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- [[WormBase Models]] == Old Model ==12 KB (1,431 words) - 19:06, 20 March 2012
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- = Agenda and Notes - BioGRID and WB interaction meeting.= ;item 1 - Mapping of Physical interaction terms/types between WB and BioGRID.1 KB (240 words) - 22:36, 22 February 2011
- == WS249 model == === ?Interaction model (Chris) ===1 KB (198 words) - 17:01, 16 April 2015
- ...ist of the most prominent classes in use in the AceDB database employed by WormBase. To display the current model of any class, include the following text in your documentation:4 KB (568 words) - 11:06, 23 May 2011
- [[WormBase Models]] == Model ==3 KB (275 words) - 01:07, 6 February 2014
- :: Remove interaction based phenotypes from existing tables-→ new table ;item 3 - Interaction Model (slides 4-5, attached .ppt in documents distributed section)3 KB (475 words) - 22:50, 17 December 2010
- [[WormBase Models]] ?Interaction700 bytes (98 words) - 09:44, 4 October 2010
- = Agenda - BioGRID and WB interaction meeting.= ;item 2 - Mapping of interaction terms between WB and BioGRID. (Attached Excel and PowerPoint)3 KB (391 words) - 22:13, 22 February 2011
- [[WormBase Models]] == Old Model ==12 KB (1,431 words) - 19:06, 20 March 2012
- == 1. Life_stage model change == Life_stage model change proposal:1 KB (205 words) - 16:55, 17 May 2012
- [[WormBase Models]] == Model ==2 KB (200 words) - 08:23, 5 October 2010
- [[WormBase Models]] == Model ==3 KB (312 words) - 15:14, 15 July 2010
- [[WormBase Models]] Interaction ?Interaction XREF Molecule_interactor // Chris WS2446 KB (543 words) - 23:29, 15 March 2016
- Physical Interaction model *Separating out from general "Interaction" model4 KB (650 words) - 17:08, 1 September 2011
- ...cycle. Please review the file [http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.376&root=ensembl&view=markup models.wrm] in the ?Interaction4 KB (503 words) - 08:30, 22 June 2012
- PPI (Protein-Protein Interaction) New pipeline proposal is to retrieve information from WormBase ftp site, which will be updated with each release.4 KB (556 words) - 12:45, 21 May 2019
- Textpresso Interaction Sentences *Need to discuss what sentences should be kept as adequate evidence of interaction and placed in remarks5 KB (847 words) - 17:49, 1 March 2012
- ...reviously only with a text description are getting updated to fit the data model === Interaction-Gene associations ===4 KB (633 words) - 19:09, 6 January 2015
- *Should we take minutes of Caltech WormBase group meetings and send around? *WormBase-wide conference call twice per month8 KB (1,282 words) - 17:08, 7 July 2011
- == The A - Z of Ace Model and Redesign Page == ...ndex of available Ace classses; see the [https://spreadsheets.google.com/a/wormbase.org/ccc?key=tygSYCz49YW5hyCcYMHUZ1Q#gid=2 Google Doc] for migration status.12 KB (1,559 words) - 18:14, 15 June 2011
- === Construct model/annotation === ...d to add "Construct" under list of "Detection methods" in the ?Interaction model4 KB (622 words) - 16:47, 6 August 2014
- [[WormBase Models]] == Model ==5 KB (471 words) - 16:07, 4 October 2010
- **Chris will add all model changes proposed for WS233 **?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an "Interactor" tag6 KB (983 words) - 18:02, 12 July 2012
- * http://wiki.wormbase.org/index.php/2018_Advisory_Board_Meeting *?RO_term proposal sent to models@wormbase list4 KB (691 words) - 17:16, 21 June 2018
- EPIC data into WormBase *Need to modify model and display for data7 KB (1,070 words) - 17:47, 1 March 2012
- [[WormBase Models]] Updated model and unused tags for WS245 elegans data from pre-merged BUILD/elegans databa4 KB (394 words) - 08:39, 16 September 2014
- * What implications does this have for the WormBase Ontology Browser? === Physical Interaction Curation ===8 KB (1,120 words) - 16:19, 5 March 2015
- Interaction model WormBase meeting announcement6 KB (903 words) - 16:37, 5 January 2012
- [[WormBase Models]] ==Updated model for WS245==13 KB (1,341 words) - 20:12, 22 September 2015
- ==== Unified Interaction model - Chris & Kimberly ==== * PaulD: The model is OK but is the web capable of displaying it?5 KB (800 words) - 10:09, 17 February 2012
