Automated semantic annotation of species names in handwritten texts

Lise Stork; Andreas Weber; Jaap van den Herik; Aske Plaat; Fons Verbeek; Katherine Wolstencroft

doi:10.1007/978-3-030-15712-8_43

Automated semantic annotation of species names in handwritten texts

Lise Stork^*, Andreas Weber, Jaap van den Herik, Aske Plaat, Fons Verbeek, Katherine Wolstencroft

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

1 Citation (Scopus)

Abstract

In this paper, scientific species names from images of handwritten species observations are automatically recognised and annotated with semantic concepts, so that they can be used for document retrieval and faceted search. Until now, automated semantic annotation of such named entities was only applied to printed or digital text. We employ a two-step approach. First, word images are classified, identifying elements of scientific species names; Genus, species, author, using (i) visual structural features, (ii) position, and (iii) context. Second, the identified species names are semantically annotated according to the NHC-Ontology, an ontology that describes species observations. Internationalised Resource Identifiers (IRIs) are assigned to the elements so that they can be linked and disambiguated at a later stage by individual researchers. For the identification of scientific species names, we achieve an average F1 score of 0.86. Moreover, we discuss how our method will function in a semi-automated annotation process, with a fruitful dialogue between system and user as the main objective.

Original language	English
Title of host publication	Advances in Information Retrieval
Subtitle of host publication	41st European Conference on IR Research, ECIR 2019, Proceedings, Part I
Editors	Leif Azzopardi, Benno Stein, Norbert Fuhr, Philipp Mayr, Claudia Hauff, Djoerd Hiemstra
Place of Publication	Cham
Publisher	Springer
Pages	667-680
Number of pages	14
ISBN (Electronic)	978-3-030-15712-8
ISBN (Print)	978-3-030-15711-1
DOIs	https://doi.org/10.1007/978-3-030-15712-8_43
Publication status	Published - 7 Apr 2019
Event	41st European Conference on Information Retrieval, ECIR 2019 - Cologne, Germany Duration: 14 Apr 2019 → 18 Apr 2019 Conference number: 41 http://ecir2019.org/

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	11437 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	41st European Conference on Information Retrieval, ECIR 2019
Abbreviated title	ECIR 2019
Country	Germany
City	Cologne
Period	14/04/19 → 18/04/19
Internet address	http://ecir2019.org/

Keywords

Deep learning
Historical biodiversity research
Ontologies
Scientific names
Semantic annotation
Taxonomy

Access to Document

10.1007/978-3-030-15712-8_43

Fingerprint Dive into the research topics of 'Automated semantic annotation of species names in handwritten texts'. Together they form a unique fingerprint.

Cite this

Stork, L., Weber, A., van den Herik, J., Plaat, A., Verbeek, F., & Wolstencroft, K. (2019). Automated semantic annotation of species names in handwritten texts. In L. Azzopardi, B. Stein, N. Fuhr, P. Mayr, C. Hauff, & D. Hiemstra (Eds.), Advances in Information Retrieval: 41st European Conference on IR Research, ECIR 2019, Proceedings, Part I (pp. 667-680). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11437 LNCS). Springer. https://doi.org/10.1007/978-3-030-15712-8_43

Stork, Lise ; Weber, Andreas ; van den Herik, Jaap ; Plaat, Aske ; Verbeek, Fons ; Wolstencroft, Katherine. / Automated semantic annotation of species names in handwritten texts. Advances in Information Retrieval: 41st European Conference on IR Research, ECIR 2019, Proceedings, Part I. editor / Leif Azzopardi ; Benno Stein ; Norbert Fuhr ; Philipp Mayr ; Claudia Hauff ; Djoerd Hiemstra. Cham : Springer, 2019. pp. 667-680 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{daa7c752e4e64d37983aaac970475788,

title = "Automated semantic annotation of species names in handwritten texts",

abstract = "In this paper, scientific species names from images of handwritten species observations are automatically recognised and annotated with semantic concepts, so that they can be used for document retrieval and faceted search. Until now, automated semantic annotation of such named entities was only applied to printed or digital text. We employ a two-step approach. First, word images are classified, identifying elements of scientific species names; Genus, species, author, using (i) visual structural features, (ii) position, and (iii) context. Second, the identified species names are semantically annotated according to the NHC-Ontology, an ontology that describes species observations. Internationalised Resource Identifiers (IRIs) are assigned to the elements so that they can be linked and disambiguated at a later stage by individual researchers. For the identification of scientific species names, we achieve an average F1 score of 0.86. Moreover, we discuss how our method will function in a semi-automated annotation process, with a fruitful dialogue between system and user as the main objective.",

keywords = "Deep learning, Historical biodiversity research, Ontologies, Scientific names, Semantic annotation, Taxonomy",

author = "Lise Stork and Andreas Weber and {van den Herik}, Jaap and Aske Plaat and Fons Verbeek and Katherine Wolstencroft",

year = "2019",

month = apr,

day = "7",

doi = "10.1007/978-3-030-15712-8_43",

language = "English",

isbn = "978-3-030-15711-1",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer",

