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Article ; Online: PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability.

Rutherford, Kim M / Lera-Ramírez, Manuel / Wood, Valerie

2024 Volume 227, Issue 1

Abstract: PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. ... ...

Abstract	PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community.
MeSH term(s)	Schizosaccharomyces/genetics ; Databases, Genetic ; Genome, Fungal
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyae007
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: JaponicusDB: rapid deployment of a model organism database for an emerging model species.

Rutherford, Kim M / Harris, Midori A / Oliferenko, Snezhana / Wood, Valerie

Genetics

2022 Volume 220, Issue 4

Abstract: The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well- ... ...

Abstract	The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.
MeSH term(s)	Databases, Factual ; Schizosaccharomyces/genetics
Language	English
Publishing date	2022-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyab223
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Fission stories: using PomBase to understand Schizosaccharomyces pombe biology.

Harris, Midori A / Rutherford, Kim M / Hayles, Jacqueline / Lock, Antonia / Bähler, Jürg / Oliver, Stephen G / Mata, Juan / Wood, Valerie

Genetics

2022 Volume 220, Issue 4

Abstract: PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into ... ...

Abstract	PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualization, PomBase also drives innovation in the MOD community.
MeSH term(s)	Biology ; Databases, Factual ; Schizosaccharomyces/genetics
Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyab222
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Molecular structure of sauropsid β-keratins from tuatara (Sphenodon punctatus).

Parry, David A D / Fraser, R D Bruce / Alibardi, Lorenzo / Rutherford, Kim M / Gemmell, Neil

Journal of structural biology

2019 Volume 207, Issue 1, Page(s) 21–28

Abstract: The birds and reptiles, collectively known as the sauropsids, can be subdivided phylogenetically into the archosaurs (birds, crocodiles), the testudines (turtles), the squamates (lizards, snakes) and the rhynchocephalia (tuatara). The structural ... ...

Abstract	The birds and reptiles, collectively known as the sauropsids, can be subdivided phylogenetically into the archosaurs (birds, crocodiles), the testudines (turtles), the squamates (lizards, snakes) and the rhynchocephalia (tuatara). The structural framework of the epidermal appendages from the sauropsids, which include feathers, claws and scales, has previously been characterised by electron microscopy, infrared spectroscopy and X-ray diffraction analyses, as well as by studies of the amino acid sequences of the constituent β-keratin proteins (also referred to as the corneous β-proteins). An important omission in this work, however, was the lack of sequence and structural data relating to the epidermal appendages of the rhynchocephalia (tuatara), one of the two branches of the lepidosaurs. Considerable effort has gone into sequencing the tuatara genome and while this is not yet complete, there are now sufficient sequence data for conclusions to be drawn on the similarity of the β-keratins from the tuatara to those of other members of the sauropsids. These results, together with a comparison of the X-ray diffraction pattern of tuatara claw with those from seagull feather and goanna claw, confirm that there is a common structural plan in the β-keratins of all of the sauropsids, and not just those that comprise the archosaurs (birds and crocodiles), the testudines (turtles) and the squamates (lizards and snakes).
MeSH term(s)	Animals ; Biological Evolution ; Epidermis/growth & development ; Extremities/anatomy & histology ; Feathers/chemistry ; Hoof and Claw/chemistry ; Molecular Structure ; Phylogeny ; Reptiles/anatomy & histology ; Reptiles/metabolism ; beta-Keratins/chemistry
Chemical Substances	beta-Keratins
Language	English
Publishing date	2019-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2019.04.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.

Wood, Valerie / Carbon, Seth / Harris, Midori A / Lock, Antonia / Engel, Stacia R / Hill, David P / Van Auken, Kimberly / Attrill, Helen / Feuermann, Marc / Gaudet, Pascale / Lovering, Ruth C / Poux, Sylvain / Rutherford, Kim M / Mungall, Christopher J

Open biology

2020 Volume 10, Issue 9, Page(s) 200149

Abstract: Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, ... ...

Abstract	Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.
MeSH term(s)	Computational Biology/methods ; Databases, Genetic ; Evolution, Molecular ; Gene Ontology ; Genome, Fungal ; Genomics/methods ; Molecular Sequence Annotation ; Quality Control ; Schizosaccharomyces/genetics ; Web Browser ; Workflow
Language	English
Publishing date	2020-09-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.200149
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Improving functional annotation for industrial microbes: a case study with Pichia pastoris

Dikicioglu, Duygu / Wood, Valerie / Rutherford, Kim M / McDowall, Mark D / Oliver, Stephen G

Trends in biotechnology. 2014 Aug., v. 32, no. 8

2014

Abstract: The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial ... ...