- *WormBase curates phenotypes, pathways, etc. *WormBase Process curation could really benefit from GO's adoption of this strategy7 KB (1,019 words) - 20:58, 12 April 2012
- *Make link on WormBase homepage *Will add note to site about how the model may be integrated into WormBase5 KB (752 words) - 17:07, 7 July 2011
- *WormBase communicate/work with DCC personnel for data wrangling during post-DCC era? *Wei wei asking about how to update with WormBase4 KB (612 words) - 17:13, 1 December 2011
- === GO data model change === * Worm pick holders (pencil grips) with WormBase logos; can they be printed on?7 KB (1,058 words) - 15:32, 2 April 2015
- Ticket: https://github.com/WormBase/website/issues/8296 Issue: Genetic Map tool down with the following error: Caught exception in WormBase::Web::Controller::Tools->tools "Could not connect to database acedb _WS280,2 KB (347 words) - 14:07, 2 July 2021
- **Performs similar to WormBase **Todd has made progress with getting Intermine for WormBase7 KB (1,158 words) - 17:20, 3 May 2012
- ...arize how the Phenotype2GO-based GO annotations will be handled for future WormBase builds and GO uploads. ...ting for a genetic interaction. To distinguish these, can we include the ?Interaction ID in the With/From column along with the WBRNAi and WBPhenotype IDs?7 KB (1,164 words) - 17:54, 19 February 2015
- == 1. Model changes (Hinxton) == 1a) Variation model sign off7 KB (1,182 words) - 13:50, 20 April 2012
- *What would WormBase look like without any manually curated data? === Interaction changes ===8 KB (1,225 words) - 16:33, 3 October 2013
- * ?Construct model === ?Construct model ===8 KB (1,218 words) - 17:46, 2 April 2014
- [[WormBase Models]] == Model ==7 KB (712 words) - 10:40, 4 October 2010
- Ranjana - Preplanning WormBase side meetings at IWM? *Two Wormbase Plenary talks9 KB (1,302 words) - 16:38, 2 June 2011
- *Yuling should contact FlyBase to make sure they're OK, once he has WormBase SVM working Physical interaction model7 KB (1,064 words) - 19:12, 3 November 2011
- =Interaction Curation= ===upload Gary and Chris RNAi-based interaction objects into OA===50 KB (5,228 words) - 15:10, 21 July 2017
- Transgene Model *Murky genetic interaction curation?7 KB (1,103 words) - 18:28, 5 May 2011
- New release of WormBase WS160, Wormpep160 and Wormrna160 Thu Jun 15 16:29:46 BST 2006 http://wwwdev.sanger.ac.uk/Projects/C_elegans/WORMBASE6 KB (706 words) - 10:50, 21 December 2011
- = The A - Z of WormBase Models = Document created from [http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?root=ensembl&view=markup&pathrev=WS218 WS218] models.16 KB (2,207 words) - 23:06, 9 January 2014
- New release of WormBase WS288 WS288 was built by Stavros Diamantakis with the input from the WormBase Community and Team. Thank you!16 KB (1,733 words) - 21:55, 11 May 2023
- ...a testing environment for curators/users. we'll have to rely on juancarlos.wormbase.org as cost/benefit analysis is unfavourable to consider other options. === Phentoype-association file: Attributing phenotypes to genes via genetic interaction ===6 KB (906 words) - 21:38, 30 September 2015
- * Wen will make the model change proposal * Many authors want to share and make links to their database/website via WormBase10 KB (1,464 words) - 17:09, 13 August 2015
- New release of WormBase WS284 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES)17 KB (1,841 words) - 21:54, 11 May 2023
- === WormBase Ontology Browser (WOBr) === === ?Expr_pattern and ?Movie model changes ===13 KB (1,983 words) - 16:40, 7 November 2013
- === WormBase Ontology Browser (WOBr) === * http://juancarlos.wormbase.org/tools/ontology_browser8 KB (1,234 words) - 12:36, 4 June 2014
- *Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..." Genetic Interaction Ontology7 KB (1,047 words) - 15:34, 4 April 2013
- [[WS241_Models.wrm | WS241 model details]] * ?Interaction and ?Feature models - linking tags changed8 KB (1,246 words) - 15:52, 12 November 2013
- **process pages will dissect the chapters and link them to entities in WormBase, * Gene interaction networks (N-browse view?)20 KB (3,088 words) - 19:17, 13 August 2020
- *Dumping process changes outlined [https://docs.google.com/a/wormbase.org/document/d/1nnuQY9OfV2VsBORj01ocoC985-5kOgxYCGOAZDeeKLQ/edit?pli=1 here *****JD started a [http://wiki.wormbase.org/index.php/WormMine Wiki Page] for documentation6 KB (864 words) - 15:32, 6 June 2013
