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  • ...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
  • == WS249 model == === ?Interaction model (Chris) ===
    1 KB (198 words) - 17:01, 16 April 2015
  • [[WormBase Models]] Unused class in wormbase and it appears that the acedb source code doesn't look for this specific cl
    816 bytes (100 words) - 15:47, 4 October 2010
  • [[WormBase Models]] ?Gene
    700 bytes (98 words) - 09:44, 4 October 2010
  • [[WormBase Models]] == Model ==
    842 bytes (93 words) - 12:59, 4 October 2010
  • [[WormBase Models]] == Model ==
    2 KB (163 words) - 15:52, 4 October 2010
  • [[WormBase Models]] == Model ==
    244 bytes (29 words) - 11:07, 10 August 2010
  • #[[Alliance - migrating WormBase papers to Alliance ABC]] #[[Getting Meeting Abstracts into WormBase]]
    1 KB (130 words) - 21:21, 15 March 2021
  • [[WormBase Models]] == Model ==
    3 KB (275 words) - 01:07, 6 February 2014
  • [[WormBase Models]] == Model ==
    2 KB (208 words) - 14:36, 4 October 2010
  • == 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
  • [[WormBase Models]] == Model ==
    2 KB (133 words) - 09:56, 10 August 2010
  • [[WormBase Models]] == Model ==
    1 KB (119 words) - 16:43, 11 April 2013
  • ==C. elegans as a model system to study disease and disease genes== ...s is used to model the biology of a disease and/or the orthologous elegans gene function is studied in detail. We have developed a method to identify and f
    5 KB (782 words) - 20:56, 8 January 2020
  • == Data Model == ...l|About the WormBase data model]] - ''how data is stored and structured at WormBase''
    2 KB (264 words) - 01:36, 1 April 2022
  • [[WormBase Models]] == Model ==
    309 bytes (39 words) - 09:49, 10 August 2010
  • [[WormBase Models]] == Model ==
    1 KB (119 words) - 10:41, 10 August 2010
  • == Model Change Sign Off == [https://github.com/WormBase/website/issues/241 issue 241] "Nucl. Aligner Tool bug."
    2 KB (294 words) - 16:14, 16 August 2012
  • [[WormBase Models]] == Model ==
    1 KB (125 words) - 15:01, 4 October 2012
  • === Linkouts to AGR from WB gene & disease pages === * Yeast gene page: https://qa.yeastgenome.org/locus/S000000364
    2 KB (250 words) - 16:12, 19 October 2017
  • [[WormBase Models]] == Model ==
    2 KB (193 words) - 14:28, 4 October 2010
  • [[WormBase Models]] Updated model and unused tags for WS245 elegans data from pre-merged BUILD/elegans databa
    4 KB (394 words) - 08:39, 16 September 2014
  • == Model Changes == Gene class
    3 KB (306 words) - 10:00, 26 October 2011
  • [[WormBase Models]] == Model ==
    3 KB (318 words) - 00:53, 7 December 2010
  • * [https://github.com/WormBase/website/issues/6841 TICKET #6841 I was looking at the modENCODE ChIP-S * [https://github.com/WormBase/website/issues/6831 TICKET #6831 Looking to buy clones of Syphacia mur
    2 KB (292 words) - 17:44, 17 January 2019
  • [[WormBase Models]] == Model ==
    5 KB (352 words) - 17:20, 25 September 2015
  • This gene encodes a protein containing an F-box, a motif predicted to mediate The protein product of this gene is predicted to contain a glutamine/asparagine
    2 KB (259 words) - 19:11, 19 February 2016
  • As the modENCODE DCC is overwhelmed with other work, she has proposed that WormBase make the data available to the public. Our position with providing primary data to users has always been that WormBase isn't a primary repository of data.
    5 KB (796 words) - 21:05, 10 March 2014
  • [[WormBase Models]] == Model ==
    3 KB (312 words) - 15:14, 15 July 2010
  • * File in /usr/local/wormbase/databases/{RELEASE}/orthology and automatically generated by orthology data ...h the associations available from the orthology data compile -- /usr/local/wormbase/databases/{RELEASE}/orthology/go_id2omim_ids.txt
    4 KB (583 words) - 20:22, 29 July 2011
  • [[WormBase Models]] == Model ==
    648 bytes (65 words) - 12:56, 4 October 2010
  • *stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/P *Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
    2 KB (325 words) - 15:24, 7 October 2021
  • [[WormBase Models]] == Model ==
    1 KB (159 words) - 09:16, 5 October 2010
  • Protein model Uncaptured gene & protein synonyms
    1,008 bytes (159 words) - 19:13, 15 December 2011
  • [[WormBase Models]] == Model ==
    1 KB (146 words) - 08:38, 5 October 2010
  • We will need to create a tab-delimited gpi file with each WormBase release. !Project_name: WormBase
    5 KB (720 words) - 20:46, 10 October 2016
  • [[WormBase Models]] == Model ==
    1 KB (139 words) - 09:51, 10 August 2010
  • == Model == ...// Ribo-zero treated to reduce the amount of ribosome gene transcripts
    3 KB (252 words) - 16:46, 9 January 2014
  • [[WormBase Models]] == Model ==
    3 KB (223 words) - 09:22, 10 August 2010
  • The WS126 release of WormBase last month featured a complete genome with no gaps remaining in the genome == WormBase launches the 'WormBook' project ==
    4 KB (621 words) - 15:38, 24 September 2007
  • New release of WormBase WS183, Wormpep183 and Wormrna183 Tue Oct 16 16:18:34 BST 2007 ...map_positions.WS183.gz - Interpolated map positions for each coding/RNA gene
    7 KB (800 words) - 10:01, 8 November 2007
  • ==Importing Undiagnosed Diseases Network (UDN) worm data into WormBase== *Initially thought it would be textual data that would go into disease model curation, but really involves other data types such as Variation, Strain, P
    3 KB (400 words) - 16:03, 15 March 2018
  • [[WormBase Models]] == Model ==
    2 KB (305 words) - 08:49, 5 October 2010
  • [[WormBase Models]] == Model ==
    5 KB (514 words) - 21:15, 7 December 2010
  • [[WormBase Models]] == Model ==
    4 KB (497 words) - 22:42, 6 December 2010
  • New release of WormBase WS185, Wormpep185 and Wormrna185 Fri Nov 30 17:11:38 GMT 2007 ...map_positions.WS185.gz - Interpolated map positions for each coding/RNA gene
    6 KB (680 words) - 07:37, 11 January 2008
  • ...is the "Working Groups" page. Working Groups are intended to be groups of WormBase staff focused on particular issues, whether they be WormBase bugs, data architecture, enhancements/proposals, etc.
    2 KB (306 words) - 15:01, 14 January 2016
  • New release of WormBase WS186, Wormpep186 and Wormrna186 Fri Dec 21 08:57:59 GMT 2007 ...map_positions.WS186.gz - Interpolated map positions for each coding/RNA gene
    6 KB (683 words) - 05:51, 3 April 2008
  • *Community annotation form needs to be very simple (e.g. gene name and empty box only) Gene file from Hinxton to populate Gene Tables
    4 KB (650 words) - 17:08, 1 September 2011
  • ===Testing data for WS278 model changes=== **Note that for gene-paper associations, we try to only associate genes that are studied in some
    3 KB (490 words) - 17:22, 18 June 2020
  • = Proposed Model changes = Link to the model changes proposed for WS236 [[WS236_Models.wrm]]
    5 KB (752 words) - 18:55, 6 December 2012
  • [[WormBase Models]] == Model ==
    4 KB (350 words) - 09:32, 17 June 2013
  • This document describes the WebApp requirements for: ''a new WormBase Molecule widget''. <br/> These requirements originate from: [[User:Kyook|Karen Yook]], a CalTech-based WormBase curator.
