2. Use systematic names and descriptions
Systematic descriptions should be used in relation to models (and
elsewhere), when systematics exists. Relevant areas in relation to
molecular models include names of organisms (taxonomy), gene and protein
names (Gray et al., 2015), variations in proteins (HGVS nomenclature)
(den Dunnen and Antonarakis, 2001), names of files (sequence and PDB
ids), variation effects and consequences (Variation Ontology annotations
(Vihinen, 2014)), etc. In the case of sequence ids, version numbers must
be included unless LRGs (Dalgleish et al., 2010) are used.
Example: Variations in human BTK gene and translated
protein (LRG_128) lead to XLA, a X-chromosomal primary immunodeficiency
(OMIM # 300755). Variant p.R28C has been identified in XLA patients.