More and more approaches for systematic biologically inspired design (BID) aim to scalably leverage large biological databases. To support the scalable systematic BID process, an automated method for mention and focus organism (FO) detection in biological strategy documents is proposed and validated to perform with 85% precision and 81% recall. Furthermore, a number of potential applications of mention and FO detection are presented, and the biodiversity of two corpora is measured.

References

References
1.
Bar-Cohen
,
Y.
,
2006
, “
Biomimetics Using Nature to Inspire Human Innovation
,”
Bioinspiration Biomimetics
,
1
(
1
), pp.
1
12
.10.1088/1748-3182/1/1/P01
2.
Bar-Cohen
,
Y.
,
2011
,
Biomimetics: Nature-Based Innovation
,
CRC/Taylor & Francis
, Boca Raton, FL.
3.
Bonser
,
R. H.
, and
Vincent
,
J. F.
,
2007
, “
Technology Trajectories, Innovation, and the Growth of Biomimetics
,”
Proc. Inst. Mech. Eng., Part C
,
221
(
10
), pp.
1177
1180
.10.1243/09544062JMES522
4.
Bajželj
,
B.
,
Allwood
,
J. M.
, and
Cullen
,
J. M.
,
2013
, “
Designing Climate Change Mitigation Plans That Add Up
,”
Environ. Sci. Technol.
,
47
(
14
), pp.
8062
8069
.10.1021/es400399h
5.
Gebeshuber
,
I. C.
,
Gruber
,
P.
, and
Drack
,
M.
,
2009
, “
A Gaze Into the Crystal Ball: Biomimetics in the Year 2059
,”
J. Mech. Eng. Sci.
,
223
(
12
), pp.
2899
2918
.10.1243/09544062JMES1563
6.
Benyus
,
J. M.
,
1997
,
Biomimicry: Innovation Inspired by Nature
,
Quill -William Morrow
,
New York
.
7.
Wilson
,
J. O.
,
Rosen
,
D.
,
Nelson
,
B. A.
, and
Yen
,
J.
,
2010
, “
The Effects of Biological Examples in Idea Generation
,”
Des. Stud.
,
31
(
2
), pp.
169
186
.10.1016/j.destud.2009.10.003
8.
Chiu
,
I.
, and
Shu
,
L. H.
,
2007
, “
Biomimetic Design Through Natural Language Analysis to Facilitate Cross-Domain Information Retrieval
,”
Artif. Intell. Eng. Des., Anal. Manuf.
,
21
(
1
), pp.
45
59
.10.10170S0890060407070138
9.
Shu
,
L. H.
,
2010
, “
A Natural-Language Approach to Biomimetic Design
,”
Artif. Intell. Eng. Des., Anal. Manuf.
,
24
(
4
), pp.
507
519
.10.1017/S0890060410000363
10.
Vincent
,
J. F. V.
,
Bogatyreva
,
O. A.
,
Bogatyrev
,
N. R.
,
Bowyer
,
A.
, and
Pahl
,
A. K.
,
2006
, “
Biomimetics: Its Practice and Theory
,”
J. R. Soc.: Interface
,
3
(
9
), pp.
471
482
.10.1098/rsif.2006.0127
11.
Deldin
,
J.-M.
, and
Schuknecht
,
M.
,
2014
, “The AskNature Database:”
Biologically Inspired Design
, pp.
17
21
.10.1007/978-1-4471-5248-4
12.
Vattam
,
S. S.
,
Wiltgen
,
B.
,
Helms
,
M.
,
Goel
,
A. K.
, and
Yen
,
J.
,
2011
, “
DANE: Fostering Creativity in and Through Biologically Inspired Design
,”
First International Conference on Design Creativity
,
Kobe, Japan
, Nov. 2010, Springer-Verlag London, pp.
115
122
.10.1007/978-1-4471-5248-4_2
13.
Nagel
,
J. K. S.
,
Nagel
,
B. I.
,
Stone
,
R. B.
, and
McAdams
,
D. A.
,
2010
, “
Function-Based, Biologically Inspired Concept Generation
,”
Artif. Intell. Eng. Des., Anal. Manuf.
