SGD Newsletter, Spring 2021

2021-09-30T15:14:36Z

Mjalexander: /* New Homology Pages */

SGD Newsletter, Spring 2021

2021-09-30T15:14:22Z

Mjalexander: /* New Homology Pages */

[[Category:Newsletter]]
'''About this newsletter:''' 

This is the Spring 2021 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_2021 newsletter] as well as previous newsletters on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

==R64.3 Annotation Update==
SGD curators periodically update the chromosomal annotations of the ''S. cerevisiae'' Reference Genome, which is derived from strain [http://www.yeastgenome.org/strain/S288C/overview S288C].

The R64.3 annotation release, dated 2021-04-21, included various updates and additions:

*7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A]
*5 new ncRNAs: [https://www.yeastgenome.org/locus/S000303802 GAL10-ncRNA], [https://www.yeastgenome.org/locus/S000303803 TBRT/XUT_2F-154], [https://www.yeastgenome.org/locus/S000303809 SUT169], [https://www.yeastgenome.org/locus/S000303814 PHO84 lncRNA], [https://www.yeastgenome.org/locus/S000303815 GAL4 lncRNA]
*2 new uORFs for [https://www.yeastgenome.org/locus/S000003139 ROK1/YGL171W]
*1 new recombination enhancer: [https://www.yeastgenome.org/locus/S000303804 RE]
*1 new LTR: [https://www.yeastgenome.org/locus/S000303805 YELWdelta27]
*3 ORFs with shifted translation starts: [https://www.yeastgenome.org/locus/S000000792 HPA3/YEL066W], [https://www.yeastgenome.org/locus/S000003773 YJR012C], [https://www.yeastgenome.org/locus/S000005204 LTO1/YNL260C]
*1 ORF with shifted translation stop plus new intron: [https://www.yeastgenome.org/locus/S000004755 LDO45/YMR147W]
*Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2]
*New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs]

Various sequence and annotation files are available on SGD's [http://sgd-archive.yeastgenome.org/sequence/S288C_reference/ Downloads] site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the [https://wiki.yeastgenome.org/index.php/Details_of_2021_Reference_Genome_Annotation_Update_R64.3#R64.3_Annotation_update_summary Details of 2021 Reference Genome Annotation Update R64.3] SGD Wiki page.
 

==New Homology Pages==

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

The information displayed on the Homology Pages is divided into several sections:

*Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
*Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
*Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
*External Identifiers: A list of external identifiers for the protein from various database sources.
 
[[File:homology1.png|650px|left|Image: 650 pixels|link=https://www.yeastgenome.org/locus/S000000364]] [[File:homology2.png|750px|Image: 650 pixels|link=https://www.yeastgenome.org/locus/S000000364/homology]]
 

[[File:test2.png|750px|Image: 650 pixels|link=https://www.yeastgenome.org/locus/S000000364/homology]]

==Functional Complementation Data Available on References Pages==
Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the [http://ppod.princeton.edu Princeton Protein Orthology Database] (P-POD).

[[File:functional_comp3.png|600px|center|upright=0.8|link=https://www.yeastgenome.org/reference/S000274440]]
 
==YeastMine Updates and New Templates==
SGD has updated the current [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=all Gene-->UTRs] YeastMine template with newly calculated 5' and 3' UTR sequence/coordinates. Additionally, transcript iso-forms for specific genes from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al., 2013] study can be accessed in YeastMine using the new [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene-->Transcripts] template. Both templates can be found under the "Templates" section of YeastMine under the "Expression" category.
[[File:ym_templates.png|600px|center|upright=0.8|Transcript and UTR YeastMine Templates|link=https://yeastmine.yeastgenome.org/yeastmine/templates.do]]

==Textpresso Central Update==
[[File:textpresso.png|600px|thumb|left|upright=0.8|Textpresso Central homepage|link=https://textpresso.yeastgenome.org/tpc/home]]
[https://textpresso.yeastgenome.org/tpc/home Textpresso] has recently been updated with a new system, adopting an overhauled user interface and introducing several new features including:
*Search results shown in the context of the full text
*Custom corpus creation
*Customizable annotation interface
*Search terms are highlighted in full-text view

Textpresso Central can also be accessed by clicking on "Full-text Search" under the Literature pull-down menu on the home page of SGD. More information about the changes and types of papers stored in Textpresso can be found in their [https://textpresso.yeastgenome.org/tpc/aboutus About Us] help section or (from [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2103-8 Müller et al., 2018]).

