Connecting molecular sequences to their voucher specimens

Groom, Quentin; Dillen, Mathias; Huybrechts, Pieter; Johaadien, R; Kyriakopoulou, N; Fjq, Fernandez; Trekels, Maarten; Wong, Wai Yeung

doi:10.37044/osf.io/93qf4

Cited by 6 publications

(3 citation statements)

References 12 publications

(12 reference statements)

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“…We also propose that GenBank will become a useful resource for species identification by gene sequences other than the current DNA barcode region in the future. We believe that our work will accelerate future life science-and museomics-associated research employing biodiversity and sequence data (Groom et al, 2021).…”

Section: Introductionmentioning

confidence: 91%

“…GenBank has been collecting sequences for over 30 years (Sayers et al, 2022b), so it will be difficult to comply with the Darwin Core anytime soon. NCBI and other bioinformatics organizations are working on data standardization and Semantic Web activities, thereby including data integration with the biodiversity field (Chawuthai et al, 2016;Groom et al, 2021;Nakazato, 2021).…”

Section: Differences Between Barcode Of Life System and Genbank Descr...mentioning

confidence: 99%

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Cross-sectional use of barcode of life data system and GenBank as DNA barcoding databases for the advancement of museomics

Nakazato¹,

Jinbo²

2022

Front. Ecol. Evol.

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Museomics is an approach to the DNA sequencing of museum specimens that can generate both biodiversity and sequence information. In this study, we surveyed both the biodiversity information-based database BOLD (Barcode of Life System) and the sequence information database GenBank, by using DNA barcoding data as an example, with the aim of integrating the data from these two databases. DNA barcoding is a method of identifying species from DNA sequences by using short genetic markers. We surveyed how many entries had biodiversity information (such as links to BOLD and specimen IDs) by downloading all fish, insect, and flowering plant data available from the GenBank Nucleotide, and BOLD ID was assigned to 26.2% of entries for insects. In the same way, we downloaded the respective BOLD data and checked the status of links to sequence information. We also investigated how many species do these databases cover, and 7,693 species were found to exist only in BOLD. In the future, as museomics develops as a field, the targeted sequences will be extended not only to DNA barcodes, but also to mitochondrial genomes, other genes, and genome sequences. Consequently, the value of the sequence data will increase. In addition, various species will be sequenced and, thus, biodiversity information such as the evidence specimen photographs used as a basis for species identification, will become even more indispensable. This study contributes to the acceleration of museomics-associated research by using databases in a cross-sectional manner.

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Section: Introductionmentioning

confidence: 91%

Section: Differences Between Barcode Of Life System and Genbank Descr...mentioning

confidence: 99%

Cross-sectional use of barcode of life data system and GenBank as DNA barcoding databases for the advancement of museomics

Nakazato¹,

Jinbo²

2022

Front. Ecol. Evol.

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“…The importance of vouchers for molecular data has been pointed out repeatedly (Mulcahy 2022, Buckner et al 2021Groom et al 2021). Voucher specimens serve as physical evidence for the taxonomic identification and enable repeatability of molecular research, ranging from molecular ecological studies and molecular systematics to genomics.…”

Section: Taxon Names Sample Metadata and Vouchersmentioning

confidence: 99%

Policies Handbook on Using Molecular Collections

Mestier¹,

Mulcahy²,

Harris³

et al. 2022

Preprint

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The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitization also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The handbook presented here proposes a workflow to follow to safely exchange materials, in accordance with international laws and legislations. We make numerous recommendations here to help the institutions and researchers to navigate the legal and administrative procedures, to manage molecular collections in the best way possible.

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Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

Abarenkov¹,

Zirk²,

Põldmaa³

et al. 2021

BISS

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Third-party annotations are a valuable resource to improve the quality of public DNA sequences. For example, sequences in International Nucleotide Sequence Databases Collaboration (INSDC) often lack important features like taxon interactions, species level identification, information associated with habitat, locality, country, coordinates, etc. Therefore, initiatives to mine additional information from publications and link to the public DNA sequences have become common practice (e.g. Tedersoo et al. 2011, Nilsson et al. 2014, Groom et al. 2021). However, third-party annotations have their own specific challenges. For example, annotations can be inaccurate and therefore must be open for permanent data management. Further, every DNA sequence (except sequences from type material) can carry different species names, which must be databased as equal scientific hypotheses. PlutoF platform provides such data management services for third-party annotations. PlutoF is an online data management platform and computing service provider for biology and related disciplines. Registered users can enter and manage a wide range of data, e.g., taxon occurrences, metabarcoding data, taxon classifications, traits, and lab data. It also features an annotation module where third-party annotations (on material source, geolocation and habitat, taxonomic identifications, interacting taxa, etc.) can be added to any collection specimen, living culture or DNA sequence record. The UNITE Community is using these services to annotate and improve the quality of INSDC rDNA Internal Transcribed Spacer (ITS) sequence datasets. The National Center for Biotechnology Information (NCBI) is linking its ITS sequences with their annotations in PlutoF. However, there is still missing an automated solution for linking annotations in PlutoF with any sequence and sample record stored in INSDC databases. One of the ambitions of the BiCIKL Project is to solve this through operating the ELIXIR Contextual Data ClearingHouse (CDCH). CDCH offers a light and simple RESTful Application Programming Interface (API) to enable extension, correction and improvement of publicly available annotations on sample and sequence records available in ELIXIR data resources. It facilitates feeding improved or corrected annotations from databases (such as secondary databases, e.g., PlutoF, which consume and curate data from repositories) back to primary repositories (databases of the three INSDC collaborative partners). In the Biodiversity Community Integrated Knowledge Library (BiCIKL) Project, the University of Tartu Natural History Museum is leading the task of linking the two components—the web interface provided by the PlutoF platform and CDCH APIs—to allow user-friendly and effortless reporting of errors and gaps in sequenced material source annotations. The API and web interface will be promoted to those communities (such as taxonomists, those abstracting from the literature, and those already using the community curated data) with the appropriate knowledge and tools who will be encouraged to report their enhanced annotations back to primary repositories.

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Connecting molecular sequences to their voucher specimens

Cited by 6 publications

References 12 publications

Cross-sectional use of barcode of life data system and GenBank as DNA barcoding databases for the advancement of museomics

Cross-sectional use of barcode of life data system and GenBank as DNA barcoding databases for the advancement of museomics

Policies Handbook on Using Molecular Collections

Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

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