Chris Freeland Director, Center for Biodiversity Informatics, Missouri Botanical Garden

1. Scribbles & Scraps:Darwin’s Library & the Online Display ofAnnotated Biodiversity Literaturehttp://biodiversitylibrary.org/collection/darwinlibrary Chris Freeland Director, Center for Biodiversity Informatics, Missouri Botanical Garden Technical Director, Biodiversity Heritage Library @chrisfreeland #bhlib #tdwg @chrisfreeland

2. 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 #bhlib #tdwg @chrisfreeland

3. 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 #bhlib #tdwg @chrisfreeland

4. Agassiz, L. Contributions to the natural history of the United States of North America. http://www.biodiversitylibrary.org/page/34117347

5. 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 #bhlib #tdwg @chrisfreeland

6. 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 #bhlib #tdwg @chrisfreeland

7. And then the fun began… • Originally envisioned simple Flickr-like notes http://www.flickr.com/photos/chrisfreeland/4928966390/ #bhlib #tdwg @chrisfreeland

8. 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

9. 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 #bhlib #tdwg @chrisfreeland

10. 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.] #bhlib #tdwg @chrisfreeland

11. 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

12. Subject indexing instructions ad adaptation af affinity an analogy behbehaviour 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 confinement ch change che chemistry chel luminescence, phosphorescence chem manure, fertilisers chet taste co coral crcreation(ism), religion cs crossing ct cell-theory, histology dg degeneration ds descent dv divergence em embryology ex extinction f fertility (vs. sterility) fa fauna fd food fdm meat fgfertilisation and generation fge eggs fgm mechanisms of fgn nectar

13. \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

14. Agassiz, L. Contributions to the natural history of the United States of North America. http://www.biodiversitylibrary.org/page/34117347

15. <insert magic here>

16. http://www.biodiversitylibrary.org/page/34117347

17. <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 #bhlib #tdwg @chrisfreeland

18. Data Model http://code.google.com/p/bhl-bits/downloads #bhlib #tdwg @chrisfreeland

19. 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 #bhlib #tdwg @chrisfreeland

20. 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 #bhlib #tdwg @chrisfreeland

21. Acknowledgements Transatlantic Digitisation Collaboration Grant, Phase 1 sponsored by: • United KingdomJISC 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. #bhlib #tdwg @chrisfreeland

22. 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 #bhlib #tdwg @chrisfreeland

23. Lyell, C. Principles of Geology. 1837. http://www.biodiversitylibrary.org/page/33949861 Awesome

24. Questions?http://biodiversitylibrary.org/collection/darwinlibraryQuestions?http://biodiversitylibrary.org/collection/darwinlibrary Chris Freeland Director, Center for Biodiversity Informatics, Missouri Botanical Garden Technical Director, Biodiversity Heritage Library Email: chris.freeland@mobot.org Twitter: @chrisfreeland #bhlib #tdwg @chrisfreeland