1 introduction to (geo)ontology barry smith
Post on 19-Dec-2015
219 views
TRANSCRIPT
![Page 1: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/1.jpg)
1
Introduction to (Geo)Ontology
Barry Smith
http://ontology.buffalo.edu/smith
![Page 2: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/2.jpg)
2
![Page 3: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/3.jpg)
3
natural language labels
to make the data cognitively accessible to human beings
and algorithmically tractable to computers
![Page 4: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/4.jpg)
4
compare: legends for mapscompare: legends for maps
![Page 5: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/5.jpg)
5
compare: legends for mapscommon legends allow (cross-border) integration
![Page 6: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/6.jpg)
6
ontologies are legends for data
![Page 7: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/7.jpg)
7
compare: legends for diagrams
![Page 8: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/8.jpg)
8
legends
help human beings use and understand complex representations of reality
help human beings create useful complex representations of reality
help computers process complex representations of reality
![Page 9: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/9.jpg)
9
computationally tractable legends
help human beings find things in very large complex representations of reality
![Page 10: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/10.jpg)
10
maps may be correct by reflecting topology, rather than geometry
![Page 11: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/11.jpg)
11
two kinds of annotations
![Page 12: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/12.jpg)
12
names of types
![Page 13: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/13.jpg)
13
names of instances
![Page 14: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/14.jpg)
14
First basic distinction
type vs. instance
(science text vs. diary)
(human being vs. Tom Cruise)
![Page 15: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/15.jpg)
15
Ontology types Instances
![Page 16: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/16.jpg)
16
Ontology = A Representation of Types
![Page 17: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/17.jpg)
17
An ontology is a representation of types
We learn about types in reality from looking at the results of scientific experiments in the form of scientific theories
experiments relate to what is particular science describes what is general
![Page 18: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/18.jpg)
18
where in the body ? where in the cell ?
what kind of organism ?
what kind of disease process ?
![Page 19: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/19.jpg)
19
to yield: distributed accessibility of the data to humansreasoning with the datacumulation for purposes of researchincrementality and evolvabilityintegration with clinical data
Creating broad-coverage semantic annotation systems for biomedicine
![Page 20: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/20.jpg)
20
The Gene Ontology
![Page 21: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/21.jpg)
21
![Page 22: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/22.jpg)
22
![Page 23: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/23.jpg)
23
The Idea of Common Controlled Vocabularies
MouseEcotope GlyProt
DiabetInGene
GluChem
sphingolipid transporter
activity
![Page 24: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/24.jpg)
24
The Idea of Common Controlled Vocabularies
MouseEcotope GlyProt
DiabetInGene
GluChem
Holliday junction helicase complex
![Page 25: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/25.jpg)
25
what cellular component?
what molecular function?
what biological process?
![Page 26: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/26.jpg)
26
Michael Ashburner
![Page 27: 1 Introduction to (Geo)Ontology Barry Smith](https://reader036.vdocuments.site/reader036/viewer/2022081519/56649d405503460f94a1a0b7/html5/thumbnails/27.jpg)
GEO.OBO• biological samples
• populations, epidemics
• speciation, evolutionary processes in space and time
• museum artifacts
27