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[VIVO-1930] - Update example.runtime.properties #194

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[VIVO-1930] - Update example.runtime.properties #194

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f585d90
adding collections process terms (#165)
diatomsRcool Sep 23, 2020
b836e87
Update example.runtime.properties
gneissone Sep 30, 2020
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56 changes: 38 additions & 18 deletions home/src/main/resources/config/example.runtime.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -72,20 +72,23 @@ argon2.time = 1000
# 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.
# Example:
# email.smtpHost = smtp.mydomain.edu
# email.replyTo = vivoAdmin@mydomain.edu
#
email.smtpHost = smtp.mydomain.edu
email.replyTo = vivoAdmin@mydomain.edu
email.smtpHost =
email.replyTo =

#
# 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
# in build.properties) + "solr"
# scheme + server_name + port + "solr" + solr_core_name
# In a standard Solr installation, the Solr service will be available on port
# 8983. The path will be /solr followed by the name used when adding a core
# for VIVO.
# Example:
# vitro.local.solr.url = http://localhost:8080/vivosolr
# vitro.local.solr.url = http://localhost:8983/solr/vivocore
#
vitro.local.solr.url = http://localhost:8080/vivosolr
vitro.local.solr.url = http://localhost:8983/solr/vivocore


# -----------------------------------------------------------------------------
Expand Down Expand Up @@ -217,26 +220,43 @@ selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
# ORCID INTEGRATION
# -----------------------------------------------------------------------------

# The Client ID from your ORCID credentials
# When your application for credentials is accepted, you will receive a Client
# ID to be used in communications with the API. If you apply for sandbox
# credentials first, and then production credentials, you will likely receive
# two different Client IDs.
# orcid.clientId = 0000-0000-0000-000X

# The Client Secret from your ORCID credentials
# When your application for credentials is accepted, you will receive a Client
# Secret to be used in communications with the API. If you apply for sandbox
# credentials first, and then production credentials, you will likely receive
# two different Client Secrets.
# orcid.clientPassword = 00000000-0000-0000-0000-000000000000

#
# The orcid.webappBaseUrl must end in a front slash (/)
# if it includes a path past the domain and (if required) port.
#
# The base URL for your VIVO application, as seen from outside.
# VIVO will use this to construct a callback URL that the ORCID API can use to
# return control to VIVO. The actual callback URL will be the string you
# provide here with the suffix of /orcid/callback added at the end.
# The orcid.webappBaseUrl must end in a front slash (/)
# if it includes a path past the domain and (if required) port.
#
# orcid.webappBaseUrl = http://vivo.mydomain.edu/vivo/
# orcid.externalIdCommonName = VIVO Cornell Identifier

# 1.2, 2.0
# The version of ORCIDs API protocol that VIVO will expect. Currently, the
# only supported version is 2.0.
# orcid.apiVersion = 2.0

# release, sandbox
# The entry point for ORCID's public API.
# This changes, depending on whether you are using the sandbox API or the
# production API. Value is either release or sandbox.
# orcid.api = sandbox

# Specify the type of API access that you have - public or member
# public - only allows you to confirm ORCID IDs
# member - allows VIVO to write a link to the VIVO profile in the ORCID record
# If you only have a public API key, ensure that you have entered public here
# Specify the type of API access that you have - public or member
# public - only allows you to confirm ORCID IDs
# member - allows VIVO to write a link to the VIVO profile in the ORCID record
# If you only have a public API key, ensure that you have entered public here
#orcid.apiLevel = public


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70 changes: 70 additions & 0 deletions home/src/main/resources/rdf/tbox/filegraph/vivo.owl
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Expand Up @@ -5982,6 +5982,32 @@ To enable other Gender/Sex codes to be used, this dataproperty has range URI. Th



