BIOS5316

Daniel Vaulot

2023-10-05

Culture information management

Outline

  • The Roscoff Culture Collection
  • Strain information: metadata
  • Keeping track of the metadata: database
  • Access and Benefit Sharing (ABS)

Station Biologique de Roscoff

Station Biologique de Roscoff

  • 1872 - Antoine Lacaze-Duthiers (150 years ago)
  • CNRS and Sorbonne Université
  • Staff: 350
  • Students : 1,000-2,000 per year

Ecologie of Marine Plankton team (ECOMAP)

  • Scientists: 10
  • Staff: ~ 40
  • Research themes:
    • Viruses
    • Bacteria
    • Cyanobacteria
    • Symbioses
    • Parasitism

Roscoff Culture Collection

  • Created 1998
  • One of the largest marine algal collection
  • 5,000 strains distributed
  • https://roscoff-culture-collection.org/

Metadata

What are metadata ?

Metadata are data related to each strain.

They are used to determine the ID-card of the strain.

  • Unique identifier
  • Strain name
  • Taxonomy
  • Origin
  • Status of strain
  • Images
  • Maintenance conditions
  • ABS status
  • Sequences
  • Publications

Strain identification

  • Unique identifier (RCC1, RCC2…)
    • This number is fixed and should be always used
    • It is given only for stable cultures
  • Strain name
    • This is given during the isolation process
    • It contains reference to cruise or project
    • Important to provide synomyms if they exists

Strain identification

  • Taxonomy
    • Follow standard (Algaebase)
    • Be consistent
    • Can be in separate table (see later)
    • RCC use 7 levels
      1. Domain
      2. Division
      3. Class
      4. Order
      5. Family
      6. Genus
      7. Species
    • Identification can be at higher level only (e.g. class)

Strain status

  • Alive ?
    • Never erase information about a strain even if it has been lost.
    • Lost: Yes/no
    • Date of loss
  • Distributed ?
    • Strains may be kept private until described
  • Clonal ?
    • Arise from single cells
  • Mixed ?
    • With heterotroph ?
  • ABS status (Nagoya convention)

Strain isolation

  • Sampling
    • Date (see ABS)
    • Position
    • Depth
    • Ocean / Regional Sea
    • Site
    • Country (see ABS)
    • Substrate (water, sediment)
    • Temperature / Salinity
  • Isolation
    • Method
    • Medium
    • Temperature
    • Light

Phenotype

  • Life mode
    • Phototrophic / Heterotrophic
    • Symbiotic
  • Morphology
    • Cell size
    • Cell shape
    • Motility
    • Colonial ?
  • Images

Other information

  • Genetic sequences
  • Pigment composition
  • References for the strain

Management

  • Culture localisation
  • Media batches
  • Cryoconservation
  • DNA
  • Distribution

Databases

How to keep track of the information ?

Excel worksheet

Advantages

  • Everyone can use Excel

Disadvantages

  • Difficult to share
  • No rule enforcement for each field
  • Too many formatting

Google worksheet

Advantages

  • More easy to share
  • Can trace who modifies

Disadvantages

  • Same as Excel

How to keep track of the information ?

SQL relational databases

Advantages

  • Allow to structure information much better
  • Relationships between different tables
  • Many choices for implementation:
    • local (SQlite or Access)
    • remote on the cloud (MySQL)

Disadvantages

  • Requires using specific tools
  • Need computer skills

The Roscoff Culture Collection solution

This solution has been elaborated over 20 years with many iterations…

  • Start from a database
    • Initially Microsoft Access
    • Since 2017 MySQL
  • Link to web site
    • 3 generations

Access and Benefit Sharing (ABS)

Using biological resources

  • Sampling/Acquisition - ABS
  • Housing
  • Utilization - ABS

Best practice

  • OECD Best Practice Guidelines for Biological Resource Centres (2007)
  • ISO 9001 : Quality Management System
  • ISO 20387:2018 : General requirements for biobanking (based on French NF S96-900 standard)

ABS: long journey

  • Before Convention on Biological Diversity (Rio 1992): Biodiversity (animals, plants, microorganisms) considered as common heritage of mankind
  • After CBD (1992): Adoption of concept that states have sovereign rights over their biological resources
  • 2010: Adoption of Nagoya Protocol (NP) to CBD: sets out core obligations for its contracting Parties to take measures in relation to access to genetic resources, benefit-sharing and compliance.
  • 2014: European ABS Directive 511-2014 defines responsibilities of Member States for enforcing compliance to NP
  • From 2014: national laws (or not…)

Nagoya protocol - 1990

United Nations Convention on the Law of the Sea (UNCLOS) - 1994

Important points

  • Unique identifier for each strain
  • Never delete information (e.g. lost strains)
  • Sampling information is critical for ABS

Questions ?