    1 KB (209 words) - 19:57, 25 July 2012
  • ;item 3 - Interaction Model (slides 4-5, attached .ppt in documents distributed section) #Chris and Gary will try to map WormBase interaction types to BioGRID interaction types and figure out what the diff
    3 KB (475 words) - 22:50, 17 December 2010
  • ...rent type (such as the DNA sequence of the gene, or the cells in which the gene is active). One can also do searches for complex data sets. ...n of WormBase available in September, 2005 (WS147 release; BioPerl/Generic Model Organism Database software).
    2 KB (365 words) - 00:06, 1 December 2010
  • 1. Model change --ticket #588 David Baillie from Vancouver group would like wormbase to fix the BC strains (gfp expression strains) display, so that users won't
    1 KB (182 words) - 10:02, 2 November 2012
  • [[WormBase Models]] == Model ==
    1 KB (120 words) - 09:24, 10 August 2010
  • == Model changes for WS246 == * This cycle we see 6 model changes effecting 7 classes:
    3 KB (413 words) - 15:51, 18 September 2014
  • ...regional and topical meetings held at various locations around the world. WormBase includes the abstracts from these meetings in our database. ...getting the regional and topical meeting abstracts into postgres and then WormBase.
    1 KB (201 words) - 16:34, 15 October 2012
  • ew release of WormBase WS184, Wormpep184 and Wormrna184 Thu Nov 8 12:09:34 GMT 2007 ...map_positions.WS184.gz - Interpolated map positions for each coding/RNA gene
    7 KB (831 words) - 07:36, 11 January 2008
  • [[WormBase Models]] == Model ==
    2 KB (183 words) - 13:25, 4 October 2010
  • ...y enthusiastic response from Chris and Nicole about including worm disease model data ...ion.WS245.wb, however this is incomplete since it doesn't have the disease model descriptions, and the manually curated OMIM connections, so also sent them
    5 KB (807 words) - 18:27, 4 September 2014
  • = 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
  • [[WormBase Models]] == Model ==
    2 KB (177 words) - 22:50, 6 December 2010
  • * Describe how to develop for the WormBase implementation **document fetching the WormBase code
    3 KB (365 words) - 19:14, 10 August 2010
  • [[WormBase Models]] == Model ==
    2 KB (152 words) - 14:44, 4 October 2010
  • * [https://github.com/WormBase/website/issues/8008 egl-1 automated gene description] * [https://github.com/WormBase/website/issues/8006 We have identified from RNAseq....]
    2 KB (239 words) - 17:32, 3 December 2020
  • [[WormBase Models]] ==Updated model for WS245==
    13 KB (1,341 words) - 20:12, 22 September 2015
  • <pre>New release of WormBase WS146, Wormpep146 and Wormrna146 Thu Jul 28 14:01:21 BST 2005 ...map_positions.WS146.gz - Interpolated map positions for each coding/RNA gene
    6 KB (670 words) - 11:09, 21 December 2011
  • === Datomic model for external links === * Hinxton will work on simplifying the model
    3 KB (493 words) - 16:08, 16 March 2017
  • === * Transposon gene reactivation - Paul === ==== Poor nomenclature in ?Gene history and Event ====
    8 KB (1,073 words) - 15:31, 14 December 2012
  • ...e here] for an archive of outdated/obsolete information about the WormBase gene association file. == Gene Association File (GAF) format ==
    12 KB (1,718 words) - 17:45, 5 February 2021
  • * We should ask users what they want: e.g. Is an Ascaris suum gene ortholog in C. elegans essential? ** Can try demo version with any S. pombe or S. cerevisiae gene names/ids
    4 KB (622 words) - 16:47, 6 August 2014
  • *BioGRID, Gene Orienteer, Interolog database, etc. *Gene Orienteer
    5 KB (847 words) - 17:49, 1 March 2012
  • WormBase staff can find this document in the "Documentation" directory and edit it t = About Groups at WormBase =
    5 KB (757 words) - 01:45, 2 June 2014
  • * There are papers in the WormBase collection that are used as paper evidence for some concise descriptions ==== LEGO (Logical Extensions of Gene Ontology) ====
    6 KB (823 words) - 19:38, 2 January 2014
  • ...is elegans] and related nematodes. WormBase is developed by an [http://www.wormbase.org/about/staff#01--10 international consortium] of researchers and compute *November 2020 -- ''[https://wiki.wormbase.org/images/Elections_Subcommittee_Proposal_toWBvote.docx Election Subcommit
    5 KB (646 words) - 17:11, 25 November 2020
  • <pre>New release of WormBase WS198, Wormpep198 and Wormrna198 Thu Dec 18 19:31:36 GMT 2008 ...map_positions.WS198.gz - Interpolated map positions for each coding/RNA gene
    6 KB (692 words) - 16:51, 21 December 2011
  • * integrated search for their gene and protein under their strain (not mixed up with the default strain) - Had conversation with GO people about gene model graph, will work on this visualization after WS252 development
    3 KB (478 words) - 15:41, 23 February 2016
  • * uncharacterized eukaryotic protein-coding gene with an intron ** https://github.com/WormBase/website/issues/7829
    3 KB (440 words) - 08:42, 3 September 2020
  • [[WormBase Models]] == Model ==
    3 KB (265 words) - 08:51, 5 October 2010
  • [[WormBase Models]] == Model ==
    5 KB (471 words) - 16:07, 4 October 2010
  • [[WormBase Models]] == Model ==
    7 KB (712 words) - 10:40, 4 October 2010
  • <pre>New release of WormBase WS192, Wormpep192 and Wormrna192 Tue Jun 24 11:23:32 BST 2008 ...map_positions.WS192.gz - Interpolated map positions for each coding/RNA gene
    6 KB (763 words) - 10:43, 21 December 2011
  • The Categories would be gene-specific and we will supply information for: 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
  • === WormBase Ontology Browser (WOBr) for WS244 release === * May be migrating to GPAD/GPI [Gene Product Annotation Data / Gene Product Information] format in future
    6 KB (801 words) - 17:29, 2 July 2014
  • **** java -cp wb-names-export.jar clojure.main -m wormbase.names.export gene genes.csv ...arriving at many: Using WormBase and the Alliance of Genome Resources for gene data. (10 mins + 5 mins for questions)** Talk 2: What tool do I use? Matchi
    7 KB (1,113 words) - 18:19, 6 April 2023
  • * ?Construct model === ?Construct model ===
    8 KB (1,218 words) - 17:46, 2 April 2014
  • ...s are being dealt with or closed, except github ticket [https://github.com/WormBase/website/issues/8156| #8156] * https://github.com/WormBase/website/issues/8156 - - needs a reply from textpresso group -Valerio will t
    4 KB (709 words) - 13:27, 5 April 2021
  • 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
  • ...l have setup the community curation portal page on staging: http://staging.wormbase.org/about/userguide/submit_data#0--10 == GO term enrichment (TE) tool for WormBase ==
    3 KB (539 words) - 10:56, 5 June 2015
  • This protocol describes how to BLAST a sequence against the sequences in WormBase. Further discusion of the BLAST algorithm can be found in ''UNITS 3.3, 3.4, ...e.org/wiki/index.php/Image:Fig_1_8_01.png). This will lead to http://blast.wormbase.org/db/searches/blat. This is the method of choice for searching the ''C. e
    3 KB (401 words) - 20:02, 11 August 2010
  • === Gene association file formats on FTP === ...current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
    6 KB (861 words) - 19:23, 5 November 2020
  • New release of WormBase WS204, Wormpep204 and Wormrna204 Fri Jun 26 20:17:06 BST 2009 ...map_positions.WS204.gz - Interpolated map positions for each coding/RNA gene
    6 KB (648 words) - 16:16, 21 December 2011
  • Gene ID mapping problems (as discussed in site-wide call) *Does CIT need to worry about consistency of gene IDs over database builds?
