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Pack bio_db -- Readme.txt


An SWI-Prolog pack/library [4] that provides a plethora of biological data in the form of Prolog predicates. The data can reside either in Prolog fact files (which are auto-compiled to fast loading .qlf files), or to back-end databases. The method of storage is trasparent to the user.

Installation :

?- pack_install(bio_db).

The library itself does not come with any data, these can be either downloaded en-masse via,

?- pack_install(bio_db_repo).

Or will be installed on demand at the first invocation of each data predicate. For instance if there have been no data installed the example below will ask permission to contact the server and install the specific dataset.

Minimal example:

?- map_hgnc_symb_hgnc( 'LMTK3', Hgnc ).

The served tables include data from

  • HGNC
  • NCBI
  • MGI (mouse)


The data are organised by organism, currently this is either hs (for human) or mouse. As the library was originally only for human data, predicates that do not specify organism of origin are assumed to be related to human databases.


[1] project page: http://stoics.org.uk/~nicos/sware/bio_db [2] docs: http://stoics.org.uk/~nicos/sware/bio_db/doc/html/bio_db.html [3] github: https://github.com/nicos-angelopoulos/bio_db [4] SWI-Prolog packs: http://eu.swi-prolog.org/pack/list

Nicos Angelopoulos

London, November 2018. (2016-2018)