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Work is currently being undertaken to refine the annotation requirements for the submission pipeline and to provide canonical gas chromatography mass spectrometry, liquid chromatography mass spectrometry and 1D NMR metabolomic experiment representations to guide submitters and developers alike.
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The practical requirements for annotation reinforces the benefits of using modular parts, rather than annotation of entire models, and of maintaining repositories of already-annotated SVPs.
Minimum requirements for annotation were a contiguous alignment of 300 bp, with 85% sequence similarity and a minimum e-value of 1 × 10−20.
The "Data collection and annotation" section describes our data requirements and the specific data sources we used, followed by the pre-processing and annotation steps required for supervised learning of VE recruitment.
Finally, the 'Augment Annotation by ANNEX' function was used to refine annotations (please see Availability & requirements for more information; [ 48]).
Rigorously, at least the osa-MIR812f, osa-MIR1848, osa-MIR1868 osa-MIR18771877 suffice the requirements for miRNA annotation.
In the case of eagle-i, the requirements for data annotation evolved as the data were collected, the ontology updated, and the guidelines enhanced.
In some cases, small RNA with highest expression was not chosen because it did not reside in a hairpin structure that meets the stringent structural requirements for miRNA annotation [ 48, 49].
The SwissProt protein IDs were used to associate the sequences with GO terms, using the file: "UniProt GO Annotations" (please see Availability and requirements for more information).
Functional enrichment analysis using Gene Ontology (GO) annotations of sensitive strains showed distinct requirements for resistance to each compound.
Sequence databases have introduced more stringent requirements for submitters meaning that running an annotation pipeline alone is not enough to ensure acceptance of the genome annotation [ 9, 10].
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