    4 KB (612 words) - 17:13, 1 December 2011
  • [[WormBase Models]] == Old Model ==
    12 KB (1,431 words) - 19:06, 20 March 2012
  • New release of WormBase WS187, Wormpep187 and Wormrna187 Fri Jan 25 20:22:16 GMT 2008 ...map_positions.WS187.gz - Interpolated map positions for each coding/RNA gene
    6 KB (647 words) - 16:43, 21 December 2011
  • * Protein aligner appears to be broken: https://github.com/WormBase/website/issues/7793 **Formally refer to the standard HGNC human gene in disease model curation and other types of curation
    3 KB (529 words) - 18:26, 16 July 2020
  • ...parate AGR orthology pipeline to link human genes and their orthologs from model organisms. !Project_name: WormBase (WB) Version WS258
    10 KB (1,599 words) - 18:53, 24 January 2019
  • <pre>New release of WormBase WS199, Wormpep199 and Wormrna199 Tue Feb 3 12:09:54 GMT 2009 ...map_positions.WS199.gz - Interpolated map positions for each coding/RNA gene
    6 KB (661 words) - 16:51, 21 December 2011
  • <nowiki>New release of WormBase WS171, Wormpep171 and Wormrna171 Thu Feb 8 15:28:27 GMT 2007 ...map_positions.WS171.gz - Interpolated map positions for each coding/RNA gene
    6 KB (652 words) - 10:55, 21 December 2011
  • New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007 ...map_positions.WS175.gz - Interpolated map positions for each coding/RNA gene
    6 KB (680 words) - 10:54, 21 December 2011
  • ...e from the Orthology WG for WB to move to a once-per-year update cycle for gene models. What do people think? * Faye Rodgers has recently joined WormBase @ Sanger to work with parasites
    2 KB (351 words) - 18:32, 15 December 2016
  • <pre>New release of WormBase WS147, Wormpep147 and Wormrna147 Thu Aug 18 16:59:45 BST 2005 ...map_positions.WS147.gz - Interpolated map positions for each coding/RNA gene
    7 KB (815 words) - 11:09, 21 December 2011
  • == WormBase SAB Meeting Date == * [https://github.com/WormBase/website/issues/6213 SNPs in specific genomic regions in Hawaiian C. elegans
    4 KB (574 words) - 01:54, 2 March 2018
  • <pre>New release of WormBase WS196, Wormpep196 and Wormrna196 Fri Oct 31 16:00:42 GMT 2008 ...map_positions.WS196.gz - Interpolated map positions for each coding/RNA gene
    6 KB (748 words) - 16:41, 21 December 2011
  • New release of WormBase WS173, Wormpep173 and Wormrna173 Fri Mar 23 18:22:22 GMT 2007 ...map_positions.WS173.gz - Interpolated map positions for each coding/RNA gene
    6 KB (639 words) - 10:55, 21 December 2011
  • New release of WormBase WS203, Wormpep203 and Wormrna203 Thu May 28 13:24:17 BST 2009 ...map_positions.WS203.gz - Interpolated map positions for each coding/RNA gene
    6 KB (662 words) - 16:50, 21 December 2011
  • This protocol presents how to conduct a general search of WormBase ...king on the Home link at the top left of any WormBase Web page (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png).
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  • [[WormBase Models]] == Model ==
    4 KB (410 words) - 17:08, 17 August 2010
  • New release of WormBase WS178, Wormpep178 and Wormrna178 Wed Jul 4 12:56:45 BST 2007 ...map_positions.WS178.gz - Interpolated map positions for each coding/RNA gene
    7 KB (762 words) - 10:53, 21 December 2011
  • <pre>New release of WormBase WS158, Wormpep158 and Wormrna158 Thu May 4 13:10:59 BST 2006 WS158 was built by Paul Davis [paul.davis@wormbase.org]
    6 KB (673 words) - 11:07, 21 December 2011
  • <pre>New release of WormBase WS191, Wormpep191 and Wormrna191 Mon Jun 2 09:50:52 BST 2008 ...map_positions.WS191.gz - Interpolated map positions for each coding/RNA gene
    6 KB (756 words) - 16:53, 21 December 2011
  • New release of WormBase WS205, Wormpep205 and Wormrna205 Wed Jul 22 10:29:27 BST 2009 ...map_positions.WS205.gz - Interpolated map positions for each coding/RNA gene
    6 KB (711 words) - 16:31, 21 December 2011
  • *Yuling should contact FlyBase to make sure they're OK, once he has WormBase SVM working Physical interaction model
    7 KB (1,064 words) - 19:12, 3 November 2011
  • New release of WormBase WS214, Wormpep214 and Wormrna214 Tue Apr 27 15:37:39 BST 2010 ...map_positions.WS214.gz - Interpolated map positions for each coding/RNA gene
    6 KB (709 words) - 16:49, 21 December 2011
  • <pre>New release of WormBase WS163, Wormpep163 and Wormrna163 Thu Aug 17 10:49:02 BST 2006 WS163 was built by Paul Davis [paul.davis@wormbase.org]
    6 KB (645 words) - 10:57, 21 December 2011
  • == OMIM links to/from WormBase == * Ranjana working on linking between WormBase and OMIM
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  • New release of WormBase WS182, Wormpep182 and Wormrna182 Thu Sep 27 11:59:39 BST 2007 ...map_positions.WS182.gz - Interpolated map positions for each coding/RNA gene
    6 KB (716 words) - 16:48, 21 December 2011
  • model? It seems pretty redundant with the Paper information and I'm not to WormBase?"
    4 KB (599 words) - 00:25, 4 May 2012
  • New release of WormBase WS209, Wormpep209 and Wormrna209 Fri Nov 27 11:57:36 GMT 2009 ...map_positions.WS209.gz - Interpolated map positions for each coding/RNA gene
    6 KB (687 words) - 16:50, 21 December 2011
  • New release of WormBase WS160, Wormpep160 and Wormrna160 Thu Jun 15 16:29:46 BST 2006 ...map_positions.WS160.gz - Interpolated map positions for each coding/RNA gene
    6 KB (706 words) - 10:50, 21 December 2011
  • == 1. Model changes (Hinxton) == 1a) Variation model sign off
    7 KB (1,182 words) - 13:50, 20 April 2012
  • <pre>New release of WormBase WS197, Wormpep197 and Wormrna197 Wed Nov 26 19:40:37 GMT 2008 ...map_positions.WS197.gz - Interpolated map positions for each coding/RNA gene
    6 KB (672 words) - 16:43, 21 December 2011
  • New release of WormBase WS201, Wormpep201 and Wormrna201 Wed Mar 25 15:30:27 GMT 2009 ...d_map_positions.WS201.gz - Interpolated map positions for each coding/RNA gene
    6 KB (665 words) - 16:42, 21 December 2011
  • * New Hinxton WormBase GTL: Sarah Dyer ...cussing further with you the idea of inserting WormCyc pathway diagrams in Wormbase pages."
