Introduction to Ontologies for Environmental Biology

Introduction to Ontologies
for Environmental Biology
Barry Smith
http://ontology.buffalo.edu/smith

2
Finnegans Web
concept
type
class
instance
model
representation
data
process
property

Disciplines here involved
GIS
Ecology
Environmental biology
Various -omics disciplines
Bioinformatics
Medical Informatics
Database science
Semantic webists
...

4
Part 1: What is an Ontology?

5
what cellular component?
what molecular function?
what biological process?

6
natural language labels
designed for use in annotations
to make the data cognitively
accessible to human beings
and algorithmically tractable
to computers

7
compare: legends for mapscompare: legends for maps

8
compare: legends for mapscommon legends allow (cross-border) integration

9
ontologies are legends for data

10
compare: legends for diagrams

Ramirez et al.
Linking of Digital Images to Phylogenetic Data Matrices Using a
Morphological Ontology
Syst. Biol. 56(2):283–294, 2007

12
computationally tractable legends
help integrate complex representations
of reality
help human beings find things in
complex representations of reality
help computers reason with complex
representations of reality

ontologies are used to annotate data

but there are two kinds of annotations

18
A basic distinction
type vs. instance
science text vs. diary
human being vs. Michael Ashburner

19
A 515287 DC3300 Dust Collector Fan
B 521683 Gilmer Belt
C 521682 Motor Drive Belt
Catalog vs. inventory

21
An ontology is a collection of
standardized names for types
We learn about types in reality from looking
at the results of scientific experiments
captured in the form of scientific theories
Ontologies provide the terminological
scaffolding of scientific theories
experiments relate to what is particular
science describes what is general

siamese
mammal
cat
organism
thing
types
animal
instances
frog
22

23
types vs. their extensions
type
c,...} class of instances
= a collections
of particulars

24
Extension =def
The extension of a type A is the class of
instances of A
(the class of all entities to which the term ‘A’
applies)

25
types vs. classes
types
{c,d,e,...} classes

26
types vs. classes
types
extensions ~ defined classes

27
Defined class =def
member of Abba aged > 50 years
pizza with > 4 different toppings
red wine to serve with fish

29
what cellular component?
what molecular function?
what biological process?

32
Five bangs for your GO buck
1. based in biological science
2. cross-species data comparability (human,
mouse, yeast, fly ...)
3. cross-granularity data integration
(molecule, cell, organ, organism)
4. cumulation of scientific knowledge in
algorithmically tractable form
5. links people to software
6. part of Open Biomedical Ontologies (OBO)
The Gene Ontology

33
Entry point for creation of web-
accessible biomedical data
GO initially low-tech to encourage users
Simple (web-service-based) tools
created to support the work of biologists
in creating annotations (data entry)
OBO  OWL DL converters now
making OBO Foundry annotated data
immediately accessible to Semantic
Web data integration projects

The OBO Foundry
A suite of high quality interoperable
reference ontologies to serve the
annotation of biomedical data
providing guidelines for those who need to
create new ontology resources
http://obofoundry.org

35
RELATION
TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical
Entity
(FMA, CARO)
Organ
Function
(FMP, CPRO) Phenotypic
Quality
(PaTO)
Biological Process
(GO)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
Cellular
Component
(FMA, GO)
Cellular
Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
(GO)
Molecular Process
(GO)
The OBO Foundry building out from the original GO

Simple guidelines
• use singular nouns
• distinguish continuants from occurrents
• distinguish things from their qualities
• distinguish types from their instances
• do not use the weasel word ‘concept’

37
 OPENNESS: The ontology is open and available to be
used by all.
 FORMAL LANGUAGE: The ontology is in, or can be
instantiated in, a common formal language.
 ORTHOGONALITY: The developers of the ontology
agree in advance to collaborate with developers of other
OBO Foundry ontology where domains overlap.
 CONVERGENCE: The developers agree to work
torwards a single ontology for each domain.
http://obofoundry.org/http://obofoundry.org/
CRITERIA

