introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/introduction... ·...
TRANSCRIPT
Introduction to conceptual modeling
and next steps
Bring Your Own Data To Link Rare Disease Registries
1Organised by Istituto Superiore di Sanità
Rome (Italy), September 21-22, 2017
and next steps
Marco Roos
Leiden University Medical Center, The Netherlands
Our data
Name Phenotype ...
Marco Big head ...Marco Big head ...
... ... ...
LegendInstance
• the human being referred to by as “Marco”
• my big head
Class
• Human being• Human being
• Abnormality of the head
Relation (aka property, aka predicate)
• has name
• has phenotype
Value
• “Marco”
• “Groot hoofd”
“...”
type
Human being
label
“Marco”
type
Name Phenotype ...
Marco Big head ...
... ... ...
type
Human beingAbnormality
of the head
type
Name Phenotype ...
Marco Big head ...
... ... ...
(Marco’s big head)
type
has
phenotype
label
“Marco”
type
Human beingAbnormality
of the head
has id Marco’s ORCID
type
Name Phenotype ...
Marco Big head ...
... ... ...
(Marco’s big head)
type
has
phenotype
label
“Marco”
Your turn...Your turn...
Conceptual modelling
with ontologieswith ontologies
Task: lookup and replace names with URIs
type
Human beingAbnormality
of the head
has id Marco’s ORCID
type
Name Phenotype ...
Marco Big head ...
... ... ...
(Marco’s big head)
type
has
phenotype
type
Human beingAbnormality
of the head http://purl.obolibrary.org/obo/VTO_0011993
has id Marco’s ORCID
type
Name Phenotype ...
Marco Big head ...
... ... ...
Marco’s big head
type
has
phenotype
type
Human beingAbnormality
of the head http://purl.obolibrary.org/obo/VTO_0011993
has id Marco’s ORCID
type
Name Phenotype ...
Marco Big head ...
... ... ...
Marco’s big head
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
type
Human beingAbnormality
of the head http://purl.obolibrary.org/obo/VTO_0011993
has id “http://orcid.org/0000-0002-8691-772X”
type
Name Phenotype ...
Marco Big head ...
... ... ...
Marco’s big head
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://orcid.org/0000-0002-5312-6729
type
Human beingAbnormality
of the head http://purl.obolibrary.org/obo/VTO_0011993
has id “http://orcid.org/0000-0002-8691-772X”
type
Name Phenotype ...
Marco Big head ...
... ... ...
Marco’s big head
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200
Marco’s Registry
type
Human beingIncreased head
circumference http://purl.obolibrary.org/obo/VTO_0011993
http://purl.obolibrary.org/obo/HP_0040194
has id “http://orcid.org/0000-0002-8691-772X”
type
Name Phenotype ...
Marco Big head ...
... ... ...“Marco’s big head”
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200label
Your turn...Your turn...
Marco’s Registry
type
Human beingIncreased head
circumference http://purl.obolibrary.org/obo/VTO_0011993
http://purl.obolibrary.org/obo/HP_0040194
has id “http://orcid.org/0000-0002-8691-772X”
type
Name Phenotype ...
Marco Big head ...
... ... ...“Marco’s big head”
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200label
Alice’s registry
type
Human beingDecreased head
circumference http://purl.obolibrary.org/obo/VTO_0011993
http://purl.obolibrary.org/obo/HP_0000252
has id “http://orcid.org/xxx”
type
Name Phenotype ...
Marco Big head ...
... ... ...“Alice’s small head”
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200label
Query
How many persons have an abnormal head-size?
Marco’s
registy
Alice’s
registyHPO
Virtual graph
type
Human beingIncreased head
circumference http://purl.obolibrary.org/obo/VTO_0011993
obo:HP_0040194
Decreased head
circumference
obo:HP_0000252
Abnormality of the Headobo/HP_0000234
has id “http://orcid.org/0000-0002-8691-772X”
type
“Marco’s big head”
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200
“http://orcid.org/xxx...”has id
“Alice’s small head”
Abnormality of the Headobo/HP_0000234
Virtual graph
type
Human beingIncreased head
circumference http://purl.obolibrary.org/obo/VTO_0011993
obo:HP_0040194
Decreased head
circumference
obo:HP_0000252
Abnormality of the Headobo/HP_0000234
Human being
http://purl.obolibrary.org/obo/VTO_0011993
has id “http://orcid.org/0000-0002-8691-772X”
type
“Marco’s big head”
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200
“http://orcid.org/xxx...”has id
“Alice’s small head”
Abnormality of the Headobo/HP_0000234
Virtual graph
type
Human beingIncreased head
circumference http://purl.obolibrary.org/obo/VTO_0011993
obo:HP_0040194
Decreased head
circumference
obo:HP_0000252
type
Abnormality of the Headobo/HP_0000234
Human being
http://purl.obolibrary.org/obo/VTO_0011993
has id “http://orcid.org/0000-0002-8691-772X”
type
“Marco’s big head”
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200
“http://orcid.org/xxx...”has id
“Alice’s small head”
type
Abnormality of the Headobo/HP_0000234
Virtual graph
type
Human beingIncreased head
circumference http://purl.obolibrary.org/obo/VTO_0011993
obo:HP_0040194
Decreased head
circumference
obo:HP_0000252
type
Abnormality of the Headobo/HP_0000234
Human being
http://purl.obolibrary.org/obo/VTO_0011993
has id “http://orcid.org/0000-0002-8691-772X”
type
“Marco’s big head”
type
has
phenotype
http://purl.org/dc/elements/1.1/identifier
http://purl.obolibrary.org/obo/RO_0002200
“http://orcid.org/xxx...”has id
“Alice’s small head”
type
Query
How many persons have an abnormal head-size?
Result:2