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  • Scripts for file dumping and conversion
    /home/acedb/ranjana/citace_upload/go_curation/protein2go_migration/split_into_curators. /home/acedb/ranjana/citace_upload/go_curation/protein2go_migration/
    539 bytes (84 words) - 19:05, 25 January 2013
  • Data mining
    #[[AceDB classes|AceDB classes]] - ''A comprehensive list of AceDB classes'' #[[AceDB classes tutorial|AceDB classes tutorial]] -''Examples and descriptions of commonly accessed classe
    2 KB (264 words) - 01:36, 1 April 2022
  • New Model Implementation Checklist
    **Status: file created, not yet checked in ACeDB **Status: file created, not yet checked in ACeDB
    1 KB (199 words) - 19:08, 10 February 2014
  • Quick response cheatsheet
    - use top command to check if sgiface is at 100%, if so restart ACeDB ==Restart AceDB==
    784 bytes (128 words) - 21:31, 5 November 2015
  • UserGuide:Display Tools
    The Tree Display shows the data relationships according to each ACeDB data model. Shown in the diagram: red color shows tags, blue color indicate ACeDB Schema
    2 KB (266 words) - 18:26, 17 August 2010
  • Xapian and wormbase
    cd /usr/local/wormbase/acedb/bin acedb> @dump_ace_for_search.script
    658 bytes (108 words) - 16:11, 5 October 2011
  • Orthology, Homology and Paralog data in WormBase
    it is in the ACeDB database on the genes as ortholog/paralog, but we also dump it since a whil ...files, as well as here: ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/acedb /Non_C_elegans_BLAST
    2 KB (336 words) - 14:08, 27 August 2015
  • Importing Protein Structure Data
    brie3:/usr/local/acedb/datasets/structure_data/ cshace: brie3:/usr/local/acedb/dumpdb/
    3 KB (408 words) - 23:36, 13 August 2010
  • Updating WormMart
    WormMart is built every 5 releases of AceDB. Currently, the machine ls2.res.oicr.on.ca is used to build WormMart, then === Get AceDB ===
    2 KB (289 words) - 18:24, 17 August 2010
  • Update Matrix Template
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    3 KB (489 words) - 18:14, 17 August 2010
  • ModENCODE TilingArray
    == Tiling Array Related ACeDB Models ==
    2 KB (220 words) - 00:19, 21 January 2011
  • General specifications
    ''Arabidopsis'': /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles/ ''Arabidopsis'': /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles
    2 KB (204 words) - 19:18, 17 November 2011
  • Update Matrix WS205
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    3 KB (530 words) - 18:14, 17 August 2010
  • Data mining:WQL tutorial
    [http://grain.jouy.inra.fr/ggpages/ggpages/aboutacedbquery.html About ACEDB Queries (not worm-specific)]
    296 bytes (41 words) - 15:12, 16 June 2011
  • Update Matrix WS209
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (717 words) - 18:20, 17 August 2010
  • Update Matrix WS214
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (719 words) - 18:21, 17 August 2010
  • Update Matrix WS208
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (738 words) - 18:20, 17 August 2010
  • WBConfCall 2021.12.16-Agenda and Minutes
    It's a acedb availability issue; Todd will investigate.
