]> NEMO_annotation_properties NEMO_annotation_properties This file contains OWL Annotation Properties that are used for curation of the NEMO ontology. 2009-06-01 2012-05-15 v2.85 annotation_type annotation_type A category designed to help data processing systems automatically determine how to process a given annotation. The only valid values for this property are DC or SKOS (core) AnnotationProperty URIs. The legal cardinality range for annotationType applied to AnnotationProperties = 0...n - i.e., it is neither required, nor is it limited to a cardinality of 1, though it is recommend there be at least one annotationType for each AnnotationProperty, whenever there is an appropriate super-class available. The current use of this meta-property is to identify types of definitions (nemo_annot:definition) and types of external source ID (dc:identifier) (BB: 2007-08-03). This is required, since sub-classing AnnotationProperties is not allowed in OWL-DL. Using this descriptive metadata AnnotationProperties, we can construct a chained code representation of a classification graph for AnnotationProperities very likely to be useful for information systems built to parse and process OWL content. http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#annotationType 2009-06-03 NEMO_annotation pref_label pref_label An underscore-delimited, human-readable name. Same as core:prefLabel. Only one label is allowed per concept. Otherwise, use nemo_annot:synonym. We are creating a new label for NEMO, which is essentially the same as rdfs:label, so as to keep all annotation properties for NEMO closed. In order to comply with Protege 4.x display properties and render concepts according to annotations, we may need to duplicate a nemo_annot:label entry with an rdfs:label entry. 2009-06-03 NEMO_annotation definition definition This definition uses natural language (English) to express the real-world (scientific) meaning defining the NEMO ontology term and adheres, as far as possible, to Aristotelian constraints. This definition "stores" the text of the formerly called textDefinition, which was previously included as the first definition within the NEMO_annot:definition. The source of this definition is often traceable and should be documented, whenever possible, using NEMO_annot:definition_source We are creating our own nemo_annot:definition so as to keep all annotation properties for NEMO closed. 2009-06-03 2010-07-21 NEMO_annotation onto_definition onto_definition This definition uses natural language (English), adheres to Aristotelian constraints and restates precisely the information that has been encoded in NEMO_annot:definition, including class restrictions, disjoint classes, and so forth. This definition "stores" the text of the formerly called ontoDefinition, which was previously included as the second definition within the NEMO_annot:definition. 2010-07-21 2011-07-16 NEMO_annotation created_date created_date The date when the current concept was created. 2009-06-03 2011-07-16 NEMO_annotation modified_date modified_date The date when the current concept was last updated. 2009-06-03 2011-07-16 NEMO_annotation comment comment A general comment. We are creating our own nemo_annot:comment so as to keep all annotation properties for NEMO closed. Otherwise, we consider nemo_annot:comment to be equivalent to rdfs:comment and core:note. 2009-06-03 NEMO_annotation example example An example of a given concept. 2009-06-03 NEMO_annotation replaced_by replaced_by 2010-03-12 NEMO_annotation This property indicates that an annotation property X has been replaced by another annotation property Y. We are using this kind property to keep track of changes we made to the old/retired/deprectated properties. source_ontology source_ontology 2010-04-23 NEMO_annotation This property indicates an ontology that a term has been imported from. synonym synonym A lexical variant carrying the same latent semantic value. http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#annotationType 2009-06-03 NEMO_annotation acronym acronym An acronym consisting of a sequence of letters typically taken from the beginning of words of which either the preferred label or another synonym are composed. http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#annotationType 2009-06-03 NEMO_annotation definition_source definition_source A traceable source for the current definition. In free-form text, a source could be a person's name, a URI, an informal publication reference, a PubMed ID, whatever most succinctly identifies a source. We originally had an EnumerationClass of Definition_Sources but decided that was too constrictive. 2009-06-03 NEMO_annotation _limbo_property _limbo_property A property that has been created by curators but has an uncertain place within the ontology. By implication, the property has no definition or one that is minimally specified. 2009-05-07 NEMO_annotation _limbo _limbo A class that has been created by curators but has not been assigned to a superclass and therefore has an uncertain place within the ontology class hierarchy. By implication, the class has no definition or one that is minimally specified. 2009-05-07 NEMO_annotation namespace namespace This property defines the NEMO namespace for a concept. 2009-06-03 2010-05-27 NEMO_annotation The following is the list of all NEMO namespaces: NEMO_annotation, NEMO_data, NEMO_erp, NEMO_functional, NEMO_imported_classes, NEMO_metrics, NEMO_relations, NEMO_spatial and NEMO_temporal. _annotation _annotation 2010-11-30 2010-11-30 NEMO_annotation This is a parent class of all annotation property value classes used in NEMO. evidence_code evidence_code 2010-09-07 2011-01-13 NEMO_annotation This property indicates a level of ERP pattern related data traceability accross available scientific literature. NEMO_evidence_code 2010-11-30 2011-01-13 NEMO_annotation This class represents a strict set of allowed values for evidence_code annotation property range. Valid values for this property are: (1) traceable_experiment_data; (2) traceable_metaanalysis_data; (3) untraceable_author_statement; (4) traceable_metaanalysis_report; (5) traceable_experiment_report; and (6) traceable_author_statement. NEMO_evidence_code untraceable_author_statement This evidence code should be used when an author (curator) provides a definition based on prior knowledge, without reference to a specific traceable (published) source. traceable_author_statement This evidence code should be used to indicate that the pattern rule is based on a traceable author statement from a peer-reviewed paper, textbook, or other source that can be retrieved from a publicly available database. The use of this code implies that the statement is made without reference to specific experiment results. traceable_experiment_report This evidence code should be used to indicate that the pattern rule is based on results from one or more published studies. The use of this code implies that the raw experiment data are not publicly available. Therefore, it is not possible to verify the report directly or to reanalyze the data using alternative methods. However, the data summary and report are