 

==Number of Curated Alleles Continues to Grow==
SGD now has approximately '''13,000''' [https://www.yeastgenome.org/search?q=&category=allele alleles] that are either fully or partially curated. To navigate to an allele page, use the search bar to find a specific allele or enter a gene name and select an allele from the autocomplete list. Additionally, these pages can be accessed by clicking on the allele name in a gene’s Phenotype Annotation table. SGD Curators continue to add new alleles or update existing ones as new information becomes available.

You can generate a list of all alleles in our database or find alleles for a specific gene using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Alleles&scope=all Genes --> Alleles] template in [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine].
 
[[File:allele_page.png|link=https://www.yeastgenome.org/allele/S000277751|600px|center|upright=.8]]
 

==Alliance of Genome Resources - Disease Associations for model organisms==
Did you know that you can find human disease associations for yeast genes and their orthologs in other key model organisms at the [https://www.alliancegenome.org Alliance of Genome Resources]?

SGD is a founding member of the Alliance of Genome Resources, which was established to facilitate the use of diverse model organisms in understanding the genetic and genomic bases of human biology, health, and disease. [https://www.alliancegenome.org/gene/SGD:S000006344 Gene pages] for [https://www.alliancegenome.org/search?category=gene&species=Saccharomyces%20cerevisiae yeast] and [https://www.alliancegenome.org/search?category=gene other model organisms] at the Alliance include a section for Disease Associations, including those for orthologous genes. Human diseases are represented using the [https://disease-ontology.org Disease Ontology (DO)].

[[File:allianceDiseaseTAZ1.png|600px|center|upright=0.8|link=https://www.alliancegenome.org/gene/SGD:S000006344#disease-associations]]
 

==Fungal Pathogen Genomics Workshop==
[[File:workshop.png|thumb|left|250px|link=https://coursesandconferences.wellcomeconnectingscience.org/event/fungal-pathogen-genomics-virtual-20210510/]]
From May 10th - 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander were instructors for the [https://coursesandconferences.wellcomeconnectingscience.org/event/fungal-pathogen-genomics-virtual-20210510/ Virtual Fungal Pathogen Genomics Workshop] hosted by [https://coursesandconferences.wellcomeconnectingscience.org Wellcome Connecting Science]. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from [https://veupathdb.org/veupathdb/app FungiDB], [https://fungi.ensembl.org/index.html EnsemblFungi], [http://www.candidagenome.org CGD], [https://mycocosm.jgi.doe.gov/mycocosm/home MycoCosm], and [https://genome.jgi.doe.gov/portal/ JGI].

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

2021-05-25T21:34:17Z

Mjalexander:

SGD Newsletter, Spring 2021

2021-05-25T21:33:19Z

Mjalexander:

[[Category:Newsletter]]
'''About this newsletter:''' 

This is the Spring 2021 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 also subscribe to SGD's RSS feed to receive updates on SGD news:
http://www.yeastgenome.org/feed 

==R64.3 Annotation Update==
SGD curators periodically update the chromosomal annotations of the ''S. cerevisiae'' Reference Genome, which is derived from strain [http://www.yeastgenome.org/strain/S288C/overview S288C].

The R64.3 annotation release included various updates and additions:

*7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A]
*5 new ncRNAs: [https://www.yeastgenome.org/locus/S000303802 GAL10-ncRNA], [https://www.yeastgenome.org/locus/S000303803 TBRT/XUT_2F-154], [https://www.yeastgenome.org/locus/S000303809 SUT169], [https://www.yeastgenome.org/locus/S000303814 PHO84 lncRNA], [https://www.yeastgenome.org/locus/S000303815 GAL4 lncRNA]
*2 new uORFs for [https://www.yeastgenome.org/locus/S000003139 ROK1/YGL171W]
*1 new recombination enhancer: [https://www.yeastgenome.org/locus/S000303804 RE]
*1 new LTR: [https://www.yeastgenome.org/locus/S000303805 YELWdelta27]
*3 ORFs with shifted translation starts: [https://www.yeastgenome.org/locus/S000000792 HPA3/YEL066W], [https://www.yeastgenome.org/locus/S000003773 YJR012C], [https://www.yeastgenome.org/locus/S000005204 LTO1/YNL260C]
*1 ORF with shifted translation stop plus new intron: [https://www.yeastgenome.org/locus/S000004755 LDO45/YMR147W]
*Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2]
*New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs]

Various sequence and annotation files are available on SGD's [http://sgd-archive.yeastgenome.org/sequence/S288C_reference/ Downloads] site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the [https://wiki.yeastgenome.org/index.php/Details_of_2021_Reference_Genome_Annotation_Update_R64.3#R64.3_Annotation_update_summary Details of 2021 Reference Genome Annotation Update R64.3] SGD Wiki page.
 
