Presentation given by William Ulate, BHL Technical Director and Global BHL Coordinator on Wednesday February 13, 2013 during the pro-iBiosphere at Leiden

1. The BHL way to content
William Ulate
BHL Technical Director
Global BHL Coordinator
Leiden, Netherlands
February 14, 2013

2. What is BHL?
The Biodiversity Heritage Library is
a consortium of natural history and botanical libraries that
cooperate to digitize and make accessible the legacy
literature of biodiversity held in their collections and to
make that literature available for open access and
responsible use as a part of a global “biodiversity
commons.”

3. Extensive

4. Global…

5. New Partners and Geographies

6. Dear Sir / Madam Can i just
congratulate you on an
The freeing of knowledge absolutely brilliant online
may lead to new resource. I am compiling a
discoveries and changes report on an invasive
hydromedusae and could not
in the way the natural believe the ease and efficiency
world is perceived of this web page which
genuinely saved me weeks of
my life
La plus grande
#bibliotheque #botanique & Research that previously
#zoologique online The took months now takes
largest online botanical &
only a few hours
zoological #library #BHL

7. More Online Content
Pages (Millions) and Volumes (in Thousands)
included in BHL
120
105.85
100
94.6
84.86
80
60
40 40.00 38.9
35.4
31.8
20 22.00 Volumes (K)
16.4
9.2
Pages (M)
-
Oct-08 Oct-09 Oct-10 Oct-11 Oct-12

8. Global Replication & Serving
Replicated Data Center Portal Application

10. > 390,000 views
in 10 months
> 1200 sets
> 60,000+ images

12. The Art of Life project: describing and providing access to
natural history illustrations from the Biodiversity Heritage Library (BHL)
Example of illustration described using Art of Life schema
Title Stictospiza formosa
Type Illustrations
Date Publication: 1898
Agent Author: Arthur G. Butler (1844-1925)
Illustrator: F.W. Frohawk (1861-1946)
Description A pair of finches with green and yellow bodies resting on reeds
Subjects Scientific name: Amandava formosa (Latham, 1790)
Vernacular Name: Green Avadavat or Green Munia
Accepted Name: Amandava formosa (Latham, 1790)
Birds, finches
Inscriptions bottom center: Green Amaduvade Waxbill (Stictospiza formosa)
Source Butler, Arthur Gardiner. Foreign finches in captivity. Hull and London: Brumby and
Clarke, limited,1889 (2nd edition). This image comes from the Biodiversity Heritage
Library, and is available online at biodiversitylibrary.org/page/17195895
Rights Public domain
Art of Life schema elements required in Red
Element Definition Examples Repea
t
Agents person or corporate entity involved in <vra:agent> Y
the creation, design, production, or <vra:name type="personal" vocab="LCNAF" refid="89015596>
publication of a visual resource. Curtis,John</vra:name>
<vra:dates type="life">
<vra:earliestDate>1791</vra:earliestDate>
<vra:latestDate>1862</vra:latestDate>
</vra:dates>
<vra:role vocab="AAT" refid="300025574">publisher</vra:role>
</vra:agent>
Copyright The copyright status of the visual <vra:rights refid=”http://creativecommons.org/licenses/by- N
resource. nc/2.0/deed.en”>Creative Commons Attribution-NonCommercial 2.0
Generic (CC BY-NC 2.0)
</vra:rights>
Date Date or range of dates associated with <vra:date type="creation"> Y
the creation or publication of the visual <vra:earliestDate>1945</vra:earliestDate>
resource. <vra:latestDate>1955</vra:latestDate>
</vra:date>
Description A free-text note about content of the <vra:description>This illustration shows a scale, coloured illustration Y
image, including comments, description, of Sepsis annulipes (now known as Encita annulipes) beside the
or interpretation, that gives additional Trifolium ochroleucum plant. Several dissections from Sepsis
information not recorded in other cylindrica Fab. (all these details are provided on the next page of this
categories. book and the subsequent page).</vra:description>
Inscriptions All marks, caption, or written words <vra:inscription> Y
added to the object at the time of <vra:position>bottom</vra:position>
production or in its subsequent history, <vra:text>Radula of L. souleyetianum on a more
including signatures, dates, dedications, reduced scale</vra:text>
texts, and colophons, as well as marks, </vra:inscription>
such as the stamps of silversmiths,
publishers, or printers.
Source A citation for the book, journal or <vra:source><vra:name type=”book”>Butler, Arthur Gardiner. N
resource that hosts the visual resource Foreign finches in captivity. HullBrumby and Clarke, limited,1889 (2nd
edition). </vra:name>
<vra:refid
type=”URI”>http://biodiversitylibrary.org/page/17195895</vra:refid>
</vra:source>
Subject Terms or phrases that describe, identify, <vra:subject><vra:term type=”personalName”>Carl Y
or interpret the visual resource. Linnaeus</vra:term></vra:subject>
<dwc:scientificName>Plant: Picea abies</dwc:scientificName>
<dwc:acceptedName>Plant: Picea abies</dwc:acceptedName>
<dwc:vernacularName>Plant: Norway spruce<dwc:vernacularName> We welcome your feedback on the schema! http://tinyurl.com/9hm7nsb
Title The title or identifying phrase given to an <vra:title xml:lang=”la”>Sepsis annulipes</vra:title> Y
Image <vra:title type=“alternate”>Orangutan</vra:title>

