diff --git a/config/example.runtime.properties b/config/example.runtime.properties index e6092d54..27d28184 100644 --- a/config/example.runtime.properties +++ b/config/example.runtime.properties @@ -1,240 +1,240 @@ -# ----------------------------------------------------------------------------- -# -# VIVO runtime properties -# -# This file is provided as example.runtime.properties. -# -# Save a copy of this file as runtime.properties in your Vitro home directory, -# and edit the properties as needed for your installation. -# -# ----------------------------------------------------------------------------- - -# -# This namespace will be used when generating URIs for objects created in the -# editor. In order to serve linked data, the default namespace must be composed -# as follows (optional elements in parentheses): -# -# scheme + server_name (+ port) (+ servlet_context) + "/individual/" -# -# For example, Cornell's default namespace is: -# -# http://vivo.cornell.edu/individual/ -# -Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/ - -# -# URL of Solr context used in local VIVO search. This will usually consist of: -# scheme + server_name + port + vivo_webapp_name + "solr" -# In the standard installation, the Solr context will be on the same server as VIVO, -# and in the same Tomcat instance. The path will be the VIVO webapp.name (specified -# above) + "solr" -# Example: -# vitro.local.solr.url = http://localhost:8080/vivosolr -vitro.local.solr.url = http://localhost:8080/vivosolr - -# -# Email parameters which VIVO can use to send mail. If these are left empty, -# the "Contact Us" form will be disabled and users will not be notified of -# changes to their accounts. -# -email.smtpHost = smtp.mydomain.edu -email.replyTo = vivoAdmin@mydomain.edu - -# -# The basic parameters for a database connection. Change the end of the -# URL to reflect your database name (if it is not "vitrodb"). Change the username -# and password to match the authorized database user you created. -# -VitroConnection.DataSource.url = jdbc:mysql://localhost/vitrodb -VitroConnection.DataSource.username = vitrodbUsername -VitroConnection.DataSource.password = vitrodbPassword - -# -# The maximum number of active connections in the database connection pool. -# Increase this value to support a greater number of concurrent page requests. -# -VitroConnection.DataSource.pool.maxActive = 40 - -# -# The maximum number of database connections that will be allowed -# to remain idle in the connection pool. Default is 25% -# of the maximum number of active connections. -# -VitroConnection.DataSource.pool.maxIdle = 10 - -# -# Parameters to change in order to use VIVO with a database other than -# MySQL. -# -VitroConnection.DataSource.dbtype = MySQL -VitroConnection.DataSource.driver = com.mysql.jdbc.Driver -VitroConnection.DataSource.validationQuery = SELECT 1 - -# -# Optional URI of a SPARQL endpoint from which VIVO should display data. -# If set, VIVO will use this endpoint as its triple store instead of the -# SDB database. -# -#VitroConnection.DataSource.endpointURI = - -# -# Optional URI to use for modifying the above endpoint via SPARQL UPDATE. -# This setting is only necessary if the endpoint does not support updates via -# its main URI. (This may be done for access control purposes.) -# If the endpointURI above is not set, this setting has no effect. -# -#VitroConnection.DataSource.updateEndpointURI = - -# -# The email address of the root user for the VIVO application. The password -# for this user is initially set to "rootPassword", but you will be asked to -# change the password the first time you log in. -# -rootUser.emailAddress = vivo_root@mydomain.edu - -# -# How is a logged-in user associated with a particular Individual? One way is -# for the Individual to have a property whose value is the username of the user. -# This value should be the URI for that property. -# -selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId - -# -# If an external authentication system like Shibboleth or CUWebAuth is to be -# used, this property says which HTTP header will contain the user ID from -# the authentication system. If such a system is not to be used, leave this -# commented out. Consult the installation instructions for more details. -# -#externalAuth.netIdHeaderName = remote_userID - -# -# The temporal graph visualization can