38
 UPDATE: The developers of each ontology commit to its
maintenance in light of scientific advance, and to
soliciting community feedback for its improvement.
 IDENTIFIERS: The ontology possesses a unique
identifier space within OBO.
 VERSIONING: The ontology provider has procedures for
identifying distinct successive versions.
 DEFINITIONS: The ontology includes textual definitions
for all terms.
CRITERIA

39
 CLEARLY BOUNDED: The ontology has a clearly
specified and clearly delineated content.
 DOCUMENTATION: The ontology is well-documented.
 USERS: The ontology has a plurality of independent
users.
 COMMON ARCHITECTURE: The ontology uses relations
which are unambiguously defined following the pattern of
definitions laid down in the OBO Relation Ontology.
CRITERIA

40
Foundry ontologies all work in the
same way
all are built to represent the types existing in a pre-
existing domain and the relations between these
types in a way which can support reasoning
– we have data
– we need to make this data available for semantic
search and algorithmic processing
– we create a consensus-based ontology for annotating
the data
– and ensure that it can interoperate with Foundry
ontologies for neighboring domains

41
Formal-Ontological Relations
is_a
part_of
located_at
depends_on
is_boundary_of
adjacent_to

42
To support integration of ontologies
relational expressions such as
is_a
part_of
...
should be used in the same way in all
ontologies involved

43
to define these relations properly
we need to take account of both types
and instances in reality

44
Kinds of relations
<instance, type>: Toronto instance_of
city
<instance, instance>: Toronto part_of
Ontario
<type, type>: waterfall part_of river

45
is_a
human is_a mammal
all instances of the type human are as a
matter of necessity instances of the type
mammal

46Karen Eilbecksong.sf.net
properties and features of
nucleic sequences
Sequence Ontology
(SO)
RNA Ontology Consortium(under development)
three-dimensional RNA
structures
RNA Ontology
(RnaO)
Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)
Protein Ontology Consortium(under development)
protein types and
modifications
Protein Ontology
(PrO)
Michael Ashburner, Suzanna
Lewis, Georgios Gkoutos
obo.sourceforge.net/cgi
-bin/ detail.cgi?
attribute_and_value
qualities of biomedical entities
Phenotypic Quality
Ontology
(PaTO)
Gene Ontology Consortiumwww.geneontology.org
cellular components,
molecular functions,
biological processes
Gene Ontology
(GO)
FuGO Working Groupfugo.sf.net
design, protocol, data
instrumentation, and analysis
Functional Genomics
Investigation Ontology
(FuGO)
JLV Mejino Jr.,
Cornelius Rosse
fma.biostr.washington.
edu
structure of the human body
Foundational Model of
Anatomy (FMA)
Melissa Haendel, Terry
Hayamizu, Cornelius Rosse,
David Sutherland,
(under development)
anatomical structures in
human and model organisms
Common Anatomy Refer-
ence Ontology (CARO)
Paula Dematos,
Rafael Alcantara
ebi.ac.uk/chebimolecular entities
Chemical Entities of Bio-
logical Interest (ChEBI)
Jonathan Bard, Michael
Ashburner, Oliver Hofman
obo.sourceforge.net/cgi-
bin/detail.cgi?cell
cell types from prokaryotes
to mammals
Cell Ontology
(CL)
CustodiansURLScopeOntology