    2 KB (279 words) - 17:17, 3 March 2022
  • ==== 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
  • * Left over bandanas? paid ~$1 per bandana before. We have enough for WormBase staff ...ng on ?Phenotype_assay (?Phenotype_experiment/?Phenotype_annotation) class model
    8 KB (1,213 words) - 15:29, 6 July 2017
  • New release of WormBase WS213, Wormpep213 and Wormrna213 Tue Mar 23 16:36:18 GMT 2010 ...map_positions.WS213.gz - Interpolated map positions for each coding/RNA gene
    6 KB (764 words) - 16:45, 21 December 2011
  • <pre>New release of WormBase WS154, Wormpep154 and Wormrna154 Fri Feb 10 12:46:08 GMT 2006 ...map_positions.WS154.gz - Interpolated map positions for each coding/RNA gene
    7 KB (749 words) - 11:08, 21 December 2011
  • New release of WormBase WS188, Wormpep188 and Wormrna188 Fri Feb 29 14:53:33 GMT 2008 WS188 was built by [Michael Han (michael.paulini@wormbase.org)]
    6 KB (769 words) - 11:01, 21 December 2011
  • New release of WormBase WS216, Wormpep216 and Wormrna216 Tue Jun 29 12:53:35 BST 2010 ...map_positions.WS216.gz - Interpolated map positions for each coding/RNA gene
    7 KB (818 words) - 11:10, 21 December 2011
  • [[WormBase Models]] == Model ==
    3 KB (399 words) - 09:55, 10 August 2010
  • New release of WormBase WS189, Wormpep189 and Wormrna189 Thu Apr 3 10:28:39 BST 2008 WS189 was built by [Paul Davis (paul.davis@wormbase.org)]
    6 KB (668 words) - 11:01, 21 December 2011
  • * Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not ...uld we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
    9 KB (1,490 words) - 15:35, 6 October 2016
  • *Issue #8919: In 2020, we corrected gene annotations of the nematode Pristionchus pacificus. ** Do we want standard Alliance gene pages for all genes from non-canonical species?
    2 KB (348 words) - 17:52, 2 February 2023
  • == WormBase Version Freeze == ...WormBase, e. g., WS100 (http://ws100.wormbase.org) and WS110 (http://ws110.wormbase.org). These reference releases are available for perpetuity on dedicated se
    10 KB (1,509 words) - 15:40, 24 September 2007
  • New release of WormBase WS210, Wormpep210 and Wormrna210 Tue Dec 22 12:35:31 GMT 2009 ...map_positions.WS210.gz - Interpolated map positions for each coding/RNA gene
    6 KB (721 words) - 16:46, 21 December 2011
  • =WormBase Curated Data Types and Curation Methods= GEO - Gene Expression Omnibus
    9 KB (1,174 words) - 18:30, 29 August 2012
  • 6 Oct 2010: The latest changes to the assembly are due to be added to WormBase in release WS221. ...this is done, we are happy to turn the ownership of the genome sequence to WormBase. - Paul Sternberg.
    3 KB (437 words) - 16:02, 15 December 2011
  • New release of WormBase WS181, Wormpep181 and Wormrna181 Fri Sep 7 11:40:20 BST 2007 ...map_positions.WS181.gz - Interpolated map positions for each coding/RNA gene
    8 KB (885 words) - 16:47, 21 December 2011
  • 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
  • <pre>New release of WormBase WS138, Wormpep138 and Wormrna138 Thu Jan 20 11:55:33 GMT 2005 ...map_positions.WS138.gz - Interpolated map positions for each coding/RNA gene
    6 KB (740 words) - 11:19, 21 December 2011
  • ...sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13229 (44.3%)<br>WormBase_approved Gene name 15596 (52.2%)<br>RNAi_result&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ...open your database, e.g.<br>&nbsp;&nbsp;&nbsp; type 'xace /users/yourname/wormbase' at the command prompt.<br><br>5. See the acedb website for more informatio
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  • ...reviously only with a text description are getting updated to fit the data model === Interaction-Gene associations ===
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  • EPIC data into WormBase *Need to modify model and display for data
    7 KB (1,070 words) - 17:47, 1 March 2012
  • *Should we take minutes of Caltech WormBase group meetings and send around? *WormBase-wide conference call twice per month
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  • New release of WormBase WS170, Wormpep170 and Wormrna170 Fri Jan 19 09:31:14 GMT 2007 ...map_positions.WS170.gz - Interpolated map positions for each coding/RNA gene
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  • new release of WormBase WS176, Wormpep176 and Wormrna176 Mon May 21 11:58:06 BST 2007 ...map_positions.WS176.gz - Interpolated map positions for each coding/RNA gene
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  • === GO data model change === * Changes to gene association file has implications for automated descriptions
    7 KB (1,058 words) - 15:32, 2 April 2015
  • New release of WormBase WS206, Wormpep206 and Wormrna206 Fri Aug 28 13:06:57 BST 2009 ...map_positions.WS206.gz - Interpolated map positions for each coding/RNA gene
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  • <nowiki>New release of WormBase WS172, Wormpep172 and Wormrna172 Fri Mar 2 16:35:57 GMT 2007 ...map_positions.WS172.gz - Interpolated map positions for each coding/RNA gene
    7 KB (783 words) - 10:55, 21 December 2011
  • 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
  • New release of WormBase WS208, Wormpep208 and Wormrna208 Tue Oct 27 13:31:22 GMT 2009 ...map_positions.WS208.gz - Interpolated map positions for each coding/RNA gene
    5 KB (581 words) - 16:50, 21 December 2011
  • ...curating phenotypes/variation for better comparability with human disease gene function *** ParaSite and integration with WormBase central.
    3 KB (438 words) - 07:19, 6 October 2014
  • New release of WormBase WS179, Wormpep179 and Wormrna179 Mon Jul 30 12:21:01 BST 2007 ...map_positions.WS179.gz - Interpolated map positions for each coding/RNA gene
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  • [[WormBase Models]] == Model ==
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  • New release of WormBase WS180, Wormpep180 and Wormrna180 Fri Aug 17 13:41:37 BST 2007 ...map_positions.WS180.gz - Interpolated map positions for each coding/RNA gene
    7 KB (771 words) - 10:52, 21 December 2011
  • ...Karen, others are welcome. Visit the construct model requests [http://wiki.wormbase.org/index.php/WormBase_Model:Construct here] ...arned enough Catalyst to create a workable ontology browser on the caltech wormbase sandbox.
    10 KB (1,583 words) - 18:16, 5 February 2014
  • *http://wiki.wormbase.org/index.php/WBConfCall_2014.07.03-Agenda_and_Minutes#List_of_Existing_WB_ === Any updates with the nurf-1 gene naming? ===
    3 KB (464 words) - 09:09, 18 July 2014
  • <pre>New release of WormBase WS190, Wormpep190 and Wormrna190 Fri Apr 25 11:03:36 BST 2008 ...map_positions.WS190.gz - Interpolated map positions for each coding/RNA gene
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  • [[WormBase Models]] == Model ==
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  • <pre>New release of WormBase WS212, Wormpep212 and Wormrna212 Mon Mar 1 11:51:04 GMT 2010 ...map_positions.WS212.gz - Interpolated map positions for each coding/RNA gene
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  • * Ontology term enrichment analysis, using ontologies other than gene ontology === Taking over Gene Orienteer ===
    10 KB (1,464 words) - 17:09, 13 August 2015
  • <pre>New release of WormBase WS193, Wormpep193 and Wormrna193 Fri Jul 25 22:12:15 BST 2008 ...map_positions.WS193.gz - Interpolated map positions for each coding/RNA gene
    8 KB (944 words) - 16:52, 21 December 2011
  • * Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc. === Gene Ontology SObA graph ===
    7 KB (1,010 words) - 17:08, 4 May 2017
  • <pre>New release of WormBase WS194, Wormpep194 and Wormrna194 Tue Sep 2 10:54:51 BST 2008 ...map_positions.WS194.gz - Interpolated map positions for each coding/RNA gene
    8 KB (936 words) - 16:48, 21 December 2011
  • * Curators will likely need to work with a models "master" to make model changes * http://juancarlos.wormbase.org , look at a gene page, open Phenotype Graph widget
    5 KB (776 words) - 16:50, 7 January 2016
  • ...map_positions.WS174.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS174.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    8 KB (938 words) - 10:54, 21 December 2011
  • New release of WormBase WS177, Wormpep177 and Wormrna177 Fri Jun 15 15:39:40 BST 2007 ...map_positions.WS177.gz - Interpolated map positions for each coding/RNA gene
    9 KB (819 words) - 10:53, 21 December 2011
  • [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
  • ...elegans'' (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous ge ...his database, termed HapPep3, available from the Superfamily repository of model organism proteomes ([http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY http://sup
    3 KB (462 words) - 16:11, 15 December 2011
  • * Collecting model/pathway diagrams from papers and reviews: should we make ?Picture objects f === WormBase Ontology Browser ===
    6 KB (974 words) - 17:28, 3 September 2014
  • WormBase Site-Wide Conference Call Meeting Minutes **1- Gene regulation networks paper
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  • ** model change to put topics in hierarchical structure. === Gene Association files ===
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  • * Further discussed capturing/registering when a curator has reviewed a gene model but not made a change ** e.g. Gene -> Variation (#Evidence), Variation -> Gene (#Molecular_change)
    5 KB (741 words) - 10:57, 21 August 2015
  • https://github.com/WormBase/website/issues/5092 * Discussion on making available on WormBase the chapters we wrote for the WormBook.