==New Homology Pages==

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

The information displayed on the Homology Pages is divided into several sections:

*Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
*Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
*Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
*External Identifiers: A list of external identifiers for the protein from various database sources.
 
[[File:homology1.png|650px|left|Image: 650 pixels]] [[File:homology2.png|750px|Image: 650 pixels]]
 
==Functional Complementation Data Available on References Pages==
Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the [http://ppod.princeton.edu Princeton Protein Orthology Database] (P-POD).

[[File:functional_comp3.png|600px|center|upright=0.8]]
 
==YeastMine Updates and New Templates==
SGD has updated the current [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=all Gene-->UTRs] YeastMine template with newly calculated 5' and 3' UTR sequence/coordinates. Additionally, transcript iso-forms for specific genes from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] study can be accessed in YeastMine using the new [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene-->Transcript] template. Both templates can be found under the "Templates" section of YeastMine under the "Expression" category.
[[File:ym_templates.png|600px|center|upright=0.8|Transcript and UTR YeastMine Templates]]

==Textpresso Central Update==
[[File:textpresso.png|600px|thumb|left|upright=0.8|Textpresso Central homepage]]
[https://textpresso.yeastgenome.org/tpc/home Textpresso] has recently been updated with a new system, adopting an overhauled user interface and introducing several new features including:
*Search results shown in the context of the full text
*Custom corpus creation
*Customizable annotation interface
*Search terms are highlighted in full-text view

Textpresso Central can also be accessed by clicking on "Full-text Search" under the Literature pull-down menu on the home page of SGD. More information about the changes and types of papers stored in Textpresso can be found in their [https://textpresso.yeastgenome.org/tpc/aboutus About Us] help section or (from [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2103-8 Müller et al]).

 

==Number of Curated Alleles Continues to Grow==
SGD now has approximately '''13,000''' alleles that are either fully or partially curated. To navigate to an allele page, use the search bar to find a specific allele or enter a gene name and select an allele from the autocomplete list. Additionally, these pages can be accessed by clicking on the allele name in a gene’s Phenotype Annotation table. SGD Curators continue to add new alleles or update existing ones as new information becomes available.

You can generate a list of all alleles in our database or find alleles for a specific gene using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Alleles&scope=all Genes --> Alleles] template in [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine].
 
[[File:allele_page.png|link=https://yeastgenome.org/allele/S000277751|600px|center|upright=.8]]
 
==Alliance Item==

==Fungal Pathogen Genomics Workshop==
From May 10th - 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander were instructors for the [https://coursesandconferences.wellcomeconnectingscience.org/event/fungal-pathogen-genomics-virtual-20210510/ Virtual Fungal Pathogen Genomics Workshop] hosted by [https://coursesandconferences.wellcomeconnectingscience.org Wellcome Connecting Science]. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from [https://veupathdb.org/veupathdb/app FungiDB], [https://fungi.ensembl.org/index.html EnsemblFungi], [http://www.candidagenome.org CGD], [https://mycocosm.jgi.doe.gov/mycocosm/home MycoCosm], and [https://genome.jgi.doe.gov/portal/ JGI].

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

[[File:workshop.png]]

SGD Newsletter, Spring 2021

2021-05-25T20:52:46Z

Mjalexander:

[[Category:Newsletter]]
'''About this newsletter:''' 

This is the Spring 2021 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 also subscribe to SGD's RSS feed to receive updates on SGD news:
http://www.yeastgenome.org/feed 

==R64.3 Annotation Update==
SGD curators periodically update the chromosomal annotations of the ''S. cerevisiae'' Reference Genome, which is derived from strain [http://www.yeastgenome.org/strain/S288C/overview S288C].

