Configuration: server and project - NCIEVS/nci-protege5 GitHub Wiki

• classes and properties need labels, user-defined (e.g. Preferred_Name) or rdfs:label, to display in GUI widgets. If none is used, display falls back to the IRI fragment in the widgets that require a label. The IRI of the label property needs to be specified in label_prop below.
• NCIt: uses rdfs:label
• NCIt configuration: add labels to rdfs:label and rdfs:comment.
• Most every annotation property declaration is left with the rdfs:range unspecified (i.e untyped literal). The rdfs:range in an annotation property declaration will be respected in the annotation of a class, except in several cases, all discussed further below. These are xsd:anyURI, "-enum" enumerated properties (pointing to user-defined datatypes), and special user-defined datatypes meant to support software: textArea, date-time-system, and user-system.
• NCIt: xsd:anyURI is used to denote properties used for "associations", they must be specified in the rdfs:range; however, in annotations on a class, the xsd:anyURI is not respected and associations are represented as rdf:resource.
• Annotations on a class with the anyURI datatype need to be set "manually" to xsd:anyURI.
• NCIt: properties with anyURI range:
  • Concept_In_Subset
  • Has_CDRH_Parent
  • Has_Data_Element
  • Has_Free_Acid_Or_Base_Form
  • Has_NICHD_Parent
  • Has_Salt_Form
  • Has_Target
  • Is_Related_To_Endogenous_Product
  • Qualifier_Applies_To
  • Related_To_Genetic_Biomarker
  • Role_Has_Domain
  • Role_Has_Parent
  • Role_Has_Range

Annotations with a restricted rdfs:range (e.g. the term types of synonyms, PT, SY, AB, so on) have as a range user-defined datatypes which define the allowed values. Although not strictly necessary, we are using a naming convention to name those datatypes using the "name" of the annotation property followed by "-enum". The conversion from OWL1 to OWL2 can automatically generate the datatypes for most enumerated properties; it doesn't handle enumerations that were specified in the config file, e.g. def-source {NCI,FDA,CDISC,...}. In NCIt the enumerated properties and their datatypes are:

annotation property	datatype	enum values
Concept_Status	Concept_Status-enum
Contributing_Source	Contributing_Source-enum
Def_Curator	Def_Curator-enum
Extensible_List	Extensible_List-enum
FDA_Table	FDA_Table-enum
Neoplastic_Status	Neoplastic_Status-enum
Project_Name	Project_Name-enum
Publish_Value_Set	Publish_Value_Set-enum
Semantic_Type	Semantic_Type-enum
TVS_Location	TVS_Location-enum
Relationship_to_Target	Relationshipt_to_Target-enum*	{"Broader Than", "Has Synonym", "Narrower Than", "Related To"}
Target_Term_Type	Target_Term_Type-enum*	{"LLT", "PT", "SY"}
Target_Terminology	Target_Terminology-enum*	{"GAIA", "MedDRA"}
def-source	def-source-enum*	{"ACC", "BIOCARTA", "BRIDG", "CADSR", "CareLex", "CDISC", "CTEP", "CRCH", "CTCAE", "DICOM", "FDA", "GAIA", "ICD03", "KEGG", "NCI", "NCI-GLOSS", "NICHD", "SPL", "CSP2000", "CSP2003", "MMHCC", "MSH2003_2003_05_12", "MSH2001", "MSH2002_06_01"}
go-source	go-source-enum*	{"NCI", "NCBI", "CGAP"}
term-group	term-group-enum*	{"AB", "AD", "AQ", "AQS", "BR", "CA2", "CA3", "CN", "CNU", "CS", "DN", "FB", "HD", "LLT", "PT", "SN", "SY"}
term-source	term-source-enum*	{"ACC", "ANSI", "BIOCARTA", "BRIDG", "CADSR", "CareLex", "CDC", "CDISC", "CRCH", "CTCAE", "CTEP", "CTRM", "DCP", "DICOM", "DTP", "FDA", "GAIA", "GENC", "HGNC", "HL7", "ICH", "JAX", "KEGG", "MTH", "MedDRA", "NCI", "NCI-GLOSS", "NICHD", "NCPDP", "PI-RADS", "PID", "SEER", "UCUM"}

* These enumerations are defined in the OWL1 version of NCIt using a configuration file. They need to be created manually in the OWL2 version after an OWL1->2 conversion.

The table above shows the annotation properties "by name". Eventually in OWL2 we will use codes for the IRI fragment identifiers hence the above will change; however, we will retain the "named" datatypes shown above.

