STOP MOTION – Post-it Note Stopmotion Stop Motion Karate – (by Corridor) Human stop motion …
STOP
-
Upload
willow-terry -
Category
Documents
-
view
22 -
download
0
description
Transcript of STOP
![Page 1: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/1.jpg)
STOPBarry Smith
http://ifomis.de
![Page 2: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/2.jpg)
Smart Terminologies via Ontological Principles
![Page 3: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/3.jpg)
http:// ifomis.de3
Thanks to
Anand Kumar
Steffen Schulze-Kremer
Jane Lomax
![Page 4: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/4.jpg)
http:// ifomis.de4
Part OneIntroduction
![Page 5: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/5.jpg)
http:// ifomis.de5
GO here an example
a. of the sorts of problems confronting life science data integration
b. of the degree to which philosophy and logic are relevant to the solution of these problems
![Page 6: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/6.jpg)
http:// ifomis.de6
When a gene is identified
three important types of questions need to be addressed:
1. Where is it located in the cell?
2. What functions does it have on the molecular level?
3. To what biological processes do these functions contribute?
![Page 7: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/7.jpg)
http:// ifomis.de7
GO’s three ontologies
molecular functions
cellular components
biological processes
![Page 8: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/8.jpg)
http:// ifomis.de8
Each of GO’s ontologies
is organized in a graph-theoretical structure involving two sorts of links or edges:
is-a (= is a subtype of )
(copulation is-a biological process)
part-of
(cell wall part-of cell)
![Page 9: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/9.jpg)
http:// ifomis.de9
Part TwoGO as ‘Controlled Vocabulary’
![Page 10: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/10.jpg)
http:// ifomis.de10
Principle of Univocity
terms should have the same meanings (and thus point to the same referents) on every occasion of use
![Page 11: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/11.jpg)
http:// ifomis.de11
Principle of Compositionality
The meanings of compound terms should be determined
1. by the meanings of component terms
together with
2. the rules governing syntax
![Page 12: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/12.jpg)
http:// ifomis.de12
Principle of Syntactic Separateness
Do not confuse sentences with terms
If you want to say:No As are Bs
do not invent a new class of non-Bs and say A is_a non-B
Holliday junction helicase complex is-a unlocalized
![Page 13: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/13.jpg)
http:// ifomis.de13
Principle of Objectivity
which classes exist in reality is not a function of our biological knowledge.
(Terms such as ‘unclassified’ or ‘unknown ligand’ or ‘not otherwise classified as peptides’ do not designate biological natural kinds, and nor do they designate differentia of biological natural kinds)
![Page 14: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/14.jpg)
http:// ifomis.de14
Keep Epistemology Separate from Ontology
If you want to say that
We do not know where As are located
do not invent a new class of
A’s with unknown locations
(A well-constructed ontology should grow linearly; it should not need to delete classes or relations because of increases in knowledge)
![Page 15: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/15.jpg)
http:// ifomis.de15
GO:0008372 cellular component unknown
cellular component unknown is-a cellular component
![Page 16: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/16.jpg)
http:// ifomis.de16
binding is_a molecular function
binding is_a English noun
![Page 17: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/17.jpg)
http:// ifomis.de17
Principle of Meta-Data
Do not include meta-data as if it were just more data
Do not confuse meta-data with data about classes in the ontology itself
![Page 18: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/18.jpg)
http:// ifomis.de18
Principle of Meta-Data
obsolete molecular function
- list of molecular function terms declared obsolete
obsolete molecular function is_a molecular function
obsolete molecular function (obsolete)
![Page 19: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/19.jpg)
http:// ifomis.de19
obsolete molecular function (obsolete) (obsolete)
![Page 20: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/20.jpg)
http:// ifomis.de20
meta-data
data
reality
![Page 21: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/21.jpg)
http:// ifomis.de21
meta-data comments on terms
data terms
reality natural kinds
![Page 22: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/22.jpg)
http:// ifomis.de22
meta-data comments on terms
data terms
‘is_a’, ‘part_of ’
reality natural kinds
is_a, part_of
![Page 23: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/23.jpg)
http:// ifomis.de23
data: nucleus part_of cell
reality: <
cellular component part_of Gene Ontology
reality: <
![Page 24: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/24.jpg)
http:// ifomis.de24
data: nucleus part_of cell
reality: <
cellular component part_of Gene Ontology
reality: <
![Page 25: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/25.jpg)
http:// ifomis.de25
Russell’s Paradox
GO names itself
SwissProt does not name itself
Consider:
the database of all biological databases that do not name themselves
this names itself if and only if it does not name itself
![Page 26: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/26.jpg)
http:// ifomis.de26
Part ThreeGO’s Relation
![Page 27: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/27.jpg)
http:// ifomis.de27
Principle of Single Inheritance
every non-root class in a classificatory hierarchy has exactly one parent
no classificatory diamonds:
![Page 28: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/28.jpg)
http:// ifomis.de28
Linnaeus
![Page 29: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/29.jpg)
http:// ifomis.de29
![Page 30: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/30.jpg)
http:// ifomis.de30
Uses of multiple inheritance associated with errors in coding
B C
is-a1 is-a2
A
because ‘is-a’ no longer univocal
![Page 31: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/31.jpg)
http:// ifomis.de31
e.g. is_a is pressed into service to express location
is-located-at and similar relations are expressed by creating special compound terms using:
site of …
… within …
… in …
extrinsic to …
yielding associated errors
![Page 32: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/32.jpg)
http:// ifomis.de32
‘is-a’ overloading
an obstacle to integration with other ontologies
and causes other problems
![Page 33: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/33.jpg)
http:// ifomis.de33
e.g. problems with ‘within’
lytic vacuole within a protein storage vacuole
lytic vacuole within a protein storage vacuole is-a protein storage vacuole
time-out within a baseball game is-a baseball game
embryo within a uterus is-a uterus
![Page 34: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/34.jpg)
http:// ifomis.de34
similar problems with part_of
extrinsic to membrane part_of membrane
.
![Page 35: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/35.jpg)
http:// ifomis.de35
two distinct terms in GO’s cellular component ontology
GO:0005716 synaptonemal complex (obsolete)
GO:0000795: synaptonemal complex
![Page 36: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/36.jpg)
http:// ifomis.de36
‘synaptonemal complex’
GO:0005716 synaptonemal complex
Definition OBSOLETE. A structure that holds paired chromosomes together during prophase I of meiosis and that promotes genetic recombination.
![Page 37: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/37.jpg)
http:// ifomis.de37
GO:0005716 synaptonemal complex
This term was made obsolete because the definition is not true for every organism.
To update annotations, use the cellular component term ‘synaptonemal complex ; GO:0000795’.
![Page 38: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/38.jpg)
http:// ifomis.de38
‘synaptonemal complex’
GO:0000795 synaptonemal complex
Definition: A proteinaceous scaffold found between homologous chromosomes during meiosis.
Yet still:
synaptonemal complex part_of chromosome
![Page 39: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/39.jpg)
http:// ifomis.de39
structural constituent of bonestructural constituent of chorion (sensu Insecta)structural constituent of chromatinstructural constituent of cuticlestructural constituent of cytoskeletonstructural constituent of epidermisstructural constituent of eye lensstructural constituent of musclestructural constituent of myelin sheathstructural constituent of nuclear porestructural constituent of peritrophic membrane
(sensu Insecta)structural constituent of ribosome – note
possibility of confusion with ‘major ribosome unit’ (check)
structural constituent of tooth enamelstructural constituent of vitelline membrane
(sensu Insecta)
Examples of GO
Functions
![Page 40: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/40.jpg)
http:// ifomis.de40
structural constituent of bone
structural constituent of tooth enamel
are molecular functions
Not biological processes
Not cellular components
![Page 41: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/41.jpg)
http:// ifomis.de41
structural constituent of bonestructural constituent of chorion (sensu Insecta)structural constituent of chromatinstructural constituent of cuticlestructural constituent of cytoskeletonstructural constituent of epidermisstructural constituent of eye lensstructural constituent of musclestructural constituent of myelin sheathstructural constituent of nuclear porestructural constituent of peritrophic membrane
(sensu Insecta)structural constituent of ribosome – note
possibility of confusion with ‘major ribosome unit’ (check)
structural constituent of tooth enamelstructural constituent of vitelline membrane
(sensu Insecta)
what is the relation between
‘constituent’ and ‘component’?
![Page 42: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/42.jpg)
http:// ifomis.de42
Units, constituents, components, parts, …
What is the relation between
structural constituent of ribosome
and
large ribosomal subunit ?
How does process relate to activity ?
these are questions of ontology in the philosophical sense
![Page 43: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/43.jpg)
http:// ifomis.de43
Part FourGO’s Definitions
![Page 44: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/44.jpg)
http:// ifomis.de44
Judith Blake:
The use of bio-ontologies … ensures consistency of data curation, supports extensive data integration, and enables robust exchange of information between heterogeneous informatics systems. ..
ontologies … formally define relationships between the concepts.
![Page 45: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/45.jpg)
http:// ifomis.de45
"Gene Ontology: Tool for the Unification of Biology"
an ontology "comprises a set of well-defined terms with well-defined relationships"
(Ashburner et al., 2000, p. 27)
![Page 46: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/46.jpg)
http:// ifomis.de46
GO’s term definitions
First problem: Circularity (and worse)
hemolysis
Definition: The processes that cause hemolysis …
![Page 47: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/47.jpg)
http:// ifomis.de47
OBO Definition of ‘part_of’:
Used for representing partonomies
The subject (child node) of the relationship is the subpart; the object (parent node) is the superpart.
