Simple Semantic Web Architecture and Protocol

The SSWAP Protocol The core classes and properties that allow any resource to use SSWAP. All your graphs should be based around the use of this canonical graph structure. OWL Ontology OWL Docs Source File Ontology Provider Description sswap SSWAP OWL Docs sswap.owl SSWAP Protocol The core ontology which defines the SSWAP Protocol util SSWAP util OWL Docs util.owl SSWAP General purpose utility terms Biology Core Set Ontologies containing core classes and properties useful for establishing a minimum vocabulary with relations to the Open Biomedical Ontologies and others. OWL Ontology OWL Docs Source File Ontology Provider Description genome genome OWL Docs genome.owl SSWAP Genome-related terms map map OWL Docs map.owl SSWAP Map-related terms marker marker OWL Docs marker.owl SSWAP Marker-related terms qtl qtl OWL Docs qtl.owl SSWAP QTL-related terms sequence sequence OWL Docs sequence.owl SSWAP Sequence-related terms sequenceServices sequenceServices OWL Docs sequenceServices.owl SSWAP Sequence Services' terms for BLAST, ClustalW, etc. taxa taxa OWL Docs taxa.owl SSWAP Taxa-related terms trait trait OWL Docs trait.owl SSWAP Plant trait-related terms Open Biomedical Ontologies A set of ontologies converted from OBO format to SSWAP format OWL Ontology OWL Docs Source File Ontology Provider Description OBO OBO OWL Docs obo.owl Open Biomedical Ontologies High level classes for major OBO ontologies; useful for specifying OBO data types for SSWAP input (sswap:Subject) and output (sswap:Object) data types OBO_REL RO OWL Docs ro.owl OBO Relation Ontology Defines core relations used in all OBO ontologies. Referred to as OBO_REL or RO. oboInOwl oboInOwl OWL Docs oboInOwl.owl OBO In OWL Ontology Ontology for mapping between OBO 1.2 and OWL. Used extensively in OBO to OWL conversions. ENVO ENVO OWL Docs envo.obo Environment Ontology A controlled vocabulary to describe different types of supplemental environments that have been reported in the experimental profiles of gene expression and phenotype (mutant and QTL) studies on cereal plants GO none gene_ontology.obo Gene Ontology A controlled vocabulary to describe gene and gene product attributes in any organism MO none MGEDOntology.owl Microarray Gene Expression Data Society A controlled vocabulary for the annotation of microarray experiments PO PO OWL Docs po_anatomy.obo po_temporal.obo Plant Ontology A controlled vocabulary of anatomy and growth and developmental stages in various plants SO SO OWL Docs so.obo Sequence Ontology A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases TO TO OWL Docs plant trait.obo Gramene Ontologies A controlled vocabulary to describe phenotypic traits in cereal plants; each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature cereal plant Third Party Ontologies Ontologies to describe domain-specific concepts OWL Ontology OWL Docs Source File Ontology Provider Description ADO none arabidopsis_development.obo TAIR Ontologies A structured controlled vocabulary for the development of Arabidopsis LIN Ontology none none none An ontology to describe terms used by LIS and CCGB in the LIN, Legume Information Network LIS Ontology LIS OWL Docs none LIS Legume Information System An ontology used to describe structural annotation terms used by LIS, the Legume Information System MOBY-S Objects MOBY-S Namespaces MOBY-S Predicates none Objects Namespaces Predicates MOBY Services at BioMoby.org Controlled vocabularies for MOBY Services Objects, Namespaces, and Predicates NAR Databases NAR Web Servers none Database Categories Web Server Categories DB Issue WS Issue NAR database and web server categories and subcategories NCBITaxonomyRecord NCBITaxonomyRecord OWL Docs none none A controlled vocabulary to describe species per NCBI QTL none none Gramene Web Services Gramene's semantic web service invocation classes TIGR Gene Ontology none none none A controlled vocabulary to describe genes and gene features per TIGR TIGRTaxonomyRecord none none none A controlled vocabulary to describe species per TIGR Ontologies Emphasizing Individuals and their Properties This is the preferred way to build modular ontologies, especially for use in semantic web services. It specifies explicit individuals (as web resources) and their properties. It relies on a reasoner to infer implicit classes from sets of individuals. OWL Ontology OWL Docs OBO Source File Ontology Provider Description OpenBiomedicalOntologies none none Open Biomedical Ontologies Defines classes and properties that authors of ontologies based on Open Biomedical Ontologies (OBO) should use to define the individuals that are included in their ontologies. The ontologies in this table are examples of this type of ontology OBOProperties OBOProperties OWL Docs OBOProperties.owl Open Biomedical Ontologies Specifies a set of properties for describing data atributes of individuals of OBO related classes. Domain specific ontologies based on OBO describe their classes and properties by creating subclasses and subproperties of the classes and properties defined in this and the OBO ontologies. The ontologies in this table are examples of this type of ontology ArabidopsisDevelopmentOntology none arabidopsis_development.obo TAIR Ontologies A structured controlled vocabulary for the development of Arabidopsis GeneOntology none gene_ontology.obo Gene Ontology A controlled vocabulary to describe gene and gene product attributes in any organism SequenceOntology none so.obo Sequence Ontology A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases TIGR Taxonomy Individuals none none TIGR database Taxonomy data from the TIGR database in OWL format as individuals. The data provides the values for properties defined in the TIGRTaxonomyRecord ontology above.