- Archived Interaction documentation may be found [[Gene_Interaction/archive | here]] ==Interaction Curation==53 KB (6,521 words) - 20:51, 7 March 2019
- '''Field 4 Experimental model for (dis_humandoid):''' <br/ > '''Field 11 Last Updated for Exp Model (dis_lastupdateexpmod):''' <br/ >14 KB (2,085 words) - 20:27, 7 July 2022
- Curators checked their model proposals in this file: WS241 pre-WS241 tagged models [[http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.396&root=ensembl&view=markup pre-WS241]]6 KB (909 words) - 21:56, 21 November 2013
- =WormBase Curated Data Types and Curation Methods= HMM - Hidden Markov Model9 KB (1,174 words) - 18:30, 29 August 2012
- [[WormBase Models]] == Model ==15 KB (1,645 words) - 18:54, 23 January 2014
- New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007 http://www.wormbase.org/wiki/index.php/Release_notes6 KB (680 words) - 10:54, 21 December 2011
- https://docs.google.com/a/wormbase.org/document/d/1oPpj8d5gibUc-gpUZorl6ETT5baE6mp-v2bMedKauiA/edit# This document describes the process of staging a new release of WormBase on the development server.25 KB (3,632 words) - 03:11, 28 October 2013
- ...ontology/evidenceontology The Evidence and Conclusion Ontology] is used in WormBase to record evidence used for assertions in curation data models. ...ence and Conclusion Ontology will be incorporated into a future release of WormBase, aiming for WS278, and is proposed to eventually fully replace ?GO_code.6 KB (834 words) - 17:56, 15 June 2020
- * Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser) ** May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape)10 KB (1,474 words) - 15:54, 30 April 2014
- ...current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/ ...e suggestion for the Alliance is to create a description based on a GO-CAM model6 KB (861 words) - 19:23, 5 November 2020
- ** model change to put topics in hierarchical structure. http://www.wormbase.org/tools/wormmine/template.do?name=Anatomy_LS_Genes&scope=all10 KB (1,485 words) - 18:08, 5 March 2014
- * WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT) * Orthology synchrony is a challenge; WormBase and FlyBase may need to pay special attention to orthology calls and discre12 KB (1,809 words) - 16:33, 1 March 2018
- == WormBase SAB Meeting Date == * [https://github.com/WormBase/website/issues/6213 SNPs in specific genomic regions in Hawaiian C. elegans4 KB (574 words) - 01:54, 2 March 2018
- [[WormBase Models]] == Model ==8 KB (853 words) - 23:50, 16 April 2014
- * WBPaper00026596.ce.mr.csv content incorrect: https://github.com/WormBase/website/issues/8101 **Alliance/Future of WormBase3 KB (511 words) - 18:54, 18 February 2021
- New release of WormBase WS231 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:16 KB (1,820 words) - 14:15, 13 September 2012
- -rwxrwxr-x 1 todd wormbase 20053 Jul 6 14:06 cell.cgi -rwxrwxr-x 1 todd wormbase 3916 Jul 6 14:06 make_pedigree.cgi16 KB (1,576 words) - 17:44, 16 August 2010
- * Wen considering adding interaction data to SimpleMine ** Want to indicate, for a query gene, genes for which multiple interaction types have been observed11 KB (1,703 words) - 15:27, 5 April 2018
- [http://intermine.wormbase.org/tools/wormmine/begin.do WormMine] [https://github.com/WormBase/intermine WormMine Github]15 KB (2,088 words) - 16:16, 15 October 2020
- Binary vs. Non-binary interaction display *Cytoscape and interaction table are only displaying interactions as binary interactions, regardless o8 KB (1,161 words) - 16:34, 7 March 2013
- ** See github ticket 2867 https://github.com/WormBase/website/issues/2867#issuecomment-48041365 *** How many new objects did you add to WormBase23 KB (3,248 words) - 12:58, 22 September 2014
- == Interaction Model as of WS231 == ...ed ?Physical_interaction model has also been consolidated into this larger model. Note that #Interaction_info and #Interaction_type have been deprecated.59 KB (8,367 words) - 22:00, 14 December 2018
- ...to be incorporated (BioID, APEX, cofractionation) – perhaps as part of an interaction viewer. * The interaction browser should have a link to Cytoscape/GeneMania for deeper interrogation11 KB (1,649 words) - 16:10, 19 July 2018
