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causal_network.yarrrml.yml
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#TODO aggregate size
#TODO check all assays reported in spreadsheet
prefixes:
rr: "http://www.w3.org/ns/r2rml#"
dc: "http://purl.org/dc/elements/1.1/"
dcterms: "http://purl.org/dc/terms/"
void: "http://rdfs.org/ns/void#"
rdfs: "http://www.w3.org/2000/01/rdf-schema#"
owl: "http://www.w3.org/2002/07/owl#"
xsd: "http://www.w3.org/2001/XMLSchema#"
rml: "http://semweb.mmlab.be/ns/rml#"
ql: "http://semweb.mmlab.be/ns/ql#"
d2rq: "http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#"
idlab-fn: "http://example.com/idlab/function/"
fnml: "http://semweb.mmlab.be/ns/fnml#"
fno: "http://w3id.org/function/ontology#"
grel: "http://users.ugent.be/~bjdmeest/function/grel.ttl#"
obo: "http://purl.obolibrary.org/obo/"
npo: "http://purl.bioontology.org/ontology/npo#"
enm: "http://purl.enanomapper.org/onto/"
amb: "http://purl.enanomapper.net/"
sio: "http://semanticscience.org/resource/SIO_"
wdt: "http://www.wikidata.org/prop/direct/"
wd: "http://www.wikidata.org/entity/"
bao: "http://www.bioassayontology.org/bao#"
efo: "http://www.ebi.ac.uk/efo/"
skos: "http://www.w3.org/2004/02/skos/core#"
cito: "http://purl.org/net/cito/"
nci: "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"
NCBITAXON: "http://purl.bioontology.org/ontology/NCBITAXON/"
sbdbel: "https://h2020-sbd4nano.github.io/sbdbel/"
nsvoc: "https://ammar257ammar.github.com/RDFied-datasets/nanosafery_vocabulary:"
fn: "https://w3id.org/imec/idlab/function#"
sbd4nano: "https://h2020-sbd4nano.github.io/sbd-data-landscape/"
placeholder: "https://purl.placeholder.enanomapper.net/"
erm: "https://nanocommons.github.io/identifiers/registry#"
cheminf: "http://semanticscience.org/resource/CHEMINF_"
base: https://h2020-sbd4nano.github.io/sbd-data-landscape/
authors:
- name: Javier Millan Acosta
website: http://orcid.org/0000-0002-4166-7093
- name: Ammar Ammar #original mappings for https://zenodo.org/badge/latestdoi/386910392
website: http://orcid.org/0000-0002-8399-8990
sources:
data-source: ['data/causal_network.csv~csv']
external:
licenseUrl: https://creativecommons.org/licenses/by/4.0/
publisherName: Javier Millan Acosta
publisherName2: Jeaphianne van Rijn
publisherName3: Egon Willighagen
datasetName: NANO_SBD_RDF
datasetTitle: NANO-SBD RDF
datasetDescription: RDF version of the literature review on nanomaterial SbD
datasetSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/dataset_
referenceSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/reference_
chemicalSubstanceSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/chemical_substance_
measureGroupSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/measurement_group_
assaySubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/assay_
protocolSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/protocol_
methodSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/method_
endpointSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/endpoint_
assertionSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/causal_assertion_
evidenceSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/evidence_
bioassayFormatSubjectUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/bioassay_format_
screeningConcentrationUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/screening_concentration_
causeUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/cause_
outcomeUrl: https://h2020-sbd4nano.github.io/sbd-data-landscape/outcome_
mappings:
dataset:
sources:
- data-source
subject:
- $(_datasetSubjectUrl)$(_datasetName)
predicateobjects:
- [a, void:DataSet~iri]
- [dcterms:title, $(_datasetTitle), en~lang]
- [dcterms:description, $(_datasetDescription), en~lang]
- [dcterms:license, $(_licenseUrl)~iri]
- [dcterms:creator, $(_publisherName)]
- [dcterms:creator, $(_publisherName2)]
- [dcterms:creator, $(_publisherName3)]
# References
reference:
sources:
- data-source
subjects:
- $(_referenceSubjectUrl)$(reference_id)
predicateobjects:
- [a, wd:Q13442814~iri]
- [owl:sameAs, $(source)~iri]
# Evidence
quoteEvidence:
sources:
- data-source
subjects:
- $(_evidenceSubjectUrl)$(row_id)
predicateobjects:
- [a, sio:000299~iri] #is a quote
- [sio:000208, $(_assertionSubjectUrl)$(row_id)~iri] #is supporting evidence for a causalAssertion
- [sbdbel:quote, $(quote), en~lang]
- [cito:containsAssertionFrom, $(_referenceSubjectUrl)$(reference_id)~iri]
# A bioassay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_$(row_id)~iri
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "bioassay"]
# A primary size assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_primary_size_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "primary size"]
# A hydrodynamic diameter assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "hydrodynamic size"]
# A surface area assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_surface_area_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "surface area"]
# A shape assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_shape_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "shape"]
# A zeta potential assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_zeta_potential_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "zeta potential"]
# A porosity assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_porosity_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "porosity"]
# A crystal structure assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_crystal_structure_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "crystal structure"]
# A polidispersity index assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_polidispersity_index_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "polidispersity"]
# A endotoxin assay
- predicate: obo:ECO_9000001 # uses (as evidence)
