From d9f9de4f435fce7b1eec3bed008ae485dacbde09 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Wed, 24 Jan 2024 17:04:55 +0000 Subject: [PATCH] Add new occupational_exposure_to_material pattern Fix #250 --- .../occupational_exposure_to_material.tsv | 4 + src/patterns/definitions.owl | 277 ++++++++++-------- .../occupational_exposure_to_material.yaml | 74 +++++ 3 files changed, 231 insertions(+), 124 deletions(-) create mode 100644 src/patterns/data/default/occupational_exposure_to_material.tsv create mode 100644 src/patterns/dosdp-patterns/occupational_exposure_to_material.yaml diff --git a/src/patterns/data/default/occupational_exposure_to_material.tsv b/src/patterns/data/default/occupational_exposure_to_material.tsv new file mode 100644 index 0000000..de23bd0 --- /dev/null +++ b/src/patterns/data/default/occupational_exposure_to_material.tsv @@ -0,0 +1,4 @@ +defined_class defined_class_name material material_name exact_synonyms xrefs orcid +ECTO:1999999 ENVO:02000112 fume https://orcid.org/0000-0001-8314-2140 +ECTO:1999998 ENVO:02000107 grain dust https://orcid.org/0000-0001-8314-2140 +ECTO:1999997 occupational exposure to urea-based herbicide CHEBI:188147 urea herbicide https://orcid.org/0000-0001-8314-2140 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index d1e9aaf..a91e709 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-01-13") + +Annotation(owl:versionInfo "2024-01-24") Declaration(Class()) Declaration(Class()) @@ -2570,6 +2570,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5581,6 +5584,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6018,8 +6023,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to environmental quality) -AnnotationAssertion( "A exposure event involving the interaction of an exposure receptor to quality.") -AnnotationAssertion( "quality exposure") +AnnotationAssertion( "A exposure event involving the interaction of an exposure receptor to characteristic.") +AnnotationAssertion( "characteristic exposure") AnnotationAssertion(rdfs:label "exposure to environmental quality") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -6200,106 +6205,106 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to apple via ingestion) -AnnotationAssertion( "An exposure to apple (whole) via ingestion.") -AnnotationAssertion( "apple (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to apple via ingestion.") +AnnotationAssertion( "apple exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to apple via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to avocado via ingestion) -AnnotationAssertion( "An exposure to avocado (whole, raw) via ingestion.") -AnnotationAssertion( "avocado (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to avocado (raw) via ingestion.") +AnnotationAssertion( "avocado (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to avocado via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to banana via ingestion) -AnnotationAssertion( "An exposure to banana (whole) via ingestion.") -AnnotationAssertion( "banana (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to banana via ingestion.") +AnnotationAssertion( "banana exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to banana via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to blueberries via ingestion) -AnnotationAssertion( "An exposure to blueberry (whole, raw) via ingestion.") -AnnotationAssertion( "blueberry (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to blueberry (raw) via ingestion.") +AnnotationAssertion( "blueberry (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to blueberries via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to cantaloupe via ingestion) -AnnotationAssertion( "An exposure to cantaloupe (whole, raw) via ingestion.") -AnnotationAssertion( "cantaloupe (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to cantaloupe (raw) via ingestion.") +AnnotationAssertion( "cantaloupe (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to cantaloupe via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to grapes via ingestion) -AnnotationAssertion( "An exposure to grape (whole, raw) via ingestion.") -AnnotationAssertion( "grape (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to grape (raw) via ingestion.") +AnnotationAssertion( "grape (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to grapes via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to grapefruit via ingestion) -AnnotationAssertion( "An exposure to grapefruit (whole, raw) via ingestion.") -AnnotationAssertion( "grapefruit (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to grapefruit (raw) via ingestion.") +AnnotationAssertion( "grapefruit (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to grapefruit via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to navel orange via ingestion) -AnnotationAssertion( "An exposure to navel orange (whole, raw) via ingestion.") -AnnotationAssertion( "navel orange (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to navel orange (raw) via ingestion.") +AnnotationAssertion( "navel orange (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to navel orange via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to peach via ingestion) -AnnotationAssertion( "An exposure to peach (whole, raw) via ingestion.") -AnnotationAssertion( "peach (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to peach (raw) via ingestion.") +AnnotationAssertion( "peach (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to peach via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to plum via ingestion) -AnnotationAssertion( "An exposure to plum (whole, raw) via ingestion.") -AnnotationAssertion( "plum (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to plum (raw) via ingestion.") +AnnotationAssertion( "plum (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to plum via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to apricot via ingestion) -AnnotationAssertion( "An exposure to apricot (whole, raw) via ingestion.") -AnnotationAssertion( "apricot (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to