16. Where are we?
• Scientific Name Extraction
– Improved algorithm (Thanks uBio!)
• Articles
– Extended BHL data model to store article metadata
– Content and Process to harvest data from BioStor in place
• Create user interfaces for adding article metadata and
associated files
– Functional requirements defined
– Process flow for adding article metadata and associated files
– Implement UI changes
• Change BHL UI to accommodate article search
• Change BHL UI to accommodate article display (TOC)

17. Scientific Name Extraction
• TaxonFinder algorithm in production since
2008
– More than 100 million candidate name strings
– More than 1.5 million unique, verified names
– Available through UI, APIs, Data Exports & Internet
Archive
• New collaboration with Global Names
– Improved algorithm, better precision & recall
– More data with TaxonFinder and Neti Neti!

18. Taxon Names
BEFORE
Name Instances 101,591,803 101,288,804
Unique Names 7,498,554 7,464,924
Verified Names 1,905,507 1,902,803
EOL Names 63,130,350 62,963,582
EOL Pages 13,579,868 13,532,684
AFTER
Name Instances 151,222,182 150,066,425
Unique Names 29,246,382 29,091,767
Verified Names 10,153,165 10,109,540
EOL Names 87,791,695 87,135,089
EOL Pages 15,466,713 15,342,867

19. Part-level metadata
• Disambiguating and locating structural
components in the corpus
• Done by automated and crowdsourced means
– Thanks Rod Page! Welcome others!
• Greatly increases semantic value of the dataset
• Addressing important – makes data addressable
and thus linkable

20. Articles in the BHL UI

21. Images

22. PDF Generator

23. Support citation reconciliation
.
.Linneaus, C. Species Plantarum, vol. 2 p. 971. 1753
.Linné, Carl von. Sp. Pl. Vol. 2 Page 971. 1753
.
Caroli Linnaei, Species Plantarum exhibentes plantas rite cognitas, ad genera
.relatas, cum Differentis Specificis, Nominibus Trivialibus,2:971. 1753 Selectis,
Locis Natalibus, secundum SYSTEMA SEXUALE digestas..
Synonymis
.L. Sp. Pl. 2: 971. 1753
.
Zea mays

24. Citations Providers

25. What we’d like to do
http://biodivlib.wikispaces.com/BHL+and+Gaming
^Challenges framed as games
• Improve OCR
• Rekeying Tables of Contents
• Researching candidate Scientific Names
• Image identification & extraction
– http://biodivlib.wikispaces.com/Art+of+Life
– Currently funded by NEH

26. 2007 Name Finding Study
>35% OCR error rate for names only
Of the 3,003 names, 1,056 were incorrectly transcribed by OCR.
Top OCR errors
1 Insert Space 8 n->v
35.16% 2 Omit Space 9 l->i
3 e->c 10 r->i
4 u->I 11 u->ii
5 u->n 12 h->l
Wei, et al. An Evaluation of Taxonomic Name Recognition (TNR) in the 6 i->l 13 h->ii
Biodiversity Heritage Library. Proceedings of TDWG. 2008.
http://www.tdwg.org/proceedings/article/view/380 7 c->e 14 e->o

27. Abbild ungen und Beschreibungen
der
Fische Syriens,
nebst
einer neuen Classification und Characteristik
sämmtlicher Gattungen
der
i
JOH. JAKOB HECKEL,
Inipectoi am k. k. Hof-Natur.-iUenkabinete in
Wien, mehr, yelelirt. UeHtllMeii. MIfglivd.
STUTTGART.
E. Schweizerbart' sehe Verlagshandlung,
1843.

28. Older material
• Great deal of material is pre-1923
• Irregular fonts – blackletter
• Multiple languages on same page – English
text with Latin scientific names
• Changes in geographic names
• Changes in scientific names

