FAIR data in Aspergillus research

Welcome to the jungle!

Sibbe Bakker

Why?

Aspergillus fumigatus–an upcoming opportunist pathogen.

• A. fumigatus is a growing health concern [1].

• A lot of research is being conducted.

  • Environmental spread.
  • Molcular biology.

• There are some un-answered questions in this domain.

  • What mechanisms of azole resistance are there?
  • How does azole resistance spread in the environment?

A. fumigatus spreads quickly through its environment [2]

How is this research shared?

What ways of sharing are there?

Types of datasharing by [3]

• It is published.
• Sometimes the excel data is shared.
• Rarely other formats are used.
• Inter operability and reusibility are the biggest issues facing us.
• Acronyms
  • OL: Open Licence, sharing is possible.
  • RE: machine REadable.
  • OF: Open Format
  • URI: Unique Resource Identifiers -LD: Connected to other dataset.

How is the data actually shared?¹

Here I’ll share what I’ve seen.

What are these data usefull for?

• A single study may be understood better using this.
• Using the data from the same study for a different question?
• Combining specific results?
• Finding specific results?
• Not possible currently!

What do we need to make it useful?

What is already available

NCBI [6]—Meta data not always standard.

Afrum database [7]—Data upload not possible.

FunResDB [8]—Data upload not possible.

Solution? The FAIRDS project [9]

• A standardised meta data solution.
• Excel templates.
• RDF output.

A quick demo!

What should be the use of the ASPAR_KR project.

What is the use of a FAIR database?

What do you think? Fill in the poll

References

1.

Parums DV (2022) Editorial: The World Health Organization (WHO) Fungal Priority Pathogens List in Response to Emerging Fungal Pathogens During the COVID-19 Pandemic. Med Sci Monit 28:e939088-1-e939088-3. https://doi.org/10.12659/MSM.939088

2.

Keller N (2017) Heterogeneity Confounds Establishment of “a” Model Microbial Strain. mBio 8:e00135–17. https://doi.org/10.1128/mBio.00135-17

3.

Spinster (2012) English: Tim Berners-Lee, the inventor of the Web and Linked Data initiator, suggested a 5-star deployment scheme for Open Data. This scheme contains the five steps that this entails.

4.

Gonçalves P, Melo A, Dias M, et al (2021) Azole-Resistant Aspergillus fumigatus Harboring the TR34/L98H Mutation: First Report in Portugal in Environmental Samples. Microorganisms 9(1, 1):57. https://doi.org/10.3390/microorganisms9010057

5.

Burks C, Darby A, Londoño LG, Momany M, Brewer MT (2021) Azole-resistant Aspergillus Fumigatus in the environment: Identifying key reservoirs and hotspots of antifungal resistance. PLOS Pathogens 17(7):e1009711. https://doi.org/10.1371/journal.ppat.1009711

6.

Barrett T, Clark K, Gevorgyan R, et al (2012) BioProject and BioSample databases at NCBI: Facilitating capture and organization of metadata. Nucleic Acids Research 40(D1):D57–D63. https://doi.org/10.1093/nar/gkr1163

7.

Sewell TR, Zhu J, Rhodes J, et al (2019) Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus. mBio 10(3):e00392–19. https://doi.org/10.1128/mBio.00392-19

8.

Weber M, Schaer J, Walther G, et al (2018) FunResDB—A web resource for genotypic susceptibility testing of Aspergillus fumigatus. Med Mycol 56(1):117–120. https://doi.org/10.1093/mmy/myx015

9.

Nijsse B, Schaap PJ, Koehorst JJ (2023) FAIR data station for lightweight metadata management and validation of omics studies. GigaScience 12:giad014. https://doi.org/10.1093/gigascience/giad014

Footnotes

1. Statements from [4], [5], caoPrevalenceAzoleResistantAspergillus2021