- New release of WormBase WS217, Wormpep217 and Wormrna217 Wed Jul 28 09:25:17 BST 2010 http://www.wormbase.org/wiki/index.php/Release_Schedule8 KB (915 words) - 11:10, 21 December 2011
- *Icons on genes indicating drug interaction, for example WormBase GO progress report9 KB (1,339 words) - 19:02, 31 January 2013
- New release of WormBase WS232 WS232 was built by Michael Paulini [michael.paulini@wormbase.org]15 KB (1,729 words) - 14:15, 13 September 2012
- ...r><br>Release notes on the web:<br>-------------------------<br>http://www.wormbase.org/wiki/index.php/Release_Schedule<br><br>Genome sequence composition:<br> ...open your database, e.g.<br> type 'xace /users/yourname/wormbase' at the command prompt.<br><br>5. See the acedb website for more informatio11 KB (1,614 words) - 16:52, 21 December 2011
- ***Integrated interaction model, genetic interaction ontology ***Need to update Gene expression model to accommodate Epic dataset (John Murray), 3D movies (Bill Mohler), and sin12 KB (1,878 words) - 15:55, 6 September 2012
- * Citace upload deadline will be 6pm Monday, November 25th (added to WormBase calendar) * We will want to provide a public notice (likely via the WormBase blog) about what topic we have focused on for that release of the database/10 KB (1,664 words) - 17:02, 4 December 2013
- New release of WormBase WS223, Wormpep223 and Wormrna223 Mon Jan 24 12:12:08 GMT 2011 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data15 KB (1,610 words) - 11:20, 21 December 2011
- * adding a Community_curator tag or Curator tag in the Expression model to acknowledge the community curators that annotated/will annotate the data * for the records- documentation on the import here: http://wiki.wormbase.org/index.php/TransgeneOme_import9 KB (1,490 words) - 15:35, 6 October 2016
- New release of WormBase WS221, Wormpep221 and Wormrna221 Tue Nov 23 12:32:16 GMT 2010 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data17 KB (1,758 words) - 16:47, 21 December 2011
- New release of WormBase WS222, Wormpep222 and Wormrna222 Mon Dec 20 12:07:08 GMT 2010 WS222 was built by Michael Paulini (michael.paulini@wormbase.org)15 KB (1,647 words) - 10:06, 22 December 2010
- New release of WormBase WS228 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:14 KB (1,572 words) - 10:37, 11 November 2011
- http://www.wormbase.org/wiki/index.php/Release_notes Confirmed introns not in a CDS gene model;8 KB (938 words) - 10:54, 21 December 2011
- New release of WormBase WS227 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:15 KB (1,738 words) - 11:20, 21 December 2011
- *We should be able to start configuring for WormBase at that point *Gary will propose appropriate model changes (e.g. Add "silencer" and "enhancer" to method for GBrowse display)7 KB (1,059 words) - 15:37, 1 August 2013
- New release of WormBase WS225, Wormpep225 and Wormrna225 Tue Apr 5 11:57:03 BST 2011 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data16 KB (1,674 words) - 11:38, 20 April 2011
- ...ing author; for a list of all labs' two-letter codes look here: http://www.wormbase.org/db/misc/laboratory?name=*;class=laboratory), date of publication (accep ...g), Phenotype observed (or not_observed), Gene Regulation objects, Genetic Interaction objects, species, and general remarks about the experiment.47 KB (7,989 words) - 23:40, 1 September 2015
- New release of WormBase WS218, Wormpep218 and Wormrna218 Tue Aug 24 genomes DIR - contains a sub dir for each WormBase species with15 KB (1,756 words) - 11:21, 21 December 2011
- New release of WormBase WS224, Wormpep224 and Wormrna224 Fri Mar 4 14:58:13 GMT 2011 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data15 KB (1,583 words) - 11:13, 21 December 2011
- New release of WormBase WS234 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:15 KB (1,653 words) - 10:13, 18 January 2013
- * GO-CAM (Gene Ontology - Causal Activity Model(ing)) ...rds, tool could pull up all relevant annotations to help start with GO CAM model building8 KB (1,229 words) - 15:31, 1 June 2017
- *We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it *Mark Blaxter offered to donate his Brugia database into WormBase10 KB (1,553 words) - 18:04, 7 February 2013
