--- Releases ---

TBD: + SWI: Harmonization of bdb and rocks db ? Rocks allows aliases. Duplicate option for rocksdb. Rocks doesn't have mode (and does not open as read only so no 2 processes can open the db?) Would be nice to have the "correct" types when opening an existing database with no options. Rocks: Enumerate connections ? 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).

4.7 @ 25.03.28 25.03.28 BUILD: Increase stack for multi/ncbi 25.01.02 BioDB: added building and using preds for reactome predicate in sus scrofa 24.10.19 FIXED: missing is_symbol/2 for chicken and pig

4.6 @ 24.10.17 24.10.16 BioDB: added ense_gg7w_* predicates to support white loghorn CHANGE: of hgnc base URL 24.10.15 REMOVE: obsolete second argument in std_chicken_maps_ense/3 FIXED: build_repo, broken gg6a:ense (was identical to chicken) 4.5 @ 24.04.05 24.04.05 FIXED: currently stoics.org certificate is not recognised added insecure(true) in url_file/3 opts 4.4 @ 24.04.05 24.03.27 BioDB: added ncbi_homs_ncbi_symb/2 (and seriously reorganised ncbi builds) 24.03.26 BioDB: added vgnc_suss_vgnc_ncbi/2 + vgnc_suss_vgnc_ensg/2 24.03.17 BioDB: added reac in human cell 24.03.16 IFACE: added bio_db_org_in_opts/2 24.03.16 DOC: errors in doc of bio_db_organims/1,2,3 + improved text 24.03.11 BioDB: activated reactome for chicken build & cell 24.03.07 BioDB: ncbi for chicken (ensg <-> ncbi + ensp <-> ncbi) - also in cell/ 23.10.17 FIXED: pig cell errors (ncbi module name), and vgnc ncbi predicates 4.3 @ 23.10.05 23.09.03 BUILD: major rewrite of Opts and helpers + new version of link_to_bio_sub/3 23.09.29 OPTS: renamed url_file_local_date_mirror:file() to dnld_file() 23.09.24 FIXED: mgim Marker Symbols was tokenised to _symb 23.09.22 BUILD: create a optionised url constructor, that uses bio_db_source_base_url/2 (bio_db_source_url/2) BUILD: created file for pretty printing messages: auxil/build_repo/lib/bio_db_build_messages.pl 23.09.21 BUILD: begin gathering the base urls into auxil/build_repo/lib/bio_db_source_base_url/2 SCRIPT: auxil/build_repo/hpc/build_bio_db_repo_slurm OPTS: verb(Verb) in url_file_local_date_mirror OPTS: iactive(Iact=false) and in_subs(InSubs=true) for hpc and non supervised running 23.09.20 CELL: cell/multi for multi-species preds BioDB: vgnc, multi + pig BioDB: NCBI taxonomy 23.09.16 FIXED: auto fill for info headers was broken LIB: added [bio_db_]cnm_token/2,3,4, mapping db column names to bio_db tokens ADDED: bio_db_organism_known/3 (internal for now) 23.09.15 CELL: mult/multi for preds across multiple species: ncbi_mult_taxo_scnm/2, ncbi_mult_taxo_gbnm/2 BUILD: scripts for the multi predicates from NCBI: ncbi_mult_taxo_scnm/2, ncbi_mult_taxo_gbnm/2 23.06.21 SCRIPT: new version of bio_db_stats.pl (via by_unix: avoid mem probs), also new csv output added 23.06.10 CHANGE: mouse unip-rot was using .versioned ensp-roteins; which was also knocking on string 23.06.07 FIXED: updated table names to new regime, + support for pig (ord_edge_strg_symb/4)

4.2 @ 23.06.06 23.06.02 CELL: sus scrofa, pig support with token suss 23.05.31 BUILD: start support for pig 23.01.02 DOC: updated numbers of records and preds at the top of the module doc

