WikiPathways
Encyclopedia
WikiPathways is a community resource for biological pathway
s.
software that powers Wikipedia
, we added a custom graphical pathway editing tool (PathVisio) and integrated databases (BridgeDb) covering major gene
, protein
, and metabolite
systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review
, editorial curation, and maintenance to the community.
, signaling
, regulatory
, etc. And all manner of species
are covered, including human
, mouse
, zebrafish, fruit fly
, C.elegans, yeast
, as well as bacteria
and plant
species. Any pathway can be edited by activating the embedded pathway editor. After editing, an updated pathway image is displayed on the wiki page along with the version history and list of component genes and proteins. Users can easily monitor and undo changes, compare differences and search for overlapping pathways. Using the search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or by the text displayed in its description. One can also browse the collection of pathways with combinations of species names and ontology-based categories.
The pathway content at WikiPathways is freely available for download in a variety of data and image formats. WikiPathways is committed to open access and open source
. All content is available under Creative Commons license terms. All source code for WikiPathways and the PathVisio editor is available under the Apache License, Version 2.0.
, Reactome
, KEGG), WikiPathways supports a variety of ways to integrate and interact with pathway content. These include directed link-outs, image maps, RSS feeds and deep web services. WikiPathways webservices can be used by bioinformaticians, e.g., to perform enrichment analysis on WikiPathways in R
and web developers, e.g. to link to relevant pathways.
WikiPathways content is used to annotate and cross-link Wikipedia articles cover various genes, proteins, metabolites and pathways. Here are a few examples:
All WikiPathways templates
Biological pathway
A biological pathway is a number of biochemical steps, linked together, with a start and an end. The activity within a pathway should is a flow of molecules. Some typical types of biochemical pathways are metabolic pathways and signaling pathways. The Reactome is a curated information source, with...
s.
What is WikiPathways
WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways represents a new model for pathway databases that enhances complementary efforts and synergizes with other science wikis. Building on the same MediaWikiMediaWiki
MediaWiki is a popular free web-based wiki software application. Developed by the Wikimedia Foundation, it is used to run all of its projects, including Wikipedia, Wiktionary and Wikinews. Numerous other wikis around the world also use it to power their websites...
software that powers Wikipedia
Wikipedia
Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Its 20 million articles have been written collaboratively by volunteers around the world. Almost all of its articles can be edited by anyone with access to the site,...
, we added a custom graphical pathway editing tool (PathVisio) and integrated databases (BridgeDb) covering major gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
, protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
, and metabolite
Metabolite
Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. Alcohol is an example of a primary metabolite produced in large-scale by industrial...
systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review
Peer review
Peer review is a process of self-regulation by a profession or a process of evaluation involving qualified individuals within the relevant field. Peer review methods are employed to maintain standards, improve performance and provide credibility...
, editorial curation, and maintenance to the community.
How Does It Work
Each article at WikiPathways is dedicated to a particular pathway. All sorts of molecular pathways are covered, including metabolicMetabolic pathway
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
, signaling
Signal transduction
Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response...
, regulatory
Regulation of gene expression
Gene modulation redirects here. For information on therapeutic regulation of gene expression, see therapeutic gene modulation.Regulation of gene expression includes the processes that cells and viruses use to regulate the way that the information in genes is turned into gene products...
, etc. And all manner of species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
are covered, including human
Human
Humans are the only living species in the Homo genus...
, mouse
Mouse
A mouse is a small mammal belonging to the order of rodents. The best known mouse species is the common house mouse . It is also a popular pet. In some places, certain kinds of field mice are also common. This rodent is eaten by large birds such as hawks and eagles...
, zebrafish, fruit fly
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
, C.elegans, yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
, as well as bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
species. Any pathway can be edited by activating the embedded pathway editor. After editing, an updated pathway image is displayed on the wiki page along with the version history and list of component genes and proteins. Users can easily monitor and undo changes, compare differences and search for overlapping pathways. Using the search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or by the text displayed in its description. One can also browse the collection of pathways with combinations of species names and ontology-based categories.
The pathway content at WikiPathways is freely available for download in a variety of data and image formats. WikiPathways is committed to open access and open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
. All content is available under Creative Commons license terms. All source code for WikiPathways and the PathVisio editor is available under the Apache License, Version 2.0.
Access and Integration
In addition to various primary data formats (e.g. GPML, BioPAXBioPAX
BioPAX is a RDF/OWL-basedstandard language to represent biological pathwaysat the molecular and cellular level. Its major use is to facilitate the exchange of pathway data....
, Reactome
Reactome
Reactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
, KEGG), WikiPathways supports a variety of ways to integrate and interact with pathway content. These include directed link-outs, image maps, RSS feeds and deep web services. WikiPathways webservices can be used by bioinformaticians, e.g., to perform enrichment analysis on WikiPathways in R
R (programming language)
R is a programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians for developing statistical software, and R is widely used for statistical software development and data analysis....
and web developers, e.g. to link to relevant pathways.
WikiPathways content is used to annotate and cross-link Wikipedia articles cover various genes, proteins, metabolites and pathways. Here are a few examples:
- Citric acid cycle#Interactive pathway map
- Dihydrolipoyl transacetylase#Interactive pathway map
- Articles that link to Citric acid cycle template...
All WikiPathways templates
See also
- ReactomeReactomeReactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
- KEGG
- GenMAPPGenMAPPGenMAPP is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways , connecting gene-level datasets to biological processes and disease. First created in 2000, GenMAPP is developed by an open-source team based in an academic...
- GenenetworkGenenetworkGeneNetwork is a database and open source bioinformatics software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence variants to corresponding differences in gene and protein expression and to differences in traits such as health and...
- CytoscapeCytoscapeCytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins...
- BioPAXBioPAXBioPAX is a RDF/OWL-basedstandard language to represent biological pathwaysat the molecular and cellular level. Its major use is to facilitate the exchange of pathway data....