apricot (raw) via ingestion.") +AnnotationAssertion( "apricot (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to apricot via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to pear via ingestion) -AnnotationAssertion( "An exposure to pear (whole, raw) via ingestion.") -AnnotationAssertion( "pear (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to pear (raw) via ingestion.") +AnnotationAssertion( "pear (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to pear via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to raspberry via ingestion) -AnnotationAssertion( "An exposure to raspberry (whole, raw) via ingestion.") -AnnotationAssertion( "raspberry (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to raspberry (raw) via ingestion.") +AnnotationAssertion( "raspberry (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to raspberry via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to strawberry via ingestion) -AnnotationAssertion( "An exposure to strawberry (whole, raw) via ingestion.") -AnnotationAssertion( "strawberry (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to strawberry (raw) via ingestion.") +AnnotationAssertion( "strawberry (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to strawberry via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to tomato via ingestion) -AnnotationAssertion( "An exposure to tomato (whole) via ingestion.") -AnnotationAssertion( "tomato (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to tomato via ingestion.") +AnnotationAssertion( "tomato exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to tomato via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6319,43 +6324,43 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to watermelon via ingestion) -AnnotationAssertion( "An exposure to watermelon (whole, raw) via ingestion.") -AnnotationAssertion( "watermelon (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to watermelon (raw) via ingestion.") +AnnotationAssertion( "watermelon (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to watermelon via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to bean via ingestion) -AnnotationAssertion( "An exposure to bean (whole) via ingestion.") -AnnotationAssertion( "bean (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to bean via ingestion.") +AnnotationAssertion( "bean exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to bean via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to lentil via ingestion) -AnnotationAssertion( "An exposure to lentil (whole) via ingestion.") -AnnotationAssertion( "lentil (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to lentil via ingestion.") +AnnotationAssertion( "lentil exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to lentil via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to bell pepper via ingestion) -AnnotationAssertion( "An exposure to bell pepper (whole) via ingestion.") -AnnotationAssertion( "bell pepper (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to bell pepper via ingestion.") +AnnotationAssertion( "bell pepper exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to bell pepper via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to broccoli via ingestion) -AnnotationAssertion( "An exposure to broccoli floret (whole, raw) via ingestion.") -AnnotationAssertion( "broccoli floret (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to broccoli floret (raw) via ingestion.") +AnnotationAssertion( "broccoli floret (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to broccoli via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to brussels sprout via ingestion) -AnnotationAssertion( "An exposure to brussels sprout (whole) via ingestion.") -AnnotationAssertion( "brussels sprout (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to brussels sprout via ingestion.") +AnnotationAssertion( "brussels sprout exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to brussels sprout via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6368,57 +6373,57 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to carrot via ingestion) -AnnotationAssertion( "An exposure to carrot root (whole) via ingestion.") -AnnotationAssertion( "carrot root (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to carrot root via ingestion.") +AnnotationAssertion( "carrot root exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to carrot via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to cauliflower via ingestion) -AnnotationAssertion( "An exposure to cauliflower floret (whole) via ingestion.") -AnnotationAssertion( "cauliflower floret (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to cauliflower floret via ingestion.") +AnnotationAssertion( "cauliflower floret exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to cauliflower via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to corn via ingestion) -AnnotationAssertion( "An exposure to corn kernel (whole) via ingestion.") -AnnotationAssertion( "corn kernel (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to corn kernel via ingestion.") +AnnotationAssertion( "corn kernel exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to corn via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to eggplant via ingestion) -AnnotationAssertion( "An exposure to eggplant (whole) via ingestion.") -AnnotationAssertion( "eggplant (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to eggplant via ingestion.") +AnnotationAssertion( "eggplant exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to eggplant via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to zucchini via ingestion) -AnnotationAssertion( "An exposure to zucchini squash (whole) via ingestion.") -AnnotationAssertion( "zucchini squash (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to zucchini squash via ingestion.") +AnnotationAssertion( "zucchini squash exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to zucchini via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to squash via ingestion) -AnnotationAssertion( "An