diff --git a/.github/workflows/shinyapps_deploy.yml b/.github/workflows/shinyapps_deploy.yml index 804c66d..3a0a71d 100644 --- a/.github/workflows/shinyapps_deploy.yml +++ b/.github/workflows/shinyapps_deploy.yml @@ -9,6 +9,7 @@ on: branches: - main - dev* + - fds* tags: - v[0-9]+.[0-9]+.[0-9]+ @@ -63,6 +64,7 @@ jobs: echo 'DFA_CLIENT_SECRET="${{ secrets.OAUTH_CLIENT_SECRET }}"' >> .Renviron echo 'DFA_DCC_CONFIG="https://raw.githubusercontent.com/Sage-Bionetworks/data_flow_config/dev/tenants.json"' >> .Renviron echo 'GITHUB_PAT="${{ secrets.GITHUB_TOKEN }}"' >> .Renviron + echo 'DFA_REF="${{ github.ref }}"' >> .Renviron # deploy app using rsconnect - name: Authorize and deploy app diff --git a/R/app_server.R b/R/app_server.R index 902f3c5..a11c95b 100644 --- a/R/app_server.R +++ b/R/app_server.R @@ -84,7 +84,7 @@ app_server <- function( input, output, session ) { # show waiter on button click waiter::waiter_show( html = shiny::tagList( - shiny::img(src = "www/loading.gif"), + shiny::img(src = "www/sage-loader.svg"), shiny::h3("Getting data. This may take a moment.", style = "color:white;")), color="#424874" ) diff --git a/R/app_ui.R b/R/app_ui.R index 73c04ad..69970f4 100644 --- a/R/app_ui.R +++ b/R/app_ui.R @@ -10,6 +10,13 @@ app_ui <- function() { shiny::tagList( # Leave this function for adding external resources golem_add_external_resources(), + + tags$head( + tags$link( + rel="shortcut icon", + href=FAVICON_URL + ) + ), # initialize shinyjs shinyjs::useShinyjs(), @@ -64,7 +71,7 @@ app_ui <- function() { waiter::use_waiter(), waiter::waiter_preloader( html = shiny::tagList( - shiny::img(src = "www/loading.gif"), + shiny::img(src = "www/sage-loader.svg"), shiny::h4("Retrieving Synapse information...", style = "color:white;") ), color = "#424874" @@ -154,7 +161,7 @@ golem_add_external_resources <- function() { ) tags$head( - favicon(), + favicon(resources_path = app_sys("app/www")), bundle_resources( path = app_sys("app/www"), app_title = "Data Flow" diff --git a/R/global.R b/R/global.R index 49a5bea..e93d2e4 100644 --- a/R/global.R +++ b/R/global.R @@ -1,3 +1,15 @@ +## SET GLOBAL VARS + +# READ IN BRANCH NAME +ref <- Sys.getenv("DFA_REF") + +# SET FAVICON URL +FAVICON_URL <- file.path( + "https://raw.githubusercontent.com/Sage-Bionetworks/data_flow", + ref, # FIXME: Automate branch via env variable + "inst/app/www/favicon.ico" +) + # READ IN TENANTS.JSON tenants_config_path <- Sys.getenv("DFA_DCC_CONFIG") if (is.null(tenants_config_path) || nchar(tenants_config_path) == 0) stop("missing DFA_DCC_CONFIG environmental variable") @@ -64,4 +76,3 @@ api <- httr::oauth_endpoint( # The 'openid' scope is required by the protocol for retrieving user information. scope <- "openid view download modify" - diff --git a/inst/app/www/favicon.ico b/inst/app/www/favicon.ico index 4c0982c..5cd5cde 100644 Binary files a/inst/app/www/favicon.ico and b/inst/app/www/favicon.ico differ diff --git a/inst/app/www/loading.gif b/inst/app/www/loading.gif deleted file mode 100644 index 3d5adab..0000000 Binary files a/inst/app/www/loading.gif and /dev/null differ diff --git a/inst/app/www/sage-loader.svg b/inst/app/www/sage-loader.svg new file mode 100644 index 0000000..5c34fe7 --- /dev/null +++ b/inst/app/www/sage-loader.svg @@ -0,0 +1,15 @@ + + + + + + \ No newline at end of file diff --git a/inst/app/www/sage_logo_mark_only.png b/inst/app/www/sage_logo_mark_only.png new file mode 100644 index 0000000..127ffad Binary files /dev/null and b/inst/app/www/sage_logo_mark_only.png differ diff --git a/inst/data_model/dataflow_component.csv b/inst/data_model/dataflow_component.csv deleted file mode 100644 index 6ee39e5..0000000 --- a/inst/data_model/dataflow_component.csv +++ /dev/null @@ -1,17 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -dataFlow,Describes data flow status,,"Component, contributor, dataset_id, dataset_name, dataset_type, upload_date, num_items, dataset_size, scheduled_release_date, release_date, status, released_destinations, released, metadata_check, governance_compliance",,TRUE,DataType,,, -contributor,"The team of a contributing user. The team reflects the contributing institution in standard DCC setups).  Note that for DCCs picking option 1 in the standard DCC setup, the Synapse project name also reflects the contributing institutions and can be used instead of the team name.",,,,TRUE,DataProperty,,,str -dataset_id,Synapse ID of manifest folder,,,,TRUE,DataProperty,,,str -dataset_name,Name of dataset,,,,TRUE,DataProperty,,,str -dataset_type,Type of dataset,,,,TRUE,DataProperty,,,str -upload_date,Date when both data records and data files (if applicable) have been uploaded,,,,TRUE,DataProperty,,,date -num_items,Number of files contained in a manifest,,,,TRUE,DataProperty,,,int -dataset_size,GB of data in a dataset,,,,TRUE,DataProperty,,,int -scheduled_release_date,Date that a dataset is scheduled for release,,,,TRUE,DataProperty,,,date -release_date,Date when a given dataset has actually been released,,,,TRUE,DataProperty,,,date -status,Data flow status of a dataset,"Not uploaded, uploaded, curated, quarantine, preprocessing, scheduled for release, ready for release, released",,,TRUE,DataProperty,,,str -released_destinations,Location that a dataset has been released to,"Not applicable, data portal, dbGaP",,,TRUE,DataProperty,,,str -released,"Whether or not a dataset has been released -","TRUE, FALSE",,,TRUE,DataProperty,,,str -metadata_check,Whether or not a dataset has passed DCA/Schematic metadata checks,"TRUE, FALSE",,,TRUE,DataProperty,,,str -governance_compliance,Whether or not