1. Information structuring in the PEER project
Back to meaning
Information structuring
in the PEER project
Foudil Bretel1, Patrice Lopez1-2, Maud Medves1-2, Alain Monteil1, Laurent Romary1-2
1INRIA
2Humboldt Univ. Berlin
PEER Publishing and the Ecology of European Research

2. Sorting out the chaos?
Vision: channelling heterogeneous (publisher’s) data into one single (meaningful) format
Material: PDF with metadata – what can the TEI do with it?
Articulating a pivot/reference format seen as a strict customization of the TEI
Exploring the possibility of automatic metadata extraction from PDFs
PEER Publishing and the Ecology of European Research

3. Why is it so difficult?
Great heterogeneity of format within publishers
Meta data (and full-text)
Proprietary, ScholarOne, NLM 2.0, NLM 3.0, …
Various issues
Affiliations
Publication date information
ISO 639 codes (countries)
Bibliographical references
Proprietary metadata fields
PEER Publishing and the Ecology of European Research

4. The information chaos Article title Journal title ISSN (print)
article-title/title | ArticleTitle | article-title | ce:title | art_title | article_title | nihms-submit/title | ArticleTitle/Title | ChapterTitle
Journal title
j-title | JournalTitle | full_journal_title | jrn_title | journal-title
ISSN (print)
JournalPrintISSN | | | PrintISSN | issn-paper
First page of a paper
spn | FirstPage | ArticleFirstPage | fpage | first-page
PEER Publishing and the Ecology of European Research

5. Sorting this out Defining a coherent infrastructure to facilitate
The long-term management of scholarly content in research institutions
Smooth interaction between publishers and research institutions
Better understanding of what each of us can provide
On-going experimental setting: the EU PEER project
PEER Publishing and the Ecology of European Research

6. The PEER project Initiated by the EU commission (DG INFSO)
Objective: study the impact of systematically archiving stage-two outputs in “institutional repositories” (cf. Romary & Armbruster 2010)
on journals and business models
on wider ecology of scientific resarch
Consortium
STM, European Science Foundation (ESF), Goettingen State and University Library (UGOE), Max Planck Gesellschaft (MPG), INRIA
PEER Publishing and the Ecology of European Research

7. Content submission - publishers
Eligible Journals / Articles
Publishers
PEER Depot
Authors
Select
100 % Metadata
50 % Manuscripts
Publishers Transfer
Publishers Deposit
Publishers Inform
PEER Publishing and the Ecology of European Research 7

8. Content submission – to repositories & LTP archive
Publishers Deposit
Authors
Deposit
PEER Depot
Transfer
Transfer
Long-Term Preservation; LTP Depot (e-Depot, KB)
Publicly Available PEER Repositories
UGOE
ULD
MPG
KTU
HAL
TDC
SSOAR
PEER Publishing and the Ecology of European Research 8

9. What has been done Publishers involved the project
BMJ Publishing Group (proprietary format)
Cambridge University Press (NLM2.2)
EDP Science (NLM3.0)
Elsevier (proprietary format)
IOP Publishing (NLM3.0)
Nature Publishing Group (proprietary format)
Oxford University Press (ScholarOne)
Portland Press (NLM2.0)
Sage Publications (proprietary format)
Springer (proprietary format)
Taylor & Francis Group (ScholarOne)
Wiley-Blackwell (ScholarOne)
PEER Publishing and the Ecology of European Research

10. The PEER deposit workflow
Repositories
Publishers
HAL
SUB-Göt
PEER Depot
MPS … KB
Preservation
PEER Publishing and the Ecology of European Research

11. TEI as a pivot format for interchange
General strategy: no information should be lost
Nearly everything in sourceDesc
+ Keywords, Summary, Copyright
Strict author description
Deep encoding of names
Deep encoding of affiliations (Web of Science - 3-level)
Deep encoding of addresses – getting the country right
Precise publishing information
Pagination, DOIs, volume, issue, journals name(s)
Yes, biblStruct is cool!
PEER Publishing and the Ecology of European Research

