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- ==C. elegans as a model system to study disease and disease genes== ...g of new ones, based on the published literature, where elegans is used to model the biology of a disease and/or the orthologous elegans gene function is st5 KB (782 words) - 20:56, 8 January 2020
- 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
- ...nants worldwide also known as red stomach worm, wire worm or Barber's pole worm, is very common parasite and one the most pathogenic nematodes of ruminants ...ving model nematode ''Caenorhabditis elegans''. This makes it an important model of parasitic nematode biology that is commonly used for experimental studie3 KB (493 words) - 16:03, 15 December 2011
- == Adding worm disease models/data to the Monarch Initiative website== *http://monarchinitiative.org/ : connects phenotypes, diseases, models, and genes for translational research across species (People involved: Melissa Haendel5 KB (807 words) - 18:27, 4 September 2014
- https://github.com/WormBase/website/issues/5092 * Discussion on making available on WormBase the chapters we wrote for the WormBook.2 KB (369 words) - 16:38, 6 October 2016
- * File in /usr/local/wormbase/databases/{RELEASE}/orthology and automatically generated by orthology data * mark the elegans/worm genes with omim ortholgs, as caltech is unable to query into the proteins (done b4 KB (583 words) - 20:22, 29 July 2011
- New release of WormBase WS185, Wormpep185 and Wormrna185 Fri Nov 30 17:11:38 GMT 2007 vii) confirmed_genes.WS185.gz - DNA sequences of all genes confirmed by EST &/or cDNA6 KB (680 words) - 07:37, 11 January 2008
- ...cial wiki site for [http://www.wormbase.org WormBase], the database of the model organism [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditi WormBase is developed by an [http://www.wormbase.org/about/staff#01--10 international consortium] of researchers and compute4 KB (507 words) - 08:46, 8 October 2014
- New release of WormBase WS183, Wormpep183 and Wormrna183 Tue Oct 16 16:18:34 BST 2007 vii) confirmed_genes.WS183.gz - DNA sequences of all genes confirmed by EST &/or cDNA7 KB (800 words) - 10:01, 8 November 2007
- New release of WormBase WS186, Wormpep186 and Wormrna186 Fri Dec 21 08:57:59 GMT 2007 vii) confirmed_genes.WS186.gz - DNA sequences of all genes confirmed by EST &/or cDNA6 KB (683 words) - 05:51, 3 April 2008
- 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
- [[WS241_Models.wrm | WS241 model details]] *These annotations need to be properly credited, so for the new GO annotation model we would like to create WBPerson objects for these groups and use Curator_c8 KB (1,246 words) - 15:52, 12 November 2013
- =WormBase Curated Data Types and Curation Methods= HMM - Hidden Markov Model9 KB (1,174 words) - 18:30, 29 August 2012
- ...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
- * WB needs Genes from nameserver, which is on AWS, so need creds or AMI ? **** java -cp wb-names-export.jar clojure.main -m wormbase.names.export gene genes.csv7 KB (1,113 words) - 18:19, 6 April 2023
- ew release of WormBase WS184, Wormpep184 and Wormrna184 Thu Nov 8 12:09:34 GMT 2007 vii) confirmed_genes.WS184.gz - DNA sequences of all genes confirmed by EST &/or cDNA7 KB (831 words) - 07:36, 11 January 2008
- ==== 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
- *When mark a paper, separate into two different types of genes :stable vs unstable **Stable genes map to stable ID4 KB (612 words) - 17:13, 1 December 2011
- *WormBase - Bitbucket, GitHub (can commit code) *Is WormBase interested connecting to it?7 KB (1,117 words) - 16:39, 4 August 2011
- **How to get GO terms for a list of genes? International Worm Meeting6 KB (864 words) - 15:32, 6 June 2013
- **90 genes >= 10 publications **20,000 genes with RNAi data9 KB (1,302 words) - 16:38, 2 June 2011
- === Upstate NY Worm Meeting === === Midwest Worm Meeting ===11 KB (1,703 words) - 15:27, 5 April 2018
- * 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
- * What implications does this have for the WormBase Ontology Browser? * WormBase has imported all worm (C. elegans) physical (protein-protein) interactions from BioGRID8 KB (1,120 words) - 16:19, 5 March 2015
- 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
- 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, ...is the method of choice for searching the ''C. elegans'' genome with a non-worm protein or nucleic acid sequence.3 KB (401 words) - 20:02, 11 August 2010
- * Explaining job posting options via the forum in new Worm Breeder's Gazette article * Wen will make the model change proposal10 KB (1,464 words) - 17:09, 13 August 2015
- == OMIM links to/from WormBase == * Ranjana working on linking between WormBase and OMIM2 KB (384 words) - 20:25, 21 May 2015
- = 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
- * 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 out8 KB (1,228 words) - 20:57, 14 July 2020
- 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
- '''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
- *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