object: $(_assaySubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_as
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(uses_assay_type)]
- [grel:string_sub, "endotoxin"]
# causalAssertions
causalAssertion:
sources:
- data-source
subjects:
- $(_assertionSubjectUrl)$(row_id)
predicateobjects:
- [a, sio:001183~iri] #is a statement
- [sio:000206, $(_evidenceSubjectUrl)$(row_id)~iri] #is supported by an evidence
- [sbdbel:hasCause, $(s_iri)~iri]
- [sbdbel:hasRelationship, sbdbel:$(p)~iri]
- [sbdbel:hasOutcome, $(o_iri)~iri]
- [sio:000339, $(_referenceSubjectUrl)$(reference_id)~iri] #is specified by a reference
- [sio:000332, $(_chemicalSubstanceSubjectUrl)$(hash)~iri] # is about a chemical substance
# causes
cause:
sources:
- data-source
subjects:
- $(_causeUrl)_$(row_id)
predicateobjects:
- [a, sbdbel:cause~iri] #is a cause
- [rdfs:about, $(o_iri)]
# relationships
relationship:
sources:
- data-source
subjects:
- sbdbel:$(p)
predicateobjects:
- [a, sbdbel:relationship~iri] #is a relationship
- [rdfs:label, $(p)]
# outcomes
outcome:
sources:
- data-source
subjects:
- $(_outcomeUrl)$(row_id)
predicateobjects:
- [a, sbdbel:outcome~iri] #is an outcome
- [rdfs:about, $(o_iri)]
# Substance
chemicalSubstance:
sources:
- data-source
subjects:
- $(_chemicalSubstanceSubjectUrl)$(hash)
predicateobjects:
#- [dcterms:title, $(material_type), en~lang]
- [dcterms:description, $(material_type): $(material_description), en~lang]
- [a, $(material_iri)]
- [dcterms:identifier, erm:$(erm)]
# Sources
- predicate: dcterms:source
object: $(_datasetSubjectUrl)$(_datasetName)~iri
- predicate: dcterms:source
object: $(source)~iri
# primary size measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_primary_size_mg~iri
# bundle diameter measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_bundle_diameter_mg~iri
# hydrodynamic diameter measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_mg~iri
# surface area measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_surface_area_mg~iri
# shape measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_shape_mg~iri
# zeta potential measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_zeta_potential_mg~iri
# porosity measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_porosity_mg~iri
# crystal structure measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_crystal_structure_mg~iri
# polidispersity index measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_polidispersity_index_mg~iri
# endotoxin impurities measurement group
- predicate: obo:BFO_0000056
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_mg~iri
# Assays
## Bioassay
bioassay:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_$(row_id)
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_bio_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_bio_ap~iri
- predicate: bao:BAO_0000555 # Has assay format
object: $(_bioassayFormatSubjectUrl)$(hash)_$(reference_id)_$(row_id)~iri
## Assay primary size
assayPrimarySize:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_primary_size_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_primary_size_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_primary_size_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_primary_size_me~iri
## Assay bundle diameter
assayBundleDiameter:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_bundle_diameter_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_bundle_diameter_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_bundle_diameter_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_bundle_diameter~iri
## Assay diameter
assayDiameter:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_diameter_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_diameter_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_diameter_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_diameter~iri
## Assay hydrodynamic diameter
assayHydrodynamicDiameter:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter~iri
## Assay surface area
assaySurfaceArea:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_surface_area_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_surface_area_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_surface_area_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_surface_area~iri
## Assay shape
assayShape:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_shape_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_shape_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_shape_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_shape~iri
## Assay zeta potential
assayZetaPotential:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_zeta_potential_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_zeta_potential_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_zeta_potential_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_zeta_potential~iri
## Assay porosity
assayPorosity:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_porosity_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_porosity_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_porosity_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_porosity~iri
## Assay crystal_structure
assayCrystalStructure:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_crystal_structure_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_crystal_structure_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_crystal_structure_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_crystal_structure~iri