47Karen Eilbecksong.sf.net
properties and features of
nucleic sequences
Sequence Ontology
(SO)
RNA Ontology Consortium(under development)
three-dimensional RNA
structures
RNA Ontology
(RnaO)
Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)
Protein Ontology Consortium(under development)
protein types and
modifications
Protein Ontology
(PrO)
Michael Ashburner, Suzanna
Lewis, Georgios Gkoutos
obo.sourceforge.net/cgi
-bin/ detail.cgi?
attribute_and_value
qualities of biomedical entities
Phenotypic Quality
Ontology
(PaTO)
Gene Ontology Consortiumwww.geneontology.org
cellular components,
molecular functions,
biological processes
Gene Ontology
(GO)
FuGO Working Groupfugo.sf.net
design, protocol, data
instrumentation, and analysis
Functional Genomics
Investigation Ontology
(FuGO)
JLV Mejino Jr.,
Cornelius Rosse
fma.biostr.washington.
edu
structure of the human body
Foundational Model of
Anatomy (FMA)
Melissa Haendel, Terry
Hayamizu, Cornelius Rosse,
David Sutherland,
(under development)
anatomical structures in
human and model organisms
Common Anatomy Refer-
ence Ontology (CARO)
Paula Dematos,
Rafael Alcantara
ebi.ac.uk/chebimolecular entities
Chemical Entities of Bio-
logical Interest (ChEBI)
Jonathan Bard, Michael
Ashburner, Oliver Hofman
obo.sourceforge.net/cgi-
bin/detail.cgi?cell
cell types from prokaryotes
to mammals
Cell Ontology
(CL)
CustodiansURLScopeOntology

Pleural
Cavity
Pleural
Cavity
Interlobar
recess
Interlobar
recess
Mesothelium
of Pleura
Mesothelium
of Pleura
Pleura(Wall
of Sac)
Pleura(Wall
of Sac)
Visceral
Pleura
Visceral
Pleura
Pleural SacPleural Sac
Parietal
Pleura
Parietal
Pleura
Anatomical SpaceAnatomical Space
Organ
Cavity
Organ
Cavity
Serous Sac
Cavity
Serous Sac
Cavity
Anatomical
Structure
Anatomical
Structure
OrganOrgan
Serous SacSerous Sac
Mediastinal
Pleura
Mediastinal
Pleura
TissueTissue
Organ PartOrgan Part
Organ
Subdivision
Organ
Subdivision
Organ
Component
Organ
Component
Organ Cavity
Subdivision
Organ Cavity
Subdivision
Serous Sac
Cavity
Subdivision
Serous Sac
Cavity
Subdivision
Foundational Model of Anatomy

Pleural
Cavity
Pleural
Cavity
Interlobar
recess
Interlobar
recess
Mesothelium
of Pleura
Mesothelium
of Pleura
Pleura(Wall
of Sac)
Pleura(Wall
of Sac)
Visceral
Pleura
Visceral
Pleura
Pleural SacPleural Sac
Parietal
Pleura
Parietal
Pleura
Anatomical SpaceAnatomical Space
Organ
Cavity
Organ
Cavity
Serous Sac
Cavity
Serous Sac
Cavity
Anatomical
Structure
Anatomical
Structure
OrganOrgan
Serous SacSerous Sac
Mediastinal
Pleura
Mediastinal
Pleura
TissueTissue
Organ PartOrgan Part
Organ
Subdivision
Organ
Subdivision
Organ
Component
Organ
Component
Organ Cavity
Subdivision
Organ Cavity
Subdivision
Serous Sac
Cavity
Subdivision
Serous Sac
Cavity
Subdivision
part_of
is_a

50
Mature OBO Foundry ontologies
now undergoing reform
Cell Ontology (CL)
Chemical Entities of Biological Interest (ChEBI)
Foundational Model of Anatomy (FMA)
Gene Ontology (GO)
Phenotypic Quality Ontology (PaTO)
Relation Ontology (RO)
Sequence Ontology (SO)

51
Ontologies being built to satisfy Foundry
principles ab initio
Ontology for Clinical Investigations (OCI)
Common Anatomy Reference Ontology
(CARO)
Ontology for Biomedical Investigations (OBI)
Protein Ontology (PRO)
RNA Ontology (RnaO)
Subcellular Anatomy Ontology (SAO)

52
Ontologies in planning phase
Biobank/Biorepository Ontology (BrO, part of OBI)
Environment Ontology (EnvO)
Immunology Ontology (ImmunO)
Infectious Disease Ontology (IDO)
Mouse Adult Neurogenesis Ontology (MANGO)

