☆ 4.4 Editorial Material

Making biological knowledge useful for humans and machines

GENETICS (2022)

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Article Genetics & Heredity

WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans

Paul Davis et al.

Summary: WormBase is a central repository for genetics and genomics research on Caenorhabditis elegans, providing data and tools to facilitate the study of this organism and related nematodes. They continually evolve to incorporate new data types and services, aiming to integrate and utilize knowledge from published nematode genetics literature. Additionally, they collaborate with the Alliance of Genome Resources to harmonize infrastructure, processes, and tools.

GENETICS (2022)

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Article Genetics & Heredity

JaponicusDB: rapid deployment of a model organism database for an emerging model species

Kim M. Rutherford et al.

Summary: The fission yeast Schizosaccharomyces japonicus has become an important system for studying cellular process evolution, utilizing similarities and differences with the established model organism Schizosaccharomyces pombe. By deploying open-source code and tools, JaponicusDB provides a central resource for S. japonicus researchers, supporting their studies and integration of new data.

GENETICS (2022)

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Article Genetics & Heredity

MOET: a web-based gene set enrichment too at the Rat Genome Database for multiontology and multispecies analyses

Mahima Vedi et al.

Summary: This article introduces the features and functions of MOET (Multi-Ontology Enrichment Tool). MOET can identify significantly overrepresented ontology terms based on input gene or protein lists using hypergeometric test and ontology term enrichment analysis. It provides statistical measures such as P-values and odds ratios. The tool integrates data from multiple databases and can be accessed freely through the website.

GENETICS (2022)

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Article Genetics & Heredity

Zebrafish information network, the knowledgebase for Danio rerio research

Yvonne M. Bradford et al.

Summary: The Zebrafish Information Network is a central repository for genetic and genomic data of Danio rerio, providing services for the zebrafish research community. It makes zebrafish research data accessible and integrable through various activities and tools, and collaborates with other model organism knowledgebases for data integration.

GENETICS (2022)

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Article Genetics & Heredity

Rectifying nematode names

Jonathan Hodgkin

Summary: This article discusses the origins and development of gene naming and genetic nomenclature system in the nematode worm Caenorhabditis elegans.

GENETICS (2022)

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Article Genetics & Heredity

FlyBase: a guided tour of highlighted features

L. Sian Gramates et al.

Summary: As FlyBase celebrates its fourth decade, it highlights its unique aspects and expresses its commitment to collaborate with other research communities. They emphasize the reports and tools dedicated to fly researchers' needs and provide multiple avenues for researchers to interact with FlyBase.

GENETICS (2022)

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Editorial Material Developmental Biology

Model organism databases are in jeopardy

Hugo J. Bellen et al.

DEVELOPMENT (2021)

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Article Biochemistry & Molecular Biology

The Gene Ontology resource: enriching a GOld mine

Seth Carbon et al.

Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.

NUCLEIC ACIDS RESEARCH (2021)

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Editorial Material Genetics & Heredity

The Descent of Databases

Howard D. Lipshitz

GENETICS (2021)

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Article Biochemistry & Molecular Biology

Alliance of Genome Resources Portal: unified model organism research platform

Julie Agapite et al.

NUCLEIC ACIDS RESEARCH (2020)

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Article Biochemistry & Molecular Biology

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

Valerie Wood et al.

OPEN BIOLOGY (2020)

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Article Mathematical & Computational Biology

Automated generation of gene summaries at the Alliance of Genome Resources

Ranjana Kishore et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2020)

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Editorial Material Genetics & Heredity

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Paul D. Thomas et al.

NATURE GENETICS (2019)

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Article Biochemistry & Molecular Biology

PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information

Antonia Lock et al.

NUCLEIC ACIDS RESEARCH (2019)

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Article Biochemical Research Methods

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature

H. -M. Muller et al.

BMC BIOINFORMATICS (2018)

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Article Mathematical & Computational Biology

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Daniela Raciti et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)

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Article Biology

Non-model model organisms

James J. Russell et al.

BMC BIOLOGY (2017)

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Editorial Material Biology

Model organism databases: essential resources that need the support of both funders and users

Stephen G. Oliver et al.

BMC BIOLOGY (2016)

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Article Multidisciplinary Sciences

Comment: The FAIR Guiding Principles for scientific data management and stewardship

Mark D. Wilkinson et al.

SCIENTIFIC DATA (2016)

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