## Assay polidispersity index
assayPolidispersityIndex:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_polidispersity_index_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_polidispersity_index_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_polidispersity_index_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_polidispersity_index~iri
## Assay endotoxin impurities
assayEndotoxinImpurities:
sources:
- data-source
subjects: $(_assaySubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_as
predicateobjects:
- [a, bao:BAO_0000015~iri]
- predicate: bao:BAO_0000209
object: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_mg~iri
- predicate: bao:BAO_0002846
object: $(_protocolSubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_ap~iri
- predicate: bao:BAO_0000207
object: $(_methodSubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities~iri
# Methods
## Method primary size
methodPrimarySize:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_primary_size_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(primary_size_instrument)
datatype: xsd:string
## Method bundle diameter
methodBundleDiameter:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_bundle_diameter_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(bundle_diameter_instrument)
datatype: xsd:string
## Method diameter
methodDiameter:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_diameter_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(diameter_instrument)
datatype: xsd:string
## Method hydrodynamic diameter
methodHydrodynamicDiameter:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(hydrodynamic_diameter_instrument)
datatype: xsd:string
## Method surface area
methodSurfaceArea:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_surface_area_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(surface_area_instrument)
datatype: xsd:string
## Method zeta potential
methodZetaPotential:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_zeta_potential_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(zeta_potential_instrument)
datatype: xsd:string
## Method porosity
methodPorosity:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_porosity_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(porosity_instrument)
datatype: xsd:string
## Method crystal structure
methodCrystalStructure:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_crystal_structure_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(crystal_structure_instrument)
datatype: xsd:string
## Method polidispersity index
methodPolidispersityIndex:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_polidispersity_index_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(polidispersity_index_instrument)
datatype: xsd:string
## Method endotoxin impurities
methodEndotoxinImpurities:
sources:
- data-source
subjects: $(_methodSubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_me
predicateobjects:
- [a, bao:BAO_0000035~iri]
- predicate: rdfs:label
object:
value: $(endotoxin_impurities_instrument)
datatype: xsd:string
# Bioassay formats
## Organism
bioassayFormatOrganism:
sources:
- data-source
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(organism_iri)]
- [grel:string_sub, "http"]
subjects: $(_bioassayFormatSubjectUrl)$(hash)_$(reference_id)_$(row_id)
predicateobjects:
#- [rdfs:type, bao:BAO_0000219~iri] # type: organism format bioassay
- [bao:BAO_0002921, $(organism_iri)~iri] # organism
- [bao:BAO_0002833, $(exposure_time)] #incubation time value
- [bao:BAO_0000338, $(_screeningConcentrationUrl)$(hash)$(row_id)~iri]
# Missing exposure type
- predicate: a # a (assay format type)
object: $(assay_iri)~iri
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(assay_iri)]
- [grel:string_sub, "http"]
## Cell
bioassayFormatCell:
sources:
- data-source
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(model_cell_iri)]
- [grel:string_sub, "http"]
subjects: $(_bioassayFormatSubjectUrl)$(hash)_$(reference_id)_$(row_id)
predicateobjects:
- [bao:BAO_0002004, $(model_cell_iri)~iri] # cell line
- [bao:BAO_0002833, $(exposure_time)] #incubation time value
- [bao:BAO_0000338, $(_screeningConcentrationUrl)$(hash)$(row_id)~iri]
- predicate: rdfs:type # a (assay format type, e.g., ELISA)
object: $(assay_iri)~iri
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(assay_iri)]
- [grel:string_sub, "http"]
## Measurement Group Bioassay
measurementGroupBioassay:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_bio_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_$(row_id)_bioassay_ep~iri
## Measurement Group primary size
measurementGroupPrimarySize:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_primary_size_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_primary_size_ep~iri
## Measurement Group bundle diameter
measurementGroupBundleDiameter:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_bundle_diameter_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_bundle_diameter_ep~iri
## Measurement Group diameter
measurementGroupDiameter:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_diameter_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_diameter_ep~iri
## Measurement Group hydrodynamic diameter
measurementGroupHydrodynamicDiameter:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_ep~iri
## Measurement Group surface area
measurementGroupSurfaceArea:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_surface_area_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_surface_area_ep~iri