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  • <pre>New release of WormBase WS169, Wormpep169 and Wormrna169 Fri Dec 22 15:09:52 GMT 2006 ...map_positions.WS169.gz - Interpolated map positions for each coding/RNA gene
    8 KB (787 words) - 10:56, 21 December 2011
  • * First draft up on WormBase development site ...notate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable
    8 KB (1,289 words) - 18:11, 10 November 2016
  • *Example: If a gene is involved in a function or process, where in the cell does this take plac *WormBase curates phenotypes, pathways, etc.
    7 KB (1,019 words) - 20:58, 12 April 2012
  • ...r00031139]). The P pacificus laboratory strain [http://www.wormbase.org/db/gene/strain?name=PS312;class=Strain PS312], used for genomic sequencing, was iso ...ution of hermaphroditism. ''BMC Evol Biol''&nbsp; '''7''':104 ([http://www.wormbase.org/db/misc/paper?name=WBPaper00030826;class=Paper WBPaper00030826])
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  • [[WormBase Models]] == Model ==
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  • === Gene descriptions === Title: WormBase 2019 - Data, Tools and Community Curation
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  • A Backbone.js + jQuery Mobile app for accessing the Wormbase database through its RESTful API. wormbase-mobile
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  • New release of WormBase WS200, Wormpep200 and Wormrna200 Tue Feb 24 12:51:18 GMT 2009 ...map_positions.WS200.gz - Interpolated map positions for each coding/RNA gene
    6 KB (722 words) - 16:43, 21 December 2011
  • *Getting real-time updates of gene list for genes in OA ...from nameserver: cgc name, public names, sequence name, live/dead status, gene IDs
    7 KB (1,059 words) - 15:37, 1 August 2013
  • ...e. This is similar to a gene being attached to more than one GO term. If a gene needs to be attached to a unrelated disease, enter all data on a new line, '''Field 4 Experimental model for (dis_humandoid):''' <br/ >
    14 KB (2,085 words) - 20:27, 7 July 2022
  • Gene Concise Description form *Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
    7 KB (1,047 words) - 15:34, 4 April 2013
  • New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009 ...map_positions.WS207.gz - Interpolated map positions for each coding/RNA gene
    6 KB (675 words) - 16:42, 21 December 2011
  • === WormBase Ontology Browser (WOBr) === * http://juancarlos.wormbase.org/tools/ontology_browser
    8 KB (1,234 words) - 12:36, 4 June 2014
  • ...ZCX1hZ3b-vDdWB4KjIvieALc_GLnYqYCTqnMaJ7Rg/edit (Need to be logged in with WormBase google account to edit it). === WormBase Workshop roll call ===
    9 KB (1,431 words) - 23:32, 23 June 2015
  • ===WormBase Webinars=== * Current schedule: https://wiki.wormbase.org/index.php/Meetings#2020_-_2021_WormBase_Webinars
    3 KB (534 words) - 17:29, 1 October 2020
  • *JD Wong started at WormBase this week; will focus on building WormBase instance of Intermine *Once in place, we can build pre-canned queries that we can embed in WormBase pages (maybe in response to help desk inquiries)
    7 KB (1,123 words) - 16:39, 6 December 2012
  • ...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
  • * What implications does this have for the WormBase Ontology Browser? * WormBase has imported all worm (C. elegans) physical (protein-protein) interactions
    8 KB (1,120 words) - 16:19, 5 March 2015
  • * Wen will create ticket to create wormbase.org URL * Working on mapping fosmids to latest release of WormBase
    8 KB (1,224 words) - 15:34, 21 July 2016
  • * I could not find an ontology that was ready built to adopt; few genetic model organisms, of those, FB has the most useful. Other mods use controlled voca * Requested model change for WS250 with new terms.
    6 KB (982 words) - 15:33, 2 July 2015
  • ...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 Reporter 3_UTR ?Gene
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  • http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks ==2. WormBase exhibit at the GSA meeting Dev., Cell Bio and Gene Expression Meeting==
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  • Interaction model WormBase meeting announcement
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  • * Any more comments about the Wiki page and the proposal? https://wiki.wormbase.org/index.php/WormBase_gene_association_file * Will change ?Expr_pattern model to possibly remove ?Author reference and add in a ?Person reference instead
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  • *Gene IDs can be found from original paper or data set AMIGO2 (Wormbase Ontology Browser)
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  • <pre>New release of WormBase WS107, Wormpep107 and Wormrna107 Fri Aug 8 13:44:00 BST 2003 ...map_positions.WS107.gz - Interpolated map positions for each coding/RNA gene
    6 KB (659 words) - 11:17, 21 December 2011
  • * We will need to learn to model in Datomic to start building curation tools that run off of Datomic ...ill want to build a curation tool directly on top of Datomic; will need to model currently un-dumped fields in Datomic
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  • === WormBase Ontology Browser (WOBr) === ...erver for the information the browser queries: gene ontology associations, gene association files
    13 KB (1,983 words) - 16:40, 7 November 2013
  • *** Updated automated gene concise descriptions? * Progress being made within the Alliance to update the automated concise gene descriptions
    8 KB (1,121 words) - 14:01, 15 July 2019
  • * WBPaper00026596.ce.mr.csv content incorrect: https://github.com/WormBase/website/issues/8101 * Eduardo has the data and can produce gene/cell-specific outputs.
    3 KB (511 words) - 18:54, 18 February 2021
  • ...a of the model nematode ''Caenorhabditis elegans'' and related nematodes. WormBase is developed by an international consortium of researchers and computer sci *[[UserGuide:General_Description|Overview of WormBase]]
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  • *WormBase - Bitbucket, GitHub (can commit code) *Is WormBase interested connecting to it?