require extensive machine resources. -# This can have a particularly noticeable impact on memory usage if -# - The organization tree is deep, -# - The number of grants and publications is large. -# VIVO 1.3 release mitigates this problem by the way of a caching mechanism & -# hence we can safely set this to be enabled by default. -# -visualization.temporal = enabled - -# -# The temporal graph visualization is used to compare different organizations/people -# within an organization on parameters like number of publications or grants. -# By default, the app will attempt to make its best guess at the top level -# organization in your instance. If you're unhappy with this selection, uncomment out -# the property below and set it to the URI of the organization individual you want to -# identify as the top level organization. It will be used as the default whenever the -# temporal graph visualization is rendered without being passed an explicit org. -# For example, to use "Ponce School of Medicine" as the top organization: -# visualization.topLevelOrg = http://vivo.psm.edu/individual/n2862 -# -# visualization.topLevelOrg = http://vivo.mydomain.edu/individual/topLevelOrgURI - -# -# Absolute path on the server of the Harvester root directory. -# You must include the final slash. -# Setting a value for harvester.location indicates that the Harvester is installed at -# this path. This will enable the Harvester functions in the Ingest Tools page. -# -# harvester.location = /usr/local/vivo/harvester/ - -# -# Default type(s) for Google Refine Reconciliation Service -# The format for this property is id, name; id1, name1; id2, name2 etc. -# See Service Metadata from this page http://code.google.com/p/google-refine/wiki/ReconciliationServiceApi -# for more information. -Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Role, core:Role; \ - http://vivoweb.org/ontology/core#AcademicDegree, core:Academic Degree; \ - http://purl.org/NET/c4dm/event.owl#Event, event:Event; \ - http://vivoweb.org/ontology/core#Location, core:Location; \ - http://xmlns.com/foaf/0.1/Organization, foaf:Organization; \ - http://xmlns.com/foaf/0.1/Person, foaf:Person; \ - http://purl.obolibrary.org/obo/IAO_0000030, obo:IAO_0000030 - -# -# Types of individual for which we can create proxy editors. -# If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing -# -proxy.eligibleTypeList = http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization - -# -# Show only the most appropriate data values based on the Accept-Language -# header supplied by the browser. Default is false if not set. -# -# RDFService.languageFilter = false - -# -# Force VIVO to use a specific language or Locale instead of those -# specified by the browser. This affects RDF data retrieved from the model, -# if RDFService.languageFilter is true. This also affects the text of pages -# that have been modified to support multiple languages. -# -# languages.forceLocale = en_US - -# -# A list of supported languages or Locales that the user may choose to -# use instead of the one specified by the browser. Selection images must -# be available in the i18n/images directory of the theme. This affects -# RDF data retrieved from the model, if RDFService.languageFilter is true. -# This also affects the text of pages that have been modified to support -# multiple languages. -# -# This should not be used with languages.forceLocale, which will override it. -# -# languages.selectableLocales = en_US, es_GO - -# -# Tell VIVO to generate HTTP headers on its responses to facilitate caching the -# profile pages that it creates. -# -# For more information, see -# https://wiki.duraspace.org/display/VIVO/Use+HTTP+caching+to+improve+performance -# -# Developers will likely want to leave caching disabled, since a change to a -# Freemarker template or to a Java class would not cause the page to be -# considered stale. -# -# http.createCacheHeaders = true - -# -# For OpenSocial integration -# The base URL of the ORNG Shindig server. Usually, this is the same host and port -# number as VIVO itself, with a context path of "shindigorng". -# -#OpenSocial.shindigURL = http://localhost:8080/shindigorng - -# -# For OpenSocial integration -# The host name and port number of the service that provides security tokens for VIVO and -# Shindig to share. For now, the host name must be the actual host, not "localhost" or "127.0.0.1" -# The port number must be 8777 -# -#OpenSocial.tokenService = myhost.mydomain.edu:8777 - -# -# For OpenSocial integration -# The path to the key file that will be used qwhen generating security tokens for VIVO and -# shindig to share. -# -#OpenSocial.tokenKeyFile = /usr/local/vivo/data/shindig/openssl/securitytokenkey.txt - -# -# For OpenSocial integration -# Only set sandbox to True for dev/test environments. Comment out or set to False in production -# -#OpenSocial.sandbox = True - -# MultiViews -# VIVO supports the simultaneous use of a full foaf:Person profile page view and a "quick" page -# view that emphasizes the individual's webpage presence. Implementing this feature requires an -# installation to develop a web service that captures images of web pages or to use an existing -# service outside of VIVO. For more information on implementing multiple profile pages, refer to -# this wiki page: https://wiki.duraspace.org/display/VIVO/Multiple+foaf%3APerson+Profile+Pages. -#MultiViews.profilePageTypes=enabled - -# Geo Focus Maps -# When the following flag is set to enabled, the VIVO home page displays a global map highlighting the -# geographical focus of foaf:person individuals. For information on the maps, refer to this wiki page: -# https://wiki.duraspace.org/display/VIVO/Home+Page+Customizations#HomePageCustomizations-TheGeographicFocusMap -#homePage.geoFocusMaps=enabled - +# ----------------------------------------------------------------------------- +# +# VIVO runtime properties +# +# This file is provided as example.runtime.properties. +# +# Save a copy of this file as runtime.properties in your Vitro home directory, +# and edit the properties as needed for your installation. +# +# ----------------------------------------------------------------------------- + +# +# This namespace will be used when generating URIs for objects created in the +# editor. In order to serve linked data, the default namespace must be composed +# as follows (optional elements in parentheses): +# +# scheme + server_name (+ port) (+ servlet_context) + "/individual/" +# +# For example, Cornell's default namespace is: +# +# http://vivo.cornell.edu/individual/ +# +Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/ + +# +# URL of Solr context used in local VIVO search. This will usually consist of: +# scheme + server_name + port + vivo_webapp_name + "solr" +# In the standard installation, the Solr context will be on the same server as VIVO, +# and in the same Tomcat instance. The path will be the VIVO webapp.name (specified +# above) + "solr" +# Example: +# vitro.local.solr.url = http://localhost:8080/vivosolr +vitro.local.solr.url = http://localhost:8080/vivosolr + +# +# Email parameters which VIVO can use to send mail. If these are left empty, +# the "Contact Us" form will be disabled and users will not be notified of +# changes to their accounts. +# +email.smtpHost = smtp.mydomain.edu +email.replyTo = vivoAdmin@mydomain.edu + +# +# The basic parameters for a database connection. Change the end of the +# URL to reflect your database name (if it is not "vitrodb"). Change the username +# and password to match the authorized database user you created. +# +VitroConnection.DataSource.url = jdbc:mysql://localhost/vitrodb +VitroConnection.DataSource.username = vitrodbUsername +VitroConnection.DataSource.password = vitrodbPassword + +# +# The maximum number of active connections in the database connection pool. +# Increase this value to support a greater number of concurrent page requests. +# +VitroConnection.DataSource.pool.maxActive = 40 + +# +# The maximum number of database connections that will be allowed +# to remain idle in the connection pool. Default is 25% +# of the maximum number of active connections. +# +VitroConnection.DataSource.pool.maxIdle = 10 + +# +# Parameters to change in order to use VIVO with a database other than +# MySQL. +# +VitroConnection.DataSource.dbtype = MySQL +VitroConnection.DataSource.driver = com.mysql.jdbc.Driver +VitroConnection.DataSource.validationQuery = SELECT 1 + +# +# Optional URI of a SPARQL endpoint from which VIVO should display data. +# If set, VIVO will use this endpoint as its triple store instead of the +# SDB database. +# +#VitroConnection.DataSource.endpointURI = + +# +# Optional URI to use for modifying the above endpoint via SPARQL UPDATE. +# This