    295 bytes (40 words) - 16:40, 16 December 2021
  • Update Matrix WS211
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (723 words) - 18:21, 17 August 2010
  • Update Matrix WS212
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (723 words) - 18:21, 17 August 2010
  • Update Matrix WS210
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (725 words) - 18:20, 17 August 2010
  • C.remanei
    == ACeDB == The default code is used to show the ACeDB data and there is a GBrowse version available to show the GFF annotation. I
    2 KB (324 words) - 19:34, 11 August 2010
  • WebDev 2009.09.23-Agenda and Minutes
    == 5. Discuss AceDB -> PF (Xiaoqi; 10 minutes) ==
    2 KB (252 words) - 09:25, 28 September 2009
  • Update Matrix WS213
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (725 words) - 18:21, 17 August 2010
  • Update Matrix WS206
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (610 words) - 18:20, 17 August 2010
  • Update Matrix WS215
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (735 words) - 18:22, 17 August 2010
  • Update Matrix WS217
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (735 words) - 18:22, 17 August 2010
  • Phenote .ace citace upload
    /home/acedb/karen/WS_upload_scripts/phenotype/use_package.pl*<br> /home/acedb/karen/WS_upload_scripts/paper_object/get_paper_object.pl*
    5 KB (749 words) - 19:47, 17 May 2018
  • Update Matrix WS207
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (762 words) - 18:20, 17 August 2010
  • Website:WormMine Builds
    ===== AceDB Dump ===== Did not specify AceDB dir in $ACEDB. Searching for tace...
    9 KB (947 words) - 18:27, 12 August 2014
  • AceDB class-Y2H
    [[Category:AceDB]]
    274 bytes (40 words) - 21:51, 11 August 2010
  • WormBase Model:Map error
    AceDB internal class
    169 bytes (19 words) - 14:38, 4 October 2010
  • WormBase Model:ManyMap
    Looks like an acedb internal as the xace code looks for it.
    206 bytes (28 words) - 14:34, 4 October 2010
  • WBConfCall 2023.10.05–Agenda and Minutes
    Example of how Strain curated in NS looks in ACeDB:
    339 bytes (48 words) - 22:45, 4 October 2023
  • UserGuide:Genetic Map
    ...forward genetic mapping. The WormBase Genetic Map inherited its look from ACeDB, however because of internet interface, many features have been changed. ACEDB MAP IMAGE SUBMENU
    4 KB (720 words) - 18:28, 17 August 2010
  • Website:WormBase::API
    The following AceDB model elements are handled generically in the reimplementation. This maxim * you should specify the name of the AceDB model element in lowercase in the configuration file
    2 KB (271 words) - 14:09, 19 June 2014
  • WS186
    The reason for that is that AceDB begins to struggle when one object is linked to 3. Obtain and install a suitable acedb binary for your system
    6 KB (683 words) - 05:51, 3 April 2008
  • WebDev 2016.02.23-Agenda and Minutes
    #*ACeDB to Datomic #**Took reorganized the folder structure when I took away the non ACeDB to Datomic from this repo .
    3 KB (478 words) - 15:41, 23 February 2016
  • WBConfCall 2020.08.20-Agenda and Minutes
    ** Want/need to synchronize Postgres with Hinxton and ACEDB * Chris G wanted to dump pathogenic species, find out how they align with acedb species. How do they get into Hinxton.
    3 KB (440 words) - 08:42, 3 September 2020
  • WBConfCall 2016.12.01-Agenda and Minutes
    Can we replace ACEDB Tree Display with Datatomic? We should continue to provide Tree Display. Ho
    450 bytes (62 words) - 16:44, 1 December 2016
  • WS185
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (680 words) - 07:37, 11 January 2008
  • InterMine Strategy Meeting: May 14, 2013
    * Create versioned folders of XML representing various acedb releases. Build mine off of these. Can be used to resurrect old mines. * Find out how to extract version of data in acedb
    2 KB (241 words) - 15:32, 15 May 2013
  • WBConfCall 2024.01.04-Agenda and Minutes
    ** WBVar02157532 - tur003 Variation page is not generated but exists in ACeDB and JBrowse #9376
    618 bytes (81 words) - 21:36, 2 January 2024
  • WormBaseComparativeGenomicsTools
    ...ailable from the Gene pages (link is called syntenic alignment). Or in the ACeDB database as Homol_data on the C.elegans and C.briggsae chromosomes. * ACeDB contains WABA homol_data on the chromosomes
    5 KB (727 words) - 17:31, 27 June 2009
  • WBConfCall 2021.03.04-Agenda and Minutes
    ...f aCeDB, an object database where modeling is easy for curators to do, and acedb handles XREFs and connecting data automatically. ** Caltech curators were writing .ace text files to load into acedb, and early forms were UIs for templates for .ace text files.
