

[Example](example 2, streptomycin)
The cells were washed three times with RPMI1640 medium (Nissui Pharmaceutical Co.). The cells (1 x10⁷) were incubated in RPMI-1640 medium containing 10% calf fetal serum (Gibco Co.), 50 µg/ml streptomycin, 50 IU/ml of penicillin, 2-mercaptoethanol (5 x 10⁻⁵ M), sheep red blood cells (5 x 10⁶ cells) and a test compound dissolved in dimethyl sulfoxide supplied on a microculture plate (NUNC Co., 24 wells) in a carbon dioxide gas incubator (TABAI ESPEC CORP) at 37°C for 5 days.

A solution of 1.18 g (4.00 mmols) of the Compound a obtained in Reference Example 1, 0.39 g (4.13 mmols) of 4-aminopyridine and 20 ml of toluene was heated to reflux for 2 hours. After cooling, the reaction mixture was poured into 1 N sodium hydroxide aqueous solution, and washed twice with chloroform. 2 N Hydrochloric acid aqueous solution was added to the aqueous layer and the precipitated white crystals were filtered and dried to give 0.73 g (yield: 53%) of Compound 3.

Atomic value

raw value: 50

raw unit name: µg/ml

normalized value: 0.00005

normalized unit name:
kg/m^4

quantified (experimental):

raw: streptomycin

normalized: streptomycin
# Plugging additional services - 2

* Re-publishing content

- Grobid-TEI as a pivot format in the publishing environment

- Generation of multiple derived format

* HTML

* ePub

* Braille

* How far are we from this?

- Improving the performances of Grobid (e.g. book)

- Partially implemented in various initiatives

* Revues.org

* Istex

* There again, a central role for the library staff

- Identifying user expectations

- Maintaining formats and transforms
Conclusion

* Digital sovereignty

- Mastering scholarly content at all stages of the publication process

- Mastering the whole scholarly process

• Understanding where and when we need to resort to the private sector

- Mastering interoperability by means of open formats

- A general culture of openness

* Focusing our efforts

- More brain, budget etc. in shaping this digital turn

- Stop losing time in “negotiating” open access: let's just do it

* Dedicated research activity on scholarly information management

- TDM breakthroughs at the service of scientific information

- Dealing with the quickly evolving digital context

- Coupling service units with adequate research teams

* Training future digital librarians

- Formats, standards and related technologies

- Data mining and visualisation
References

* Mabe M. A., Scholarly communication: A long view, *New Review of Academic Librarianship*, 2010 - Taylor & Francis

* Hopfield J. J., Neural networks and physical systems with emergent collective computational abilities, *Proc. Natl. Acad. Sci. U.S.A.*, 79 (1982), pp. 2554–2558

* Berthaud Christine, Laurent Capelli, Jens Gustedt, Claude Kirchner, Kevin Loiseau, et al.. EPISCIENCES - an overlay publication platform. *ELPUB2014*, Jun 2014, Thessalonique, Greece. <http://www.ebooks.iospress.nl/publication/36552>. <10.3233/978-1-61499-409-1-78>. <hal-01002815v2>

* Romary Laurent. Scholarly Communication. Mehler, Alexander and Romary, Laurent. *Handbook of Technical Communication*, de Gruyter, 2012, 978-3-11-022494-8. <inria-00593677>