- **Virtual worm web page & FTP *Virtual worm access to data7 KB (1,074 words) - 17:19, 4 October 2012
- * Some genes have human orthology mentioned in automated descriptions, even though the o * WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)12 KB (1,809 words) - 16:33, 1 March 2018
- WORM paper Interaction model6 KB (903 words) - 16:37, 5 January 2012
- *Up-to-date mapping to genes is not currently done AMIGO2 (Wormbase Ontology Browser)5 KB (850 words) - 15:32, 5 September 2013
- === Model changes === * SAB suggested continuing site visits for WormBase tutorials7 KB (1,062 words) - 14:41, 2 August 2018
- *Prioritize with genes with little to no known information *Focus on genes in other species9 KB (1,339 words) - 19:02, 31 January 2013
- * Valerio generated new files to ignore/filter-out problematic genes Title: WormBase 2019 - Data, Tools and Community Curation9 KB (1,364 words) - 15:39, 7 February 2019
- ...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 t4 KB (709 words) - 13:27, 5 April 2021
- * After worm meeting, (June 27th) * Left over bandanas? paid ~$1 per bandana before. We have enough for WormBase staff8 KB (1,213 words) - 15:29, 6 July 2017
- * 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 Datomic4 KB (571 words) - 16:48, 3 March 2016
- * Invited to give 25+5 minute talk at Worcester Area Worm Meeting on November 14th * Would be good to meet with individual labs and lab members to discuss WormBase11 KB (1,664 words) - 16:29, 7 December 2017
- * http://wiki.wormbase.org/index.php/2014_Advisory_Board_Meeting Paul will begin meeting with “ What is WormBase” and his talk will include an introduction to the following topics (not n5 KB (763 words) - 00:51, 19 September 2014
- *Once exposed to worm community at International Meeting, can develop focus groups to enhance/imp Virtual Worm Site5 KB (752 words) - 17:07, 7 July 2011
- * Wen will create ticket to create wormbase.org URL * Working on mapping fosmids to latest release of WormBase8 KB (1,224 words) - 15:34, 21 July 2016
- ...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. * Enter list of genes, get a list of anatomy terms6 KB (906 words) - 21:38, 30 September 2015
- * Weird genes ** Handful of genes in C.elegans that have contrived structures to accommodate an frameshift /5 KB (741 words) - 10:57, 21 August 2015
- * Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue * Genes that are detected at convincing levels (present call) in cell/tissue9 KB (1,490 words) - 15:35, 6 October 2016
- === WormBase Ontology Browser (WOBr) for WS244 release === * Final data model may still need refinement?6 KB (801 words) - 17:29, 2 July 2014
- * Worm in apple graphic? Dragon worm cartooon? Maybe some variation on it? * Make modification to ACEDB model?11 KB (1,676 words) - 15:28, 2 May 2019
- * There shouldn't be model changes (that affect Caltech) for this next upload * Wen can talk with Ranjana to incorporate (particularly for info-sparse genes)6 KB (921 words) - 16:52, 4 January 2018
- 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
- It would be great to focus on data types that are unique and powerful in worm, including single cell transcriptomics/sequence analysis, neural circuits, * Metabolomics is an increasing area of concentration in the worm community and elsewhere, and a focus on how to treat this type of data will11 KB (1,649 words) - 16:10, 19 July 2018
- ...gle public name is assigned to multiple WBgene ID, Wen has a list of these genes **overlapped or dicistronic genes, ex. mrpl-44 and F02A9.109 KB (1,369 words) - 22:47, 5 August 2020
- *How to use annotation extensions for LEGO model? *Can we build a "worm-version" of FlyMine (existing classes, e.g.)?8 KB (1,161 words) - 16:34, 7 March 2013
- * 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
- *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
- * ?Construct model * miRNA analyses have used completely different platforms than protein-coding genes, so requires a different dataset for each8 KB (1,218 words) - 17:46, 2 April 2014
- 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
- * Karen will need to become part time at WormBase (needs to be more than half time on SBIR) * Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements10 KB (1,527 words) - 15:32, 6 April 2017
- ...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
- <pre>New release of WormBase WS112, Wormpep112 and Wormrna112 Fri Oct 17 18:38:57 BST 2003 vii) confirmed_genes.WS112.gz - DNA sequences of all genes confirmed by EST &/or cDNA6 KB (735 words) - 11:17, 21 December 2011
- **Reasonably satisfied with coverage of human disease genes **Performs similar to WormBase7 KB (1,158 words) - 17:20, 3 May 2012
- 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
- **Worm Phenotype ontology; attempt applying to other species? Some has been done a ***Benefit of curating phenotypes in other species? Particularly useful for genes not in C. elegans, for example12 KB (1,878 words) - 15:55, 6 September 2012
- * First draft up on WormBase development site === Expr_pattern model change ===8 KB (1,289 words) - 18:11, 10 November 2016
- * 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 widget5 KB (776 words) - 16:50, 7 January 2016