![Page 48: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/48.jpg)
http:// ifomis.de48
Principle of Intelligibility
The terms used in a definition should be simpler (more intelligible, more logically or ontologically basic) than the term to be defined – for otherwise the definition would provide no assistance to the understanding
-- not enough just to avoid circularity
![Page 49: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/49.jpg)
http:// ifomis.de49
Example:
GO:0016894: endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters
Definition: Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks to yield 3'-phosphomonoesters,
![Page 50: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/50.jpg)
http:// ifomis.de50
Problems with GO’s definitions
GO:0003673: cell fate commitment
Definition: The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells.
x is a cell fate commitment =def
x is a cell fate commitment and p
![Page 51: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/51.jpg)
http:// ifomis.de51
Principle:
Don’t confuse defining the meaning of a term with providing extra information about the world
![Page 52: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/52.jpg)
http:// ifomis.de52
Request
If GO is to introduce logical definitions, please make sure that people are involved who know some logic.
![Page 53: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/53.jpg)
http:// ifomis.de53
Part FourIs this all just
PHILOSOPHY ?
![Page 54: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/54.jpg)
http:// ifomis.de54
Is this all just philosophy ?
![Page 55: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/55.jpg)
http:// ifomis.de55
CONCLUSION (1)Problems caused by GO’s problems with formal rigor
1. Coding errors constant updating
2. Obstacles to ontology integration
3. Unclear what kinds of reasoning permitted
![Page 56: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/56.jpg)
http:// ifomis.de56
Conclusion (2)Quality assurance and ontology
maintenance must be automated
Automation requires robust formal architecture
Robust formal architecture requires that one respects ontological principles
(DL will go only some way to solving these problems)
![Page 57: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/57.jpg)
http:// ifomis.de57
The End
![Page 58: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/58.jpg)
http:// ifomis.de58
Why Description Logic is not enough
First reason:
semantics for DL is exclusively set-theoretic
is_a is not set-theoretic inclusion
NOT: adult is_a child
NOT: animal owned by the emperor is_a animal weighing less than 200 Kg
NOT: animal in Leipzig is_a animal
![Page 59: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/59.jpg)
http:// ifomis.de59
Why Description Logic is not enough
Second reason:
DL will not tell you how
complex
unit
subunit
constituent
component
part …
are related to each other – for that you need a philosophical analaysis
![Page 60: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/60.jpg)
http:// ifomis.de60
GO’s three ontologies are separate
No links or edges defined between them
molecular functions
cellular components
biological processes
![Page 61: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/61.jpg)
http:// ifomis.de61
Three granularities:
Molecular (for ‘functions’)
Cellular (for components)
Whole organism (for processes)
![Page 62: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/62.jpg)
http:// ifomis.de62
GO has cells
but it does not include terms for molecules or organisms within any of its three ontologies
except when it makes mistakes,
e.g. GO:0018995 host
=Df Any organism in which another organism spends part or all of its life cycle
![Page 63: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/63.jpg)
http:// ifomis.de63
Are the relations between functions and processes a matter of granularity?
Molecular activities are the ‘building blocks’ of biological processes ?
But they not allowed to be represented in GO as parts of biological processes
![Page 64: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/64.jpg)
http:// ifomis.de64
GO’s three ontologies
molecular functions
cellular components
biological processes
![Page 65: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/65.jpg)
http:// ifomis.de65
GO’s three ontologies
molecular functions
cellular components
organism-level
biological processes
cellularprocesses
![Page 66: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/66.jpg)
http:// ifomis.de66
‘part-of’; ‘is dependent on’
molecular functions
moleculecomplexe
s
cellularprocesses
cellular components
organism-level
biological processes
organisms
![Page 67: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/67.jpg)
http:// ifomis.de67
molecular functions
moleculecomplexe
s
cellularprocesses
cellular components
organism-level
biological processes
organisms
![Page 68: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/68.jpg)
http:// ifomis.de68
moleculecomplexes
cellular component
s
molecular function
s
cellularfunctions
organism-level
biological functions
organisms
molecular processe
s
cellularprocesses
organism-level
biological processes
![Page 69: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/69.jpg)
http:// ifomis.de69
moleculecomplexes
cellular component
s
molecular function
s
cellularfunctions
organism-level
biological functions
organisms
molecular processe
s
cellularprocesses
organism-level
biological processes
functioningsfunctionings functionings
![Page 70: STOP](https://reader036.fdocuments.in/reader036/viewer/2022062720/56813488550346895d9b6b6a/html5/thumbnails/70.jpg)
http:// ifomis.de70
moleculecomplexe
s
cellular component
s
molecular function
s
cellularfunctions
organism-level
biological functions
organisms
molecular processe
s
cellularprocesses
organism-level
biological processes
functioningsfunctionings functionings
molecularlocations
cellular locations
organism-level
locations