    7 KB (1,117 words) - 16:39, 4 August 2011
  • * GO-CAM (Gene Ontology - Causal Activity Model(ing)) ...rds, tool could pull up all relevant annotations to help start with GO CAM model building
    8 KB (1,229 words) - 15:31, 1 June 2017
  • 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 data
    17 KB (1,758 words) - 16:47, 21 December 2011
  • <pre>New release of WormBase WS142, Wormpep142 and Wormrna142 Fri Apr 15 18:22:51 BST 2005 ...map_positions.WS142.gz - Interpolated map positions for each coding/RNA gene
    7 KB (720 words) - 11:09, 21 December 2011
  • <pre>New release of WormBase WS131, Wormpep131 and Wormrna131 Tue Sep 7 15:06:49 BST 2004 ...map_positions.WS131.gz - Interpolated map positions for each coding/RNA gene
    6 KB (669 words) - 11:18, 21 December 2011
  • *GeneWiki for human gene annotation **One page for each gene; already have ~10,000 articles
    7 KB (1,158 words) - 17:20, 3 May 2012
  • 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 data
    15 KB (1,610 words) - 11:20, 21 December 2011
  • [[WS241_Models.wrm | WS241 model details]] ...ne_cluster - Karen would like to use this underused class for phylogenetic gene clusters
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  • *Focus on: Gene function, transcriptional networks, pathways *Try to use GO annotations to make more expressive statements about gene function, pathways and processes
    6 KB (944 words) - 16:25, 1 November 2012
  • <pre>New release of WormBase WS135, Wormpep135 and Wormrna135 Thu Nov 11 13:32:31 GMT 2004 ...map_positions.WS135.gz - Interpolated map positions for each coding/RNA gene
    6 KB (689 words) - 11:19, 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
  • 2. Find and follow the repo WormBase/website project: https://github.com/WormBase/website
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  • WormBase will import expression data (Images, constructs, and annotations) from the ...original data is always present on the Max Planck Institute (MPI) website. WormBase will fetch the data periodically (Release-basis) to have the collection up-
    11 KB (1,190 words) - 19:16, 26 September 2019
  • <pre>New release of WormBase WS211, Wormpep211 and Wormrna211 Fri Jan 29 13:26:05 GMT 2010 ...map_positions.WS211.gz - Interpolated map positions for each coding/RNA gene
    6 KB (766 words) - 16:38, 21 December 2011
  • === Automated gene descriptions - orthology === * WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)
    12 KB (1,809 words) - 16:33, 1 March 2018
  • ===Gene names issue in SimpleMine and other mining tools=== *Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
    9 KB (1,369 words) - 22:47, 5 August 2020
  • ** Should have a guide for users [http://www.wormbase.org/about/Frequently_asked_questions#f--10 Here] * User needs WormBase official response.
    3 KB (423 words) - 16:35, 7 September 2017
  • ...n received latest update, CGC very busy with strains generated through new gene engineering techniques Main outline [https://docs.google.com/a/wormbase.org/document/d/1l6pExlCMI88pi_-djk8jt7IzNsMDV-nIEY9Z1gBNh-A/edit here]- not
    10 KB (1,453 words) - 18:52, 4 February 2015
  • 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
  • Transgene Model *Kimberly working on Physical Interaction model
    7 KB (1,103 words) - 18:28, 5 May 2011
  • 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
  • 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
  • *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 documentation
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  • <pre>New release of WormBase WS127, Wormpep127 and Wormrna127 Tue Jul 6 13:12:51 BST 2004 ...map_positions.WS127.gz - Interpolated map positions for each coding/RNA gene
    7 KB (872 words) - 11:18, 21 December 2011
  • *Update spelling to Descendant in ?GO_term model *Model changes - added Status and Synonym tags.
    15 KB (1,936 words) - 16:29, 29 June 2018
  • === Model changes === * SAB suggested continuing site visits for WormBase tutorials
    7 KB (1,062 words) - 14:41, 2 August 2018
  • **Chris will add all model changes proposed for WS233 **?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an "Interactor" tag
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  • New release of WormBase WS217, Wormpep217 and Wormrna217 Wed Jul 28 09:25:17 BST 2010 ...map_positions.WS217.gz - Interpolated map positions for each coding/RNA gene
    8 KB (915 words) - 11:10, 21 December 2011
  • * Todd working on a spell.wormbase.org site for doing worm SPELL analyses === Expression Pattern Model ===
    6 KB (906 words) - 15:34, 6 December 2018
  • 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 data
    16 KB (1,674 words) - 11:38, 20 April 2011
  • [[WormBase Models]] == Model ==
    15 KB (1,645 words) - 18:54, 23 January 2014
  • New release of WormBase WS202, Wormpep202 and Wormrna202 Tue Apr 28 16:02:08 BST 2009 ...map_positions.WS202.gz - Interpolated map positions for each coding/RNA gene
    6 KB (770 words) - 11:06, 21 December 2011
  • 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
  • ** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/ === WormBase Ontology Browser WS248 online on Dev ===
    8 KB (1,147 words) - 15:33, 7 May 2015
  • New release of WormBase WS218, Wormpep218 and Wormrna218 Tue Aug 24 genomes DIR - contains a sub dir for each WormBase species with
    15 KB (1,756 words) - 11:21, 21 December 2011
  • * Make modification to ACEDB model? ...ence is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C.
    11 KB (1,676 words) - 15:28, 2 May 2019
  • 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
  • === Gene ACE Dumps === *Looked at gene objects specifically
    8 KB (1,225 words) - 16:33, 3 October 2013
  • 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 data
    15 KB (1,583 words) - 11:13, 21 December 2011
  • -rwxrwxr-x 1 todd wormbase 20053 Jul 6 14:06 cell.cgi -rwxrwxr-x 1 todd wormbase 3916 Jul 6 14:06 make_pedigree.cgi
    16 KB (1,576 words) - 17:44, 16 August 2010
  • <pre>New release of WormBase WS117, Wormpep117 and Wormrna117 Tue Jan 20 10:22:06 GMT 2004 ...map_positions.WS117.gz - Interpolated map positions for each coding/RNA gene
    6 KB (695 words) - 11:17, 21 December 2011
  • 2. Find and follow the tharris/wormbase project: http://bitbucket.org/tharris/wormbase/
    4 KB (616 words) - 18:35, 17 August 2010
  • * Would be good to meet with individual labs and lab members to discuss WormBase ...al to make Remark entry unique; Raymond asking to remove the UNIQUE in the model
    11 KB (1,664 words) - 16:29, 7 December 2017
  • Ranjana - Preplanning WormBase side meetings at IWM? *Two Wormbase Plenary talks
    9 KB (1,302 words) - 16:38, 2 June 2011
  • ...me and cell type/anatomy/developmental stage. This is currently done using gene expression markers of known cell types, but there is no current database of * Reliable cell marker gene curation for single cell transcriptome data/FACS-transcriptome datasets. A
    11 KB (1,649 words) - 16:10, 19 July 2018
  • ''This is a running list of proposed features at WormBase'' ...human diseases. This is a benefit both to people who use C. elegans as a model system (most grants at least true to touch on the relevance of given projec
    6 KB (842 words) - 17:01, 21 October 2011
  • ...al or published name of a genotype and the components that are inferred by WormBase * We have a "Gene" tag in the ?Genotype model for capturing relevant genes
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  • <pre>New release of WormBase WS122, Wormpep122 and Wormrna122 March 26th 2004 ...d_map_positions.WS122.gz - Interpolated map positions for each coding/RNA gene
    6 KB (721 words) - 11:18, 21 December 2011
  • ='''WormBase Gene Ontology Progress Report, December 2011'''= Developer, WormBase, Caltech, Pasadena, CA.
    13 KB (1,830 words) - 16:40, 13 December 2012
  • * Commonly referenced gene sets * Topics commonly studied in C. elegans due to its advantages as a model system
    10 KB (1,279 words) - 18:20, 18 October 2013
  • * Have a simple mockup for the display of disease data on a gene report page: https://docs.google.com/presentation/d/1YuD4_-mPS2AhIfaX41M8II * We should remove underscores from "is_model_of" and translate to "is a model of"
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  • ...oduct XREF Interaction #Interactor_info // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments ...Sequence XREF Interaction #Interactor_info // Sequence of the interacting gene or protein
    50 KB (5,228 words) - 15:10, 21 July 2017
  • New release of WormBase WS220, Wormpep220 and Wormrna220 Mon Oct 25 13:22:36 BST 2010 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data
    16 KB (1,762 words) - 11:10, 21 December 2011
  • New release of WormBase WS226 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    21 KB (2,346 words) - 11:15, 21 December 2011
  • New release of WormBase WS235 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    15 KB (1,708 words) - 10:14, 18 January 2013
  • ** Some species (e.g. P. pac) have few/no gene model changes, but could do with being brought up to latest models and have newes ** MP to create summary of gene model changes for each species
    11 KB (1,714 words) - 11:04, 27 July 2015
  • ...an) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene ...ce new ?Phenotype_experiment model is in place, to just refer to perturbed gene
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  • == WormBase User's Survey == ...ll have a chance to win a WormBase mug with Thomas Boulin√ïs award-winning WormBase Logo.