OBO Foundry Success Story
Model organism research seeks results valuable for
the understanding of human disease.
This requires the ability to make reliable cross-
species comparisons, and for this anatomy is crucial.
But different MOD communities have developed their
anatomy ontologies in uncoordinated fashion.
53

Ontologies facilitate grouping of annotations
brain 20
hindbrain 15
rhombomere 10
Query brain without ontology 20
Query brain with ontology 45
54

CARO – Common Anatomy
Reference Ontology
for the first time provides guidelines for model
organism researchers who wish to achieve
comparability of annotations
for the first time provides guidelines for those
new to ontology work
See Haendel et al., “CARO: The Common Anatomy Reference Ontology”,
in: Burger (ed.), Anatomy Ontologies for Bioinformatics: Springer, in press.55

56
CARO-conformant ontologies
already in development:
Fish Multi-Species Anatomy Ontology (NSF funding
received)
Ixodidae and Argasidae (Tick) Anatomy Ontology
Mosquito Anatomy Ontology (MAO)
Spider Anatomy Ontology
Xenopus Anatomy Ontology (XAO)
undergoing reform: Drosophila and Zebrafish
Anatomy Ontologies

Initial hypothesis:
Environments are holes

environment
place
site
niche
habitat
setting
hole
spatial region
interior
location

66
RELATION
TO TIME
GRANULARITY
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical
Entity
(FMA, CARO)
Organ
Function
Quality
(PaTO)
Biological Process
(GO)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
Cellular
Component
(FMA, GO)
Cellular
Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
(GO)
Molecular Process
(GO)
No place for environments

A Neglected Major Category in
Ontologies thus far
Things (e.g. organisms)
Qualities / Features
Functions
Processes
Environments = that into which
organisms (etc.) fit

68
RELATION
TO TIME
GRANULARITY
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical
Entity
(FMA,
CARO)
Organ
Function
Quality
(PaTO)
Biological
Process
(GO)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
Cellular
Component
(FMA, GO)
Cellular
Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
(GO)
Molecular Process
(GO)
Environments are holes in which
organisms, cells, molecules ... can live
environments
arehere

Double Hole Structure of the
Occupied Niche
Medium
(filling the environing hole)
Tenant
(occupying the central hole)
Retainer
(a boundary ofsome
surrounding structure)

Tenant, medium and retainer
the medium of the bear’s niche is a
circumscribed body of air
medium might be body of water, cytosol,
nasal mucosa, epithelium, endocardium,
synovial tissue ...

The Empty Niche
Fiat boundary Physical boundary

Two Types of Boundary
Fiat boundary Physical boundary

Positive and negative parts
positive
part
negative
part
or hole
(made of matter)
(not made
of matter)

Four Basic Niche Types
(Niche as generalized hole)
1 2 3 4
1: a womb; an egg; a house (better: the interior thereof)
2: a snail’s shell;
3: the niche of a pasturing cow;
4: the niche around a circling buzzard (fiat boundary)

Types of relations for EnvO
in
on (surface of)
surrounds
lives_in
attaches to
realizes
occupies (spatial region)
...

Lexical Semantics
the fruit is in the bowl
the bird is in the nest
the lion is in the cage
the pencil is in the cup
the fish is in the river
the river is in the valley
the water is in the lake
the car is in the garage
the fetus is in the cavity in the uterine lining
the colony of whooping crane is in its breeding grounds

Double Hole Structure
Medium
(filling the environing hole)
Tenant
(occupying the central hole)
Retainer
(a boundary ofsome
surrounding structure)
when a tenant leaves its niche the gap
left by the tenant is filled immediately
by the surrounding medium

A hole in the ground
Solid physical boundaries at the floor
and walls
but with a fiat lid:
hole

Part 4: Not every hole is an
environment

An environment is a special kind
of (generalized) hole
but what kind?