<!-- http://purl.obolibrary.org/obo/BCO_0000003 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BCO_0000003">
<rdfs:label xml:lang="en">Data Collection Process</rdfs:label>
<rdfs:subClassOf rdf:resource="http://vivoweb.org/ontology/core#CollectionProcess"/>
<obo:IAO_0000112 xml:lang="en">Observing and recording the presence or absence of butterflies during a transect walk.; A trip camera capture of an image of a jaguar is an observation, because it is &quot;selected&quot; by the camera as worthy of obsevation simply by virtue of moving in front of the camera.; Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Under development</obo:IAO_0000116>
<vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A collection process in which an information content entity is collected for research or scholarly purposes. The immediate use case is recording observations of taxa (presence/absence). Need to figure out how this relates to OBI assay OBI:0000070. maybe has broader synonym OBI:0000070</vitro:descriptionAnnot>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BCO_0000042 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BCO_0000042">
<rdfs:label xml:lang="en">Taxonomic Identification Process</rdfs:label>
<rdfs:subClassOf rdf:resource="http://vivoweb.org/ontology/core#IdentificationProcess"/>
<obo:IAO_0000112 xml:lang="en">Using a key to identify a plant in the field.; Using DNA barcoding to identify a plant species.; Associating a museum specimen with a specific taxonomic concept based on its characters.; Using BLAST to identify the taxa present in an environmental (metagenomic) sample.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A curation process in which a taxonomic name is appied to a biological entity to denote membership in a taxon.</obo:IAO_0000115>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
Expand Down Expand Up @@ -9754,6 +9780,20 @@ This class allows for linking an author to a publication while indicating inform



<!-- http://vivoweb.org/ontology/core#GeoreferencingProcess -->

<owl:Class rdf:about="http://vivoweb.org/ontology/core#GeoreferencingProcess">
<rdfs:subClassOf rdf:resource="http://vivoweb.org/ontology/core#CurationProcess"/>
<obo:IAO_0000111>Georeferenced</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A curation process in which a material entity is annotated with geo-coordinates to indicate the location of a collection</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Under development</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Anne Thessen</obo:IAO_0000117>
<rdfs:label xml:lang="en">Georeferencing Process</rdfs:label>
</owl:Class>



<!-- http://vivoweb.org/ontology/core#GovernmentAgency -->

<owl:Class rdf:about="http://vivoweb.org/ontology/core#GovernmentAgency">
Expand Down Expand Up @@ -9846,6 +9886,21 @@ This class allows for linking an author to a publication while indicating inform



<!-- http://vivoweb.org/ontology/core#IdentificationProcess -->

<owl:Class rdf:about="http://vivoweb.org/ontology/core#IdentificationProcess">
<rdfs:subClassOf rdf:resource="http://vivoweb.org/ontology/core#CurationProcess"/>
<obo:IAO_0000111>Identified</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A curation process in which a term is appied to a material entity to denote its type or kind</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Under development</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Anne Thessen</obo:IAO_0000117>
<vitro:descriptionAnnot>This is intended to apply to a wide variety of material entities, not just biological specimens.</vitro:descriptionAnnot>
<rdfs:label xml:lang="en">Identification Process</rdfs:label>
</owl:Class>



<!-- http://vivoweb.org/ontology/core#Institute -->

<owl:Class rdf:about="http://vivoweb.org/ontology/core#Institute">
Expand Down Expand Up @@ -10028,6 +10083,21 @@ This class allows for linking an author to a publication while indicating inform



<!-- http://vivoweb.org/ontology/core#MeasurementProcess -->

<owl:Class rdf:about="http://vivoweb.org/ontology/core#MeasurementProcess">
<rdfs:subClassOf rdf:resource="http://vivoweb.org/ontology/core#CurationProcess"/>
<obo:IAO_0000111>Measured</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A curation process in which data are collected about a specimen in a collection</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Under development</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Anne Thessen</obo:IAO_0000117>
<vitro:descriptionAnnot>possibly has broader synonym OBI assay OBI:0000070 because all measurement processes will be assays, but not all assays will be performed on a material entity in a collection</vitro:descriptionAnnot>
<rdfs:label xml:lang="en">Measurement Process</rdfs:label>
</owl:Class>



<!-- http://vivoweb.org/ontology/core#MedicalResidency -->

<owl:Class rdf:about="http://vivoweb.org/ontology/core#MedicalResidency">
Expand Down