Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally considered a weed.
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.
The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.
The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL). As of March 2008, a pre-release version of the ontology was made available at the project's SVN repository.
The Arabidopsis Information Resource (TAIR) is a community resource and online model organism database of genetic and molecular biology data for the model plant Arabidopsis thaliana, commonly known as mouse-ear cress.
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of admins, but the bulk of peer review, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is built using MediaWiki software, a custom graphical pathway editing tool (PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems.
DNA annotation or genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. An annotation is a note added by way of explanation or commentary. Once a genome is sequenced, it needs to be annotated to make sense of it. Genes in a eukaryotic genome can be annotated using various annotation tools such as FINDER. A modern annotation pipeline can support a user-friendly web interface and software containerization such as MOSGA. Modern annotation pipelines for prokaryotic genomes are Bakta, Prokka and PGAP.
Lincoln David Stein is a scientist and Professor in bioinformatics and computational biology at the Ontario Institute for Cancer Research.
The iPlant Collaborative, renamed Cyverse in 2017, is a virtual organization created by a cooperative agreement funded by the US National Science Foundation (NSF) to create cyberinfrastructure for the plant sciences (botany). The NSF compared cyberinfrastructure to physical infrastructure, "... the distributed computer, information and communication technologies combined with the personnel and integrating components that provide a long-term platform to empower the modern scientific research endeavor". In September 2013 it was announced that the National Science Foundation had renewed iPlant's funding for a second 5-year term with an expansion of scope to all non-human life science research.
Suzanna (Suzi) E. Lewis was a scientist and Principal investigator at the Berkeley Bioinformatics Open-source Project based at Lawrence Berkeley National Laboratory until her retirement in 2019. Lewis led the development of open standards and software for genome annotation and ontologies.
Blast2GO, first published in 2005, is a bioinformatics software tool for the automatic, high-throughput functional annotation of novel sequence data. It makes use of the BLAST algorithm to identify similar sequences to then transfers existing functional annotation from yet characterised sequences to the novel one. The functional information is represented via the Gene Ontology (GO), a controlled vocabulary of functional attributes. The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species.
Gene Ontology (GO) term enrichment is a technique for interpreting sets of genes making use of the Gene Ontology system of classification, in which genes are assigned to a set of predefined bins depending on their functional characteristics. For example, the gene FasR is categorized as being a receptor, involved in apoptosis and located on the plasma membrane.
Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with disease phenotypes. The method uses statistical approaches to identify significantly enriched or depleted groups of genes. Transcriptomics technologies and proteomics results often identify thousands of genes which are used for the analysis.
Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.
Christopher Roland Somerville is a Canadian-American biologist known as a pioneer of Arabidopsis thaliana research. Somerville is currently Professor Emeritus at the University of California, Berkeley and a Program Officer at the Open Philanthropy Project.
A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA fragments that are obtained from different types of sequencing technology.
The Plant Phenology Ontology (PPO) is a collection of OBO Foundry ontologies that facilitate integration of heterogeneous data about seed plant phenology from various sources. These data sources include observations networks, such as the National Ecological Observatory Network (NEON), the National Phenology Network (NPN), and the Pan-European Phenology Database (PEP725), remote sensing, herbarium specimens, and citizen science observations. The initial focus during ontology development was to capture phenological data about one plant or a population of plants as observed by a person, and this enabled integration of data across disparate observation network sources. Because phenological scorings vary in their methods and reporting, this allows these data to be aggregated and compared. Changes in plant phenology can be linked to different climate factors depending on the species, such precipitation or growing degree days. Aggregated data about the timing of plant life cycle stages at different places and times can provide information about spatiotemporal patterns within and among species, and potentially offer insight into how plants may change or shift their life cycles in response to climate change. These shifts can have implications for agriculture and various biodiversity research avenues, such as shifts in pollinator and host life cycles.
Judith Anne Blake is a computational biologist at the Jackson Laboratory and Professor of Mammalian Genetics.
Carolyn Joy Lawrence-Dill is an American plant biologist and academic administrator. She develops computational systems and tools to help plant science researchers use plant genetics and genomics data for basic biology applications that advance plant breeding.
