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|Pack bio_db -- doc/Releases.txt|
rocks_current(X). --- 21.12.03 make sure existing handles are checked before opening another handle to same predicate (map_ense_mouse_enst_chrl/5 was opening map_ense_enst_chrl/5).
organism(gallus)with aliases chicken and gallus_gallus 22.12.17 IFACE: added Relation to gont for mouse predicates, and updated docs CELL: gallus, full name: gallus gallus (token gallus) 22.12.16 CHANGED: iface for url_file in graph_strg (hs and mouse) was changed to wget 21.12.04 SCRIPT: examples/bio_db_stats.pl added output directory bio_db_stats & comment on versions kept there SCRIPT: moved examples/bio_db_stats.pl to scripts/ (spuds finds there for docs)
csv(version)21.12.03 SCRIPT: bio_db_stats.pl @version 0.2 2021/12/03, options, sort predicates FIXED: pack_errors in prolog/bio_db.pl now use the, modern, options version of throw/2 FIXED: fixed map_ense_mouse_enst_chrl/5 (was opening map_ense_nest_chrl/5) 21.07.19 CHANGE: update test_repo.pl
arg(3), which gene_name uses to fall back on gene_id 20.09.24 DEPS: explicit loading of library(archive)
optval for cascading options BUILD: auto detection of ense latest gtf file BUILD: started on mouse ense maps (based on human scripts) 20.09.08 DEPS: explicit loading of library(debug) 20.07.18 DEPS: explicit loading of autoloaded SWI libs
iface(wget)'cause of a couple of ftp-ing problems with SWI's URL getter
2.7 @ 19.05.12 19.05.09 CHANGE: edge_strg_symb/4 -> org_edge_strg_symb/4
pack(bio_analytics)FIXED: argument switch copy paste in edge_gont_includes/2 IFACE: is_symbol/2 + entz_symb/3 19.04.06 FIXED: make sure weights in string graphs are arithmetic BUILD: map_gont_mouse_gont_symb/2 IFACE: map_gont_mouse_gont_symb/2 DATA: GO terms in human are now without GO:
convert(false)in csv_read_file/3 call
2.1 @ 18.11.27 18.11.27 FIXED: new dependency to write_message/3 was pointing to wrong directory...
pack(lib)in auxil/build_repo/std.pl CHANGED: std_repo to look into new dir structure (bio_db_repo... rather than bio_db) ADDED: auto detection of latest string version ADDED: use of new tables in building std tables that depend on existing bio_db relations 18.03.13 DEL: moved url_url/3 to
pack(stoics_lib)17.10.14 FIXED: mislocated map_uniprot.pl FIXED: bio_db stem in aliases to bio_db_repo CHANGED: std_maps_psit.pl to new structure RENAME: std_maps_psit.pl std_maps_pros.pl 1.1 17.10.13 VER: 1.1 CHANGED: Huge restructuring of auxil/ 1.0 17.10.09 VER: 1.0 17.09.27 FIXED: man_ense_esg_hgncvcsv -> man_ense_esg_hgnc.csv typo CHANGE: parts of the URL for string CHANGE: bio_db_pl_info now from bio_db FIXED: std_maps_psit.pl untested yet 17.08.15 VER: 1.0 (candidate) 17.08.11 CHANGED: implementation of pl_prosqlite now .sqlite file is removed if op fails/excepts CHANGED: examples/cpu/cpu.pl 17.08.10 REMOVED: spurious loading of break_list_on/4 from has_extension/3 FIXED: en_list/2 loads from stoics_lib now not options (various auxil sources) 17.06.27 ADDED: examples/gene_map_compare.pl UPDTE: load via message_report/3 in auxil/lib/link_to_bio_sub.pl FIXED: dependency of std_maps_ense is now to std_maps_hgnc and not to absolute file locations
pack(lib)v1.1 16.11.28 ADDED: rule in asserting alias, that does not complain if New==Old 0.8 16.11.22 DISTRO: back to stoics.org.uk (github gives no adequate statistics) 0.7 16.11.21 EXAMPLES cpu/ 16.11.20 DOC: added rocks in bio_db_interface/1 blur and corrected typo. DOC: fixed prediate -> predicate x2 ADDED: bio_interface/2 FIXED: bio_db_rocks_multi_key_args -> bio_db_rocks_multi_key_value FIXED: failure on call mode
bio_db_info_gen( -, -, -, - ). And doc format. ADDED: examples/cpu/ with all code neccessary to reproduce cpu comparison graphs ADDED: bio_db_install/2,3 ADDED: bio_db_info/2 ADDED: full support for .qlf 16.11.14 REPO: Started a GitHub repository Jan Wielemaker found bug for obsolete call to map_gont_include/2 (and assoc. preds) added flag bio_db_qcomplie (def: true) to control the following addition: a retractall/1 fix and
qcompile(large)options in lad_files/2 by Jan Wielemaker 16.10.28 added map_ncbi_dnuc_symb/2 16.10.27 ADDED: map_hgnc_hgnc_ccds/2 & map_hgnc_ccds_hgnc/2 16.10.13 DOC: minor doc fix about what repo contains
16.09.11 IFACE: bio_db_citation/2 (2 clauses added) IFACE: bio_db_close_connections/0 and register it with at_halt/1 IFACE: Handle N-ary tables in berkeley and IFACE: bio_db_info( [Inteface,] +Pid, ?Key, -Value ). IFACE: Can now close current connections with pack_error if not open IFACE: bio_db_interface/1 prints a proper error message now LIBS: Started using lib(pack_errors) (arg_enumerating/3 was the first one) 16.09.08 - SCRIPT: Updates to almost all std_ scripts in auxil LIBS: new helper independent preds in auxil/lib DATA: Full successful download of data and creation of prolog dbs. LIBS: Check script auxil/bio_db_check.pl IFACE: Shortened bio_db_load_prolog_map/2 -> bio_db_serve/1 (load as 2nd arg) 16.09.06 IFACE: Added auto-reply via prolog_flag(bio_db_ok,true). DATA: Canonical downloads are now from .zip files. LIBS: Many improvements to the downloads logic. DATA: pl-> berkeley and pl-> sqlite are now user. DATA: pl-> sqlite are done in batches of 500, so there is no need for sqlite exec now
0.4 @ 15.09.16
15.09.13 DATA: Added Berkeley DB interface (via SWI's own library(bdb)).
15.07.25 - DATA: Added edges for is-a (and reverses
inc(cludes)) from GO.
15.07.25 - IFACE: Added bio_db_version.
0.3 Spring 2015 First releases including maps from hgnc, ncbi and uniprot. Graph edges from string (with weights).