Connecting molecular sequences to their voucher specimens

Abstract

When sequencing molecules from an organism it is standard practice to create voucher specimens. This ensures that the results are repeatable and that the identification of the organism can be verified. It also means that the sequence data can be linked to a whole host of other data related to the specimen, including traits, other sequences, environmental data, and geography. It is therefore critical that explicit, preferably machine readable, links exist between voucher specimens and sequence. However, such links do not exist in the databases of the International Nucleotide Sequence Database Collaboration (INSDC). If it were possible to create permanent bidirectional links between specimens and sequence it would not only make data more findable, but would also open new avenues for research. In the Biohackathon we built a semi-automated workflow to take specimen data from the Meise Herbarium and search for references to those specimens in the European Nucleotide Archive (ENA). We achieved this by matching data elements of the specimen and sequence together and by adding a “human-in-the-loop” process whereby possible matches could be confirmed. Although we found that it was possible to discover and match sequences to their vouchers in our collection, we encountered many problems of data standardization, missing data and errors. These problems make the process unreliable and unsuitable to rediscover all the possible links that exist. Ultimately, improved standards and training would remove the need for retrospective relinking of specimens with their sequence. Therefore, we make some tentative recommendations for how this could be achieved in the future.

Authors 7

1. Quentin Groom

   Meise Botanic Garden

   Affiliation as printed

   1 Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium

2. Mathias Dillen

   Meise Botanic Garden

   Affiliation as printed

   1 Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium

3. Pieter Huybrechts

   Meise Botanic Garden

   Affiliation as printed

   1 Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium

4. Rukaya Johaadien

   University of Oslo

   Affiliation as printed

   Natural History Museum, University of Oslo, Sars Gate 1, 0562, Oslo, Norway

5. Niki Kyriakopoulou Aachen Naturalis Biodiversity Center

   Naturalis Biodiversity Center

   Affiliation as printed

   Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, Netherlands

6. Francisco Jose Quevedo Fernandez
7. Maarten Trekels

   Meise Botanic Garden

   Affiliation as printed

   1 Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium