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Development of the FAIR Genomes schema has taken place in the context of human genomics. This has resulted in a human-centered schema, but we are eager to expand into other organisms to achieve cross-…
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"LinkML is a flexible modeling language that allows you to author schemas in YAML that describe the structure of your data". Perhaps we can represent the FAIR Genomes schema in LinkML to increase oper…
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I think this issue is related to something that has been mentioned previously here, but I'm not sure that it is resolved.
I am using GSalign to align and call variants from a series of assembled ge…
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Define SPARQL queries that can be used to answer the information needs described in the use case flash card and the mindmap linked from #57 by relying on the information models defined in the Virtual …
mroos updated
10 hours ago
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I'm working on scaffolding a HiCanu assembly for a shark species that has had duplicates purged. It was assembled with ~45x PacBio Hifi (Median length: 13,710 bp; Mean length: 13,590 bp; Max. length: …
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Hello,
I was using GTDBtk to classify several genomes and found a file with RED values for pairs of genomes in the dabatase used, which I assumed was calculated from the Bac120 tree (and confirmed us…
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We may need ERNs to be included in FAIR Genomes. David Ruvolo compiled a complete ERN list that can be reused at https://github.com/molgenis/rd-datamodel/blob/main/data/ern_metadata.csv
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The use case described in #57 will be used to identify requirements on the interfaces between the VP[^1] and the connected resources, on the data objects that are communicated, and the services that p…
mroos updated
11 hours ago
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Suggestion for potential improvement. Within the FAIR Genomes project (https://www.nature.com/articles/s41597-022-01265-x) there have been many discussions on a Dutch national level on how to best rep…
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Hello I'm writting because I'm facing when I run RepeatModeler.
Here is the code I used :
```
Sp_name=Tryphoninae_B
ASSEMBLY=/beegfs/data/these/Genomes/Tryphoninae_B/Tryphoninae_B.fa
c…