    4 KB (743 words) - 12:22, 5 March 2021
  • WBConfCall 2022.04.07-Agenda and Minutes
    ...take a look. Tree display + schema viewer + genetic map stop working when acedb goes down.
    2 KB (279 words) - 16:01, 7 July 2022
  • WS183
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (800 words) - 10:01, 8 November 2007
  • Linking To WormBase
    == Linking to Acedb Format == ...cal ACeDB database, create a link to <code>http://www.wormbase.org/db/misc/acedb?name=X;class=Y</code>, where X and Y are again replaced with the object nam
    6 KB (1,087 words) - 15:07, 19 June 2014
  • Relations Ontology
    **/home/acedb/kimberly/citace_upload/ro/ontology2ace/ro_obo_to_ro_ace.pl #In the /home/acedb/kimberly/citace_upload/ro/ontology2ace directory on tazendra, use the wget
    3 KB (453 words) - 18:27, 20 September 2023
  • Design Specs: Database Connectivity
    *do "reconnect" if dbh is not set, undef or time-out(AceDB) *http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API/Service/acedb.pm
    6 KB (980 words) - 18:48, 11 August 2010
  • AceOjbect Redesign Page
    |No API necessary; AceDB internals. |No API necessary; AceDB internals.
    12 KB (1,559 words) - 18:14, 15 June 2011
  • WS230 Models.wrm
    ...models to supplement the new gff3 dumping functionality being added to the acedb code. Ace2SO class: gives a mapping from Acedb objects to their SO terms.
    3 KB (368 words) - 10:15, 1 February 2012
  • WS184
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (831 words) - 07:36, 11 January 2008
  • WormBase-Caltech Weekly Calls February 2016
    === Postgres data not in ACEDB === * Should we this data get into ACEDB to be converted to Datomic (via the existing pipeline)? Maybe, but only tem
    4 KB (571 words) - 16:48, 3 March 2016
  • Specifications for data submission to the Alliance
    |+Mapping of acedb tags to objects in JSON ! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Ob
    2 KB (318 words) - 17:43, 26 October 2023
  • Building Frozen Releases
    acedb/ == AceDB ==
    8 KB (1,087 words) - 17:35, 19 June 2014
  • Dumping Script
    The papers cronjob is on the acedb account : ...le names in postgres (pap_nnnnn) and the tag names in the ?Paper model for ACeDB. At the top of the script, there is a list that maps postgres paper table
    2 KB (329 words) - 15:21, 7 August 2014
  • WBConfCall 2023.02.02-Agenda and Minutes
    ...63926 has no title in ACeDB. The paper title exists in postgres but not in ACeDB. In WS287, there are 8 papers from MEDLINE that have no title.
    2 KB (348 words) - 17:52, 2 February 2023
  • Alliance - migrating WormBase papers to Alliance ABC
    ...tech postgres not in acedb, and I thought that anything user-facing was in acedb, but it turns out corresponding author flags are not. It'd be mildly helpf ** The lag between data being updated at Caltech -> Built into acedb -> released into Alliance.
    3 KB (492 words) - 18:48, 17 March 2021
  • Physical Interactions
    ACeDB data models [http://wiki.wormbase.org/index.php/Gene_Interaction#Interactio
    559 bytes (71 words) - 20:41, 13 June 2011
  • WormBase Model:Transcript
    Start_not_found #acedb magic tag End_not_found #acedb magic tag
    4 KB (350 words) - 09:32, 17 June 2013
  • WBConfCall 2018.11.15-Agenda and Minutes
    * For now, we model in ACeDB and convert at Hinxton to Datomic. Curators don’t need to be too concerne ...to think about: what’s the advantage in modelling Datomic vs Modelling in ACeDB?