all files in a manifest have passed governance requirements,"TRUE, FALSE",,,TRUE,DataProperty,,,str \ No newline at end of file diff --git a/inst/data_model/dataflow_component.jsonld b/inst/data_model/dataflow_component.jsonld deleted file mode 100644 index 1c32498..0000000 --- a/inst/data_model/dataflow_component.jsonld +++ /dev/null @@ -1,2589 +0,0 @@ -{ - 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"@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesAbundanceOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest", - "rdfs:label": "decreasesAbundanceOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest", - "rdfs:label": "affectsActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - 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"@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest", - "rdfs:label": "affectsExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest", - "rdfs:label": "increasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest", - "rdfs:label": "decreasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other ", - "rdfs:label": "affectsFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other ", - "rdfs:label": "increasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other ", - "rdfs:label": "decreasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest", - "rdfs:label": "affectsLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - 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"@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest", - "rdfs:label": "affectsMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "increasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "decreasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "affectsMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "increasesMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - 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}, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other", - "rdfs:label": "decreasesSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest", - "rdfs:label": "affectsDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest", - "rdfs:label": "increasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest", - "rdfs:label": "decreasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "affectsMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "increasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "decreasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "affectsResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "increasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "decreasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA", - "rdfs:label": "affectsSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:increasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA", - "rdfs:label": "increasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:decreasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA", - "rdfs:label": "decreasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:affectsStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest", - "rdfs:label": "affectsStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest", - "rdfs:label": "increasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest", - "rdfs:label": "decreasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "affectsTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "increasesTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "decreasesTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "affectsSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "increasesSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "decreasesSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "affectsUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "increasesUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "decreasesUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:regulates,ProcessToProcess", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "regulates,ProcessToProcess", - "schema:domainIncludes": { - "@id": "bts:Occurrent" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Occurrent" - } - }, - { - "@id": "bts:regulates,EntityToEntity", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "regulates,EntityToEntity", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:hasGeneProduct", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene and a transcribed and/or translated product generated from it", - "rdfs:label": "hasGeneProduct", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneProduct" - } - }, - { - "@id": "bts:inPathwayWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are part of in the same biological pathway", - "rdfs:label": "inPathwayWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:inComplexWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex", - "rdfs:label": "inComplexWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:inCellPopulationWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are expressed in the same cell type or population ", - "rdfs:label": "inCellPopulationWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:geneAssociatedWithCondition", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with", - "rdfs:label": "geneAssociatedWithCondition", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:treats", - "@type": "rdf:Property", - "rdfs:comment": "holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat", - "rdfs:label": "treats", - "schema:domainIncludes": { - "@id": "bts:Treatment" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:correlatedWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "correlatedWith", - "schema:domainIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:hasBiomarker", - "@type": "rdf:Property", - "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "hasBiomarker", - "schema:domainIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:biomarkerFor", - "@type": "rdf:Property", - "rdfs:comment": "holds