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Packs (add-ons) for SWI-Prolog

Package "bio_db"

Title:Access, use and manage big, biological datasets.
Rating:Not rated. Create the first rating!
Latest version:2.2
SHA1 sum:0ee3ea6a5b5d30641d0e6881f3f61dc1d9774a40
Author:Nicos Angelopoulos http://stoics.org.uk/~nicos
Maintainer:Nicos Angelopoulos http://stoics.org.uk/~nicos
Packager:Nicos Angelopoulos http://stoics.org.uk/~nicos
Home page:http://stoics.org.uk/~nicos/sware/bio_db
Download URL:http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-*.tgz
Requires:lib

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Details by download location

VersionSHA1#DownloadsURL
0.13dd7e10dc7cb559d5de8da3a92dde50b09857dd61http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.1.tgz
0.2a99702e47dceb153070ca4b306add17d451206c62http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.2.tgz
0.3764e8c4cdab38aad24b1aaf237e72e53d0aaf0ec3http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.3.tgz
0.4ac338d8d45a9edd482dd33ab5466a5c45e5714644http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.4.tgz
0.5688b9165a8791f488b98a5c0a05a7401498499394http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.5.tgz
0.60a3fa770e5ad9448f914bd39d8b49732417beff83http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.6.tgz
0.7d29b4e3381fb49a0b019078ada2c09cb504c2e011https://github.com/nicos-angelopoulos/bio_db/archive/0.7.zip
0.8d718f494da239333be2a0b16151bc32a314961fe2http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.8.tgz
0.91cc842530028e2765f4843aceadf63d7c85c20f06http://www.stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-0.9.tgz
1.08dbf1931f396064d6d30522e6d3a6916e42964231http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-1.0.tgz
1.19acd752e73dcb701becc340a58138db5e1a3a9ca11http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-1.1.tgz
2.0f28bfd91fd211d5b6ee6a8c69f3c7d9fb4fd3c4b1http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-2.0.tgz
2.1afd131df1bb82b9193720bdbabc78df9c19c55f11http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-2.1.tgz
2.20ee3ea6a5b5d30641d0e6881f3f61dc1d9774a401http://stoics.org.uk/~nicos/sware/packs/bio_db/bio_db-2.2.tgz

bio_db

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
  • ENSEMBL
  • NCBI
  • UNIPROT
  • PROSITE
  • STRING
  • GENE ONTOLOGY
  • MGI (mouse)

Organisms

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.

Links

[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)

Contents of pack "bio_db"

Pack contains 171 files holding a total of 557K bytes.