Challenges to sharing sample metadata in computational genomics

Sheffield, Nathan C.; LeRoy, Nathan J.; Khoroshevskyi, Oleksandr

doi:10.3389/fgene.2023.1154198

Cited by 5 publications

(2 citation statements)

References 33 publications

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“…Accordingly, our study had three specific objectives: (i) to assemble the genomes of strains FSP34 and KS17 by making use of both second-and third-generation sequencing technologies; (ii) to annotate the genomes in terms of gene content, chromosome number and chromosome identity, as well as their telomeric and centromeric features; and (iii) to compile for both strains a detailed set of relevant biological and ecological metadata (i.e., a description of the attributes of the samples from which the genome data were generated). The latter is increasingly regarded as essential for achieving timely and impactful outcomes in genome-based investigations [28,29]. This study would thus aid future research into the chromosomal architecture, as well as the genic content, of each genome, delivering essential resources for studying this destructive plant pathogen.…”

Section: Introductionmentioning

confidence: 97%

Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum

De Vos,

van der Nest,

Santana

et al. 2024

Pathogens

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The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome’s distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.

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Section: Introductionmentioning

confidence: 97%

Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum

De Vos,

van der Nest,

Santana

et al. 2024

Pathogens

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“…However, most effort has focused on biological data . Less emphasis has been placed on increasing the availability of biological metadata [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

LeRoy,

Khoroshevskyi,

O’Brien

et al. 2024

GigaScience

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Background As biological data increase, we need additional infrastructure to share them and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important and in some ways has a wider scope than sharing data themselves. Results Here, we present PEPhub, an approach to improve sharing and interoperability of biological metadata. PEPhub provides an API, natural-language search, and user-friendly web-based sharing and editing of sample metadata tables. We used PEPhub to process more than 100,000 published biological research projects and index them with fast semantic natural-language search. PEPhub thus provides a fast and user-friendly way to finding existing biological research data or to share new data. Availability https://pephub.databio.org

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PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

LeRoy,

Khoroshevskyi,

O’Brien

et al. 2023

Preprint

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Background: As biological data increases, we need additional infrastructure to share it and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important, and in some ways has a wider scope than sharing data itself. Results: Here, we present PEPhub, a new tool focused on improving sharing and interoperability of biological metadata. PEPhub provides an API, natural language search, and user-friendly web-based sharing and editing of sample metadata tables. These features will help researchers to share biological metadata more broadly. Availability: https://pephub.databio.org

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Challenges to sharing sample metadata in computational genomics

Cited by 5 publications

References 33 publications

Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum

Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

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