The R64.3 annotation release included various updates and additions:

*7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A]
*5 new ncRNAs: [https://www.yeastgenome.org/locus/S000303802 GAL10-ncRNA], [https://www.yeastgenome.org/locus/S000303803 TBRT/XUT_2F-154], [https://www.yeastgenome.org/locus/S000303809 SUT169], [https://www.yeastgenome.org/locus/S000303814 PHO84 lncRNA], [https://www.yeastgenome.org/locus/S000303815 GAL4 lncRNA]
*2 new uORFs for [https://www.yeastgenome.org/locus/S000003139 ROK1/YGL171W]
*1 new recombination enhancer: [https://www.yeastgenome.org/locus/S000303804 RE]
*1 new LTR: [https://www.yeastgenome.org/locus/S000303805 YELWdelta27]
*3 ORFs with shifted translation starts: [https://www.yeastgenome.org/locus/S000000792 HPA3/YEL066W], [https://www.yeastgenome.org/locus/S000003773 YJR012C], [https://www.yeastgenome.org/locus/S000005204 LTO1/YNL260C]
*1 ORF with shifted translation stop plus new intron: [https://www.yeastgenome.org/locus/S000004755 LDO45/YMR147W]
*Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2]
*New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs]

Various sequence and annotation files are available on SGD's [http://sgd-archive.yeastgenome.org/sequence/S288C_reference/ Downloads] site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the [https://wiki.yeastgenome.org/index.php/Details_of_2021_Reference_Genome_Annotation_Update_R64.3#R64.3_Annotation_update_summary Details of 2021 Reference Genome Annotation Update R64.3] SGD Wiki page.
 
==New Homology Pages==

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

The information displayed on the Homology Pages is divided into several sections:

*Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
*Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
*Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
*External Identifiers: A list of external identifiers for the protein from various database sources.
 
[[File:homology1.png|650px|left|Image: 650 pixels]] [[File:homology2.png|650px|Image: 650 pixels]]
 
==Functional Complementation Data Available on References Pages==
[[File:functional_comp3.png|800px|left|upright=0.8]]
Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD).

==YeastMine Updates and New Templates==
SGD has updated the current [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=all Gene-->UTRs] YeastMine template with newly calculated 5' and 3' UTR sequence/coordinates. Additionally, transcript iso-forms for specific genes from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] study can be accessed in YeastMine using the new [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene-->Transcript] template. Both templates can be found under the "Templates" section of YeastMine under the "Expression" category.
 
[[File:ym_templates.png|600px|center|upright=0.8|Transcript and UTR YeastMine Templates]]

==Textpresso Central Update==
[[File:textpresso.png|800px|thumb|left|upright=0.8|Textpresso Homepage]]
[https://textpresso.yeastgenome.org/tpc/home Textpresso] has recently been updated with a new system, adopting an overhauled user interface and introducing several new features including:
*Search results shown in the context of the full text
*Custom corpus creation
*Customizable annotation interface
*Search terms are highlighted in full-text view

Textpresso Central can also be accessed by clicking on "Full-text Search" under the Literature pull-down menu on the home page of SGD. More information about the changes and types of papers stored in Textpresso can be found in their [https://textpresso.yeastgenome.org/tpc/aboutus About Us] help section or (from [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2103-8 Müller et al]).

 

==Number of Curated Alleles Continues to Grow==
[[File:allele_page.png|link=https://yeastgenome.org/allele/S000277751|300px|left|upright=.8|The cdc28-13 allele page.]]

SGD now has approximately '''13,000''' alleles that are either fully or partially curated. You can generate a list of all alleles in our database using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Alleles&scope=all Genes --> Alleles] template in [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine], or search for a specific allele in the website search bar.
 
==Alliance Item==

==Fungal Pathogen Genomics Workshop==
From May 10th - 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander were instructors for the [https://coursesandconferences.wellcomeconnectingscience.org/event/fungal-pathogen-genomics-virtual-20210510/ Virtual Fungal Pathogen Genomics Workshop] hosted by [https://coursesandconferences.wellcomeconnectingscience.org Wellcome Connecting Science]. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from [https://veupathdb.org/veupathdb/app FungiDB], [https://fungi.ensembl.org/index.html EnsemblFungi], [http://www.candidagenome.org CGD], [https://mycocosm.jgi.doe.gov/mycocosm/home MycoCosm], and [https://genome.jgi.doe.gov/portal/ JGI].

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

[[File:workshop.png]]

SGD Newsletter, Spring 2021

2021-05-25T20:52:18Z

Mjalexander: /* Textpresso Central Update */

[[Category:Newsletter]]
'''About this newsletter:''' 

This is the Spring 2021 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 also subscribe to SGD's RSS feed to receive updates on SGD news:
http://www.yeastgenome.org/feed 

==R64.3 Annotation Update==
SGD curators periodically update the chromosomal annotations of the ''S. cerevisiae'' Reference Genome, which is derived from strain [http://www.yeastgenome.org/strain/S288C/overview S288C].