pages = "667--680",

editor = "Leif Azzopardi and Benno Stein and Norbert Fuhr and Philipp Mayr and Claudia Hauff and Djoerd Hiemstra",

booktitle = "Advances in Information Retrieval",

address = "Netherlands",

note = "41st European Conference on Information Retrieval, ECIR 2019, ECIR 2019 ; Conference date: 14-04-2019 Through 18-04-2019",

url = "http://ecir2019.org/",

}

Stork, L, Weber, A, van den Herik, J, Plaat, A, Verbeek, F & Wolstencroft, K 2019, Automated semantic annotation of species names in handwritten texts. in L Azzopardi, B Stein, N Fuhr, P Mayr, C Hauff & D Hiemstra (eds), Advances in Information Retrieval: 41st European Conference on IR Research, ECIR 2019, Proceedings, Part I. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11437 LNCS, Springer, Cham, pp. 667-680, 41st European Conference on Information Retrieval, ECIR 2019, Cologne, Germany, 14/04/19. https://doi.org/10.1007/978-3-030-15712-8_43

Automated semantic annotation of species names in handwritten texts. / Stork, Lise; Weber, Andreas; van den Herik, Jaap; Plaat, Aske; Verbeek, Fons; Wolstencroft, Katherine.

Advances in Information Retrieval: 41st European Conference on IR Research, ECIR 2019, Proceedings, Part I. ed. / Leif Azzopardi; Benno Stein; Norbert Fuhr; Philipp Mayr; Claudia Hauff; Djoerd Hiemstra. Cham : Springer, 2019. p. 667-680 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11437 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

TY - GEN

T1 - Automated semantic annotation of species names in handwritten texts

AU - Stork, Lise

AU - Weber, Andreas

AU - van den Herik, Jaap

AU - Plaat, Aske

AU - Verbeek, Fons

AU - Wolstencroft, Katherine

N1 - Conference code: 41

PY - 2019/4/7

Y1 - 2019/4/7

N2 - In this paper, scientific species names from images of handwritten species observations are automatically recognised and annotated with semantic concepts, so that they can be used for document retrieval and faceted search. Until now, automated semantic annotation of such named entities was only applied to printed or digital text. We employ a two-step approach. First, word images are classified, identifying elements of scientific species names; Genus, species, author, using (i) visual structural features, (ii) position, and (iii) context. Second, the identified species names are semantically annotated according to the NHC-Ontology, an ontology that describes species observations. Internationalised Resource Identifiers (IRIs) are assigned to the elements so that they can be linked and disambiguated at a later stage by individual researchers. For the identification of scientific species names, we achieve an average F1 score of 0.86. Moreover, we discuss how our method will function in a semi-automated annotation process, with a fruitful dialogue between system and user as the main objective.

AB - In this paper, scientific species names from images of handwritten species observations are automatically recognised and annotated with semantic concepts, so that they can be used for document retrieval and faceted search. Until now, automated semantic annotation of such named entities was only applied to printed or digital text. We employ a two-step approach. First, word images are classified, identifying elements of scientific species names; Genus, species, author, using (i) visual structural features, (ii) position, and (iii) context. Second, the identified species names are semantically annotated according to the NHC-Ontology, an ontology that describes species observations. Internationalised Resource Identifiers (IRIs) are assigned to the elements so that they can be linked and disambiguated at a later stage by individual researchers. For the identification of scientific species names, we achieve an average F1 score of 0.86. Moreover, we discuss how our method will function in a semi-automated annotation process, with a fruitful dialogue between system and user as the main objective.

KW - Deep learning

KW - Historical biodiversity research

KW - Ontologies

KW - Scientific names

KW - Semantic annotation

KW - Taxonomy

UR - http://www.scopus.com/inward/record.url?scp=85064860066&partnerID=8YFLogxK

UR - https://rdcu.be/bFzrr

U2 - 10.1007/978-3-030-15712-8_43

DO - 10.1007/978-3-030-15712-8_43

M3 - Conference contribution

AN - SCOPUS:85064860066

SN - 978-3-030-15711-1

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 667

EP - 680

BT - Advances in Information Retrieval

A2 - Azzopardi, Leif

A2 - Stein, Benno

A2 - Fuhr, Norbert

A2 - Mayr, Philipp

A2 - Hauff, Claudia

A2 - Hiemstra, Djoerd

PB - Springer

CY - Cham

T2 - 41st European Conference on Information Retrieval, ECIR 2019

Y2 - 14 April 2019 through 18 April 2019

ER -

Stork L, Weber A, van den Herik J, Plaat A, Verbeek F, Wolstencroft K. Automated semantic annotation of species names in handwritten texts. In Azzopardi L, Stein B, Fuhr N, Mayr P, Hauff C, Hiemstra D, editors, Advances in Information Retrieval: 41st European Conference on IR Research, ECIR 2019, Proceedings, Part I. Cham: Springer. 2019. p. 667-680. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-030-15712-8_43