setting is only necessary if the endpoint does not support updates via +# its main URI. (This may be done for access control purposes.) +# If the endpointURI above is not set, this setting has no effect. +# +#VitroConnection.DataSource.updateEndpointURI = + +# +# The email address of the root user for the VIVO application. The password +# for this user is initially set to "rootPassword", but you will be asked to +# change the password the first time you log in. +# +rootUser.emailAddress = vivo_root@mydomain.edu + +# +# How is a logged-in user associated with a particular Individual? One way is +# for the Individual to have a property whose value is the username of the user. +# This value should be the URI for that property. +# +selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId + +# +# If an external authentication system like Shibboleth or CUWebAuth is to be +# used, this property says which HTTP header will contain the user ID from +# the authentication system. If such a system is not to be used, leave this +# commented out. Consult the installation instructions for more details. +# +#externalAuth.netIdHeaderName = remote_userID + +# +# The temporal graph visualization can require extensive machine resources. +# This can have a particularly noticeable impact on memory usage if +# - The organization tree is deep, +# - The number of grants and publications is large. +# VIVO 1.3 release mitigates this problem by the way of a caching mechanism & +# hence we can safely set this to be enabled by default. +# +visualization.temporal = enabled + +# +# The temporal graph visualization is used to compare different organizations/people +# within an organization on parameters like number of publications or grants. +# By default, the app will attempt to make its best guess at the top level +# organization in your instance. If you're unhappy with this selection, uncomment out +# the property below and set it to the URI of the organization individual you want to +# identify as the top level organization. It will be used as the default whenever the +# temporal graph visualization is rendered without being passed an explicit org. +# For example, to use "Ponce School of Medicine" as the top organization: +# visualization.topLevelOrg = http://vivo.psm.edu/individual/n2862 +# +# visualization.topLevelOrg = http://vivo.mydomain.edu/individual/topLevelOrgURI + +# +# Absolute path on the server of the Harvester root directory. +# You must include the final slash. +# Setting a value for harvester.location indicates that the Harvester is installed at +# this path. This will enable the Harvester functions in the Ingest Tools page. +# +# harvester.location = /usr/local/vivo/harvester/ + +# +# Default type(s) for Google Refine Reconciliation Service +# The format for this property is id, name; id1, name1; id2, name2 etc. +# See Service Metadata from this page http://code.google.com/p/google-refine/wiki/ReconciliationServiceApi +# for more information. +Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Role, core:Role; \ + http://vivoweb.org/ontology/core#AcademicDegree, core:Academic Degree; \ + http://purl.org/NET/c4dm/event.owl#Event, event:Event; \ + http://vivoweb.org/ontology/core#Location, core:Location; \ + http://xmlns.com/foaf/0.1/Organization, foaf:Organization; \ + http://xmlns.com/foaf/0.1/Person, foaf:Person; \ + http://purl.obolibrary.org/obo/IAO_0000030, obo:IAO_0000030 + +# +# Types of individual for which we can create proxy editors. +# If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing +# +proxy.eligibleTypeList = http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization + +# +# Show only the most appropriate data values based on the Accept-Language +# header supplied by the browser. Default is false if not set. +# +# RDFService.languageFilter = false + +# +# Force VIVO to use a specific language or Locale instead of those +# specified by the browser. This affects RDF data retrieved from the model, +# if RDFService.languageFilter is true. This also affects the text of pages +# that have been modified to support multiple languages. +# +# languages.forceLocale = en_US + +# +# A list of supported languages or Locales that the user may choose to +# use instead of the one specified by the browser. Selection images must +# be available in the i18n/images directory of the theme. This