An RDF/OWL representation of the PCORnet Common Data Model Version 3.0 Contains Demographic Table birth time birth date sex - male/female/ambigous Hispanic - refusal to answer Hispanic - Hispanic, non-Hispanic race - refusal to answer To Do Demographic Table sex - other/unknown (working on a general strategy for other and unknown null flavors) race -
RDFized PCORnet CDM
BFO OWL specification label
BFO CLIF specification label
example of usage
definition
editor note
imported from
elucidation
has associated axiom(nl)
has associated axiom(fol)
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
exists at
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
has proper occurrent part
[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life.
[copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
has temporal part
Mary’s 5th birthday occurrent_part_of Mary’s life
The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
the first set of the tennis match occurrent_part_of the tennis match.
[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
part of occurrent
[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]
proper part of occurrent
the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
the process boundary which separates the 3rd and 4th years of your life.
your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
temporal part of
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
occupies temporal region
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
during which exists
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
database extract, transform, and load process
A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
ETL
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A quality that inheres in an entire organism or part of an organism.
answer to ID question
response to an ID question asking process
ID question asking process
refusal to answer datum
response to a question asking process
ethnic ID question asking process
race ID question asking process
PCORnet racial identification process
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
Of or pertaining to the period of time immediately following birth, or to the newborn.
A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
A life cycle temporal boundary that marks the end of the life cycle of the organism.
A life cycle temporal boundary that marks the start of the neonate stage of the organism.
PROMIS response data item
question asking process
Amanda Hicks
A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process.
PCORnet racial identity datum
question text
answer set
PCORnet American Indian or Alaska Native identity datum
PCORnet Asian identity datum
material information bearer of question text plus answer set
PCORnet black or African American identity datum
PCORnet CDM item identifier
PCORnet item
option as member of answer set
PCORnet Native Hawaiian or other Pacific Islander identity datum
PCORnet white identity datum
PCORnet multiple race identity datum
From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race."
PCORnet Hispanic identity datum
PCORnet not Hispanic identity datum
PCORnet ethnic identity datum
A centrally registered identifier that denotes a person in a PCORnet data mart and is used to link across tables. This identifier is not necessarily unique within PCORnet.
PCORnet patient identifier
John Doe
John Doe's birth
John Doe's neonate stage
1D temporal interval occuped by John Doe's neonate stage
rta1
eiqap1
Jane Doe
ridqap1
Jane Doe's American Indian or Alaska Native identity datum
rta2
Jane Doe's racial identification process
ETL process of Jane Doe’s racial identity datum
John Doe's patient role
John Doe's Hispanic or Latino identity datum
John Doe’s ethnic identification process
John Doe’s PCORnet Hispanic identity datum
ETL process of John Doe’s ethnic identity datum
Jane Doe's not Hispanic or Latino identity datum
Jane Doe’s ethnic identification process
Jane Doe’s PCORnet not Hispanic identity datum
ETL process of Jane Doe’s ethnic identity datum