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Table 1 Possible annotations within DNAmod’s curated (A) sequencing method data and (B) natural occurrence information

From: DNAmod: the DNA modification database

(A) Sequencing method annotations
Field Terms
 Mapping method 〈method abbreviation〉
 Method detail affinity-based, chemical conversion, chemical conversion and immunoprecipitation, chemical tagging, direct detection, DNMT1 conversion, enzyme-mediated chemical tagging, excision repair enzyme-based, restriction endonuclease
 Resolution low, high, single-base
 Qualifier 5hmU:G mismatch only, CpG contexts only, [low-input or] single-cell, [methylation-insensitive] restriction digestion, microarray probes, salt gradient stratification, specific fragments, strand-specific, target sequences
  1. Each row lists a field and all terms ever used to annotate it. [square brackets]: optional prefixes. 〈angle brackets〉: description of term, rather than the complete enumeration provided for other terms
  2. aEach row contains all possible instantiations of the field on the left, except that terms within the “Function” field are often combined, as conjunctions
(B) Natural occurrence annotations
Field Terms
 Functiona damage, demethylation intermediate, [possible] epigenetic mark, hypermodified nucleobase, restriction-modification
 Functional detail [highly] cytotoxic, mutagenic, reactive oxygen species, specific transcriptional roles, transcription terminator
 Origin natural, synthetic, synthetic and RNA
 Organism 〈binomial name〉
  1. Each row lists a field and all terms ever used to annotate it. [square brackets]: optional prefixes. 〈angle brackets〉: description of term, rather than the complete enumeration provided for other terms
  2. aEach row contains all possible instantiations of the field on the left, except that terms within the “Function” field are often combined, as conjunctions