    2 KB (323 words) - 18:24, 15 November 2018
  • WS211
    The Non-elegans blastx data is no longer loaded into the full acedb database release. install acedb as usual from
    6 KB (766 words) - 16:38, 21 December 2011
  • WormBase-Caltech Weekly Calls March 2021
    === Spreadsheet for Data not in ACEDB === ...alena/Hinxton would like to know how much data at Caltech doesn't get into ACEDB
    5 KB (777 words) - 13:18, 1 April 2021
  • WormBase-Caltech Weekly Calls November 2020
    ...9 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new === Curating to human genes in ACEDB ===
    4 KB (695 words) - 14:44, 3 December 2020
  • WBConfCall 2018.09.06-Agenda and Minutes
    Due to ACeDB (which does not support unicode due to it's ancientness), not currently pos
    896 bytes (138 words) - 16:10, 6 September 2018
  • WBConfCall 2020.04.16-Agenda and Minutes
    As we winnow down the number of items at WormBase.org that directly depend on ACEDB (and there are very few left), # Hosting data at AceDB and automatic update from AGR update
    2 KB (303 words) - 18:23, 16 April 2020
  • WormMine
    | Orthology || ACeDB gene class (Ortholog and Ortholog_other tags) and there is also a OICR crea | Interaction || AceDB interaction class
    15 KB (2,088 words) - 16:16, 15 October 2020
  • WormBase Model:Multi counts
    Unused class in wormbase and it appears that the acedb source code doesn't look for this specific class.
    816 bytes (100 words) - 15:47, 4 October 2010
  • Data mining:AQL tutorial
    '''Documentation at AceDB web site''' [http://www.acedb.org/Software/whelp/AQL/ [2]]
    834 bytes (137 words) - 15:09, 16 June 2011
  • WebDev 2010.02.17-Agenda and Minutes
    * connection to AceDB and GBrowse -- persistent
    907 bytes (113 words) - 14:27, 19 February 2010
  • WBConfCall 2021.07.01-Agenda and Minutes
    ...in WormBase::Web::Controller::Tools->tools "Could not connect to database acedb _WS280, host: 7e85f19c6634" User wants to: This WBG article says, "Map data have been deposited in ACeDB." I would like to know the flanking markers used to map ccIs4251 and the ob
    2 KB (347 words) - 14:07, 2 July 2021
  • Software Life Cycle: 4. Updating The Production Servers
    Remove build WSXXX -- including acedb, mysql, and support DBs -- from the staging cluster: Remove build WSXXX -- including acedb, mysql, and support DBs -- from the production cluster:
    8 KB (1,229 words) - 16:17, 30 December 2013
  • WBConfCall 2014.08.07-Agenda and Minutes
    *Example data already accessible in the acedb database * the data is hidden in ACeDB and quite inaccessible
    3 KB (450 words) - 16:07, 7 August 2014
  • WBConfCall 2020.05.06-Agenda and Minutes
    22nd June-17th July - ACeDB production 8th June-3rd July - ACeDB production <!!!!!!EBI Farm move 22nd June - 3rd July!!!!!!!>
    2 KB (378 words) - 17:04, 11 May 2020
  • WBConfCall 2020.05.07-Agenda and Minutes
    22nd June-17th July - ACeDB production 8th June-3rd July - ACeDB production <!!!!!!EBI Farm move 22nd June - 3rd July!!!!!!!>
    2 KB (376 words) - 17:03, 11 May 2020
  • Building WormMart
    In simple terms, WormMart is built by transforming WormBase's AceDB database into a BioMart schema MySQL database. Standard BioMart tools are t 1a. Install the ACeDB Software
    6 KB (786 words) - 19:13, 18 June 2014
  • WS207
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (675 words) - 16:42, 21 December 2011
  • WS208
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    5 KB (581 words) - 16:50, 21 December 2011
  • WS212
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    5 KB (582 words) - 11:16, 21 December 2011
  • AceDB classes
