Virtual Biodiversity ViBRANT Literature Mining and Mark-up ViBRANT’s text processing tools David Morse, The Open University, UK, [email protected] Dauvit King, The Open University, UK, [email protected] ViBRANT/BeBOL/JEMU workshop, RBINS, 11 June 2013 ViBRANT Virtual Biodiversity
Virtual Biodiversity ViBRANT Literature Mining and Mark-up ViBRANT’s text processing tools David Morse, The Open University, UK, [email protected]@open.ac.uk.
Dec 28, 2015
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Virtual BiodiversityViBRANT
Literature Mining and Mark-upViBRANT’s text processing tools
David Morse, The Open University, UK, [email protected] King, The Open University, UK, [email protected]
ViBRANT/BeBOL/JEMU workshop, RBINS, 11 June 2013
ViBRANTVirtual Biodiversity
Virtual BiodiversityViBRANT
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Literature Mining
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ViBRANT is for taxonomists, so we look for:• Taxon names• Authors• Locations
Also interested in:• Citations• Relationships
Mining for Names and Concepts
Virtual BiodiversityViBRANT
Literature Mining – harder than you thinkM
BRITISH MUSEUM
(NATURAL HiSi
26JU
PRESENTED GENERAL UC.-lARY
Bulletin ofthe
BritishMuseum (Natural History)
The ichneumon-fly genus Banchus in the OldWorld
(Hymenoptera)
M. G. Fitton series
Entomology Vol51 Nol 25 July 1985
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Virtual BiodiversityViBRANT
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GoldenGATE
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Sautter, G., Agosti, D., and Böhm. K. (2007) Semi-Automated XML Markup of Biosystematics Legacy Literature with the GoldenGATE Editor. In Proceedings of PSB 2007, Wailea, HI, USA, 2007
Downloadable from http://psb.stanford.edu/psb-online/proceedings/psb07/sautter.pdf
Virtual BiodiversityViBRANT
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GoldenGATE
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Virtual BiodiversityViBRANT
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GoldenGATE in OBOE
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Virtual BiodiversityViBRANT
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GoldenGATE in OBOE
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Virtual BiodiversityViBRANT
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GoldenGATE in OBOE
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Virtual BiodiversityViBRANT
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GoldenGATE in OBOE
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Virtual BiodiversityViBRANT
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Visualising mark up
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Virtual BiodiversityViBRANT
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Taxonomic XML schemas
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Lyubomir Penev, Christopher Lyal, Anna Weitzman, David Morse, David King, Guido Sautter, Teodor Georgiev, Robert Morris, Terry Catapano, and Donat Agosti. (2011) XML schemas and mark-up practices of taxonomic literature. ZooKeys 150: 89-116.
Downloadable from http://dx.doi.org/10.3897/zookeys.150.2213
Virtual BiodiversityViBRANT
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Linked Open Data
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Virtual BiodiversityViBRANT
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Other tools
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KEAKeyphrase Extraction Algorithm
GNRDGlobal Names Recognition and Discovery
LinnaeusUsed for molecular data
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Conclusion
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Developing Literature Mining services deployed through OBOE.
Initially aimed at ViBRANT’s core audience.
Setting up workflow integrated with Scratchpads.
Yet still permitting large, slow jobs.
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