The R64.3 annotation release included various updates and additions:

*7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A]
*5 new ncRNAs: [https://www.yeastgenome.org/locus/S000303802 GAL10-ncRNA], [https://www.yeastgenome.org/locus/S000303803 TBRT/XUT_2F-154], [https://www.yeastgenome.org/locus/S000303809 SUT169], [https://www.yeastgenome.org/locus/S000303814 PHO84 lncRNA], [https://www.yeastgenome.org/locus/S000303815 GAL4 lncRNA]
*2 new uORFs for [https://www.yeastgenome.org/locus/S000003139 ROK1/YGL171W]
*1 new recombination enhancer: [https://www.yeastgenome.org/locus/S000303804 RE]
*1 new LTR: [https://www.yeastgenome.org/locus/S000303805 YELWdelta27]
*3 ORFs with shifted translation starts: [https://www.yeastgenome.org/locus/S000000792 HPA3/YEL066W], [https://www.yeastgenome.org/locus/S000003773 YJR012C], [https://www.yeastgenome.org/locus/S000005204 LTO1/YNL260C]
*1 ORF with shifted translation stop plus new intron: [https://www.yeastgenome.org/locus/S000004755 LDO45/YMR147W]
*Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2]
*New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs]

Various sequence and annotation files are available on SGD's [http://sgd-archive.yeastgenome.org/sequence/S288C_reference/ Downloads] site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the [https://wiki.yeastgenome.org/index.php/Details_of_2021_Reference_Genome_Annotation_Update_R64.3#R64.3_Annotation_update_summary Details of 2021 Reference Genome Annotation Update R64.3] SGD Wiki page.
 
==New Homology Pages==

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

The information displayed on the Homology Pages is divided into several sections:

*Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
*Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
*Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
*External Identifiers: A list of external identifiers for the protein from various database sources.
 
[[File:homology1.png|650px|left|Image: 650 pixels]] [[File:homology2.png|650px|Image: 650 pixels]]
 
==Functional Complementation Data Available on References Pages==
[[File:functional_comp3.png|800px|left|upright=0.8]]
Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD).

==YeastMine Updates and New Templates==
SGD has updated the current [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=all Gene-->UTRs] YeastMine template with newly calculated 5' and 3' UTR sequence/coordinates. Additionally, transcript iso-forms for specific genes from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] study can be accessed in YeastMine using the new [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene-->Transcript] template. Both templates can be found under the "Templates" section of YeastMine under the "Expression" category.
 
[[File:ym_templates.png|600px|center|upright=0.8|Transcript and UTR YeastMine Templates]]

==Textpresso Central Update==
[[File:textpresso.png|800px|thumb|center|upright=0.8|Textpresso Homepage]]
[https://textpresso.yeastgenome.org/tpc/home Textpresso] has recently been updated with a new system, adopting an overhauled user interface and introducing several new features including:
*Search results shown in the context of the full text
*Custom corpus creation
*Customizable annotation interface
*Search terms are highlighted in full-text view

Textpresso Central can also be accessed by clicking on "Full-text Search" under the Literature pull-down menu on the home page of SGD. More information about the changes and types of papers stored in Textpresso can be found in their [https://textpresso.yeastgenome.org/tpc/aboutus About Us] help section or (from [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2103-8 Müller et al]).

 

==Number of Curated Alleles Continues to Grow==
[[File:allele_page.png|link=https://yeastgenome.org/allele/S000277751|300px|left|upright=.8|The cdc28-13 allele page.]]

SGD now has approximately '''13,000''' alleles that are either fully or partially curated. You can generate a list of all alleles in our database using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Alleles&scope=all Genes --> Alleles] template in [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine], or search for a specific allele in the website search bar.
 
==Alliance Item==

==Fungal Pathogen Genomics Workshop==
From May 10th - 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander were instructors for the [https://coursesandconferences.wellcomeconnectingscience.org/event/fungal-pathogen-genomics-virtual-20210510/ Virtual Fungal Pathogen Genomics Workshop] hosted by [https://coursesandconferences.wellcomeconnectingscience.org Wellcome Connecting Science]. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from [https://veupathdb.org/veupathdb/app FungiDB], [https://fungi.ensembl.org/index.html EnsemblFungi], [http://www.candidagenome.org CGD], [https://mycocosm.jgi.doe.gov/mycocosm/home MycoCosm], and [https://genome.jgi.doe.gov/portal/ JGI].