12. Example Source (Springer proprietary format) PEER format (TEI)
<Author AffiliationIDS="Aff1" CorrespondingAffiliationID="Aff1"> <AuthorName DisplayOrder="Western"> <GivenName>Hucheng</GivenName>
<FamilyName>Qi</FamilyName>
</AuthorName>
<Contact> </Contact> </Author> ….
<Affiliation ID="Aff1"> <OrgName>Durisol, A division of Armtec Limited Partnership</OrgName> <OrgAddress> <Street>51 Arthur Street South</Street> <Postcode>N0K 1N0</Postcode> <City>Mitchell</City> <State>ON</State> <Country>Canada</Country> </OrgAddress> </Affiliation>
Source (Springer proprietary format)
PEER format
(TEI)
<author>
<persName>
<forename type="first">Hucheng</forename>
<surname>Qi</surname>
</persName>
<affiliation>
<orgName type="institution">Durisol, A division of Armtec Limited Partnership</orgName>
<address>
<street>51 Arthur Street South</street>
<postCode>N0K 1N0</postCode>
<settlement>Mitchell</settlement>
<region>ON</region>
<country key="CA">CANADA</country>
</address>
</affiliation>
</author>
PEER Publishing and the Ecology of European Research

13. Example PEER format (TEI) Source (Springer proprietary format)
<sourceDesc> <biblStruct>
<analytic>… <title level="a" type="main" xml:lang="en"> The investigation of basic processes of rapidly hardening wood-cement-water mixture with CO<hi rend="subscript">2</hi> </title>
<title level="a" type="main" xml:lang="de"> Untersuchung der Vorgänge bei der schnellen Härtung einer Holz-Zement-Wasser-Mischung mit CO<hi rend="subscript">2</hi> </title> </analytic> <monogr> <imprint> <date when=" "/>
<biblScope type="fpage">1</biblScope> <biblScope type="lpage">7</biblScope> </imprint>
</monogr> <idno type="DOI"> /s z</idno> <idno type="publisherID">s z</idno> <idno type="articleID">351</idno> </biblStruct> </sourceDesc>
</fileDesc>
PEER format
(TEI)
<ArticleID>351</ArticleID> <ArticleDOI> /s z</ArticleDOI> <ArticleSequenceNumber>0</ArticleSequenceNumber> <ArticleTitle Language="En"> The investigation of basic processes of rapidly hardening wood-cement-water mixture with CO<Subscript>2</Subscript> </ArticleTitle> <ArticleTitle Language="De"> Untersuchung der Vorgänge bei der schnellen Härtung einer Holz-Zement-Wasser-Mischung mit CO<Subscript>2</Subscript> </ArticleTitle> <ArticleCategory>Originals Originalarbeiten </ArticleCategory> <ArticleFirstPage>1</ArticleFirstPage> <ArticleLastPage>7</ArticleLastPage> <ArticleHistory> <RegistrationDate> <Year>2009</Year> <Month>05</Month> <Day>14</Day> </RegistrationDate> <Received> <Year>2008</Year><Month>12</Month><Day>9</Day></Received> <OnlineDate> <Year>2009</Year> <Month>5</Month><Day>30</Day></OnlineDate> </ArticleHistory> <ArticleCopyright> <CopyrightHolderName>Springer-Verlag</CopyrightHolderName> <CopyrightYear>2009</CopyrightYear> </ArticleCopyright> <ArticleContext> <JournalID>107</JournalID> </ArticleContext> </ArticleInfo>
Source (Springer proprietary format)
PEER Publishing and the Ecology of European Research

14. … And when no metadata is available
PEER Publishing and the Ecology of European Research

15. GROBID GeneRation Of BIbliographic Data
A text mining tool for extracting bibliographical metadata at large
Input:
Technical and scientific domains
Scholar documents, technical manuals and patents
Raw text or text with layout information (PDF)
Machine learning approach
PEER Publishing and the Ecology of European Research