affects +# RDF data retrieved from the model, if RDFService.languageFilter is true. +# This also affects the text of pages that have been modified to support +# multiple languages. +# +# This should not be used with languages.forceLocale, which will override it. +# +# languages.selectableLocales = en_US, es_GO + +# +# Tell VIVO to generate HTTP headers on its responses to facilitate caching the +# profile pages that it creates. +# +# For more information, see +# https://wiki.duraspace.org/display/VIVO/Use+HTTP+caching+to+improve+performance +# +# Developers will likely want to leave caching disabled, since a change to a +# Freemarker template or to a Java class would not cause the page to be +# considered stale. +# +# http.createCacheHeaders = true + +# +# For OpenSocial integration +# The base URL of the ORNG Shindig server. Usually, this is the same host and port +# number as VIVO itself, with a context path of "shindigorng". +# +#OpenSocial.shindigURL = http://localhost:8080/shindigorng + +# +# For OpenSocial integration +# The host name and port number of the service that provides security tokens for VIVO and +# Shindig to share. For now, the host name must be the actual host, not "localhost" or "127.0.0.1" +# The port number must be 8777 +# +#OpenSocial.tokenService = myhost.mydomain.edu:8777 + +# +# For OpenSocial integration +# The path to the key file that will be used qwhen generating security tokens for VIVO and +# shindig to share. +# +#OpenSocial.tokenKeyFile = /usr/local/vivo/data/shindig/openssl/securitytokenkey.txt + +# +# For OpenSocial integration +# Only set sandbox to True for dev/test environments. Comment out or set to False in production +# +#OpenSocial.sandbox = True + +# MultiViews +# VIVO supports the simultaneous use of a full foaf:Person profile page view and a "quick" page +# view that emphasizes the individual's webpage presence. Implementing this feature requires an +# installation to develop a web service that captures images of web pages or to use an existing +# service outside of VIVO. For more information on implementing multiple profile pages, refer to +# this wiki page: https://wiki.duraspace.org/display/VIVO/Multiple+foaf%3APerson+Profile+Pages. +#multiViews.profilePageTypes=enabled + +# Geo Focus Maps +# When the following flag is set to enabled, the VIVO home page displays a global map highlighting the +# geographical focus of foaf:person individuals. For information on the maps, refer to this wiki page: +# https://wiki.duraspace.org/display/VIVO/Home+Page+Customizations#HomePageCustomizations-TheGeographicFocusMap +#homePage.geoFocusMaps=enabled + diff --git a/rdf/tbox/filegraph/research-resource.owl b/rdf/tbox/filegraph/research-resource.owl index 997bd64d..1718a798 100644 --- a/rdf/tbox/filegraph/research-resource.owl +++ b/rdf/tbox/filegraph/research-resource.owl @@ -55,6 +55,13 @@ + + + + + + + A flow cytometer. Material entity that is designed to have a function and play a role in scientific investigation. PERSON: Melissa Haendel diff --git a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 index 312850e6..b2e38164 100644 --- a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 +++ b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 @@ -523,7 +523,8 @@ vivo:relates rdfs:label "relates"@en-US . obo:ERO_0000007 - rdfs:label "Technique"@en-US . + rdfs:label "Technique"@en-US ; + vitro:inClassGroup . vcard:hasCalendarLink rdfs:label "has calendar link"@en-US . @@ -536,7 +537,8 @@ vivo:SubnationalRegion vitro:displayLimitAnnot "-1"^^xsd:int ; vitro:displayRankAnnot - "-1"^^xsd:int ; + "10"^^xsd:int ; + vitro:inClassGroup ; vitro:hiddenFromDisplayBelowRoleLevelAnnot ; vitro:prohibitedFromUpdateBelowRoleLevelAnnot @@ -2452,7 +2454,15 @@ obo:ARG_2000083 rdfs:label "American Board of Plastic Surgery"@en-US . obo:ERO_0000398 - rdfs:label "is performed by"@en-US . + rdfs:label "is performed by"@en-US ; + vitro:hiddenFromDisplayBelowRoleLevelAnnot + ; + vitro:inPropertyGroupAnnot + ; + vitro:prohibitedFromUpdateBelowRoleLevelAnnot + ; + vitro:selectFromExistingAnnot + "true"^^xsd:boolean . vcard:hasCalenderBusy rdfs:label "has calendar busy"@en-US . @@ -4445,6 +4455,8 @@ geo:nameShortAR "5"^^xsd:int ; vitro:displayRankAnnot "5"^^xsd:int ; + vitro:inClassGroup + ; vitro:hiddenFromDisplayBelowRoleLevelAnnot ; vitro:prohibitedFromUpdateBelowRoleLevelAnnot