  Software is a central part of modern science, and knowledge of its use is
crucial for the scientific community with respect to reproducibility and
attribution of its developers. Several studies have investigated in-text
mentions of software and its quality, while the quality of formal software
citations has only been analyzed superficially. This study performs an in-depth
evaluation of formal software citation based on a set of manually annotated
software references. It examines which resources are cited for software usage,
to what extend they allow proper identification of software and its specific
version, how this information is made available by scientific publishers, and
how well it is represented in large-scale bibliographic databases. The results
show that software articles are the most cited resource for software, while
direct software citations are better suited for identification of software
versions. Moreover, we found current practices by both, publishers and
bibliographic databases, to be unsuited to represent these direct software
citations, hindering large-scale analyses such as assessing software impact. We
argue that current practices for representing software citations -- the
recommended way to cite software by current citation standards -- stand in the
way of their adaption by the scientific community, and urge providers of
bibliographic data to explicitly model scientific software.
