Post on 26-May-2015
description
Scribbles & Scraps:Darwin’s Library & the Online Display of
Annotated Biodiversity Literaturehttp://biodiversitylibrary.org/collection/darwinlibrary
Chris FreelandDirector, Center for Biodiversity Informatics,
Missouri Botanical GardenTechnical Director, Biodiversity Heritage Library
@chrisfreeland@chrisfreeland #bhlib #tdwg
About Darwin’s Library
• Digital edition & virtual reconstruction of surviving books owned by Charles Darwin.
• Darwin’s son Francis transferred “Darwin’s Library” to the Botany School at Cambridge University in 1908
• More detail about the collection at:http://biodiversitylibrary.org/collection/darwinlibrary
@chrisfreeland #bhlib #tdwg
Funded Project
• Digitize most heavily annotated volumes in Darwin’s Library
• Funded via JISC / NEH: Transatlantic Digitisation Collaboration Grant
• Partners:– Cambridge University Library– Natural History Museum, London– American Museum of Natural History• Subaward to BHL via Missouri Botanical Garden
@chrisfreeland #bhlib #tdwg
http://www.biodiversitylibrary.org/page/34117347 Agassiz, L. Contributions to the natural history of the United States of North America.
The scribbly bits
Charles Darwin’s Marginalia, vol. 1 (1990)• Compiled by Mario Di Gregorio & Nicholas Gill• Painstaking work to :– transcribe Darwin’s annotations & markings– assign subjects & concepts– crosslink marginalia & related annotations on
loose slips or end papers• Data encoded in purpose-driven form &
format intended for print
@chrisfreeland #bhlib #tdwg
Digitization Considerations
• BHL had already digitized some of the titles through mass scanning
• Some materials couldn’t be scanned at CUL for fear of damage – Truly unique documents
• Higher per page scanning cost at CUL for special handling
Compromise:• Scan the most heavily annotated volumes at CUL• Include existing content in BHL• Scan “surrogates” via BHL mass scanning from NHM
@chrisfreeland #bhlib #tdwg
And then the fun began…• Originally envisioned simple Flickr-like notes
@chrisfreeland #bhlib #tdwg http://www.flickr.com/photos/chrisfreeland/4928966390/
And then the reality• Realized true complexity of data parsing after
getting Di Gregorio & Gill’s data\n0015.v01.p01.c0117 |n0015.v01.p01.c0117:m01= 10—14 m / 13 w $ mere analogy $ / from_\
n0015.v01.p01.f1000 w \m4a $ 117    On combinations of characters in old Forms $
|n0015.v01.p01.c0117:m01i an /b |n0015.v01.p01.c0117:m01i fos /B/c |n0015.v01.p01.c0117:m01i rsa- /b |n0015.v01.p01.c0117:m01i tm /B/c |n0015.v01.p01.c0117:m01j faz:bird /e |n0015.v01.p01.c0117:m01j faz:dolphin /e |n0015.v01.p01.c0117:m01j faz:fish, sauroid /e |n0015.v01.p01.c0117:m01j faz:Ichthyosauri /e |n0015.v01.p01.c0117:m01j faz:Pterodactyl /e |n0015.v01.p01.c0117:m01j faz:reptile /e |n0015.v01.p01.c0117:m01j tiz:ancient /D
Structural markup instructions
+n[4-digits] starts a book; then =a author =t title =e edition data =v volume data =p publication details =d date =l location [CUL (Cambridge University Library) or Down (Down
House, Kent)] =b Beagle-era / on board =x book has a Darwin signature (S) and/or is inscribed to him
@chrisfreeland #bhlib #tdwg
In the body of the item:
\n starts a new page or other piece |n flags the other data entries
The 4-digit title number is followed by .v?? volume number (00 = 'only’) .p?? part number
page or other piece designator .b???r [roman-numbered front-matter] .c???? [arabic-numbered page-count] .d??? [end-matter with its own pagination] .f???? [Darwin's final end-notes/slips: f0? end-note (f00 'only') f1? end-slip last 2 digits numbering the sides] [A note or slip can have a 'head-note', flagged \H, describing the physical
characteristics of the piece.]