16. Metadata extraction from front page
PEER Publishing and the Ecology of European Research

17. Metadata extraction from front page
Extraction of bibliographical information from article header
Fields: title, authors, date, abstract, location, affiliation, book title, journal title, , publication number, web, degree, keywords, etc.
As features, exploitation of
position information (begin/end of line, in the doc.)
lexical information (vocabulary, large gazetteers)
layout information (font size, font style, etc.)
Conditional Random Fields (CRF) (Peng & McCallum 04)
Current training corpus: global examples affiliations/addresses blocks authors sequences, etc.
PEER Publishing and the Ecology of European Research

18. Layout & Block Analysis: XY-Cut algorithm
PEER Publishing and the Ecology of European Research

19. Metadata extraction from header
PEER Publishing and the Ecology of European Research

20. Metadata extraction from header
PEER Publishing and the Ecology of European Research

21. Metadata consolidation
Exploitation of external bibliographical databases for correcting/completing results based on extraction results
Crossref: The full bibliographical record can be obtained based on:
DOI
Journal title, volume, first page
Title + author first name ➞ frequent!
Other databases: xISSN, xISBN, Amazon Web Service
Real time: online requests between seconds
PEER Publishing and the Ecology of European Research

22. Accuracy overview: corpus CORA
Features
Accuracy
Precision
Recall F1
Token
99.65
97.37
94.19
95.75
Field
94.7
Instance
74.91
Instance after consolidation
82.20
Title
99.70
98.24
95.48
96.84
Author
99.38
90.27
96.36
93.21
Date
99.86
97.53
81.07
87.29
Affiliation
99.52
98.25
93.26
95.69
Abstract
98.95
99.64
98.81
99.22
(+9.7%)
PEER Publishing and the Ecology of European Research

23. Extraction from header
Collection
Pre-
processing
Token + features
CRF models
Header
Authors
Affiliations
+ catalog
+ catalog
+ expected result
Document
segmentation
- text segmentation
- feature generation
train
PEER Publishing and the Ecology of European Research

24. Extraction from header
Collection
Pre-
processing
Token + features
CRF models
Header
Authors
Affiliations
+ catalog
+ catalog
+ expected result
Document
segmentation
- text segmentation
- feature generation
train /
classify
post-processing
consolidation
Segmented
document
Term candidates
+ features
terms +
labels
Final biblio.
record
Document
PEER Publishing and the Ecology of European Research

25. Why GROBID ? Cataloguing: mass digitalization User needs:
self-archiving of scholar papers by authors in open archives
metadata not easily available
Extraction of additional metadata: references, keywords, etc. for enriching/correcting existing ones
improvement in search & retrieval
Ease document access from citation strings
Playground for experimenting with CRF models for text mining
PEER Publishing and the Ecology of European Research

26. Lessons
Reusable infrastructure for various types of academic-publisher relation (e.g. Gold OA agreements)
biblStruct is cool
Cf. Michael’s talk: deeply structured
Standardization in the publishing world is still an open issue
… diplomatically put
The TEI has a role to play in the publishing world
Coherence between publication material and other sources
E.g. central role of attribution/authorship/affiliation
Stylesheets to be made available in OxGarage

27. A TEI customization for scholarly publishing
A family of formats based on the TEI customization facilities
Core editing customization (to be further extended – minimal tool support)
Reference customization family for archiving
Can be extended to specific domains: Maths, physics, SVG graphics, etc.
Precise representation of bibliographic information
Specific support through associated tool:
XSLT stylesheets (html, pdf TEI2NLM)
PDF 2 TEI facility (Grobid)
Open Office 2 TEI facilities (maintained at Oxford)
MSWord 2 TEI facilities (TEI project with ISO)
AccessTEI
PEER Publishing and the Ecology of European Research