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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
