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1.
Development ; 151(3)2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38230566

ABSTRACT

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the comprehensive and systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways in Drosophila.


Subject(s)
Databases, Genetic , Drosophila , Animals , Drosophila/genetics , Gene Ontology , Signal Transduction , Drosophila melanogaster/genetics
2.
Data Brief ; 50: 109602, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37780462

ABSTRACT

In this article, the results of experimental explosive research of a dome-shaped protective device (made of St20 steel, 90 cm diameter, 130 kg weight) with a load have been given. These studiesused standard statistical procedures with a 0.95 reliability level to establish the validity of the existing mathematical model for emergency prevention. These are associated with the threat of the explosion of a small-sized explosive object. That allowed to substantiate the features that must be taken into account by the personnel of pyrotechnic divisions in operational activities (compliance with the additional load on the body of small-sized explosives trinitrotoluene (TNT), the need for passive protective embankment, stock in the pyrotechnic division of protective load, for example in the form of bags with sand).

3.
bioRxiv ; 2023 Sep 15.
Article in English | MEDLINE | ID: mdl-37645956

ABSTRACT

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a comprehensive and dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways in Drosophila . Summary statement: Comprehensive curation of Drosophila signaling pathways and new visual displays of the pathways provides a new FlyBase resource for researchers, and new insights into signaling pathway architecture.

4.
Genetics ; 224(1)2023 05 04.
Article in English | MEDLINE | ID: mdl-36866529

ABSTRACT

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.


Subject(s)
Databases, Genetic , Proteins , Gene Ontology , Proteins/genetics , Molecular Sequence Annotation , Computational Biology
5.
Genetics ; 220(4)2022 04 04.
Article in English | MEDLINE | ID: mdl-35266522

ABSTRACT

FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.


Subject(s)
Databases, Genetic , Drosophila melanogaster , Animals , Drosophila melanogaster/genetics , Genome , Genomics
6.
Nucleic Acids Res ; 49(D1): D899-D907, 2021 01 08.
Article in English | MEDLINE | ID: mdl-33219682

ABSTRACT

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.


Subject(s)
Computational Biology/methods , Databases, Genetic , Drosophila melanogaster/genetics , Genome, Insect/genetics , Genomics/methods , Animals , Genes, Insect/genetics , Knowledge Bases , Molecular Sequence Annotation/methods , Search Engine/methods , Web Browser
7.
Nucleic Acids Res ; 47(D1): D759-D765, 2019 01 08.
Article in English | MEDLINE | ID: mdl-30364959

ABSTRACT

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called 'experimental tools' consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research.


Subject(s)
Databases, Genetic , Drosophila melanogaster/genetics , Genome, Insect/genetics , Genomics , Animals , Protein Domains/genetics , Software
8.
Nucleic Acids Res ; 45(D1): D663-D671, 2017 01 04.
Article in English | MEDLINE | ID: mdl-27799470

ABSTRACT

Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.


Subject(s)
Computational Biology/methods , Databases, Genetic , Drosophila/genetics , Genomics/methods , Animals , Disease Models, Animal , Genetic Association Studies , Humans , Web Browser
9.
G3 (Bethesda) ; 5(8): 1721-36, 2015 Jun 24.
Article in English | MEDLINE | ID: mdl-26109357

ABSTRACT

We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase (http://flybase.org). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3' UTRs (up to 15-18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.


Subject(s)
Drosophila melanogaster/genetics , Molecular Sequence Annotation , 3' Untranslated Regions , Animals , Databases, Genetic , Exons , Female , Male , Models, Genetic , RNA, Small Untranslated/chemistry , RNA, Small Untranslated/metabolism , Sequence Analysis, RNA , Transcription Initiation Site , Transcriptome
10.
Nucleic Acids Res ; 43(Database issue): D690-7, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25398896

ABSTRACT

Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly. In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase (http://flybase.org) and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.


