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add Otu reference sequence table #12

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mdoering opened this issue Mar 21, 2019 · 2 comments
Open

add Otu reference sequence table #12

mdoering opened this issue Mar 21, 2019 · 2 comments
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enhancement New feature or request
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@mdoering
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to hold information about reference sequence incl cluster method metadata for OTU based taxa.

@mdoering mdoering added the enhancement New feature or request label Mar 21, 2019
@thomasstjerne
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thomasstjerne commented Mar 25, 2019

Starting an attribute list here. Should all metadata about clustering method etc be repeated on each OTU?
There are conceptually two entities, the cluster and the chosen representative sequence, but for now these are flattened in one entity.

FieldName Description Example data
ID BOLD:ACG2675, SH1519649.08FU
doi Doi for the OTU 10.15156/BIO/SH215668.07FU
marker The Marker (region) of the DNA ITS2, COI-5P
referenceSequence A sequence choosen to represent the cluster (OTU) AACACTTTATTTTATTTTTGGAATTTGATCTGGAATAAT......
genbankAccessionNumber Link to the ref seq in GenBank DQ350842
typeStatus If the rep seq was taken from a type HOLOTYPE, ISOTYPE
memberCount Number of sequences in this cluster 5
averageInternalDistance The average distance between members of the OTU 0.94
maximumInternalDistance The max distance between members of the OTU 1.79
distanceToNearestNeighbor Distance to nearest neighbor OTU 9.12
clusteringMethodDesciption A short description of the clustering method. (Tree-based, Threshold-based, Ref Seq selection, centroid) OTU Designation Through Refined Single Linkage (RESL) Analysis

@mdoering
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If feasable I think we should put all fields into one flattened entity and repeat metadata - it is not safe to assume the entire dataset shares them. We might surely mix some in the catalogue and potentially derived "downloads". The clustering method description is obviously not nice.

As for ID and DOI I guess that is already part of the taxon entity that this links to? but it needs a taxonID to refer to the taxon

@mdoering mdoering added this to the Verison 2 milestone Apr 19, 2021
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