exposure to squash (whole) via ingestion.") -AnnotationAssertion( "squash (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to squash via ingestion.") +AnnotationAssertion( "squash exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to squash via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to kale via ingestion) -AnnotationAssertion( "An exposure to kale leaf (whole, raw) via ingestion.") -AnnotationAssertion( "kale leaf (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to kale leaf (raw) via ingestion.") +AnnotationAssertion( "kale leaf (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to kale via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to collard greens via ingestion) -AnnotationAssertion( "An exposure to collard leaf (whole, raw) via ingestion.") -AnnotationAssertion( "collard leaf (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to collard leaf (raw) via ingestion.") +AnnotationAssertion( "collard leaf (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to collard greens via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6431,43 +6436,43 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to swiss chard via ingestion) -AnnotationAssertion( "An exposure to swiss chard leaf (whole) via ingestion.") -AnnotationAssertion( "swiss chard leaf (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to swiss chard leaf via ingestion.") +AnnotationAssertion( "swiss chard leaf exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to swiss chard via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to onion via ingestion) -AnnotationAssertion( "An exposure to onion (whole, raw) via ingestion.") -AnnotationAssertion( "onion (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to onion (raw) via ingestion.") +AnnotationAssertion( "onion (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to onion via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to peas via ingestion) -AnnotationAssertion( "An exposure to pea (whole) via ingestion.") -AnnotationAssertion( "pea (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to pea via ingestion.") +AnnotationAssertion( "pea exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to peas via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to lima bean via ingestion) -AnnotationAssertion( "An exposure to baby lima bean (whole) via ingestion.") -AnnotationAssertion( "baby lima bean (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to baby lima bean via ingestion.") +AnnotationAssertion( "baby lima bean exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to lima bean via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to spinach leaf (whole) via ingestion) -AnnotationAssertion( "An exposure to spinach leaf (whole) via ingestion.") -AnnotationAssertion( "spinach leaf (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to spinach leaf via ingestion.") +AnnotationAssertion( "spinach leaf exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to spinach leaf (whole) via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to spinach leaf (whole, raw) via ingestion) -AnnotationAssertion( "An exposure to spinach leaf (whole, raw) via ingestion.") -AnnotationAssertion( "spinach leaf (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to spinach leaf (raw) via ingestion.") +AnnotationAssertion( "spinach leaf (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to spinach leaf (whole, raw) via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6480,8 +6485,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to green bean via ingestion) -AnnotationAssertion( "An exposure to green bean pod (whole) via ingestion.") -AnnotationAssertion( "green bean pod (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to green bean pod via ingestion.") +AnnotationAssertion( "green bean pod exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to green bean via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6508,36 +6513,36 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to soybean via ingestion) -AnnotationAssertion( "An exposure to soybean (whole) via ingestion.") -AnnotationAssertion( "soybean (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to soybean via ingestion.") +AnnotationAssertion( "soybean exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to soybean via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to winter squash via ingestion) -AnnotationAssertion( "An exposure to squash (whole, raw) via ingestion.") -AnnotationAssertion( "squash (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to squash (raw) via ingestion.") +AnnotationAssertion( "squash (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to winter squash via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to yam via ingestion) -AnnotationAssertion( "An exposure to yam (whole) via ingestion.") -AnnotationAssertion( "yam (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to yam via ingestion.") +AnnotationAssertion( "yam exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to yam via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to sweet potato via ingestion) -AnnotationAssertion( "An exposure to sweet potato (whole) via ingestion.") -AnnotationAssertion( "sweet potato (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to sweet potato via ingestion.") +AnnotationAssertion( "sweet potato exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to sweet potato via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to egg via ingestion) -AnnotationAssertion( "An exposure to hen egg (whole) via ingestion.") -AnnotationAssertion( "hen egg (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to hen egg via ingestion.") +AnnotationAssertion( "hen egg exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to egg via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6914,8 +6919,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to white rice via ingestion) -AnnotationAssertion( "An exposure to white rice (whole) via ingestion.") -AnnotationAssertion( "white rice (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to white rice via ingestion.") +AnnotationAssertion( "white rice exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to white rice via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6935,8 +6940,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to couscous via ingestion) -AnnotationAssertion( "An exposure to couscous (whole, dried) via ingestion.") -AnnotationAssertion( "couscous (whole, dried) exposure via ingestion") +AnnotationAssertion( "An exposure to couscous (dried) via ingestion.") +AnnotationAssertion( "couscous (dried) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to couscous via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -6956,8 +6961,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to potato via ingestion) -AnnotationAssertion( "An exposure to potato (whole) via ingestion.") -AnnotationAssertion( "potato (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to potato via ingestion.") +AnnotationAssertion( "potato exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to potato via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -7124,22 +7129,22 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to peanut via ingestion) -AnnotationAssertion( "An exposure to peanut (whole) via ingestion.") -AnnotationAssertion( "peanut (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to peanut via ingestion.") +AnnotationAssertion( "peanut exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to peanut via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to walnuts via ingestion) -AnnotationAssertion( "An exposure to walnut (whole, raw) via ingestion.") -AnnotationAssertion( "walnut (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to walnut (raw) via ingestion.") +AnnotationAssertion( "walnut (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to walnuts via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to nuts via ingestion) -AnnotationAssertion( "An exposure to nut (whole or parts) via ingestion.") -AnnotationAssertion( "nut (whole or parts) exposure via ingestion") +AnnotationAssertion( "An exposure to nut (whole or pieces) via ingestion.") +AnnotationAssertion( "nut (whole or pieces) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to nuts via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -7292,29 +7297,29 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to Williams pear via ingestion) -AnnotationAssertion( "An exposure to Williams pear (whole) via ingestion.") -AnnotationAssertion( "Williams pear (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to Williams pear via ingestion.") +AnnotationAssertion( "Williams pear exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to Williams pear via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to red onion via ingestion) -AnnotationAssertion( "An exposure to red onion (whole, raw) via ingestion.") -AnnotationAssertion( "red onion (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to red onion (raw) via ingestion.") +AnnotationAssertion( "red onion (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to red onion via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to white onion via ingestion) -AnnotationAssertion( "An exposure to white onion (whole, raw) via ingestion.") -AnnotationAssertion( "white onion (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to white onion (raw) via ingestion.") +AnnotationAssertion( "white onion (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to white onion via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to yellow onion via ingestion) -AnnotationAssertion( "An exposure to yellow onion (whole, raw) via ingestion.") -AnnotationAssertion( "yellow onion (whole, raw) exposure via ingestion") +AnnotationAssertion( "An exposure to yellow onion (raw) via ingestion.") +AnnotationAssertion( "yellow onion (raw) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to yellow onion via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -7334,15 +7339,15 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to plant leaf vegetable food product via ingestion) -AnnotationAssertion( "An exposure to plant leaf vegetable food product via ingestion.") -AnnotationAssertion( "plant leaf vegetable food product exposure via ingestion") +AnnotationAssertion( "An exposure to plant leaf food product via ingestion.") +AnnotationAssertion( "plant leaf food product exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to plant leaf vegetable food product via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (exposure to bacon (whole cut or parts) via ingestion) -AnnotationAssertion( "An exposure to bacon (whole cut or parts) via ingestion.") -AnnotationAssertion( "bacon (whole cut or parts) exposure via ingestion") +AnnotationAssertion( "An exposure to bacon (whole cut or pieces) via ingestion.") +AnnotationAssertion( "bacon (whole cut or pieces) exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to bacon (whole cut or parts) via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -7446,8 +7451,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to winter squash (whole) via ingestion) -AnnotationAssertion( "An exposure to winter squash (whole) via ingestion.") -AnnotationAssertion( "winter squash (whole) exposure via ingestion") +AnnotationAssertion( "An exposure to winter squash via ingestion.") +AnnotationAssertion( "winter squash exposure via ingestion") AnnotationAssertion(rdfs:label "exposure to winter squash (whole) via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -7537,8 +7542,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to chlorpyrifos in apple via ingestion) -AnnotationAssertion( "An exposure to chlorpyrifos mixed in apple (whole) via ingestion.") -AnnotationAssertion( "chlorpyrifos exposure in apple (whole) via ingestion") +AnnotationAssertion( "An exposure to chlorpyrifos mixed in apple via ingestion.") +AnnotationAssertion( "chlorpyrifos exposure in apple via ingestion") AnnotationAssertion(rdfs:label "exposure to chlorpyrifos in apple via ingestion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -8907,6 +8912,30 @@ AnnotationAssertion( "exposure to landspout") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (occupational exposure to urea-based herbicide) + +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/occupational_exposure_to_material") "Exposure to urea herbicide which is related to some occupation(s).") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/proportion_of_attributes") "occupational exposure to urea herbicide") +AnnotationAssertion(rdfs:label "occupational exposure to urea-based herbicide") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( )))) + +# Class: (occupational grain dust exposure) + +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/occupational_exposure_to_material") "Exposure to grain dust which is related to some occupation(s).") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/proportion_of_attributes") "occupational exposure to grain dust") +AnnotationAssertion(rdfs:label "occupational grain dust exposure") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( )))) + +# Class: (occupational fume exposure) + +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/occupational_exposure_to_material") "Exposure to fume which is related to some occupation(s).") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/proportion_of_attributes") "occupational exposure to fume") +AnnotationAssertion(rdfs:label "occupational fume exposure") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( )))) + # Class: (exposure to medical action) AnnotationAssertion( "An exposure to medical action.") @@ -8937,8 +8966,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to theraputic insulin treatment) -AnnotationAssertion( "An exposure to therapeutic insulin treatment.") -AnnotationAssertion( "exposure to therapeutic insulin treatment") +AnnotationAssertion( "An exposure to insulin treatment.") +AnnotationAssertion( "exposure to insulin treatment") AnnotationAssertion(rdfs:label "exposure to theraputic insulin treatment") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -9119,8 +9148,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to theraputic tranquilizers) -AnnotationAssertion( "An exposure to tranquilizing agent therapy.") -AnnotationAssertion( "exposure to tranquilizing agent therapy") +AnnotationAssertion( "An exposure to obsolete tranquilizing agent therapy.") +AnnotationAssertion( "exposure to obsolete tranquilizing agent therapy") AnnotationAssertion(rdfs:label "exposure to theraputic tranquilizers") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -9252,8 +9281,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to angiography) -AnnotationAssertion( "An exposure to Angiography.") -AnnotationAssertion( "exposure to Angiography") +AnnotationAssertion( "An exposure to X-ray Angiography.") +AnnotationAssertion( "exposure to X-ray Angiography") AnnotationAssertion(rdfs:label "exposure to angiography") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -9280,8 +9309,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to kidney implantation) -AnnotationAssertion( "An exposure to kidney transplantation.") -AnnotationAssertion( "exposure to kidney transplantation") +AnnotationAssertion( "An exposure to whole kidney transplantation.") +AnnotationAssertion( "exposure to whole kidney transplantation") AnnotationAssertion(rdfs:label "exposure to kidney implantation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -9399,8 +9428,8 @@ EquivalentClasses( ObjectIntersecti # Class: (exposure to change) -AnnotationAssertion( "A exposure event involving the interaction of an exposure receptor to deviation (from_normal) of quality.") -AnnotationAssertion( "exposure to deviation (from_normal) in quality") +AnnotationAssertion( "A exposure event involving the interaction of an exposure receptor to deviation (from_normal) of characteristic.") +AnnotationAssertion( "exposure to deviation (from_normal) in characteristic") AnnotationAssertion(rdfs:label "exposure to change") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) diff --git a/src/patterns/dosdp-patterns/occupational_exposure_to_material.yaml b/src/patterns/dosdp-patterns/occupational_exposure_to_material.yaml new file mode 100644 index 0000000..12257b4 --- /dev/null +++ b/src/patterns/dosdp-patterns/occupational_exposure_to_material.yaml @@ -0,0 +1,74 @@ +--- +pattern_name: occupational_exposure_to_material +pattern_iri: http://purl.obolibrary.org/obo/ecto/patterns/occupational_exposure_to_material.yaml + +description: 'Use this pattern to create compound term that categorise + exposures to various materials from the environment related to some + occupations.' + +# examples +# occupational fume exposure +# occupational grain dust exposure +# occupational exposure to urea-based herbicide + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + +classes: + occupation: NCIT:C25193 + exposure_event: ExO:0000002 + material: BFO:0000040 # material entity + +relations: + has_exposure_stimulus: RO:0002309 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym + xref: oio:hasDbXref + contributor: dct:contributor + +vars: + material: "'material'" + +data_list_vars: + orcid: xsd:anyURI # ORCID of contributor + exact_synonyms: xsd:string # add a list of exact synonyms + xrefs: xsd:anyURI # add a list of external references + +name: + text: "occupational %s exposure" + vars: + - material + +def: + text: "Exposure to %s which is related to some occupation(s)." + vars: + - material + annotations: + - annotationProperty: xref + text: "AUTO:patterns/patterns/occupational_exposure_to_material" + +annotations: + - annotationProperty: exact_synonym + text: "occupational exposure to %s" + vars: + - material + annotations: + - annotationProperty: xref + text: "AUTO:patterns/patterns/proportion_of_attributes" + + - annotationProperty: contributor + value: orcid + +exact_synonym: + value: exact_synonyms + +xref: + value: xrefs + +equivalentTo: + text: "'exposure_event' + and ('has_exposure_stimulus' some ('occupation' and %s))" + vars: + - material