|Number of classes:||1269|
|Number of individuals:||0|
|Number of properties:||8|
|Maximum number of siblings:||28|
|Average number of siblings:||1|
|Classes with a single subclass:||
Classes with a single subclass
|Classes with more than 25 subclasses:||
Classes with more than 25 subclasses
|Classes with no definition:||
Classes with no definition
|Contact||Victoria Petri, firstname.lastname@example.org|
|Description||The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD. Mapping of pathways in other databases to terms in PW as synonyms further increased the content of the ontology. It also provided the means to bring in annotations made by these databases and link to their sites via automatic pipelines built at RGD. The ontology allows for the standardized annotation of rat as well as human and mouse genes to pathway terms. It also serves as a vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within a diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. Metabolic, regulatory or signaling pathway terms have associated terms for the altered version of the pathway and the level at which the alteration(s) may occur. Proteins with mutations known to affect a particular pathway can be annotated to the normal and altered version(s) of the pathway and to a disease pathway, if known. Both the provision of terms for the altered versions of pathways and the representation of disease pathway diagrams as a collection of altered pathways are unique to the PW ontology and RGD's pathway data. The Pathway ontology is distributed under the terms of the Creative Commons Attribution license version 3.0 Unported (CC BY 3.0), see http://creativecommons.org/licenses/by/3.0 for details.|
|Version||Release Date||Upload Date||Downloads|
|4.8||05/09/2013||05/09/2013||Ontology / Diff|
|4.4||04/18/2013||04/18/2013||Ontology / Diff|
|4.3||02/28/2013||02/28/2013||Ontology / Diff|
NCBO Resource Index
The NCBO Resource Web service is a system for ontology based a...
The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts.
High level abstraction API (Java/REST/R) for interacting with o...
High level abstraction API (Java/REST/R) for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal.
Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz
|EMBL-EBI, University of Groningen|
OntoMaton is a google spreadsheet application allowing for onto...
OntoMaton is a google spreadsheet application allowing for ontology search and tagging directly within google spreadsheets. More information can be found here: https://github.com/ISA-tools/OntoMaton
A Web service that tags free text with ontology concepts. NCBO ...
A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.
The Pathway Portal is a multi-tier approach offering dynamic gr...
The Pathway Portal is a multi-tier approach offering dynamic graphic representation of pathways along with associated annotations, integration with other portals and navigational capabilities. It uses one ontology as the vehicle that connects its elements.
|Medical College of Wisconsin|