,
24
(
4
), pp.
521
535
.10.1017/S0890060410000375
14.
Nagel
,
J. K. S.
, and
Stone
,
R. B.
,
2012
, “
A Computational Approach to Biologically Inspired Design
,”
Artif. Intell. Eng. Des., Anal. Manuf.
,
26
(
1
), pp.
161
176
.10.1017/S0890060412000054
15.
Chakrabarti
,
A.
,
Sarkar
,
P.
,
Leelavathamma
,
B.
, and
Nataraju
,
B. S.
,
2005
, “
A Functional Representation for Aiding Biomimetic and Artificial Inspiration of New Ideas
,”
Artif. Intell. Eng. Des., Anal. Manuf.
,
19
(
2
), pp.
113
132
.10.1017/S0890060405050109
16.
Sartori
,
J.
,
Pal
,
U.
, and
Chakrabarti
,
A.
,
2010
, “
A Methodology for Supporting “Transfer” in Biomimetic Design
,”
Artif. Intell. Eng. Des., Anal. Manuf.
,
24
(
4
), pp.
483
505
.10.1017/S0890060410000351
17.
Vandevenne
,
D.
,
Verhaegen
,
P.
,
Dewulf
,
S.
, and
Duflou
,
J. R.
,
2011
, “
A Scalable Approach for the Integration of Large Knowledge Repositories in the Biologically-Inspired Design Process
,”
Proceedings of the 18th International Conference on Engineering Design (ICED11)
,
Denmark
, Aug. 15–19, Vol.
6
, pp.
210
219
.
18.
Vattam
,
S.
, and
Goel
,
A.
,
2011
, “
Semantically Annotating Research Articles for Interdisciplinary Design
,”
Proceedings of the Sixth International Conference on Knowledge Capture
,
New York
, pp.
165
166
.
19.
Cheong
,
H.
,
Chiu
, I
.
,
Shu
,
L. H.
,
Stone
,
R.
, and
McAdams
,
D.
,
2011
, “
Biologically Meaningful Keywords for Functional Terms of the Functional Basis
,”
ASME J. Mech. Des.
,
133
(
2
), p.
021007
.10.1115/1.4003249
20.
Vandevenne
,
D.
,
Verhaegen
,
P.-A.
,
Dewulf
,
S.
, and
Duflou
,
J. R.
,
2014
, “
Product and Organism Aspects for Scalable Systematic Biologically-Inspired Design
,”
Proceedings of TRIZ Future Conference
,
Paris
, Oct. 29–31, pp.
401
409
.
21.
Hanisch
,
D.
,
Fundel
,
K.
,
Mevissen
,
H. T.
,
Zimmer
,
R.
, and
Fluck
,
J.
,
2005
, “
ProMiner: Rule-Based Protein and Gene Entity Recognition
,”
BMC Bioinf.
,
6
(
Suppl 1
), p.
S14
.10.1186/1471-2105-6-S1-S14
22.
Koning
,
D.
,
Sarkar
, I
. N.
, and
Moritz
,
T.
,
2006
, “
TaxonGrab: Extracting Taxonomic Names From Text
,”
Biodiversity Inf.
,
2
, pp.
79
82
.
23.
Koning
,
D.
, “
TaxonGrab
,” http://sourceforge.net/projects/taxongrab/
24.
Sautter
,
G.
,
Böhm
,
K.
, and
Agosti
,
D.
, “
A Combining Approach to Find all Taxon Names (FAT) in Legacy Biosystematic Literature
,”
Biodiversity Inf.
,
3
, pp.
41
53
.
25.
Linnaeus
,
C.
,
1767
, “
Systema Naturae
,”
26.
McEntyre
,
J.
, and
Ostell
,
J.
, eds.,
2002
,
The NCBI Handbook
,
National Center for Biotechnology Information (US)
,
Bethesda, MD
.
27.
Ding
,
J.
,
Viswanathan
,
K.
,
Berleant
,
D.
,
Hughes
,
L.
,
Wurtele
,
E.
,
Ashlock
,
D.
,
Dickerson
,
J.
,
Fulmer
,
A.
