@inproceedings{corvi-etal-2021-biomaterials,
title = "The Biomaterials Annotator: a system for ontology-based concept annotation of biomaterials text",
author = "Corvi, Javier and
Fuentesl{\'o}pez, Carla and
Fern{\'a}ndez, Jos{\'e} and
Gelpi, Josep and
Ginebra, Maria-Pau and
Capella-Guitierrez, Salvador and
Hakimi, Osnat",
editor = "Beltagy, Iz and
Cohan, Arman and
Feigenblat, Guy and
Freitag, Dayne and
Ghosal, Tirthankar and
Hall, Keith and
Herrmannova, Drahomira and
Knoth, Petr and
Lo, Kyle and
Mayr, Philipp and
Patton, Robert M. and
Shmueli-Scheuer, Michal and
de Waard, Anita and
Wang, Kuansan and
Wang, Lucy Lu",
booktitle = "Proceedings of the Second Workshop on Scholarly Document Processing",
month = jun,
year = "2021",
address = "Online",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2021.sdp-1.5/",
doi = "10.18653/v1/2021.sdp-1.5",
pages = "36--48",
abstract = "Biomaterials are synthetic or natural materials used for constructing artificial organs, fabricating prostheses, or replacing tissues. The last century saw the development of thousands of novel biomaterials and, as a result, an exponential increase in scientific publications in the field. Large-scale analysis of biomaterials and their performance could enable data-driven material selection and implant design. However, such analysis requires identification and organization of concepts, such as materials and structures, from published texts. To facilitate future information extraction and the application of machine-learning techniques, we developed a semantic annotator specifically tailored for the biomaterials literature. The Biomaterials Annotator has been implemented following a modular organization using software containers for the different components and orchestrated using Nextflow as workflow manager. Natural language processing (NLP) components are mainly developed in Java. This set-up has allowed named entity recognition of seventeen classes relevant to the biomaterials domain. Here we detail the development, evaluation and performance of the system, as well as the release of the first collection of annotated biomaterials abstracts. We make both the corpus and system available to the community to promote future efforts in the field and contribute towards its sustainability."
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<abstract>Biomaterials are synthetic or natural materials used for constructing artificial organs, fabricating prostheses, or replacing tissues. The last century saw the development of thousands of novel biomaterials and, as a result, an exponential increase in scientific publications in the field. Large-scale analysis of biomaterials and their performance could enable data-driven material selection and implant design. However, such analysis requires identification and organization of concepts, such as materials and structures, from published texts. To facilitate future information extraction and the application of machine-learning techniques, we developed a semantic annotator specifically tailored for the biomaterials literature. The Biomaterials Annotator has been implemented following a modular organization using software containers for the different components and orchestrated using Nextflow as workflow manager. Natural language processing (NLP) components are mainly developed in Java. This set-up has allowed named entity recognition of seventeen classes relevant to the biomaterials domain. Here we detail the development, evaluation and performance of the system, as well as the release of the first collection of annotated biomaterials abstracts. We make both the corpus and system available to the community to promote future efforts in the field and contribute towards its sustainability.</abstract>
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%0 Conference Proceedings
%T The Biomaterials Annotator: a system for ontology-based concept annotation of biomaterials text
%A Corvi, Javier
%A Fuenteslópez, Carla
%A Fernández, José
%A Gelpi, Josep
%A Ginebra, Maria-Pau
%A Capella-Guitierrez, Salvador
%A Hakimi, Osnat
%Y Beltagy, Iz
%Y Cohan, Arman
%Y Feigenblat, Guy
%Y Freitag, Dayne
%Y Ghosal, Tirthankar
%Y Hall, Keith
%Y Herrmannova, Drahomira
%Y Knoth, Petr
%Y Lo, Kyle
%Y Mayr, Philipp
%Y Patton, Robert M.
%Y Shmueli-Scheuer, Michal
%Y de Waard, Anita
%Y Wang, Kuansan
%Y Wang, Lucy Lu
%S Proceedings of the Second Workshop on Scholarly Document Processing
%D 2021
%8 June
%I Association for Computational Linguistics
%C Online
%F corvi-etal-2021-biomaterials
%X Biomaterials are synthetic or natural materials used for constructing artificial organs, fabricating prostheses, or replacing tissues. The last century saw the development of thousands of novel biomaterials and, as a result, an exponential increase in scientific publications in the field. Large-scale analysis of biomaterials and their performance could enable data-driven material selection and implant design. However, such analysis requires identification and organization of concepts, such as materials and structures, from published texts. To facilitate future information extraction and the application of machine-learning techniques, we developed a semantic annotator specifically tailored for the biomaterials literature. The Biomaterials Annotator has been implemented following a modular organization using software containers for the different components and orchestrated using Nextflow as workflow manager. Natural language processing (NLP) components are mainly developed in Java. This set-up has allowed named entity recognition of seventeen classes relevant to the biomaterials domain. Here we detail the development, evaluation and performance of the system, as well as the release of the first collection of annotated biomaterials abstracts. We make both the corpus and system available to the community to promote future efforts in the field and contribute towards its sustainability.
%R 10.18653/v1/2021.sdp-1.5
%U https://aclanthology.org/2021.sdp-1.5/
%U https://doi.org/10.18653/v1/2021.sdp-1.5
%P 36-48
Markdown (Informal)
[The Biomaterials Annotator: a system for ontology-based concept annotation of biomaterials text](https://aclanthology.org/2021.sdp-1.5/) (Corvi et al., sdp 2021)
ACL