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 Ontology Browser Source File Ontology Provider Description sswap Browse SSWAP sswap.owl SSWAP Protocol The core ontology which defines the SSWAP Protocol Upper Ontologies Generic ontologies useful across domains. Domain-specific ontologies may subClass and subProperty these terms to specialize for specific use. OWL Ontology Ontology Browser Source File Ontology Provider Description data Browse data data.owl SSWAP Data and data formats exec -- -- SSWAP Program and command execution mime -- -- SSWAP IANA MIME types util Browse util 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 Ontology Browser Source File Ontology Provider Description genome Browse genome genome.owl SSWAP Genome-related terms map Browse map map.owl SSWAP Map-related terms marker Browse marker marker.owl SSWAP Marker-related terms qtl Browse qtl qtl.owl SSWAP QTL-related terms sequence Browse sequence sequence.owl SSWAP Sequence-related terms sequenceServices Browse sequenceServices sequenceServices.owl SSWAP Sequence Services' terms for BLAST, ClustalW, etc. taxa Browse taxa taxa.owl SSWAP Taxa-related terms trait Browse trait trait.owl SSWAP Plant trait-related terms Open Biomedical Ontologies A set of ontologies converted from OBO or OboInOwl to modular URIs. OWL Ontology Ontology Browser Source File Ontology Provider Description OBO Browse OBO 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 Browse RO ro.owl OBO Relation Ontology Defines core relations used in all OBO ontologies. Referred to as OBO_REL or RO. oboInOwl Browse oboInOwl oboInOwl.owl OBO In OWL Ontology Ontology for mapping between OBO 1.2 and OWL. Used extensively in OBO to OWL conversions. ENVO Browse ENVO 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 - gene_ontology.obo Gene Ontology A controlled vocabulary to describe gene and gene product attributes in any organism MO - MGEDOntology.owl Microarray Gene Expression Data Society A controlled vocabulary for the annotation of microarray experiments PO Browse PO po_anatomy.obo po_temporal.obo Plant Ontology A controlled vocabulary of anatomy and growth and developmental stages in various plants SO Browse SO 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 Browse TO 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 Ontology Browser Source File Ontology Provider Description ADO - arabidopsis_development.obo TAIR Ontologies A structured controlled vocabulary for the development of Arabidopsis LIS Ontology - none none An ontology to describe terms used by LIS and CCGB in the LIN, Legume Information Network LIN Ontology Browse LIS none LIS Legume Information System An ontology used to describe structural annotation terms used by LIS, the Legume Information System MOBY-S - Objects Namespaces Predicates MOBY Services at BioMoby.org Controlled vocabularies for MOBY Services Objects, Namespaces, and Predicates NAR Databases NAR Web Servers - Database Categories Web Server Categories DB Issue WS Issue NAR database and web server categories and subcategories NCBITaxonomyRecord Browse NCBITaxonomyRecord NCBITaxonomyRecord.owl none A controlled vocabulary to describe species per NCBI QTL none none Gramene Web Services Gramene's semantic web service invocation classes 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 Ontology Browser OBO Source File Ontology Provider Description OpenBiomedicalOntologies - 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 Browse OBOProperties 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 - arabidopsis_development.obo TAIR Ontologies A structured controlled vocabulary for the development of Arabidopsis GeneOntology - gene_ontology.obo Gene Ontology A controlled vocabulary to describe gene and gene product attributes in any organism SequenceOntology - 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