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- ==C. elegans as a model system to study disease and disease genes== [[C. elegans models for human disease in the literature]]5 KB (782 words) - 20:56, 8 January 2020
- = Disease = == Disease search ==4 KB (583 words) - 20:22, 29 July 2011
- == 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
- = 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 ==3 KB (275 words) - 01:07, 6 February 2014
- ...1,000 request emails for community submissions of phenotypes on October 18 and October 20 * Todd working on a spell.wormbase.org site for doing worm SPELL analyses6 KB (906 words) - 15:34, 6 December 2018
- === * Transposon gene reactivation - Paul === ==== Poor nomenclature in ?Gene history and Event ====8 KB (1,073 words) - 15:31, 14 December 2012
- =WormBase Curated Data Types and Curation Methods= ...ally updated as both data types curated, and curation methods used, change and improve.''9 KB (1,174 words) - 18:30, 29 August 2012
- ===Ontology Annotator for disease data=== ...ptions have been removed from the concise descriptions OA and moved to the disease OA.14 KB (2,085 words) - 20:27, 7 July 2022
- * Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not * There's difficulty in reconciling small and large datasets (or different data types)9 KB (1,490 words) - 15:35, 6 October 2016
- ==New DAF specs as specified by the AGR Disease Working Group== *These specifications have been discussed and specified by the Disease Working Group of the AGR10 KB (1,599 words) - 18:53, 24 January 2019
- *BioGRID, Gene Orienteer, Interolog database, etc. *Gene Orienteer5 KB (847 words) - 17:49, 1 March 2012
- ''This is a running list of proposed features at WormBase'' == New displays, analysis, and data integration ==6 KB (842 words) - 17:01, 21 October 2011
- === WormBase Ontology Browser (WOBr) for WS244 release === * User interface: would be good if curators could have a look and review again6 KB (801 words) - 17:29, 2 July 2014
- *Community annotation form needs to be very simple (e.g. gene name and empty box only) *What are they using for anatomy annotation? they use standard Anatomy Ontology (Daniela double checked with Mihail)4 KB (650 words) - 17:08, 1 September 2011
- * ?Construct model === ?Construct model ===8 KB (1,218 words) - 17:46, 2 April 2014
- * Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate) * Paul's lab will do marathon bibs to show lab affiliation and graphical abstract8 KB (1,121 words) - 14:01, 15 July 2019
- * Collecting model/pathway diagrams from papers and reviews: should we make ?Picture objects for these? ** Do we want to display these published diagrams on ?Paper pages and/or ?Topic pages6 KB (974 words) - 17:28, 3 September 2014
- * Chris and Mary Ann will be in touch with individuals about section writing ...hese questions highlight a need to revisit the pharyngeal phenotype branch and clarify how we should be focused on annotating these reported annotations.7 KB (1,073 words) - 16:26, 2 March 2017
- 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
- * Ranjana working with Juancarlos to run and update automated descriptions pipeline * First draft up on WormBase development site8 KB (1,289 words) - 18:11, 10 November 2016
- === Gene descriptions === ...out poll if you are interested in attending; have responses from Kimberly and Gary S.9 KB (1,364 words) - 15:39, 7 February 2019
- * Current projects and report the steady state ...an) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene6 KB (912 words) - 01:40, 15 September 2017
- * Wen will create ticket to create wormbase.org URL * Wen, Chris, and Juancarlos have been working on updating older timestamps for OA entries in8 KB (1,224 words) - 15:34, 21 July 2016
- ===Dates and Location=== * Monday 6th October: whole-group advisory board meeting (talks and discussion), EBI3 KB (438 words) - 07:19, 6 October 2014
- ='''WormBase Gene Ontology Progress Report, December 2011'''= Developer, WormBase, Caltech, Pasadena, CA.13 KB (1,830 words) - 16:40, 13 December 2012
- * Michael and Valerio were awarded AWS credits, more than they can use === Automated gene descriptions ===5 KB (670 words) - 15:31, 3 June 2021
- *May take longer than previously expected to get up and running *Yuling should contact FlyBase to make sure they're OK, once he has WormBase SVM working7 KB (1,064 words) - 19:12, 3 November 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
- * There are papers in the WormBase collection that are used as paper evidence for some concise descriptions * Many of these were coming up in the disease paper pipeline6 KB (823 words) - 19:38, 2 January 2014
- === WormBase Ontology Browser (WOBr) === ...erver for the information the browser queries: gene ontology associations, gene association files13 KB (1,983 words) - 16:40, 7 November 2013
- = 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
- * Juancarlos and Raymond looking for feedback; let them know ...leMine is Caltech hosted so we'd need to look at Tazendra logs to see who (and how many people) are using the tool (cannot rule out bots etc.)6 KB (911 words) - 17:13, 6 June 2019
- * 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
- === 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
- *WormBase - Bitbucket, GitHub (can commit code) *Is WormBase interested connecting to it?7 KB (1,117 words) - 16:39, 4 August 2011
- * Apologies from Mary Ann - in Strasboug. Might try and Skype in. - Mary Ann joined in at the end of the call. ...Karen, others are welcome. Visit the construct model requests [http://wiki.wormbase.org/index.php/WormBase_Model:Construct here]10 KB (1,583 words) - 18:16, 5 February 2014
- * Life_stage and Anatomy_term * Couples (or attempts to) time-and-space (life_stage-and-anatomy) annotation of expression pattern6 KB (857 words) - 16:01, 2 October 2014
- * Would be good to meet with individual labs and lab members to discuss WormBase * Will probably decline this offer and wait until a longer talk next year11 KB (1,664 words) - 16:29, 7 December 2017