    7 KB (1,180 words) - 11:00, 21 December 2011
  • <pre>New release of WormBase WS112, Wormpep112 and Wormrna112 Fri Oct 17 18:38:57 BST 2003 ...map_positions.WS112.gz - Interpolated map positions for each coding/RNA gene
    6 KB (735 words) - 11:17, 21 December 2011
  • * Changes requested here: https://github.com/WormBase/website/issues/7900 * Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
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  • === Automated gene descriptions === * Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
    5 KB (670 words) - 15:31, 3 June 2021
  • * https://github.com/WormBase/website/issues/8262 * ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
    5 KB (670 words) - 16:00, 5 August 2021
  • ...arize how the Phenotype2GO-based GO annotations will be handled for future WormBase builds and GO uploads. ...d based upon the presence of a phenotype associated with a perturbation of gene activity.
    7 KB (1,164 words) - 17:54, 19 February 2015
  • *Complex gene information will still be best handled manually *Applying gene (GO) annotations across all species
    9 KB (1,339 words) - 19:02, 31 January 2013
  • ** chromosome map tool (https://github.com/WormBase/website/issues/1103). Requires comment from web team ==WormBase Survey==
    4 KB (684 words) - 19:43, 5 December 2015
  • ** Want to indicate, for a query gene, genes for which multiple interaction types have been observed * Adding functionality to WormMine that preserves original gene list
    11 KB (1,703 words) - 15:27, 5 April 2018
  • * WormBook mirror: will move from wormbase.sanger.ac.uk to * WormBase mirror: will go offline next week Friday
    7 KB (1,220 words) - 15:50, 25 November 2011
  • [[WormBase Models]] ...sion_cluster XREF Regulated_by_molecule //Added for molecule regulation of gene expression by Wen
    6 KB (543 words) - 23:29, 15 March 2016
  • * 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
  • New release of WormBase WS230 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    17 KB (1,950 words) - 09:37, 7 February 2012
  • *[https://github.com/WormBase/website/issues/6423 Not sure if this falls under content....] * User asked about phenotype information being incorporated into the gene description
    14 KB (2,226 words) - 15:31, 7 June 2018
  • **Gene Function ***Integrated interaction model, genetic interaction ontology
    12 KB (1,878 words) - 15:55, 6 September 2012
  • **Example: Gene page; only update information relevant to gene class to be displayed Karen: Transgene model
    13 KB (2,097 words) - 22:48, 7 April 2011
  • New genome assemblies and gene names across species *How do we handle independent, conflicting genome assemblies and gene models?
    8 KB (1,161 words) - 16:34, 7 March 2013
  • * Can we track who is using this tool (and others)? SObA is hosted by WormBase so we'd have to ask Todd (Google analytics); SimpleMine is Caltech hosted s * To implement on Gene pages. One vs. Five widgets?
    6 KB (911 words) - 17:13, 6 June 2019
  • 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
  • New release of WormBase WS219, Wormpep219 and Wormrna219 Tue Oct 5 16:04:14 BST 2010 WS219 was built by [Michael Paulini (michael.paulini@wormbase.org)]
    15 KB (1,622 words) - 11:11, 21 December 2011
  • * Portal for larger biomedical community into C. elegans gene function.<br> **process pages will dissect the chapters and link them to entities in WormBase,
    20 KB (3,088 words) - 19:17, 13 August 2020
  • === Past meetings posted on the WormBase Meeting page === **[C. elegans topic meeting: Development, Cell Biology, and Gene Expression](http://conferences.union.wisc.edu/cedevelopment/)**<br>
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  • * There shouldn't be model changes (that affect Caltech) for this next upload * Such data not currently incorporated into automated gene descriptions
    6 KB (921 words) - 16:52, 4 January 2018
  • ...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. === Logical Extensions of Gene Ontology (LEGO) ===
    6 KB (906 words) - 21:38, 30 September 2015
  • ...eral discussion on DOI handling for micropublications and using the ?Paper model * Micropublications were displayed on ?Expr_pattern pages on WormBase/WormBook
    10 KB (1,475 words) - 16:57, 5 November 2015
  • ...to link elegans gene variations and phenotypes to homologous human disease gene variations. This is separate from any automated pipeline that can be set up * Authors refer to C. elegans mutations as a model; may or may not be strictly conserved
    8 KB (1,305 words) - 23:24, 3 June 2015
  • ==Antibody Model== Gene ?Gene XREF Antibody #Evidence
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  • '''Gene name.''' ''mpk-1'' → Gene Summary page: <http://www.wormbase.org/db/gene/gene?name=mpk-1;class=Gene><br>
    14 KB (2,365 words) - 21:14, 23 July 2013
  • ===WormBase Webinars=== === Proposal: Tie WormBase releases to the Alliance release schedule ===
    5 KB (890 words) - 18:36, 5 November 2020
  • ...note, if users are accessing the from through the 'Submit data' button on WormBase they should be asked: Changes to the current Allele-phenotype form located here: http://www.wormbase.org/submissions/phenotype.cgi
    5 KB (800 words) - 18:29, 16 August 2017
  • ...ity scientific findings directly to a well established central repository (WormBase). Data will be publically shared and could be mined alongside data curated ...localization experiments (e.g. ISH, smFISH, immunohistochemistry). If the model will prove to be successful, we will scale it up to include submission of o
    21 KB (3,194 words) - 02:08, 17 May 2018
  • * Who from WormBase will go? * Working out how inferred annotations propagate from Noctua/LEGO model to GAF
    9 KB (1,377 words) - 16:44, 2 February 2017
  • New release of WormBase WS233 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    17 KB (2,002 words) - 14:17, 13 September 2012
  • * Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room * We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
    8 KB (1,228 words) - 20:57, 14 July 2020
  • ** Transgene-phenotype curation currently specifies causative gene, but would be more complicated for strains * Eppendorf tube openers with WormBase logo?
    12 KB (1,930 words) - 17:12, 1 February 2018
  • **Documenting elements of WormBase workflow to ease transition for new staff and keep track of changes made **Added information and links for getting started with WormBase
    29 KB (4,254 words) - 20:25, 27 April 2012
  • * Can use outreach@wormbase.org for consistency * Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?