between a measurable molecular entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "biomarkerFor", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:expressedIn", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene or gene product and an anatomical entity in which it is expressed", - "rdfs:label": "expressedIn", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:AnatomicalEntity" - } - }, - { - "@id": "bts:expresses", - "@type": "rdf:Property", - "rdfs:comment": "holds between an anatomical entity and gene or gene product that is expressed there", - "rdfs:label": "expresses", - "schema:domainIncludes": { - "@id": "bts:AnatomicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:hasPhenotype", - "@type": "rdf:Property", - "rdfs:comment": "holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). ", - "rdfs:label": "hasPhenotype", - "schema:domainIncludes": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:precedes", - "@type": "rdf:Property", - "rdfs:comment": "holds between two processes, where one completes before the other begins", - "rdfs:label": "precedes", - "schema:domainIncludes": { - "@id": "bts:Occurrent" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Occurrent" - } - }, - { - "@id": "bts:subclassOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two classes where the domain class is a specialization of the range class", - "rdfs:label": "subclassOf", - "schema:domainIncludes": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:OntologyClass" - } - }, - { - "@id": "bts:DataFlow", - "@type": "rdfs:Class", - "rdfs:comment": "Describes data flow status", - "rdfs:label": "DataFlow", - "rdfs:subClassOf": [ - { - "@id": "bts:DataType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "dataFlow", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Contributor" - }, - { - "@id": "bts:DatasetId" - }, - { - "@id": "bts:DatasetName" - }, - { - "@id": "bts:DatasetType" - }, - { - "@id": "bts:UploadDate" - }, - { - "@id": "bts:NumItems" - }, - { - "@id": "bts:DatasetSize" - }, - { - "@id": "bts:ScheduledReleaseDate" - }, - { - "@id": "bts:ReleaseDate" - }, - { - "@id": "bts:Status" - }, - { - "@id": "bts:ReleasedDestinations" - }, - { - "@id": "bts:Released" - }, - { - "@id": "bts:MetadataCheck" - }, - { - "@id": "bts:GovernanceCompliance" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Contributor", - "@type": "rdfs:Class", - "rdfs:comment": "The team of a contributing user. 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"rdfs:subClassOf": [ - { - "@id": "bts:DataProperty" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "dataset_name", - "sms:required": "sms:true", - "sms:validationRules": [ - "str" - ] - }, - { - "@id": "bts:DatasetType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of dataset", - "rdfs:label": "DatasetType", - "rdfs:subClassOf": [ - { - "@id": "bts:DataProperty" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "dataset_type", - "sms:required": "sms:true", - "sms:validationRules": [ - "str" - ] - }, - { - "@id": "bts:UploadDate", - "@type": "rdfs:Class", - "rdfs:comment": "Date when both data records and data files (if applicable) have been uploaded", - "rdfs:label": "UploadDate", - "rdfs:subClassOf": [ - { - "@id": "bts:DataProperty" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "upload_date", - "sms:required": "sms:true", - "sms:validationRules": [ - 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} - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scheduled_release_date", - "sms:required": "sms:true", - "sms:validationRules": [ - "date" - ] - }, - { - "@id": "bts:ReleaseDate", - "@type": "rdfs:Class", - "rdfs:comment": "Date when a given dataset has actually been released", - "rdfs:label": "ReleaseDate", - "rdfs:subClassOf": [ - { - "@id": "bts:DataProperty" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "release_date", - "sms:required": "sms:true", - "sms:validationRules": [ - "date" - ] - }, - { - "@id": "bts:Status", - "@type": "rdfs:Class", - "rdfs:comment": "Data flow status of a dataset", - "rdfs:label": "Status", - "rdfs:subClassOf": [ - { - "@id": "bts:DataProperty" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Notuploaded" - }, - { - "@id": "bts:Uploaded" - }, - { - "@id": "bts:Curated" - }, - { - "@id": "bts:Quarantine" - 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}, - { - "@id": "bts:Uploaded", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Uploaded", - "rdfs:subClassOf": [ - { - "@id": "bts:Status" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "uploaded", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Curated", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Curated", - "rdfs:subClassOf": [ - { - "@id": "bts:Status" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "curated", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Quarantine", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Quarantine", - "rdfs:subClassOf": [ - { - "@id": "bts:Status" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "quarantine", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Preprocessing", - 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