DNAmod: the DNA modification database

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

(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

(B) Natural occurrence annotations
Field	Terms
Function^a	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〉

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
^aEach row contains all possible instantiations of the field on the left, except that terms within the “Function” field are often combined, as conjunctions

ISSN: 1758-2946