## Measurement Group zeta_potential
measurementGroupZetaPotential:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_zeta_potential_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_zeta_potential_ep~iri
## Measurement Group porosity
measurementGroupPorosity:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_porosity_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_porosity_ep~iri
## Measurement Group crystal structure
measurementGroupCrystalStructure:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_crystal_structure_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_crystal_structure_ep~iri
## Measurement Group polidispersity index
measurementGroupPolidispersityIndex:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_polidispersity_index_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_polidispersity_index_ep~iri
## Measurement Group endotoxin impurities
measurementGroupEndotoxinImpurities:
sources:
- data-source
subjects: $(_measureGroupSubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_mg
predicateobjects:
- [a, bao:BAO_0000040~iri]
- predicate: bao:BAO_0000208
object: $(_endpointSubjectUrl)$(hash)_$(reference_id)_endotoxin_impurities_ep~iri
# Endpoints
## Bioassay
endpointBioassay:
sources:
- data-source
subjects: $(_endpointSubjectUrl)$(hash)_$(reference_id)_$(row_id)_bioassay_ep
predicateobjects:
- predicate: a
object: $(endpoint_iri)~iri
condition:
function: grel:string_contains
parameters:
- [grel:valueParameter, $(endpoint_iri)]
- [grel:string_sub, "http"]
- [bao:BAO_0000182, $(endpoint_units)] # has response units, TODO change to UO
- [bao:BAO_0000108, $(endpoint_measurement)] # has response value
#TODO for now label is from spreadsheet as some classes are missing in enm
- [rdfs:label, $(endpoint)]
#- [bao:BAO_0002668, $(exposure_time_units)] # has time units TODO change to UO
#- [bao:BAO_0002669, $(exposure_time)] # has time value
#- [bao:BAO_0000338, $(_screeningConcentrationUrl)$(hash)$(row_id)~iri] # has screeninig concentration
screeningConcentration:
sources:
- data-source
subjects: $(_screeningConcentrationUrl)$(hash)$(row_id)
predicateobjects:
- [a, bao:BAO_0000098]
- [bao:BAO_0000183, $(dose_units)] # has concentration units
- [bao:BAO_0002666, $(dose)]
## Primary Size
endpointPrimarySize:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_primary_size_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300 # For non-ranges
object:
value: $(primary_size)
datatype: xsd:float
#TODO - predicate: sio:madeup # For ranges
#TODO object:
#TODO value: $(primary_size)
#TODO datatype: xsd:string
#TODO condition:
#TODO function: grel:string_contains
#TODO parameters:
#TODO - [grel:valueParameter, $(primary_size)]
#TODO - [grel:string_sub, "-"]
#TODO qualifiers
endpointHydrodynamicDiameter:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_hydrodynamic_diameter_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300 # For non-ranges
object:
value: $(hydrodynamic_diameter)
datatype: xsd:float
#- predicate: sio:000221 # unit
# object:
# value: $(hydrodynamic_diameter_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers
endpointSurfaceArea:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_surface_area_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300 # For non-ranges
object:
value: $(surface_area)
datatype: xsd:float
#- predicate: sio:000221 # unit
# object:
# value: $(surface_area_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers
endpointShape:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_shape_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300
object:
value: $(shape)
datatype: xsd:string
#- predicate: sio:000221 # unit
# object:
# value: $(surface_area_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers
endpointZetaPotential:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_zeta_potential_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri] #TODO annotate
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300
object:
value: $(zeta_potential)
datatype: xsd:float
#- predicate: sio:000221 # unit
# object:
# value: $(surface_area_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers
endpointPorosity:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_porosity_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300
object:
value: $(porosity)
datatype: xsd:float
#- predicate: sio:000221 # unit
# object:
# value: $(surface_area_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers
endpointCrystalStructure:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_crystal_structure_ep
predicateobjects:
- [a, bao:BAO_000017]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300
object:
value: $(porosity)
datatype: xsd:float
#- predicate: sio:000221 # unit
# object:
# value: $(surface_area_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers
endpointPolidispersityIndex:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_polidispersity_index_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300
object:
value: $(polidispersity_index)
datatype: xsd:float
#- predicate: sio:000221 # unit
# object:
# value: $(surface_area_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers
endpointEndotoxin:
sources:
- data-source
subjects:
- $(_endpointSubjectUrl)$(hash)_$(reference_id)_endotoxin_ep
predicateobjects:
- [a, bao:BAO_0000179~iri]
- [a, obo:PATO_0000117~iri]
- [sio:000221, obo:UO_0000018~iri]
- predicate: sio:000300
object:
value: $(endotoxin)
datatype: xsd:float
#- predicate: sio:000221 # unit
# object:
# value: $(surface_area_unit) #TODO change for ontology unit
# datatype: xsd:float
#TODO qualifiers