    This is a list of the most prominent classes in use in the AceDB database employed by WormBase. [[Category:AceDB]]
    4 KB (568 words) - 11:06, 23 May 2011
  • WormBase-Caltech Weekly Calls April 2013
    **ACEDB software problem ***Possible but difficult to upgrade ACEDB software
    4 KB (651 words) - 16:11, 2 May 2013
  • WormBase gene association file/archive
    In the acedb user account on Tazendra at:/home/acedb/ranjana/GO: #copy the right go.go.<date> file from /home/acedb/ranjana/citace_upload/go_curation/go_dumper_files/ to this directory,change
    4 KB (629 words) - 18:27, 23 November 2020
  • WBConfCall 2021.04.01-Agenda and Minutes
    ...ags data that doesn't make it into acedb). We loose foreign characters in acedb, so we'll be able to keep those in postgres and pass them on to Alliance.<b Raymond: One postgres, two data streams one to acedb and a second to alliance<br>
    4 KB (709 words) - 13:27, 5 April 2021
  • AceDB class-Interaction
    [[Category:AceDB]]
    1 KB (143 words) - 21:51, 11 August 2010
  • WBConfCall 2013.10.17-Agenda and Minutes
    **acedb + website flat file **website flat file only with only database name and description stored in acedb
    2 KB (361 words) - 16:32, 17 October 2013
  • WBConfCall 2013.02.07-Agenda and Minutes
    ****Needs testing as may have implications for acedb. *Data will be kept in acedb for purposes of Cytoscape?
    2 KB (383 words) - 11:59, 15 February 2013
  • WBConfCall 2016.10.06-Agenda and Minutes
    *** Orthology data in WormMine seems *not* to come from WormBase / AceDB ...in WormMine came directly from Pather (via InterMine loader), rather than AceDB
    2 KB (369 words) - 16:38, 6 October 2016
  • InterMine Strategy Meeting: May 21, 2013
    * Find out how to extract version of data in acedb
    1 KB (169 words) - 16:51, 28 May 2013
  • WS196
    ...he GFF files and so visible in the genome browser but not via querying the acedb database. 3. Obtain and install a suitable acedb binary for your system
    6 KB (748 words) - 16:41, 21 December 2011
  • WS204
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (648 words) - 16:16, 21 December 2011
  • Populating the OA and New Dumping Script
    Can likely borrow a lot from the gpad parsing script on tazendra /home/acedb/kimberly/citace_upload/go/go_gpad_parser.pl Currently, that file is on tazendra here: /home/acedb/kimberly/citace_upload/go/gp_annotation.ace
    3 KB (484 words) - 22:19, 21 February 2015
  • WS173
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (639 words) - 10:55, 21 December 2011
  • WormBase-Caltech Weekly Calls February 2017
    === ACEDB dependencies === * Raymond was asked to collect all CIT curator uses of ACEDB, e.g. programmatic access via ACE Perl
    7 KB (1,073 words) - 16:26, 2 March 2017
  • Developer notes
    A number of elements are repeated across the AceDB schema. To make the external model easier to maintain, fetching and parsing <tr><th>Expected AceDB model tag</th><th>Object.pm method</th><th>config field</th><th>template ma
    3 KB (485 words) - 15:37, 19 June 2014
  • WS187
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (647 words) - 16:43, 21 December 2011
  • WS199
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (661 words) - 16:51, 21 December 2011
  • WS171
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (652 words) - 10:55, 21 December 2011
  • Movie
    There were 513 movies in acedb, all pertaining the RNAi class. We are going to generate the movie OA and i /home/acedb/draciti/Movies
    5 KB (814 words) - 18:48, 17 September 2018
  • WS179
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (843 words) - 10:53, 21 December 2011

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