    9 KB (1,366 words) - 15:19, 6 September 2018
  • New release of WormBase WS229 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    17 KB (1,988 words) - 11:15, 21 December 2011
  • ...loss-of-function mutation in that gene, hence providing evidence as to the gene's biological function. ...s with multiple mutations in the strain receiving the dsRNA, multiple RNAi gene targets, complex genetic interactions, and/or missing descriptions from the
    29 KB (4,152 words) - 20:29, 30 July 2019
  • = WormBase Coding Standards and Style Guide = foreach my $gene (@genes) {
    6 KB (950 words) - 15:36, 19 June 2014
  • * The following 3 items are linked and the Gene has been named and a new lab created: ** Has anyone replied to Montserrat Elías regarding naming of same gene, Y53C10A.5? - This name has been agreed by Tim S. and the issue can be clos
    5 KB (857 words) - 14:36, 9 March 2020
  • [[WormBase-Caltech_Weekly_Calls_January_2022|January]] [[WormBase-Caltech_Weekly_Calls_February_2022|February]]
    10 KB (1,547 words) - 21:31, 2 January 2024
  • === Mapping gene product-to-term relation names to RO ids. === ** Latest WB gpi file: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.canonic
    10 KB (1,456 words) - 17:43, 9 November 2023
  • * gene product(s) ==Model Changes==
    29 KB (4,575 words) - 16:23, 3 March 2022
  • == 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
  • *Trying to display site-of-action data on relevant gene pages *We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it
    10 KB (1,553 words) - 18:04, 7 February 2013
  • <pre>New release of WormBase WS215, Wormpep215 and Wormrna215 Thu May 27 18:15:29 BST 2010 ...map_positions.WS215.gz - Interpolated map positions for each coding/RNA gene
    19 KB (1,735 words) - 11:07, 21 December 2011
  • ...ed ?Physical_interaction model has also been consolidated into this larger model. Note that #Interaction_info and #Interaction_type have been deprecated. ...XREF Interaction #Interactor_info // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
    53 KB (6,521 words) - 20:51, 7 March 2019
  • ...orm IDs as an additional line in the gp2protein file; hopefully with a new model, they will be handled appropriately. ...notations that are at the top of the file and map to an unknown gene, i.e. Gene : " "
    23 KB (3,744 words) - 15:12, 23 December 2022
  • * Karen will need to become part time at WormBase (needs to be more than half time on SBIR) * WB enzyme gene pages link out to respective gene pages on WormFlux
    10 KB (1,527 words) - 15:32, 6 April 2017
  • ===WormBase Uploads=== ...produced weekly to the WormBase .ace file for upload: [[UniProtKB gpad to WormBase .ace]]
    30 KB (3,904 words) - 18:45, 13 May 2020
  • ...document describes how to install and configure the Intermine instance at WormBase. ...tyle="color: red">'''Previous build examples are available at: http://wiki.wormbase.org/index.php/Website:WormMine_Builds'''</span>
    25 KB (3,652 words) - 23:06, 25 December 2014
  • ...ormat gpad and gpi file format specifications]. This allows us to map all gene products mentions in a paper to a MOD identifier and to a UniProtKB identif **Gene product - this allows you to search sentences for a gene product. Searches are case-insensitive and you can search using:
    11 KB (1,765 words) - 15:10, 18 February 2014
  • ...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 ...obe(s) (i.e. the dsRNA sequence used to knockdown expression of the target gene). This information may be submitted in the form of a PCR product object (e.
    47 KB (7,989 words) - 23:40, 1 September 2015
  • * Wen needs a couple days from model tagging to prepare the final upload ** WormBase generated expression clusters (custom algorithm?)
    6 KB (857 words) - 16:01, 2 October 2014
  • **We could extend the WormBase web app to interact with SPELL data ****WormBase person would check on case-by-case basis the accuracy of data (e.g. express
    7 KB (1,074 words) - 17:19, 4 October 2012
  • ...ercontent.com/WormBase/wormbase-pipeline/master/wspec/models.wrm variation model]<br> ...the summaries of a gene's variations and display them on the corresponding gene pages.
    36 KB (5,076 words) - 01:38, 2 March 2016
  • ** [https://github.com/WormBase/website/issues/1438 #1438 Track errors on RNA seq GBrowse view] ** [https://github.com/WormBase/website/issues/1091 #1091 OP50 sequence data deposition]
    8 KB (1,291 words) - 21:09, 23 June 2013
  • ...ww.wormbase.org/about/Frequently_asked_questions FAQ pages] on the new www.wormbase.org site. === How should I cite WormBase? ===
    67 KB (10,954 words) - 09:22, 19 February 2013
  • * 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
  • ...ber of functional annotations for genes, provided both in free text and as Gene Ontology terms (Harris et al., 2004; ''UNIT 7.2''). ...elopers group actively invites suggestions for improvement from users, and WormBase's source code is freely available for local installation and improvement.
    30 KB (4,765 words) - 20:03, 11 August 2010
  • * Trained a small GPT model with C. elegans literature. Reporting some results. ** Current data model at the ABC has negated as a Boolean (true/false).
    36 KB (4,994 words) - 17:27, 14 February 2024
  • .../p><h2>Genomes, assemblies, clones and contigs</h2><p>Reference genomes in WormBase are given version names, for example <i>C. elegans</i> has the version name ...<b>AscSuum_1.0</b> and <b>ASU_2.0</b></p><p>The genomes of most species in WormBase are incompletely assembled, being left as various sizes of contig. Only <i>
    56 KB (9,520 words) - 11:51, 21 October 2015
  • .../p><h2>Genomes, assemblies, clones and contigs</h2><p>Reference genomes in WormBase are given version names, for example <i>C. elegans</i> has the version name ...<b>AscSuum_1.0</b> and <b>ASU_2.0</b></p><p>The genomes of most species in WormBase are incompletely assembled, being left as various sizes of contig. Only <i>
    56 KB (9,514 words) - 09:48, 23 October 2015
  • ...ble mostly contains legacy information that was imported from the CGC when WormBase starting curating paper data, as PubMed currently does not curate all autho ...hould be treated in subsequent pipelines, RNAi data, and the status of the gene-paper associations.
    25 KB (3,238 words) - 16:42, 8 November 2019
  • http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.404&root=ensembl&view=markup ...ata that only has person communication as evidence. How should users cite WormBase ? How should we make it clear to users that some is published and some isn
    15 KB (2,374 words) - 16:00, 17 July 2014
  • ...and educators who use ''C. elegans'' or related nematodes as their primary model organism. WormBoard will meet in odd-numbered years at the biennial Interna * PI of the WormBase consortium
    16 KB (2,224 words) - 17:36, 25 August 2023
  • Karen Yook/wormbase- Caltech/@wbperson712 Whole-microbiome gene expression profiling (’meta-transcriptomics’) has emerged as a powerful
    29 KB (4,082 words) - 19:15, 11 April 2014
  • == Model changes for WS244 == * This cycle we see 5 model changes in 4 classes:
    235 KB (23,325 words) - 10:33, 3 July 2014
  • ** See github ticket 2867 https://github.com/WormBase/website/issues/2867#issuecomment-48041365 ** in the expression section on the gene page highlight the objects that are Sequence feature related. Add in the ta
    23 KB (3,248 words) - 12:58, 22 September 2014
  • ...iverse nature which are used for high-throughput screening analysis of the gene function, protein interaction, cellular processing, biochemical pathways, o ==Model==
    50 KB (6,966 words) - 19:15, 13 August 2020
  • ==Picture Data Model== ...he literature and individual laboratories and display them in the WormBase gene expression page.
    120 KB (19,719 words) - 16:44, 20 October 2023
  • http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?root=ensembl&view=log WormBook chapters will be a good source of gene lists for these annotations; links to select chapters that contain lists of
    47 KB (6,852 words) - 04:27, 8 December 2020
  • Karen Yook/WormBase-Caltech/@wbperson712 financial reporting: business model before (subjective) - now quants (big data trends)
    37 KB (5,533 words) - 19:17, 11 April 2014
  • Karen Yook/WormBase-Caltech/@wbperson712 financial reporting: business model before (subjective) - now quants (big data trends)
    37 KB (5,533 words) - 19:17, 11 April 2014
  • WormBase is updated with each new build of the database released from Sanger. The li ...g or troubleshooting. This is especially true during cycles where the data model changes significantly.
    34 KB (5,450 words) - 18:24, 17 August 2010
  • ...rent type (such as the DNA sequence of the gene, or the cells in which the gene is active). One can also do searches for complex data sets. ...n of WormBase available in September, 2005 (WS147 release; BioPerl/Generic Model Organism Database software).
    103 KB (16,375 words) - 23:39, 30 November 2010
  • Current model (WS280) ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence
    104 KB (15,303 words) - 19:39, 11 May 2023
  • [[http://www.wormbase.org/wiki/index.php?title=How_to_FirstPass&action=submit back]] ...t listed by the author either. Sequences can be found by searching for the gene names : cehd-3,4,5,7,8,9,13,15,17,20,22,28,39. ||2/2/02 21:01
    40 KB (4,083 words) - 23:02, 13 August 2010
  • ...u don't use it, is it in the emails you send out or in the submit forms in WormBase ? -- J answer Please keep form, must be the one linking to old papers asso http://www.wormbase.org/db/misc/person?name=WBPerson1823;class=Person
    119 KB (18,888 words) - 00:05, 2 May 2014