• annotation property required with datatype xsd:boolean to flag annotation properties used to annotate required property values. The property IRI doesn't need to be "required", but whatever the IRI, it needs to be entered in the metaproject as the value of the key "required" (i.e. two things the key in the metaproject, and the property name - here both use the term "required"). When "required" is asserted on the declaration, that annotation must have a value before the edit is deemed valid and Saved. Optional properties used to annotate annotations do not need to be annotated themselves as required, however, they must still be specified in the metaproject configuration so they are displayed in the GUI tables (section below).

key	value	required for
classifiable	deprecated; whether the pellet server will classify this project, the value is boolean true	NA
code_prop	the IRI of the annotation property to use for the source's identifier/code	edit panel
complex_properties	collection of IRIs of qualified properties	complex properties
def_source	used in business rule to check source is NCI	edit panel
default	legacy property used as fallback	edit panel and property editing
default_on_create_class	used in datatype declaration as the default when class is created	edit panel and batch edit
default_on_edit_class	used in datatype declaration as the default when class is being edited	edit panel and batch edit
definition	property used for NCI definition sync rule	business rules
deprecated_assoc	property used to reference properties pointing to other classes that are deleted	retirement
deprecated_child	property used to referenced child classes of retired class	retirement
deprecated_concept_status	continas two items, a property to use to annotate a deprecated class, and the value for that property	retirement and merge
deprecated_in_assoc	property used to reference that pointed into the retired class through some propery	retirement
deprecated_in_role	property used to reference classes pointing in to retired class through some role	retirement
deprecated_parent	property used to reference parent class of retired class	retirement and merge
deprecated_role	property used to reference classes pointed to by retired class through some role	retirement
design_note	property used to capture date of retirement and notes of interest	retirement and merge
editor_note	property used to capture date, modeler name, and notes of interest	retirement and merge
fully_qualified_syn	identifies the property containing a fully qualified term; the value is the property's IRI	business rule
immutable_properties	IRI of properties that can't be modified on a merge, copy, or split. At the very least, the value of the code_prop key should be immutable	edit panel
label_prop	the IRI of the display property (e.g. rdfs:label, see above)	edit panel
merge_source	IRI of property holding the IRI of the first class in a merge - the surviving class	merge
merge_target	IRI of property holding the IRI of the second class in a merge - the retired class	merge
pref_name	IRI of property denoting the preferred term of the class	business rule
premerged_root	root class under which to tree class after merging by modeler that has not yet been approved by manager	merge
preretired_root	root class under which to tree class after retiring by modeler that has not yet been approved by manager	retirement
required	applied to the property declaration; the value is the boolean true	edit panel
retired_concepts_root	the root concept of the retirement bin branch, if it's not the same as the retirement bin, e.g. Retired_Concepts vs Retired_Concepts_Current_Year.	navigator
retired_root	retired root for current year, under retired_concepts_root	retirement
review_date	used for DEFINITION and other complex properties	edit panel
reviewer_name	name of modeler editing DEFINITION	edit panel
semantic_type	type associates with class, once specified it is inherited	edit panel
split_from	annotation property on source class used for a split	split
syn_source	qualifier on full_syn	business rule
syn_type	qualifier on full_syn	business rule

key	value	comment
authenticate	full name of java class performing authentication, values can be: org.protege.editor.owl.server.security.DefaultLoginService, for authentication by protege server org.protege.editor.owl.server.security.LDAPLoginService, for authentication by an LDAP server
autoupdate_interval	time interval in milliseconds between update calls from the client to the server
codegen_delimiter	can be null if no delimiters are used	global, can be overriden if specified on the project
codegen_file	file keeping track of code numeric values
codegen_prefix	the prefix used by the vocabulary's code; can be null	global, can be overriden if specified on the project
codegen_suffix	can be null if no suffixes are used	global, can be overriden if specified on the project
conhistory_file	file generated after baseline reconciliation (concept_history)
evshistory_file	file where the runtime evs_history is recorded
ldap_dn_prefix	ldap distinguished name string preceeding the username "CN=" in the case of the NIH AD/LDAP
ldap_dn_suffix	ldap distinguished name string following the username ",OU\u003dUsers,OU\u003dNCI,OU\u003dNIH,OU\u003dAD,DC\u003dNih,DC\u003dGOV" in the case of NIH AD/LDAP
login_timeout_period	value in milliseconds