bhl markup efforts and plans
DESCRIPTION
Presentation about past BHL Markup Efforts and present Plans for the pro-iBiosphere Markup Workshop.TRANSCRIPT
Efforts and plans towards Markup of the BHL Content
William Ulate R.BHL Technical Director
Missouri Botanical Garden
Berlin, Feb. 10, 2014
pro-iBiosphere Markup Workshop
BHL Mission and Vision
22.00
40.00
84.86 94.6
105.85
120.09 130.68
9.2 16.4
31.8 35.4 38.9 41.9 42.6
-
20
40
60
80
100
120
140
Oct-08 Oct-09 Oct-10 Oct-11 Oct-12 Oct-13
Pages (Millions) and Volumes (in Thousands) included in BHL
Volumes (K)
Pages (M)
More Online Content
Subjects
New Types of Content
New Types of Content
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 project
– Improved algorithm, better precision & recall– More data with TaxonFinder and Neti Neti!– http://gnrd.globalnames.org/
Taxon NamesBEFORE Name Instances 101,591,803 101,288,804Unique Names 7,498,554 7,464,924Verified Names 1,905,507 1,902,803EOL Names 63,130,350 62,963,582EOL Pages 13,579,868 13,532,684 AFTER Name Instances 151,222,182 150,066,425Unique Names 29,246,382 29,091,767Verified Names 10,153,165 10,109,540EOL Names 87,791,695 87,135,089EOL Pages 15,466,713 15,342,867
Article-level metadata
Chapter-level metadata
Treatment-level metadata
Part-level metadata
Articles in the BHL UI
See also:
Related Titles
Smithsonian
San Francisco
Woods Hole
London
Alexandria
Beijing
Global Replication & ServingReplicated Data Center Portal Application
BHL-Europe Term Expansion
Taxonomic Literature II (TL-2)
BioStor articles marked up with JATS
Art of Life
Art of Life
Art of Life
Art of Life
Macaw
https://github.com/cajunjoel/macaw-book-metadata-tool
Reviewing Metadata
Reviewing Metadata
Manually built:
1,693 sets
87,879 images
The Art of Life schema: describing and providing access to natural history illustrations from the Biodiversity Heritage Library (BHL)
by William Ulate, Trish Rose-Sandler, Gaurav Vaidya, Robert Guralnick
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 MuniaAccepted Name: Amandava formosa (Latham, 1790) Birds, finches
Inscriptions bottom center: Green Amaduvade Waxbill (Stictospiza formosa)
SourceButler, 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
Element Definition Examples Repeat
Agents person or corporate entity involved in the creation, design, production, or publication of a visual resource.
<vra:agent> <vra:name type="personal" vocab="LCNAF" refid="89015596> 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>
Y
Copyright The copyright status of the visual resource. <vra:rights refid=”http://creativecommons.org/licenses/by-nc/2.0/
deed.en”>Creative Commons Attribution-NonCommercial 2.0 Generic (CC BY-NC 2.0)</vra:rights>
N
Date Date or range of dates associated with the creation or publication of the visual resource.
<vra:date type="creation"> <vra:earliestDate>1945</vra:earliestDate> <vra:latestDate>1955</vra:latestDate></vra:date>
Y
Description A free-text note about content of the image, including comments, description, or interpretation, that gives additional information not recorded in other categories.
<vra:description>This illustration shows a scale, coloured illustration of Sepsis annulipes (now known as Encita annulipes) beside the Trifolium ochroleucum plant. Several dissections from Sepsis cylindrica Fab. (all these details are provided on the next page of this book and the subsequent page).</vra:description>
Y
Inscriptions All marks, caption, or written words added to the object at the time of production or in its subsequent history, including signatures, dates, dedications, texts, and colophons, as well as marks, such as the stamps of silversmiths, publishers, or printers.
<vra:inscription> <vra:position>bottom</vra:position> <vra:text>Radula of L. souleyetianum on a more reduced scale</vra:text></vra:inscription>
Y
Source A citation for the book, journal or resource that hosts the visual resource
<vra:source><vra:name type=”book”>Butler, Arthur Gardiner. 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>
N
Subject Terms or phrases that describe, identify, or interpret the visual resource.
<vra:subject><vra:term type=”personalName”>Carl 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>
Y
Title The title or identifying phrase given to an Image <vra:title xml:lang=”la”>Sepsis annulipes</vra:title>
<vra:title type=“alternate”>Orangutan</vra:title>Y
Type Identifies a general category for the visual resource
<vra:type>maps</vra:type><vra:type>forestry maps</vra:type>
Y
Example of illustration described using Art of Life schema
Art of Life schema elements required in Red
We welcome your feedback on the schema! http://tinyurl.com/9hm7nsb
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OCR Improvements
• Gaming• Transcription
OCR Improvements• Transcription• Purposeful Gaming
• Looking at…– Crowdsource Markup
Purposeful GamingDIGITALKOOT
• 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.
