introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/introduction... ·...
TRANSCRIPT
![Page 1: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/1.jpg)
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
![Page 2: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/2.jpg)
Our data
Name Phenotype ...
Marco Big head ...Marco Big head ...
... ... ...
![Page 3: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/3.jpg)
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”
“...”
![Page 4: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/4.jpg)
type
Human being
label
“Marco”
type
Name Phenotype ...
Marco Big head ...
... ... ...
![Page 5: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/5.jpg)
type
Human beingAbnormality
of the head
type
Name Phenotype ...
Marco Big head ...
... ... ...
(Marco’s big head)
type
has
phenotype
label
“Marco”
![Page 6: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/6.jpg)
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”
![Page 7: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/7.jpg)
Your turn...Your turn...
![Page 8: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/8.jpg)
Conceptual modelling
with ontologieswith ontologies
![Page 9: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/9.jpg)
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
![Page 10: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/10.jpg)
![Page 11: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/11.jpg)
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
![Page 12: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/12.jpg)
![Page 13: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/13.jpg)
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
![Page 14: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/14.jpg)
![Page 15: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/15.jpg)
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
![Page 16: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/16.jpg)
![Page 17: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/17.jpg)
![Page 18: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/18.jpg)
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
![Page 19: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/19.jpg)
![Page 20: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/20.jpg)
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
![Page 21: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/21.jpg)
Your turn...Your turn...
![Page 22: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/22.jpg)
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
![Page 23: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/23.jpg)
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
![Page 24: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/24.jpg)
Query
How many persons have an abnormal head-size?
Marco’s
registy
Alice’s
registyHPO
![Page 25: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/25.jpg)
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”
![Page 26: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/26.jpg)
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”
![Page 27: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/27.jpg)
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
![Page 28: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/28.jpg)
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
![Page 29: Introduction to conceptual modeling and next stepsold.iss.it/binary/cnmr4/cont/Introduction... · Introduction to conceptual modeling and next steps Bring Your Own Data To Link Rare](https://reader034.vdocument.in/reader034/viewer/2022042601/5fa01eed140b6630eb46d3d0/html5/thumbnails/29.jpg)
Query
How many persons have an abnormal head-size?
Result:2