available and can be retrieved from a publicly available database. traceable_experiment_data This evidence code should be used to indicate that the pattern rule is based on a traceable author statement from a peer-reviewed paper, textbook, or other source that can be retrieved from a publicly available database. The use of this code implies that the statement is made without reference to specific experiment results. traceable_metaanalysis_report This evidence code should be used to indicate that the pattern rule is based on results from one or more published meta-analyses. The use of this code implies that the raw experiment data are not publicly available. Therefore, it is not possible to verify the report directly or to reanalyze the data using alternative methods. However, the meta-analysis summary and report are available and can be retrieved from a publicly available database. traceable_metaanalysis_data This evidence code should be used to indicate that the pattern rule is based on results from one or more publicly available, annotated datasets that include data from multiple experiments (and, ideally, from multiple labs). The data and methods used to preprocess and analyze the data are assumed to be clearly documented and publicly available. Therefore, it should be possible to verify the meta-analysis results directly or to reanalyze the data using alternative methods. curator curator This property provides information about the NEMO ontology curators who've contributed to ontology terms' defining and annotating. 2009-06-03 2010-11-30 NEMO_annotation Names of NEMO curators should be written strictly in following manner: first name - underscore - last name; For example "Gwen_Frishkoff" More than one instance of this property is valid. NEMO_curator 2009-11-30 2010-11-30 NEMO_annotation Names of NEMO curators should be written strictly in following manner: first name - underscore - last name; For example "Gwen_Frishkoff" This property defines the NEMO ontology curators who've contributed to the definition of a class. More than one instance of this property is valid. In the case of multiple curators, the individual curator name may also be associated with the definition, if that person was primarily responsible for it. NEMO_curator Gwen_Frishkoff Snezana_Nikolic Paea_LePendu Dejing_Dou Allen_Malony Robert_Frank Jason_Sydes Haishan_Liu Usman_Khan Kurt_Mueller Tim_Curran Kerry_Kilborn Dennis_Molfese Chuck_Perfetti Don_Tucker John_Connolly Jessica_Turner Anita_Bandrowski Angela_Laird Chris_Bird Stephanie_Connel Srinivas_Kota Caitlin_Hudac Sivaram_Arabandi Alex_Beaverston curation_status curation_status This provides specific information on the level of curation a given class has received and is specifically design to promote automated reporting on the status of classes in an ontology. It is likely some classes will require more than one instance of this property to fully describe their status. Is a type of skos_editorial_note. 2009-06-03 2010-11-30 NEMO_annotation NEMO_curation_status NEMO_curation_status This provides specific info on the level of curation a given class has received and is specifically design to promote automated reporting on the status of classes in an ontology. It is likely some classes will require more than one instance of this property to fully describe their status. Is a type of skos_editorial_note. 2009-06-03 2011-01-13 Valid values for this property are: (1) limbo_class; (2) limbo_property; (3) definition_incomplete; (4) pending_final_vetting; (5) curation_complete; (7) direct_import; (8) metadata_incomplete and (9) deprecated. limbo_class Indicates a class has been created by curators but has not been assigned to a superclass and therefore has an uncertain place within the ontology class hierarchy. By implication, such class has no definition or one that is minimally specified. By implication, the next curation steps required are to: identify a valid definition_source, specify the definition_source, update the curation_status from limbo_class to definition_incomplete or pending_final_vetting. limbo_property Indicates a property has been created by curators but has an uncertain place within the ontology. By implication, the property has no definition or one that is minimally specified. By implication, the next steps required are to: identify a valid definition_source, specify the definition_source, update the curation_status from limbo_property to definition_incomplete or pending_final_vetting. definition_incomplete Indicates a class has been assigned to a superclass and therefore has a clear place within the ontology class hierarchy and at least a minimal definition. However, the definition may require considerable amending before it complies with Aristotelian/OBO requirements for a good, noncircular definition. By implication, the next steps required are to: verify the definition adheres to Aristotelian constraints, update curation_status from definition_incomplete to pending_final_vetting. pending_final_vetting Indicates a class needs to be vetted by two or more NEMO curation authorities. By implication, the next steps required are to: vet the definition among NEMO consortium members, update curation_status from pending_final_vetting curation_complete. curation_complete Indicates a class has been fully vetted by NEMO curation authorities and deemed ready for use. direct_import Indicates that a class or an object property has been imported from another ontology (i.e., the class URI is the URI assigned within the source_ontology). The annotation property source_ontology is used to specify the ontology from which the term has been is imported. metadata_incomplete Indicates that other annotation properties' values for this term, other than value for definition, are incomplete or missing. This annotation property value is similar, but not parallel, to OBI curation status value "metadata incomplete", because in NEMO ontologies "metadata_incomplete" excludes the "incompleteness" of a term definition which has already been defined by curation status value "definition_incomplete". deprecated Indicates that a term has been deprecated (i.e. not longer used in NEMO ontologies). Once a term has been deprecated, no further changes will be made to the term annotations. Accordingly, curation_status of such a term should be "deprecated". deprecation_reason deprecation_reason This property provides an information about the specific reason for term deprecation. 2010-04-23 2010-11-30 NEMO_annotation NEMO_deprecation_reason NEMO_deprecation_reason This class is created to enumerate a valid set of deprecation_reason values. Valid values for this property are: (1) retired; (2) replaced and (3) equivalent_term_imported. 2010-04-23 2011-01-13 NEMO_annotation retired Indicates that a class, instance, object property, or annotation property is no longer used in NEMO ontology. replaced Indicates that a class, instance, object property, or annotation property has been replaced by a different term. equivalent_term_imported Indicates that a class, instance, object property, or annotation property has been replaced by an imported term from another ontology.