Abstract	The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.
Keywords	Komagataella pastoris ; pipelines ; gene ontology ; Saccharomyces cerevisiae ; biotechnology ; microorganisms ; biological models ; case studies ; Escherichia coli
Language	English
Dates of publication	2014-08
Size	p. 396-399.
Publishing place	Elsevier Ltd
Document type	Article
Note	2019-12-06
ZDB-ID	47474-5
ISSN	1879-3096 ; 0167-7799
ISSN (online)	1879-3096
ISSN	0167-7799
DOI	10.1016/j.tibtech.2014.05.003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change.

Todd, Erica V / Ortega-Recalde, Oscar / Liu, Hui / Lamm, Melissa S / Rutherford, Kim M / Cross, Hugh / Black, Michael A / Kardailsky, Olga / Marshall Graves, Jennifer A / Hore, Timothy A / Godwin, John R / Gemmell, Neil J

Science advances

2019 Volume 5, Issue 7, Page(s) eaaw7006

Abstract: Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data ... ...

Abstract	Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis and that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.
MeSH term(s)	Androgens/genetics ; Androgens/metabolism ; Animals ; Epigenesis, Genetic/physiology ; Estrogens/genetics ; Estrogens/metabolism ; Female ; Fishes/genetics ; Fishes/metabolism ; Male ; Sex Determination Processes/physiology
Chemical Substances	Androgens ; Estrogens
Language	English
Publishing date	2019-07-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.aaw7006
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Canto: an online tool for community literature curation.

Rutherford, Kim M / Harris, Midori A / Lock, Antonia / Oliver, Stephen G / Wood, Valerie

Bioinformatics (Oxford, England)

2014 Volume 30, Issue 12, Page(s) 1791–1792

Abstract: Motivation: Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional ... ...

Abstract	Motivation: Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature. We have developed Canto, a web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase. Canto supports curation using OBO ontologies, and can be easily configured for use with any species. Availability: Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/).
MeSH term(s)	Biological Ontologies ; Databases, Factual ; Internet ; Schizosaccharomyces ; Software
Language	English
Publishing date	2014-02-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btu103
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Improving functional annotation for industrial microbes: a case study with Pichia pastoris.

Dikicioglu, Duygu / Wood, Valerie / Rutherford, Kim M / McDowall, Mark D / Oliver, Stephen G

Trends in biotechnology

2014 Volume 32, Issue 8, Page(s) 396–399

Abstract	The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.
MeSH term(s)	Biotechnology/methods ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Fungal Proteins/physiology ; Industrial Microbiology/methods ; Molecular Sequence Annotation/methods ; Pichia/genetics ; Pichia/metabolism ; Pichia/physiology
Chemical Substances	Fungal Proteins
Language	English
Publishing date	2014-06-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	47474-5
ISSN	1879-3096 ; 0167-7799
ISSN (online)	1879-3096
ISSN	0167-7799
DOI	10.1016/j.tibtech.2014.05.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: ACT: the Artemis Comparison Tool.

Carver, Tim J / Rutherford, Kim M / Berriman, Matthew / Rajandream, Marie-Adele / Barrell, Barclay G / Parkhill, Julian

Bioinformatics (Oxford, England)

2005 Volume 21, Issue 16, Page(s) 3422–3423

Abstract: The Artemis Comparison Tool (ACT) allows an interactive visualisation of comparisons between complete genome sequences and associated annotations. The comparison data can be generated with several different programs; BLASTN, TBLASTX or Mummer comparisons ...

Abstract	The Artemis Comparison Tool (ACT) allows an interactive visualisation of comparisons between complete genome sequences and associated annotations. The comparison data can be generated with several different programs; BLASTN, TBLASTX or Mummer comparisons between genomic DNA sequences, or orthologue tables generated by reciprocal FASTA comparison between protein sets. It is possible to identify regions of similarity, insertions and rearrangements at any level from the whole genome to base-pair differences. ACT uses Artemis components to display the sequences and so inherits powerful searching and analysis tools. ACT is part of the Artemis distribution and is similarly open source, written in Java and can run on any Java enabled platform, including UNIX, Macintosh and Windows.
MeSH term(s)	Algorithms ; Base Sequence ; Chromosome Mapping/methods ; Computer Graphics ; Molecular Sequence Data ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; Software ; User-Computer Interface
Language	English
Publishing date	2005-08-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4803
ISSN	1367-4803
DOI	10.1093/bioinformatics/bti553
Database	MEDical Literature Analysis and Retrieval System OnLINE

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