SGD Newsletter, Spring 2025 - Revision history

Stacia at 20:27, 30 April 2025

2025-04-30T20:27:25Z

Suzia: /* Alliance of Genome Resources - Latest Release 8.10.0 */

2025-04-24T20:55:19Z

‎Alliance of Genome Resources - Latest Release 8.10.0

Suzia: /* Pathway Annotations Now Available as GO Annotations */

2025-04-24T19:47:51Z

‎Pathway Annotations Now Available as GO Annotations

Suzia: /* Alliance of Genome Resources - Latest Release 8.0.0 */

2025-04-24T19:44:47Z

‎Alliance of Genome Resources - Latest Release 8.0.0

Suzia at 17:29, 24 April 2025

2025-04-24T17:29:37Z

Suzia: Suzia moved page SGD Newsletter, Summer 2025 to SGD Newsletter, Spring 2025: newsletter was completed early

2025-04-24T17:22:03Z

Suzia moved page SGD Newsletter, Summer 2025 to SGD Newsletter, Spring 2025: newsletter was completed early

Stacia: /* Alliance of Genome Resources - Latest Release 8.0.0 */

2025-04-24T16:35:16Z

‎Alliance of Genome Resources - Latest Release 8.0.0

Stacia: /* microPublications - Latest Yeast Papers */

2025-04-24T16:28:43Z

‎microPublications - Latest Yeast Papers

Stacia: /* New Yeast Phenome Links in Phenotype Resources */

2025-04-24T16:27:21Z

‎New Yeast Phenome Links in Phenotype Resources

Stacia: /* New Yeast Phenome Links in Phenotype Resources */

2025-04-24T16:24:26Z

‎New Yeast Phenome Links in Phenotype Resources

@@ Line 1: / Line 1: @@
 [[Category: Newsletter]]
-'''About this newsletter:''' <br> This is the Spring 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2025 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].
+'''About this newsletter:''' <br> This is the Spring 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.
 ==Give a Gift / Support SGD: Credit Cards Now Accepted==

@@ Line 73: / Line 73: @@
 All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].
-==Alliance of Genome Resources - Latest Release 8.10.0==
+==Alliance of Genome Resources - Latest Release 8.1.0==
 [[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]

@@ Line 30: / Line 30: @@
 ==Pathway Annotations Now Available as GO Annotations==
-[[File:figure1GENETICS2025.jpg|thumb|left|upright=.75]]YeastPathways, the database of metabolic pathways and enzymes in the budding yeast ''Saccharomyces cerevisiae'', is manually curated and maintained by the biocuration team at SGD.
+[[File:figure1GENETICS2025.jpg|thumb|left|upright=.75]][https://pathway.yeastgenome.org/ YeastPathways], the database of metabolic pathways and enzymes in the budding yeast ''Saccharomyces cerevisiae'', is manually curated and maintained by the biocuration team at SGD.
 This resource is jam-packed with information, but was somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Initially, we added a new section with pathways links on the relevant gene pages (ex. [https://yeastgenome.org/locus/S000005762#pathway DFR1]). Additionally, we made the pathways available in SGD Search. Now, we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. [https://yeastgenome.org/locus/S000005762/go#comp DFR1]).

@@ Line 73: / Line 73: @@
 All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].
-==Alliance of Genome Resources - Latest Release 8.0.0==
+==Alliance of Genome Resources - Latest Release 8.10.0==
 [[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
-The 8.0.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
+The 8.1.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
-Pathway Viewer Update:
+Recent changes in 8.0.0 and 8.1.0 include:
 * Redesign of the legend corrects issues with casual relationship representation; interface visuals have been refined; all defined causal relationships are now depicted using standardized glyphs with a matching color legend.

