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Leveraging Semantic Web Technologies for Veracity Assessment of Big Biodiversity Data
Published in Archana Patel, Narayan C. Debnath, Bharat Bhushan, Semantic Web Technologies, 2023
Zaenal Akbar, Yulia A. Kartika, Dadan R. Saleh, Hani F. Mustika, Lindung P. Manik, Foni A. Setiawan, Ika A. Satya
To be able to measure the three types of data consistency, we introduce several definitions and formalizations as follows: Vocabulary: Vocabulary is a collection of data attributes that can be used to describe an object. Each attribute has a name and an expected type of value. As an illustration, to describe a biological specimen, it is necessary to have a few data attributes such as the name of the specimen, where and when the specimen was collected, and so on. Further, an attribute “name” should have a textual value, an attribute “date” should have a date value, etc. In the field of biodiversity, several existing vocabularies have been used widely. One of them is Darwin Core,7 a data standard for publishing and integrating biodiversity information [26]. We use this vocabulary due to its wide adoption.Dataset: Dataset is a collection of data objects, where each object is described with one or more attributes that are available in the selected vocabulary.Dataset vocabulary: Dataset vocabulary is a collection of data attributes, where each object is described with one or more attributes that are available in the selected vocabulary. It is worthy to mention that every dataset could use less or a greater number of attributes available in the vocabulary.
The future of molecular ecology in Aotearoa New Zealand: an early career perspective
Published in Journal of the Royal Society of New Zealand, 2022
Libby Liggins, Vanessa Arranz, Heather E. Braid, David Carmelet-Rescan, Joane Elleouet, Ekaterina Egorova, Michael R. Gemmell, Simon F. K. Hills, Lyndsey P. Holland, Emily M. Koot, Alexandra Lischka, Kimberley H. Maxwell, Laura J. McCartney, Hang T. T. Nguyen, Cory Noble, Pamela Olmedo Rojas, Elahe Parvizi, William S. Pearman, Jenny Ann N. Sweatman, Te Rangitākuku Kaihoro, Kerry Walton, J. David Aguirre, Lucy C. Stewart
Internationally, groups such as the Biodiversity Information Standards Organization (TDWG, administering the Darwin Core Standard, Wieczorek et al. 2012) and the Genomic Standards Consortium (GSC, Wooley et al. 2009) have defined appropriate vocabularies and metadata standards for genetic biodiversity studies (e.g. Field et al. 2008; Yilmaz et al. 2011 defining the ‘Minimum Information about any (x) Sequence’, MIxS standard). The retention and stewardship of these metadata have now been operationalised by GEOME, and some repositories of the INSDC. Provisioning these metadata for genetic data can help make sure our molecular ecological research is reproducible, future-proofed, and useful to the next generation of our nation (see statements G., H., J., K.). Taking precedent over such openness, however, is consideration of Māori data sovereignty. When collected for taonga (treasured) species, some metadata may also be considered taonga (Collier-Robinson et al. 2019), meaning that collaborating iwi and hapū may prefer to protect or redact certain metadata fields from the public domain. In Aotearoa, GEOME’s infrastructure has been used by the Ira Moana Project to provide Aotearoa’s molecular ecologists with a template to guide collation, upload, and on-going storage of metadata relevant to the nation’s interests, including a TDWG field ‘informationWithheld’ that can name metadata that exist, but are not shared, for reasons of sensitivity.