- 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==7 KB (1,249 words) - 17:23, 7 January 2016
- 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
- ** 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 species11 KB (1,714 words) - 11:04, 27 July 2015
- * Topics commonly studied in C. elegans due to its advantages as a model system **Essential genes10 KB (1,279 words) - 18:20, 18 October 2013
- 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
- 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
- === 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
- 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
- * Want to have common interface but two instances (yeast & worm) * Worm data in SPELL may be more complicated than the yeast data (different specie8 KB (1,189 words) - 14:10, 5 July 2018
- 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
- Worm Processes Worm Biology20 KB (3,088 words) - 19:17, 13 August 2020
- ...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 ...ation on editors of paper objects, mostly books. The current ACeDB ?Paper model dumps Editors as ?Text, but there is not a separate ?Editor class like ther25 KB (3,238 words) - 16:42, 8 November 2019
- * Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340) * Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)14 KB (2,226 words) - 15:31, 7 June 2018
- Transgene Model *Kimberly working on Physical Interaction model7 KB (1,103 words) - 18:28, 5 May 2011
- ** Michael Paulini is adding Species information for the WBGene IDs in the genes.ace file ** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/8 KB (1,147 words) - 15:33, 7 May 2015
- 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
- * 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 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
- 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
- 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 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
- *Paper .ACE file: Would include bibliographic info, journals, authors, genes associated from abstract or added manually ...l formal release; weird things about diff; new reference associations with genes; a lot of duplications?13 KB (2,097 words) - 22:48, 7 April 2011
- [[WormBase-Caltech_Weekly_Calls_January_2022|January]] [[WormBase-Caltech_Weekly_Calls_February_2022|February]]10 KB (1,547 words) - 21:31, 2 January 2024
- * Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser) * Problems with handling inferred expression of genes in cells10 KB (1,474 words) - 15:54, 30 April 2014
- ...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
- .../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
- 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
- * Who from WormBase will go? * Working out how inferred annotations propagate from Noctua/LEGO model to GAF9 KB (1,377 words) - 16:44, 2 February 2017
- ...a that express dsRNA from a plasmid, and transgenic expression (within the worm) of dsRNA. For efficient and specific knockdown of gene expression, the dsR ...of RNAi curation is to associate RNAi-mediated phenotypes with the target genes knocked down in RNAi experiments, as found in the literature pertaining to29 KB (4,152 words) - 20:29, 30 July 2019
- ...03). Finally, there are an increasing number of functional annotations for genes, provided both in free text and as Gene Ontology terms (Harris et al., 2004 ...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
- ...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 An important point here is that RNAi target genes for an RNAi experiment are not submitted directly using the name of the tar47 KB (7,989 words) - 23:40, 1 September 2015
- ===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
- ...l traits such as gene expression patterns and neuronal connectivity. Also, WormBase contains sequence and gene structures of C. briggsae and C. remanei, two cl ...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
- http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?root=ensembl&view=log Before dumping the papers file, double-check the 'Find Dead Genes' list on the paper editor and make any necessary updates.47 KB (6,852 words) - 04:27, 8 December 2020
- == Model changes for WS244 == * This cycle we see 5 model changes in 4 classes:235 KB (23,325 words) - 10:33, 3 July 2014
- ...emical and drug entities that have been shown to effect the biology of the worm. We provide links to other databases that deal with these molecule entitie ==Model==50 KB (6,966 words) - 19:15, 13 August 2020
- ==Picture Data Model== ...ta from the literature and individual laboratories and display them in the WormBase gene expression page.120 KB (19,719 words) - 16:44, 20 October 2023
- [[http://www.wormbase.org/wiki/index.php?title=How_to_FirstPass&action=submit back]] ...753959 ||Check mPals-1 versus worm genomic DNA, and compare to C01B7.4 vs. worm genome: no grossly obvious discrepancies. ||2/2/02 21:0140 KB (4,083 words) - 23:02, 13 August 2010
- Current model (WS280) ...CDS ?CDS XREF Expr_pattern // for coding genes104 KB (15,303 words) - 19:39, 11 May 2023