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

[[File:workshop.png]]

2021-05-25T17:36:04Z

Mjalexander:

[[Category:Newsletter]]
'''About this newsletter:''' 

This is the Spring 2021 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 also subscribe to SGD's RSS feed to receive updates on SGD news:
http://www.yeastgenome.org/feed 

==R64.3 Annotation Update==
SGD curators periodically update the chromosomal annotations of the ''S. cerevisiae'' Reference Genome, which is derived from strain [http://www.yeastgenome.org/strain/S288C/overview S288C].

The R64.3 annotation release included various updates and additions:

*7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A]
*5 new ncRNAs: [https://www.yeastgenome.org/locus/S000303802 GAL10-ncRNA], [https://www.yeastgenome.org/locus/S000303803 TBRT/XUT_2F-154], [https://www.yeastgenome.org/locus/S000303809 SUT169], [https://www.yeastgenome.org/locus/S000303814 PHO84 lncRNA], [https://www.yeastgenome.org/locus/S000303815 GAL4 lncRNA]
*2 new uORFs for [https://www.yeastgenome.org/locus/S000003139 ROK1/YGL171W]
*1 new recombination enhancer: [https://www.yeastgenome.org/locus/S000303804 RE]
*1 new LTR: [https://www.yeastgenome.org/locus/S000303805 YELWdelta27]
*3 ORFs with shifted translation starts: [https://www.yeastgenome.org/locus/S000000792 HPA3/YEL066W], [https://www.yeastgenome.org/locus/S000003773 YJR012C], [https://www.yeastgenome.org/locus/S000005204 LTO1/YNL260C]
*1 ORF with shifted translation stop plus new intron: [https://www.yeastgenome.org/locus/S000004755 LDO45/YMR147W]
*Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2]
*New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs]

Various sequence and annotation files are available on SGD's [http://sgd-archive.yeastgenome.org/sequence/S288C_reference/ Downloads] site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the [https://wiki.yeastgenome.org/index.php/Details_of_2021_Reference_Genome_Annotation_Update_R64.3#R64.3_Annotation_update_summary Details of 2021 Reference Genome Annotation Update R64.3] SGD Wiki page.

==Alliance Item==

==YeastMine Updates and New Templates==
[[File:ym_templates.png|400px|left|thumb|upright=0.8|Transcript and UTR YeastMine Templates]]
 SGD has updated the current [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=all Gene-->UTRs] YeastMine template with newly calculated 5' and 3' UTR sequence/coordinates. Additionally, Transcript iso-forms for specific genes from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] study can be accessed in YeastMine using the new [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Transcript&scope=all Gene-->Transcript] template. Both templates can be found under the "Templates" section of YeastMine under the "Expression" category.

==Textpresso Central Update==
[[File:textpresso.png|600px|left|upright=0.8|Textpresso Homepage]]
[https://textpresso.yeastgenome.org/tpc/home Textpresso] has recently been updated with a new system, adopting an overhauled user interface and introducing several new features. The updated Textpresso still allows users to search the corpus of texts with specialized queries using keywords and related categories, but now search results are shown in the context of the full text. More information about the changes and types of papers stored in Textpresso can be found in their [https://textpresso.yeastgenome.org/tpc/aboutus About Us] help section.

==Fungal Pathogen Genomics Workshop==
From May 10th - 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander attended the Virtual Fungal Pathogen Genomics Workshop. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from other fungal databases at FungiDB, EnsemblFungi, PomBase, CGD, MycoCosm, and JGI.

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

[[File:workshop.png]]

==New Homology Pages==

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

The information displayed on the Homology Pages is divided into several sections:

*Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
*Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
*Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
*External Identifiers: A list of external identifiers for the protein from various database sources.

[[File:homology1.png|650px|left|Image: 650 pixels]] [[File:homology2.png|650px|Image: 650 pixels]]

==Functional Complementation Data Available on References Pages==
[[File:functional_comp.png|500px|left|upright=0.8]]
Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD).

==Number of Curated Alleles Continues to Grow==
[[File:allele_page.png|link=https://yeastgenome.org/allele/S000277751|300px|thumb|left|upright=.8|The cdc28-13 allele page.]]

SGD now has approximately '''13,000''' alleles that are either fully or partially curated. You can generate a list of all alleles in our database using the [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Alleles&scope=all Genes --> Alleles] template in [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine], or search for a specific allele in the website search bar.