@@ Line 1: / Line 1: @@
 [[Category: Newsletter]]
-'''About this newsletter:''' <br> This is the Summer 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2025 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].
+'''About this newsletter:''' <br> This is the Spring 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Spring_2025 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].
 ==Give a Gift / Support SGD: Credit Cards Now Accepted==

← Older revision	Revision as of 17:22, 24 April 2025
(No difference)

← Older revision		Revision as of 16:35, 24 April 2025
Line 83:		Line 83:

	There is now an Event Calendar with the schedule of upcoming Alliance office hours and webinars: https://www.alliancegenome.org/event-calendar		There is now an Event Calendar with the schedule of upcoming Alliance office hours and webinars: https://www.alliancegenome.org/event-calendar
		+
		+	* View the video of the latest Alliance of Genome Resources webinar:
		+	**[https://www.youtube.com/watch?v=iaOE8-kbxqo How AI informs literature curation at the Alliance]
		+	**Presented on April 17, 2025 by Kimberly Van Auken and Valerio Arnaboldi of WormBase, and Chris Tabone of FlyBase.

	==Upcoming Conferences & Courses==		==Upcoming Conferences & Courses==

@@ Line 55: / Line 55: @@
 Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]:
 *[https://www.yeastgenome.org/reference/S100000262 Andrade Latino A, Biggins S (2025)] Analysis of a cancer-associated mutation in the budding yeast Nuf2 kinetochore protein. MicroPubl Biol 2025
-*[https://www.yeastgenome.org/reference/S100000150 Thota K, Fredette-Roman JD, Sharp NP (2025)] Yeast mutation rates in alternative carbon sources reflect the influence of reactive oxygen species. MicroPubl Biol 2025
+*[https://www.yeastgenome.org/reference/S100000243 Butcher C, VanderVen K, Li J (2025)] Proteasome condensates repeatedly "contact and release" at the nuclear periphery during dissolution. MicroPubl Biol 2025
-*[https://www.yeastgenome.org/reference/S100000243 Butcher C, VanderVen K, Li J (2025)] Proteasome condensates repeatedly "contact and release" at the nuclear periphery during dissolution. MicroPubl Biol 2025
+*[https://www.yeastgenome.org/reference/S100000186 Eftimie A, Meyer D (2025)] Transcription Regulatory Protein ''SIN3'' (YOL004W) Influences Mutation Rates in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
 *[https://www.yeastgenome.org/reference/S100000338 James M, Klain GK, Brito SO, Trejo L, Okello TMA, Segarra VA (2025)] Autophagy-deficient budding yeast cells are sensitive to freeze-thaw stress. MicroPubl Biol 2025
-*[https://www.yeastgenome.org/reference/S100000186 Eftimie A, Meyer D (2025)] Transcription Regulatory Protein ''SIN3'' (YOL004W) Influences Mutation Rates in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025
+*[https://www.yeastgenome.org/reference/S000378976 Law S, et al. (2024)] The Role of hBRCA2 in the Repair of Spontaneous and UV DNA Damage in Saccharomyces cerevisiae. MicroPubl Biol 2024

@@ Line 43: / Line 43: @@
 The [https://www.yeastphenome.org/ Yeast Phenome] is a collaborative project from the Baryshnikova lab at Calico Life Sciences to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast ''Saccharomyces cerevisiae''.
-The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection. Locus-specific links to the Yeast Phenome are now available in the Resources section of the Phenotype tab and will take you directly to the corresponding page of the Yeast Phenome data library. Try it now: the SGD phenotype page for [https://yeastgenome.org/locus/S000001171/phenotype#resources ARP1], and the linked [https://www.yeastphenome.org/genes/1096/ ARP1] page at Yeast Phenome.
+The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection.
 ==microPublications - Latest Yeast Papers==

@@ Line 41: / Line 41: @@
 [[File:calico_life_sciences_llc_logo.jpg|link=https://www.calicolabs.com/|thumb|left|upright=.4]]
-The [https://www.yeastphenome.org/ Yeast Phenome] is a collaborative project from the Baryshnikova lab at Calico Life Sciences to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast Saccharomyces cerevisiae.
+The [https://www.yeastphenome.org/ Yeast Phenome] is a collaborative project from the Baryshnikova lab at Calico Life Sciences to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast ''Saccharomyces cerevisiae''.
 The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection. Locus-specific links to the Yeast Phenome are now available in the Resources section of the Phenotype tab and will take you directly to the corresponding page of the Yeast Phenome data library. Try it now: the SGD phenotype page for [https://yeastgenome.org/locus/S000001171/phenotype#resources ARP1], and the linked [https://www.yeastphenome.org/genes/1096/ ARP1] page at Yeast Phenome.