Subject(s)
Databases, Genetic , Drosophila melanogaster/genetics , Genome, Insect , Molecular Sequence Annotation , Animals , Genomics/standards , High-Throughput Nucleotide Sequencing , Internet , Models, Genetic , Molecular Sequence Data , Reference Standards , Sequence Alignment , Software
11.
Nucleic Acids Res ; 41(Database issue): D751-7, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23125371

ABSTRACT

An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the bibliography provides a set of references that are specific to the field served by the MOD. Moreover, it serves as a backbone to which all curated biological data can be attributed. Here, we describe the organization and main features of the bibliography in FlyBase (flybase.org), the MOD for Drosophila melanogaster. We present an overview of the current content of the bibliography, the pipeline for identifying and adding new references, the presentation of data within Reference Reports and effective methods for searching and retrieving bibliographic data. We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources. Although this article is focused on bibliographic data, many of the features and tools described are applicable to browsing and querying other datasets in FlyBase.


Subject(s)
Bibliographies as Topic , Databases, Genetic , Drosophila melanogaster/genetics , Animals , Drosophila/genetics , Internet
12.
Genetics ; 179(3): 1601-55, 2008 Jul.
Article in English | MEDLINE | ID: mdl-18622037

ABSTRACT

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.


Subject(s)
Chromosomes/genetics , Drosophila/genetics , Genome, Insect/genetics , Physical Chromosome Mapping , Animals , Genetic Markers , Karyotyping , Sequence Alignment , Synteny
13.
Nucleic Acids Res ; 36(Database issue): D588-93, 2008 Jan.
Article in English | MEDLINE | ID: mdl-18160408

ABSTRACT

FlyBase (http://flybase.org) is the primary resource for molecular and genetic information on the Drosophilidae. The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder. Furthermore, these search tools have been integrated with Batch Download and new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.


Subject(s)
Databases, Genetic , Drosophila melanogaster/genetics , Drosophilidae/genetics , Genes, Insect , Animals , Computer Graphics , Genome, Insect , Internet , Software , Systems Integration , User-Computer Interface
14.
Nucleic Acids Res ; 35(Database issue): D486-91, 2007 Jan.
Article in English | MEDLINE | ID: mdl-17099233

ABSTRACT

FlyBase (http://flybase.org/) is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied species in this family, but recent determination of the genomic sequences of an additional 11 Drosophila species opens up new avenues of research for other Drosophila species. This extensive sequence resource, encompassing species with well-defined phylogenetic relationships, provides a model system for comparative genomic analyses. FlyBase has developed tools to facilitate access to and navigation through this invaluable new data collection.


Subject(s)
Databases, Genetic , Drosophilidae/genetics , Genome, Insect , Animals , Drosophila/classification , Drosophila/genetics , Drosophilidae/classification , Genomics , Internet , Phylogeny , Software , User-Computer Interface
15.
Nucleic Acids Res ; 34(Database issue): D484-8, 2006 Jan 01.
Article in English | MEDLINE | ID: mdl-16381917

ABSTRACT

FlyBase (http://flybase.org/) is a database of genetic and genomic data on the model organism Drosophila melanogaster and the entire insect family Drosophilidae. The FlyBase Consortium curates, annotates, integrates and maintains a wide variety of data within this domain. Access to the data is provided through graphical and textual user interfaces tailored to particular types of data. FlyBase data types include maps at the cytological, genetic and sequence levels, genes and alleles including their products, functions, expression patterns, mutant phenotypes and genetic interactions as well as aberrant chromosomes, annotated genomes, genetic stock collections, transposons, transgene constructs and insertions, anatomy and images, bibliographic data, and community contact information.


Subject(s)
Databases, Genetic , Drosophila melanogaster/anatomy & histology , Drosophila melanogaster/genetics , Animals , Computer Graphics , Drosophila Proteins/genetics , Drosophila Proteins/physiology , Drosophila melanogaster/growth & development , Drosophilidae/genetics , Gene Expression , Genome, Insect , Genomics , Internet , Phenotype , Systems Integration , User-Computer Interface , Vocabulary, Controlled
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