- ...e are automated conversion systems being established to convert ACEDB data and models into Datomic * The Datomic data models and querying language may take some time to get used to5 KB (776 words) - 16:50, 7 January 2016
- === Disease variants === ...to link elegans gene variations and phenotypes to homologous human disease gene variations. This is separate from any automated pipeline that can be set up8 KB (1,305 words) - 23:24, 3 June 2015
- *Focus on: Gene function, transcriptional networks, pathways *Not caught up on RNAi and allele curation by end of this term6 KB (944 words) - 16:25, 1 November 2012
- * Citace upload deadline will be 6pm Monday, November 25th (added to WormBase calendar) * Ranjana is still waiting on finalization of the Disease paper flagging pipeline10 KB (1,664 words) - 17:02, 4 December 2013
- * Will we be able to automate the process and eventually port to WikiPathways or other pathway visualizer? ...ic curation: a single (or pair of) curator(s) focusing on pulling together and drawing a pathway for a topic8 KB (1,234 words) - 12:36, 4 June 2014
- * Can someone send Paul the latest AFP form location and documentation * Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?11 KB (1,676 words) - 15:28, 2 May 2019
- *Dedicated time during release cycle to fix bugs and address GitHub issues *JD Wong started at WormBase this week; will focus on building WormBase instance of Intermine7 KB (1,123 words) - 16:39, 6 December 2012
- Process and Pathways Overview Pathways and Processes20 KB (3,088 words) - 19:17, 13 August 2020
- * Can use outreach@wormbase.org for consistency * Todd and Chris have email credentials9 KB (1,366 words) - 15:19, 6 September 2018
- ...leles with multiple lesions (one name, many mutations), need to be curated and mapped * Ontology term enrichment analysis, using ontologies other than gene ontology10 KB (1,464 words) - 17:09, 13 August 2015
- = Agenda and Minutes = Q1: What new data types (and data) are coming soon?11 KB (1,649 words) - 16:10, 19 July 2018
- *Learning an ontology may be difficult, but she can stick to familiar material Ranjana - Preplanning WormBase side meetings at IWM?9 KB (1,302 words) - 16:38, 2 June 2011
- *Complex gene information will still be best handled manually *''Brugia malayi'' good starting point; Also, ''Pristionchus'' and ''C. briggsae''9 KB (1,339 words) - 19:02, 31 January 2013
- * Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser) * As one-offs, Raymond can take newly generated GAFs from curators and process for testing.10 KB (1,474 words) - 15:54, 30 April 2014
- **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
- * 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
- New release of WormBase WS288 ...as 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
- * Kimberly and Wen reached out to organizers about WB presentation ** 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
- *Curators can now edit links and add custom widgets ...a standards, how to educate users of database materials and how to use it (and think critically)7 KB (1,158 words) - 17:20, 3 May 2012
- * Now with more papers for positive and negative training set, shifting to SVM identification * Karen will need to become part time at WormBase (needs to be more than half time on SBIR)10 KB (1,527 words) - 15:32, 6 April 2017
- 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
- === Strain data import to AGR for disease === * Will need to think about how genotypes are built and stored at other MODs12 KB (1,930 words) - 17:12, 1 February 2018
- *Trying to display site-of-action data on relevant gene pages ...announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it10 KB (1,553 words) - 18:04, 7 February 2013
- **Worm Phenotype ontology; attempt applying to other species? Some has been done already (e.g. C. bri **Anatomy ontology12 KB (1,878 words) - 15:55, 6 September 2012
- * Considering removing general terms in an ontology when more specific terms exist * Curators will send group Skype handle and requested time to talk14 KB (2,226 words) - 15:31, 7 June 2018
- Tested by todd, gb1 and gb2 compliant, tested on freeze1 -rwxrwxr-x 1 todd wormbase 20053 Jul 6 14:06 cell.cgi16 KB (1,576 words) - 17:44, 16 August 2010
- *Need to coordinate with Juancarlos and Todd *Will need to be vigilant about checking for errors and inconsistencies before sending to Todd to put up on website13 KB (2,097 words) - 22:48, 7 April 2011
- * Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room ...ampus, you need to take your temperature and assess your symptoms (if any) and submit info on form8 KB (1,228 words) - 20:57, 14 July 2020
- 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 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
- ...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
- We curate all integrated (Is, In, Si, Ti), and select extrachromosomal (Ex) transgenes. * method of integration, and to what LG it was mapped, if known29 KB (4,575 words) - 16:23, 3 March 2022
- ===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
- **Documenting elements of WormBase workflow to ease transition for new staff and keep track of changes made **Added diagram and explanation for Tools data loading29 KB (4,254 words) - 20:25, 27 April 2012
- http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?root=ensembl&view=log ...e 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
- ...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
- ...<i>C. elegans</i> has the version names: <b>WBcel215</b> (an old version) and <b>WBcel235</b> (the current version). ...y assembled, being left as various sizes of contig. Only <i>C. elegans</i> and <i>C. briggsae</i> have been assembled into chromosomes.56 KB (9,520 words) - 11:51, 21 October 2015
- ...<i>C. elegans</i> has the version names: <b>WBcel215</b> (an old version) and <b>WBcel235</b> (the current version). ...y assembled, being left as various sizes of contig. Only <i>C. elegans</i> and <i>C. briggsae</i> have been assembled into chromosomes.56 KB (9,514 words) - 09:48, 23 October 2015
- ...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