, and
Schnable
,
P.
,
2005
, “
Using the Biological Taxonomy to Access Biological Literature With PathBinderH
,”
Bioinformatics
,
21
(
10
), pp.
2560
2562
.10.1093/bioinformatics/bti381
28.
Rebholz-Schuhmann
,
D.
,
Arregui
,
M.
,
Gaudan
,
M.
,
Kirsch
,
H.
, and
Jimeno
,
A.
,
2007
, “
Text Processing Through Web Services: Calling Whatizit
,”
Bioinformatics
,
23
(
2
), pp.
e237
e244
.10.1093/bioinformatics/btl302
29.
Gerner
,
M.
,
Nenadic
,
G.
, and
Bergman
,
C. M.
,
2010
, “
LINNAEUS: A Species Name Identification System for Biomedical Literature
,”
BMC Bioinf.
,
11
(
85
).10.1186/1471-2105-11-85
30.
Gerner
,
M.
, and
Bergman
,
C. M.
, “
LINNAEUS
,” http://sourceforge.net/projects/linnaeus/
31.
Lenau
,
T.
,
Dentel
,
A.
,
Ingvarsdóttir
,
Þ.
, and
Guðlaugsson
,
T.
,
2010
, “
Engineering Design of an Adaptive Leg Prosthesis Using Biological Principles
,”
Proceedings of DESIGN
,
Glasgow
, pp.
331
340
.
32.
Miller
,
G. A.
,
1995
, “
WordNet: A Lexical Database for English
,”
Commun. ACM
,
38
(
11
), pp.
39
41
.10.1145/219717.219748
33.
Kappeler
,
T.
,
Kaljurand
,
K.
, and
Rinaldi
,
F.
,
2009
, “
TX Task: Automatic Detection of Focus Organisms in Biomedical Publications
,”
Proceedings of the BioNLP 2009 Workshop; Boulder, Colorado: Association for Computational Linguistics
,
Boulder, CO
, pp.
80
88
.
34.
The UniProt Consortium
,
2009
, “
The Universal Protein Resource (UniProt)
,”
Nucleic Acids Res.
,
37
, pp.
D169
D174
.10.1093/nar/gkn664
35.
Kerrien
,
S.
,
Alam-Faruque
,
Y.
,
Aranda
,
B.
,
Bancarz
, I
.
,
Bridge
,
A.
,
Derow
,
C.
,
Dimmer
,
E.
,
Feuermann
,
M.
,
Friedrichsen
,
A.
, and
Huntley
,
R.
,
2007
, “
IntAct—Open Source Resource for Molecular Interaction Data
,”
Nucleic Acids Res.
,
35
, pp.
D561
D565
.10.1093/nar/gkl958
36.
Randolph
,
J. J.
,
2005
, “
Free-Marginal Multirater Kappa: An Alternative to Fleiss' Fixed-Marginal Multirater Kappa
,”
Joensuu University Learning and Instruction Symposium
,
Joensuu, Finland
.
37.
Vandevenne
,
D.
,
Verhaegen
,
P.-A.
,
Dewulf
,
S.
, and
Duflou
,
J. R.
,
2014
, “
A Scalable Approach for Ideation in Biologically Inspired Design
,”
Artif. Intell. Eng. Des., Anal. Manuf
, FirstView(8), pp.
1
13
.10.1017/S0890060414000122
38.
Puthoff
,
J. B.
,
Prowse
,
M. S.
,
Wilkinson
,
M.
, and
Autumn
,
K.
,
2010
, “
Changes in Materials Properties Explain the Effects of Humidity on Gecko Adhesion
,”
J. Exp. Biol.
,
213
(
21
), pp.
3699
3704
.10.1242/jeb.047654
39.
Autumn
,
K.
,
Hsieh
,
S. T.
,
Dudek
,
D. M.
,
Chen.
,
J.
,
Chitaphan
,
C.
, and
Full
,
R. J.
,
2006
, “
Dynamics of Geckos Running Vertically
,”
J. Exp. Biol.
,
209
(
2
), pp.
260
272
.10.1242/jeb.01980
You do not currently have access to this content.