4.1 @ 22.12.29 22.12.26 BUILD: remove dependency to R in csv_ids_map.pl CELL: hgnc and ncbi now produce ncbi rather than entz tokens 22.12.25 IFACE: start work on 4.0, all predicates to be 4x4 22.12.24 REPO: build script for reactome maps (all organisms) 22.12.20 IFACE: 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) 3.6 @ 21.12.04 21.12.04 VERS: 3.5 was spoiled by a 3.4 in bio_db_version/2 DEPS: added library(lists) to examples/bio_db_stats.pl DOC: moved version comments to module tags DOC: fixed 3:5:0 example in version predicate SCRIPT: examples/bio_db_stats.pl sumlist/2 -> sum_list/2 SCRIPT: bio_db_stats.pl option 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 3.4 @ 21.05.10 UPDATE: bio_db_version/2 IFACE: commented out: edge_gont_includes/2 (reciprocal of is_a), and edge_gont_consists_of/2 (reciprocal of part_of/2) 3.3 @ 21.05.10 21.05.10 DOC: minor typos CHANGE: generated new src/bio_db_data_predicate.pl 21.05.07 CHANGE: deep changes to std_graphs_gont, re-write of std_maps_gont with no dependency to FIXED: explicit removal of obsolete entries in std_{maps,graphs}_gont CHANGE: ense_info/4 has a def/1 option in arg(3), which gene_name uses to fall back on gene_id 20.09.24 DEPS: explicit loading of library(archive) 3.2 @ 20.09.18 20.09.14 BUILD: link_to_maps_sub/2->4, link_to_bio_sub/3 optionised 20.09.13 BUILD: fixed typo on reporting task: start -> stop 20.09.11 BUILD: added debug argument to csv_to_pl/1 FIXED: finalised support for mouse ense CHANGE: use library(csv) facilites for skipping comments in ense 20.09.10 IFACE: use passoptval 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 3.1 @ 20.03.08 20.03.07 CHANGE: many debug(,,true) to debug_call(,,true) as SWI 8 has changed this to an error REMOVE: map_unip_unip_unig/2 info don't seem to be in the source file any longer... HUMAN_9606_idmapping UPDATE: auxil URLs. using more iface(wget) 'cause of a couple of ftp-ing problems with SWI's URL getter 3.0 @ 19.05.15 UPDATE: many changes to IFACE: cell loading support

2.7 @ 19.05.12 19.05.09 CHANGE: edge_strg_symb/4 -> org_edge_strg_symb/4

2.6 @ 19.05.08 19.05.07 FIX: move to /3 version throughout (map_gont_mouse_gont_symb/3) 19.05.06 FIXED: correct go id and remove all traces of go_term_symbols CHANGE: entrez ids are now read as integers .... 19.05.04 DATA: added evidence to map_gont_symb_gont/2 and gont_symb/2 IFACE: map_gont_gont_symb/2 -> 3, and symb_gont/2->3 19.05.03 DATA: map_gont_gont_gomn/2, both new Gont id (as integer) and changes in go source files 19.05.02 IFACE: bio_db_organism_alias/2 and changed bio_db_organism/2 2.5 @ 19.04.22 19.04.08 IFACE: edge_strg_symb/4 IFACE: bio_db_organism/1,2 19.04.07 FIXED: logic for partial builds IFACE: go_id/2,3 MOVED: go_term_symbols/3 to 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: 2.4 @ 19.04.02 19.04.01 FIXED: setting up bio_db_repo_version/1,2 correctly from date repo was created UPDATE: auto generate bio_db_data_predicate/4 19.02.13 DOC: fixed copy paste mistakes from human onto mouse 19.02.12 BUILD: scripts for map_ncbi_mouse_syno_symb/2 IFACE: map_ncbi_mouse_syno_symb/2 19.02.11 DOC: arity of bio_db predicate in example query and typos ADDED: build script map_mgim_mouse_mgim_entz/2 IFACE: map_mgim_mouse_mgim_entz/2 DOC: 1 example per mgi_mouse predicate 2.3 @ 19.02.11 19.02.11 UPDATE: example bio_db_stats with output ADDED: version query and stats output 19.02.08 DELETE: message_report.pl/3 (now in stoics_lib) UPDATE: comprehensive overhaul, as location of source file its contents and header names, had changed UPDATE: gene_association.mgi.gz is now mgi.gaf.gz IFACE: removed dead interace predicates UPDATE: use normal calls for prev and synonyms via | sep call 19.01.30 UPDATE: new way of locating STRING version (valid from STRING 11.0) ADDED: convert(false) in csv_read_file/3 call 2.2 @ 18.12.06 18.12.06 FIXED: cpu deterioration of celled predicates 18.12.03 IFACE: map_unip_mouse_gyno_unip/2. IFACE: map_mgim_mouse_syno_mgim/2

2.1 @ 18.11.27 18.11.27 FIXED: new dependency to write_message/3 was pointing to wrong directory...

2.0 @ 18.11.17 18.11.27 FLAGS: bio_db_pl_from_zip and bio_db_del_zip REPO: make sure mouse_maps_unip.pl writes out with no flag allow_dot_in_atoms as false 18.11.26 IFACE: bio_db_data_predicate/4 18.11.26 DOC: document latest repo and cells. 18.11.25 LOAD: load full cell version when loading main file 18.03.30 FIXED: load 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 0.9 17.03.10 VERSION: works with 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 0.6 @ 16.10.13 16.10.13 DOC: fixed doc to more interface predicates. DATA: added prosite zip files to web-server (were missing) IFACE: added map_unip_hgnc_unip/2 16.09.19 DOC: added bio_db_info/4 to the documentation 16.09.17 FIXED: pl_bdb correction to open call and now more aware that it can be called from within bio_db DOC: a couple of small typos in bio_db.pl

0.5 @16.09.11

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).

0.2

0.1