.
Purposeful GamingDIGITALKOOT
• 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.
• .
Purposeful gaming and BHL: engaging the public in improving and
enhancing access to digital texts
• IMLS Grant Program: National Leadership Grants for Libraries
• Partners:– Missouri Botanical Garden– Harvard University– Cornell University– New York Botanical Garden
• P.I.: Trish Rose-Sandler, Missouri Botanical Garden• Dates: Dec 2013 – Nov. 2015
Project objectives and benefits
• Test new means of crowdsourcing to support the enhancement of content in BHL
• Demonstrate if digital games are an effective tool for analyzing and improving digital outputs from OCR and transcription
• Benefits of gaming include:– improved access to content by providing richer and more accurate
data; – an extension of limited staff resources; and – exposure of library content to communities who may not know
about the collections otherwise.
OCR Improvements
German text interpreted by the OCR process as: “unb auf ben ©elnrgen be6 fublic{)en”
OCR Improvements
Different resulting texts from parsing the phrase:“und auf den Gebirgen des südlichen Deutschlands”
(“and on the mountains of southern Germany”)
IA OCR OCR 2 Transcription 1 Transcription 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
Purposeful Gaming
iDigBio’s aOCR Hackathon
• Improve OCR parsing of labels with clear metrics (datasets, output formats, scoring algorithm)
• Libraries of regular expr. to clean up each field (different error correction for latitude/longitude coordinates than personal names or herbarium catalog numbers)
• Tool for classifying segments of the image before submitting to OCR
• Do a first pass of OCR to clean images before sending them to a second, 'real' pass of OCR
iDigBio’s CITScribe Hackathon
1. Interoperability betweenpublic participation tools and biodiversity data systems,
2. Transcription quality assessment/quality control (QA/QC) and the reconciliation of replicatetranscriptions,
3. Integration of optical character recognition (OCR) into thetranscription workflow
4. User engagement
NfN & iDigBio’s CITScribe Hackathon
• Jason Best’s DarwinScore • Ben Brumfield’s Handwriting Gibberish Detector• Dictionaries to improve crowdsourcing consensus
(e.g., names of collectors, scientific names)• Word Clouds created using n-gram scoring, faceting,
and Solr for indexing + Carrot2 for specimen selection (visualize and explore of the use with a word of interest from the word cloud) and a data cleaning step (highlight infrequent words by the system).
NESCent EOL-BHL Research SprintThere is no place like home: Defining “habitat” for biodiversity science
Robert D. StevensonUMass Boston, Dept. of Biology, 100 Morrissey Blvd., Boston, MA 02125-3393
Carl Nordman (Natureserve) and
Evangelos Pafilis Hellenic Centre for Marine Research, P.O. Box 2214, Heraklion, 71003, Crete, Greece
NESCent EOL-BHL Research Sprint
Assessing Risk Status of Mexican Amphibians Through Data Mining.
Esther Quintero and Bárbara AyalaNational Commission for Knowledge and Use of Biodiversity (CONABIO)
and
Anne ThessenMarine Biological Laboratory and Arizona State University
NESCent EOL-BHL Research Sprint
Evolution in the usage of anatomical concepts in the biodiversity literature
Todd Vision ([email protected]),
Prashanti Manda ([email protected]), and
Dongye MengUniversity of North Carolina at Chapel Hill
MiBIO: Mining Biodiversity
• Mining Biodiversity: Enriching Biodiversity Heritage with Text Mining and Social Media
• One of the international projects that won in the third round of the 2013 Digging Into Data Challenge
• Promote the development of innovative computational techniques to apply into big data in the humanities and social sciences– The National Centre for Text Mining (UK)– Missouri Botanical Garden (US) – Dalhousie University's Big Data Analytics Institute (Canada) – Social Media Lab (Canada)
MiBIO: Mining Biodiversity
1. Automatic error correction of OCR text errors.
2. Crowdsource annotation of legacy texts with semantic metadata.
3. Adapt text mining techniques to extract terminology, entities and significant events automatically and to track terminology evolution over time.
4. Use Interactive visualization techniques to help users manage search results through next generation browsing capabilities, assisted by a semantic similarity network of important terms and entities.
5. Design of a social media layer, serving as an environment for diverse users to interact and collaborate on science, public education, awareness and outreach.
MiBIO: Mining Biodiversity
•
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
Thank youWilliam UlateGlobal BHL Project Manager / Technical DirectorMissouri Botanical [email protected]: william_ulate_r