Service status: Enrichment, ontology browser and graph display tools are now working at WormBase
Enrichment, ontology browser and graph display tools are all working again. Thank-you for your patience. (Source: WormBase)
Source: WormBase - July 23, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news service status Source Type: news
Enrichment, ontology browser and graph display tools temporarily down at WormBase
A disk failure on one of our servers has brought the gene set enrichment analysis tool (TEA), the Ontology Browser (WoBr) and the graph display tool on the gene page down. We are working to restore these tools as soon as possible and apologize for any inconvenience caused. We will let the community know as soon as these are restored. (Source: WormBase)
Source: WormBase - July 19, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news service status service outtage Source Type: news
Promoting equity in the C. elegans community
From the WormBoard:Some of you have received this message already via the “LabHeads” or other mailing lists. We are now aware of many lab heads who are not on the list. If you are a PI and did not receive this message from the LabHeads list on July 9, please request to join the LabHeads Google Group.
This message is meant to be shared with the entire community. Please read and forward this message to everyone in your lab. If you have comments about the content of the message or the survey, please email Jane Hubbard.
The last month has highlighted the undeniable history of violence and inequity toward the Blac...
Source: WormBase - July 18, 2020 Category: Genetics & Stem Cells Authors: The WormBoard Tags: news wormboard Source Type: news
New Chapter in WormBook, GENETICS
Check out the new chapter in WormBook, GENETICS: mRNA Editing, Processing and Quality Control in Caenorhabditis elegans by Joshua Arribere, Hidehito Kuroyanagi and Heather Hundley. (Source: WormBase)
Source: WormBase - July 8, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news
WormBase updates in WS277 – new protein schematic images!
We have released the 277th version of WormBase! As always, for a detailed report please look at the WS277 release notes.
New features: We’ve updated the protein schematic image in the homology widget on protein pages (see, for example, the UNC-2, isoform a page.) This image displays protein domains and exons mapped to amino acid coordinates, making it easy to see which regions of a transcript correspond to specific features. Driven by JBrowse — the genome browser at WormBase — users can click through the image to an interactive view in amino acid coordinates. From that familiar interface, one can scroll, export...
Source: WormBase - July 3, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new datasets new features news release notes data release new release WS277 Source Type: news
Alliance of Genome Resources 3.1 released
The Alliance of Genome Resources is a portal for data related to six of the major model organisms and human data. The Alliance has been updated to the 3.0.1 release and contains new features and new data. Key new features include a refined home page and an allele page that includes transgenic alleles and shows variant consequences for transcripts. The Alliance also provides a Java API for access to the data. For a complete list of 3.0.1 features please see the release notes. (Source: WormBase)
Source: WormBase - July 1, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news release notes Alliance of Genome Resources Source Type: news
WormBase updated to WS276
A new release of WormBase, WS276 is live on the website. Please see the release notes which contain complete information about this release.
Note that C. elegans gene descriptions in the “Overview” section of gene pages have improved orthology statements to human genes. WormBase uses the DIOPT orthology data from the Alliance of Genome Resources and has increased stringency by displaying only those human orthologs that have been determined by three or more methods. This should significantly improve the orthology data in WormBase which is also reflected in the gene descriptions.
Known Issues: the ci...
Source: WormBase - June 19, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes Uncategorized new release WS276 Source Type: news
microPublication Biology is now indexed in PubMed
WormBase is happy to announce that the microPublication Biology journal is now fully listed in PubMed!
To make articles easier to cite and discover, every microPublication now receives a PubMed ID, a PubMed Central ID, and a DOI. If you have published with us in the past, consider updating your citations. Indexing is retroactive for all past articles.
You can see microPublications in PubMed by browsing the full index at
PubMed Central. Or look for microPublications during normal searches at PubMed or PubMed Central.
We look forward to receiving more submissions! (Source: WormBase)
Source: WormBase - June 19, 2020 Category: Genetics & Stem Cells Authors: Todd Harris Tags: news Uncategorized micropublication Source Type: news
Check out Venn diagrams for interaction data in WormBase
WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. Check out the micropublication which describes the Vennter tool. This tool is integrated into the interactions widget on WormBase gene pages and allows the visualization and analyses of interaction data. (Source: WormBase)
Source: WormBase - May 29, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news paper of interest interactions micropublication tools Source Type: news
Textpresso for coronovirus
Announcing the special edition of Textpresso covering coronavirus literature– it contains 31,000 articles from the PMC open access archive. (Source: WormBase)
Source: WormBase - May 15, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news text mining Textpresso Source Type: news
Model Organism research data related to COVID-19 at the Alliance
The Alliance of Genome Resources has been updated to the 3.0.1 release with a new resource for COVID-19 relevant model organism research data. Check it out! (Source: WormBase)
Source: WormBase - May 14, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources Source Type: news
Open Publishing Fest
microPublication will participate in the Open Publishing Fest organized by the Collaborative Knowledge Foundation. We will host four events or ‘tents’ which will focus on different aspects of microPublication and its role in scholarly communication. Mark your calendar for the following events and keep an eye on the festival website for conference channels details!
Tent 1: microPublication: A Welcome Alternative in Scholarly Communication – May 20th, 10am Pacific
Join us for an hour packed of fun to learn how microPublication is shaping the future of scholarly communication! microPublication is a de...
Source: WormBase - May 11, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news meetings Uncategorized micropublication Source Type: news
Coming orthology data changes in WormBase WS276
Many of you have written to us in the past and pointed out some spurious human orthology calls for elegans genes, most of these have been noticed in the gene descriptions that appear in the Overview widget on the gene page. WormBase now uses the DIOPT orthology data from the Alliance of Genome Resources and has increased stringency by displaying only those human orthologs that have been determined by three or more methods. This should significantly improve the orthology data in WormBase which is reflected in the gene descriptions. Note that this change will go live in the WS276 version of WormBase coming soon (late April, ...
Source: WormBase - April 22, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Uncategorized orthologs WS276 Source Type: news
Alliance of Genome Resources updated
The Alliance (alliancegenome.org) 3.0 version released yesterday, has new features and new data related to the use of model organisms in understanding the genetic and genomic basis of human biology, health and disease. Salient features of the 3.0 release include new allele pages with variant and transcript data, new disease models on gene and disease pages, data files available for download, etc. To learn more about the latest features and data, check out the release notes. (Source: WormBase)
Source: WormBase - April 9, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources new release Source Type: news
Still have time on your hands? Submit data via our ‘Submit Data’ page
You can submit various types of data via our data specific forms found here. The ‘Submit Data’ button is also prominently displayed on our menu bar on the home page on the left hand side. Click on this to be taken to the various data submission forms. (Source: WormBase)
Source: WormBase - March 27, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news
