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Towards a scientific workflow featuring Natural Language Processing for the digitisation of natural history collections.[Version 2]

Owen, David ORCID:, Groom, Quentin, Hardisty, Alex ORCID:, Leegwater, Thijs, Livermore, Laurence, van Walsum, Myriam, Wijkamp, Noortje and Spasic, Irena ORCID: 2020. Towards a scientific workflow featuring Natural Language Processing for the digitisation of natural history collections.[Version 2]. Research Ideas and Outcomes 6 , e58030. 10.3897/rio.6.e58030

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We describe an effective approach to automated text digitisation with respect to natural history specimen labels. These labels contain much useful data about the specimen including its collector, country of origin, and collection date. Our approach to automatically extracting these data takes the form of a pipeline. Recommendations are made for the pipeline's component parts based on some of the state-of-the-art technologies.Optical Character Recognition (OCR) can be used to digitise text on images of specimens. However, recognising text quickly and accurately from these images can be a challenge for OCR. We show that OCR performance can be improved by prior segmentation of specimen images into their component parts. This ensures that only text-bearing labels are submitted for OCR processing as opposed to whole specimen images, which inevitably contain non-textual information that may lead to false positive readings. In our testing Tesseract OCR version 4.0.0 offers promising text recognition accuracy with segmented images.Not all the text on specimen labels is printed. Handwritten text varies much more and does not conform to standard shapes and sizes of individual characters, which poses an additional challenge for OCR. Recently, deep learning has allowed for significant advances in this area. Google's Cloud Vision, which is based on deep learning, is trained on large-scale datasets, and is shown to be quite adept at this task. This may take us some way towards negating the need for humans to routinely transcribe handwritten text.Determining the countries and collectors of specimens has been the goal of previous automated text digitisation research activities. Our approach also focuses on these two pieces of information. An area of Natural Language Processing (NLP) known as Named Entity Recognition (NER) has matured enough to semi-automate this task. Our experiments demonstrated that existing approaches can accurately recognise location and person names within the text extracted from segmented images via Tesseract version 4.0.0. Potentially, NER could be used in conjunction with other online services, such as those of the Biodiversity Heritage Library to map the named entities to entities in the biodiversity literature ( have highlighted the main recommendations for potential pipeline components. The document also provides guidance on selecting appropriate software solutions. These include automatic language identification, terminology extraction, and integrating all pipeline components into a scientific workflow to automate the overall digitisation process.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Computer Science & Informatics
Additional Information: This is an updated version of record
Publisher: Pensoft Publishers
ISSN: 2367-7163
Funders: H2020-EU. - Developing new world-class research infrastructures
Related URLs:
Date of First Compliant Deposit: 3 July 2020
Date of Acceptance: 3 July 2020
Last Modified: 10 Dec 2022 02:25

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