BioNerDS is a dictionary and rule based named entity recogniser for databases and software. The input and output will be in text files. Examples of files annotated by BioNerds can be found here. Lists of Databases and software can be found in CSV format here.
The new version of BioNerDS is updated in 2020 by Alexandra Dumitriu. It is a Maven project that run with Java 8 or higher. The installation instructions can be found here. If you intened to annotate a large number of files, it is recommended to use the script sheet runBioNer.sh which loop through the files and save the annotations.
The original BioNerDS developed in 2016 by Geraint Duck. The code and corpora used can be found here.