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WikiPathways
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. Pathway content Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, signaling, regulatory, etc. and the supported species include human, mouse, zebrafish, fruit fly, C. elegans, yeast, rice and arabidopsis, as well as bacteria and plant species. Using a search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PathVisio
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins. : History PathVisio was created primarily at Maastricht University and Gladstone Institutes. The software is developed in Java and it's also used as part of the WikiPathways framework as an applet. Starting from version 3.0 (released in 2012) plugins are OSGi compliant and plugin directory describing them, was developed. In 2015 version 3.2 was released. This was the first signed version with a certificate issued by a certification authority. Many of the running issues introduced by java 1.7 and 1.8 with the new security rules were solved. Since 2013 a javascript version (PV ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reactome
Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is authored by biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format. The website can be used to browse pathways and submit data to a suite of data analysis tools. The underlying data is fully downloadable in a number of standard formats including PDF, SBML and BioPAX. Pathway diagrams use a Systems Biology Graphical Notation (SBGN)-based style. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioPAX
BioPAX (Biological Pathway Exchange) is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are availab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Pathway
A biological pathway is a series of interactions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move.{{Cite web , url=https://www.genome.gov/about-genomics/fact-sheets/Biological-Pathways-Fact-Sheet , title = Biological Pathways Fact Sheet Some of the most common biological pathways are involved in metabolism, the regulation of gene expression and the transmission of signals. Pathways play a key role in advanced studies of genomics. Most common types of biological pathways: *Metabolic pathway *Genetic pathway *Signal transduction pathway Pathways databases * KEGG Pathway database is a popular pathway search database highly used by biologists. * WikiPathways is a community curated pathway database using the "wiki" concept. All pathways have an open license and can be freely used. * Reactome is a free and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Plant
Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclude the fungi and some algae, as well as the prokaryotes (the archaea and bacteria). By one definition, plants form the clade Viridiplantae (Latin name for "green plants") which is sister of the Glaucophyta, and consists of the green algae and Embryophyta (land plants). The latter includes the flowering plants, conifers and other gymnosperms, ferns and their allies, hornworts, liverworts, and mosses. Most plants are multicellular organisms. Green plants obtain most of their energy from sunlight via photosynthesis by primary chloroplasts that are derived from endosymbiosis with cyanobacteria. Their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic or mycotrophic and have lost the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Yeast
Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constitute 1% of all described fungal species. Yeasts are unicellular organisms that evolved from multicellular ancestors, with some species having the ability to develop multicellular characteristics by forming strings of connected budding cells known as pseudohyphae or false hyphae. Yeast sizes vary greatly, depending on species and environment, typically measuring 3–4 µm in diameter, although some yeasts can grow to 40 µm in size. Most yeasts reproduce asexually by mitosis, and many do so by the asymmetric division process known as budding. With their single-celled growth habit, yeasts can be contrasted with molds, which grow hyphae. Fungal species that can take both forms (depending on temperature or other conditions) are ca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rice
Rice is the seed of the grass species ''Oryza sativa'' (Asian rice) or less commonly ''Oryza glaberrima ''Oryza glaberrima'', commonly known as African rice, is one of the two domesticated rice species. It was first domesticated and grown in West Africa around 3,000 years ago. In agriculture, it has largely been replaced by higher-yielding Asian r ...'' (African rice). The name wild rice is usually used for species of the genera ''Zizania (genus), Zizania'' and ''Porteresia'', both wild and domesticated, although the term may also be used for primitive or uncultivated varieties of ''Oryza''. As a cereal, cereal grain, domesticated rice is the most widely consumed staple food for over half of the world's World population, human population,Abstract, "Rice feeds more than half the world's population." especially in Asia and Africa. It is the agricultural commodity with the third-highest worldwide production, after sugarcane and maize. Since sizable portions of sugarcane and ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Arabidopsis
''Arabidopsis'' (rockcress) is a genus in the family Brassicaceae. They are small flowering plants related to cabbage and mustard. This genus is of great interest since it contains thale cress (''Arabidopsis thaliana''), one of the model organisms used for studying plant biology and the first plant to have its entire genome sequenced. Changes in thale cress are easily observed, making it a very useful model. Status Currently, the genus ''Arabidopsis'' has nine species and a further eight subspecies recognised. This delimitation is quite recent and is based on morphological and molecular phylogenies by O'Kane and Al-Shehbaz and others. Their findings confirm the species formerly included in ''Arabidopsis'' made it polyphyletic. The most recent reclassification moves two species previously placed in ''Cardaminopsis'' and ''Hylandra'' and three species of ''Arabis'' into ''Arabidopsis'', but excludes 50 that have been moved into the new genera '' Beringia, Crucihimalaya, Ianhedge ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in symbiotic and parasitic relationsh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Biomedical Ontologies
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 OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in bioinformatics. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a phenotype in a mouse model and its related phenotype in zebrafish). Introduction The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using controlled vocabularies. Ideally, such controlled vocabularies take the form of ontologies, which su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Access (publishing)
Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre open access, barriers to copying or reuse are also reduced or removed by applying an open license for copyright. The main focus of the open access movement is "peer reviewed research literature". Historically, this has centered mainly on print-based academic journals. Whereas non-open access journals cover publishing costs through access tolls such as subscriptions, site licenses or pay-per-view charges, open-access journals are characterised by funding models which do not require the reader to pay to read the journal's contents, relying instead on author fees or on public funding, subsidies and sponsorships. Open access can be applied to all forms of published research output, including peer-reviewed and non peer-reviewed academic journal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