29. *E.xvi�c�piteI von c. cXx.WptdvonfnrWmn
bu�fbe;bcn.5 am cix bIa � S &3rn~ 41X
a�m cv(f b1air�'o�et ert oiensr �; �',
:�hlrfc�c wa ff�4am.diug bist a
6aiw~s ff oJrJtwt nof bL4ecImt& blfafra mem
b t wag `wr 4 cn wiu 4 e8t5m.ed bvUratflb ck
wuo, ma144'*4I bttE5rmbebt =rt3'kn am4ra
tif vrmr Waff C * t6rmnli an `tn�ciblatGteaM
w ?ffoaifrn w4wmeu nu weib e , wpiteI
voE5teiri ct c ober gtUcr cit cm` 91 cLi biar J '
>bSciatl�Oiff ;Bruet wacfttc n qmcx b1a bl:
bt5c lttmtt bb9 lkr w.llr#e iti ncn xoa ff cu :r
trtuft *e t � B Rn "� trv W1Rt' ?Cm c blas
waIwutr Ober �ci ti 1V Ces ' wt
gbtiemwwajfu tpctt, afferain 9 c: b�titbfof
�r f eran m rs bra wlg auig4;f aer�m *mc vrt
blatcabtfm wfru an'deg~m rt blas Iaum
bwWt� run f ncmai b14ianf tJobrrfan
ebrut4net vnber Brwt Ober awawi*m.crriii
btafwfm uww c on$ 'it ttu wttkc 5,10 $ m~C
fca trc* cx u W�e�&mcyfbq4 Mabtt mmw
rc a iiu bc Jcn ncI.end.*, blat s. a u:�rprd3
rw4ftf wm c ii,+ ttCC tn wa frr9fr orfab fcfbt
enb c optiti bt -r9 ceDa ttDcn i34M sn Sem i

30. Expanding scope
• Manuscripts, field notebooks –mostly
handwritten, often with drawings
• Global expansion means dealing with non-
Western script systems and a whole new set
of OCR problems – Arabic materials from
Bibliotheca Alexandria in Egypt

31. Images

32. OCR Improvements
• Gaming
• Transcription

33. OCR Improvements
• Transcription
• Purposeful Gaming
• Crowdsource Markup

34. Transcribe Bentham
• A collaboration of the University of London Computer
Centre, UCL Library Services and UCL Learning and Media
Services with consultation from the UCL Centre for Digital
Humanities
• Volunteer users can log-in and transcribe previously
unstudied and unpublished manuscripts from the Bentham
Papers collection in UCL Library's Special Collections in the
Transcription Desk.
• Since launch, volunteers from around the world have
transcribed several thousand Bentham manuscripts to an
extremely high standard.
• Results and findings:
http://www.digitalhumanities.org/dhq/vol/6/2/000125/000125.html

35. Transcribe Bentham
• Who were the volunteers?
• http://www.digitalhumanities.org/dhq/vol/6/2/000125/000125.html

36. Transcribe Bentham
• Age ranges
• http://www.digitalhumanities.org/dhq/vol/6/2/000125/000125.html

37. http://blog.winepresspublishing.com/2011/05/pubtoons-23-angry-books/

38. Purposeful Gaming
Space Climate
Humanities
Nature Biology

39. Purposeful Gaming
DIGITALKOOT
• Joint project run by the National Library
of Finland and Microtask to index the
library's enormous archives so that they
are searchable on the Internet for easier
access to the Finnish cultural heritage.
• Launched on Feb 8 2011, nearly 110 000
participants completed over 8 million
word fixing tasks by Nov 29 2012
• DigiTalkoot enabled volunteers to
participate in this fixing work by playing
games.

40. Purposeful Gaming
DIGITALKOOT
• Joint project run by the National Library
of Finland and Microtask to index the
library's enormous archives so that they
are searchable on the Internet for easier
access to the Finnish cultural heritage.
• Launched on Feb 8 2011, nearly 110 000
participants completed over 8 million
word fixing tasks by Nov 29 2012
• DigiTalkoot enabled volunteers to
participate in this fixing work by playing
games.

41. Purposeful Gaming
DIGITALKOOT
• Joint project run by the National Library
of Finland and Microtask to index the
library's enormous archives so that they
are searchable on the Internet for easier
access to the Finnish cultural heritage.
• Launched on Feb 8 2011, nearly 110 000
participants completed over 8 million
word fixing tasks by Nov 29 2012
• DigiTalkoot enabled volunteers to
participate in this fixing work by playing
games.

42. OCR Improvements
German text interpreted by the OCR process as:
“unb auf ben ©elnrgen be6 fublic{)en”

43. OCR Improvements
Transcription Transcription
IA OCR OCR 2
1 2
1 unb und und und Ok
2 den ben den den Ok
3 ©elnrgen ©ebirgen Bebirgen Gebirgen X
4 be6 des de5 des Chk
5 fublic{)en fublichen Füdlichen Südlichen X
6 £)eittfc{)(anb6 Deutfchlanbs Deutfchlands Deutschlands X
Different resulting texts from parsing the phrase:
“und auf den Gebirgen des südlichen Deutschlands”
(“and on the mountains of southern Germany”)

44. Crowdsource Markup
Display text Species Profile Model category
General/summary TaxonBiology
Geographic range Distribution
Habitat Habitat
Food sources and feeding behavior TrophicStrategy
Physical description (general) Description
Physical description (detailed morphology) DiagnosticDescription

45. Thank you
William Ulate
Global BHL Project Manager / Technical Director
Missouri Botanical Garden
william.ulate@mobot.org
Skype: william_ulate_r