@chrisfreeland #bhlib #tdwg
Textual-feature markup encountered in these items:
\0 characters faint/faded or \0[erased] erased
\1 characters deleted
\2 characters crossed
\3 lines counted from bottom of text
\4 word illegible
\5 doubtful transcription
\6 word partly illegible
\8 vertical
\9 line across page
\m medium:
m1 pencil,
1a pale
1b 'nondescript' [undeclared default]
1c dark
m2 'red' crayon
2a pinkish-orange
2b orangy-red
2c reddish-brown
m3 blue crayon
m4a 'standard' brown ink
m5a grey ink
m6a dark brown ink
m6g dark grey ink
\p0 text 'ringed' (circled, boxed, etc)
\p8 opening editor's bracket
\p9 closing editor's bracket
\a italics
\c end-italics
\b line-break in the layout
\N 'paragraph' break
\H head-note
\o overwrite
\q arrow -->
\R characters 'retouched'
\t not in Darwin's hand
\T in Darwin's hand
\u start of underline \U double-underline
\v end of underline \V
/^ insert with caret
|^ end-insert
//^ insert without caret
||^ end-insert
\[male] \[female] signs needed
\+ \- superscript
\- \+ subscript
\! pin-hole
Subject indexing instructionsad adaptationaf affinityan analogybeh behaviour beha animal locomotion
(other than flight) behb breeding (natural) behc communication behd direction-finding,
navigation behe expression, emotion behf flight behh habit behi instinct behl learning/memory behm mind/cognition behn nesting, other
'home'-making
behp perception, sensation
c2- criticism (negative)c2+ (positive)cc conditions, climate cce elevation (as fact, not
process) ccf fresh-water ccs salt-water cct terrestrial ccw weather, wind ccx confinementch changeche chemistry chel luminescence,
phosphorescence chem manure, fertilisers chet taste
co coralcr creation(ism), religioncs crossingct cell-theory, histologydg degenerationds descentdv divergenceem embryologyex extinctionf fertility (vs. sterility)fa faunafd food fdm meatfg fertilisation and
generation fge eggs fgm mechanisms of fgn nectar
\n0015.v01.p01.c0117 |n0015.v01.p01.c0117:m01= 10—14 m / 13 w $ mere analogy $ / from_\n0015.v01.p01.f1000 w \m4a $ 117    On combinations of characters in old Forms $ |n0015.v01.p01.c0117:m01i an /b |n0015.v01.p01.c0117:m01i fos /B/c |n0015.v01.p01.c0117:m01i rsa- /b |n0015.v01.p01.c0117:m01i tm /B/c |n0015.v01.p01.c0117:m01j faz:bird /e |n0015.v01.p01.c0117:m01j faz:dolphin /e |n0015.v01.p01.c0117:m01j faz:fish, sauroid /e |n0015.v01.p01.c0117:m01j faz:Ichthyosauri /e |n0015.v01.p01.c0117:m01j faz:Pterodactyl /e |n0015.v01.p01.c0117:m01j faz:reptile /e |n0015.v01.p01.c0117:m01j tiz:ancient /D |n0015.v01.p01.c0117:m02= 14 u "Ichthyosauri" / @14 w $ ⸮ $ |n0015.v01.p01.c0117:m02i rsq /b |n0015.v01.p01.c0117:m02j faz:Ichthyosauri /e |n0015.v01.p01.c0117:m03= 22—24m / from_\n0015.v01.p01.f1000 w \m4a $ 117    On combinations of characters in old Forms $ |n0015.v01.p01.c0117:m03i fos /B/c |n0015.v01.p01.c0117:m03i sph /c |n0015.v01.p01.c0117:m03i tm /B/c |n0015.v01.p01.c0117:m03j faz:fish /e |n0015.v01.p01.c0117:m03j faz:reptile /e |n0015.v01.p01.c0117:m03j tiz:ancient /D |n0015.v01.p01.c0117:m04= 25 c "Crustacea" \a[corrected to `Cetacea']\c |n0015.v01.p01.c0117:m04i rsz /b
http://www.biodiversitylibrary.org/page/34117347 Agassiz, L. Contributions to the natural history of the United States of North America.
<insert magic here>
<magic> = code
• Regular expressions & SQL inserts• No UI for adding annotations, all data driven• Parsing completed by:– Scholars & programmers, not generalists &
enthusiasts• Parsing code is reusable within project,
unlikely to be useful outside due to data input– Purpose-driven, specific
@chrisfreeland #bhlib #tdwg
Data Model
http://code.google.com/p/bhl-bits/downloads @chrisfreeland #bhlib #tdwg
Future
Extensibility• Delivered the scholarly, nth degree option• Can be reused for simpler annotations
Phase II• New Darwin originals from CUL• Replace surrogates with originals• Refine user interface / user experience
@chrisfreeland #bhlib #tdwg
Outcomes & Perspective
• Incorporation of unique material of interest to many domains– Biology– Humanities– General public
• A glimpse into Darwin’s mind– And the minds of historians of science
@chrisfreeland #bhlib #tdwg
AcknowledgementsTransatlantic Digitisation Collaboration Grant, Phase 1 sponsored by:• United Kingdom
JISC Joint Information Systems Committee of the Higher Education Founding Council of England & Wales (HEFCE) to Cambridge University Library and Natural History Museum (Award CCICP002)
• United StatesNEH National Endowment for the Humanities to Darwin Manuscripts Project of the American Museum of Natural History, with subaward to the Missouri Botanical Garden (Award PX-50026-09)
Contributors • Cambridge University Library (http://www.lib.cam.ac.uk)• Natural History Museum, London (http://www.nhm.ac.uk)• Darwin Manuscripts Project (http://darwin.amnh.org)The project wishes to express its gratitude to William Huxley Darwin for
permission to reproduce the Darwin manuscripts.@chrisfreeland #bhlib #tdwg
Credits• Edition of Darwin's annotations and other marks. Mario Di
Gregorio and Nicholas Gill, updated by Gill and produced as part of the Darwin Manuscripts Project of the American Museum of Natural History. Adam Goldstein and Huw Jones served as bibliographers. David Kohn, PI
• Digitisation of original Darwin copies by Cambridge University Library. Grant Young, PI
• Digitisation of surrogate copies by the Library of the Natural History Museum (London). Jane Smith and Judith McGee
• Additional surrogates drawn from works digitised by member libraries of the Biodiversity Heritage Library and contributors to the Internet Archive.
• Transcription interface developed by the Biodiversity Heritage Library Technical Unit at Missouri Botanical Garden. Chris Freeland and Mike Lichtenberg
@chrisfreeland #bhlib #tdwg
http://www.biodiversitylibrary.org/page/33949861
Lyell, C. Principles of Geology. 1837.
Awesome
Questions?
http://biodiversitylibrary.org/collection/darwinlibrary
Email: chris.freeland@mobot.org
Twitter: @chrisfreeland
Chris FreelandDirector, Center for Biodiversity Informatics, Missouri Botanical Garden
Technical Director, Biodiversity Heritage Library
@chrisfreeland #bhlib #tdwg