Elton – niche as role
the ‘niche’ of an animal means
its place in the biotic environment, its
relations to food and enemies. [...]
When an ecologist says ‘there goes a
badger’ he should include in his thoughts
some definite idea of the animal’s place in
the community to which it belongs,
just as if he had said ‘there goes the vicar’
(Elton 1927, pp. 63f.)

G.E. Hutchinson: niche as volume
in a functionally defined space
the niche = an n-dimensional hyper-
volume whose dimensions correspond to
resource gradients over which species are
distributed

Hypervolume niche = a location
in an attribute space
defined by a specific constellation of
environmental variables such as degree of
slope, exposure to sunlight, soil fertility,
foliage density, salinity...

Niche Construction
Lewontin: niches normally arise in symbiosis
with the activities of organisms or groups of
organisms (“ecosystem engineering”);
they are not already there, like vacant rooms in
a gigantic evolutionary hotel, awaiting organisms
who would evolve into them. (The Triple Helix,
Gene Organism, Environment)

Part Last: Bringing Together the
Spatial and Functional Approaches
to Environment Ontology
The environment is not a location in an
attribute space, but it must have features
have such location

Every environment must have
some spatial location
The functional niche presupposes the
spatial-structural niche
Ontology of environment + ontology of
associated environmental features

J. J. Gibson’s Ecological
Psychology
The terrestrial environment is [best]
described in terms of a medium,
substances, and the surfaces that
separate them. (Gibson 1979, p. 16)

Gibson’s theory of surface layout
‘a sort of applied geometry that is
appropriate for the study of perception and
behavior’ (1979, p. 33)
ground, open environment, enclosure,
detached object, attached object, hollow
object, place, sheet, fissure, stick, fiber,
dihedral, etc.

Gibson’s theory of surface layout
as an anatomy of environments
• systems of barriers, doors, pathways to
which the behavior of organisms is
specifically attuned,
• temperature gradients, patterns of
movement of air or water molecules
• water holes, food sources (features)
• apertures (mouths, sphincters ...)

Two sets of issues
Environments, as spatial structures, and
their parts
Environmental attributes (qualities,
functions), determining multidimensional
loci à la Hutchinson

Aim
To define structural properties such as:
open, closed,
connected, compact,
spatial coincidence,
integrity,
aggregate,
boundary
RCC (Region Connection Calculus) plus
extensions

Ecological Niche Concepts
niche as particular place or subdivision of an
environment that an organism or
population occupies
vs.
niche as function of an organism or
population within an ecological
community

Next steps
Our data needs are to link niche features
with geo-locations

Scale: From geographic to
microbiological
From locations of organisms/samples,
sources of museum artifacts ...
to organism interactions, e.g. on bacterial
infection – how the interior of one
organism or organism part serves as
environment for another organism

Hosts for bacterial infection
(interior of) lung
blood (bacteremia)
erythrocyte - plasmodium inhabits red blood
cells
hepatocyte – plasmodium infects liver cells
macrophage
gut and oral mucosa, nasal mucosa, vaginal
mucosa
kidney
bladder
portion of epithelial tissue

C: bacteria (arrows) adhering to and
penetrating the epithelial cells (×3,000)
D: abscess (Ab) formation in subepithelial
region with a colony of bacteria (arrows)
and a red blood cell (RBC) in it (×2,000)

106
RELATION
TO TIME
GRANULARITY
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical
Entity
(FMA, CARO)
Organ
Function
Quality
(PaTO)
Biological Process
(GO)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
Cellular
Component
(FMA, GO)
Cellular
Function
(GO)
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
(GO)
Molecular Process
(GO)
Environments, environment parts (features),
environment qualities

Ontologies needed
Environment -- Taxonomy
place, habitat, city, farm, building (interior), oral cavity,
uterine cavity, gut ...
Environment part – Anatomy of
environments (Surface, conduit, entry ...)
city wall, uterine wall, water source, ...
Environment function
protection, supply of food,...
Environment quality – (Phenotypes)
ambient temperature, salinity, ...

Introduction to Ontologies for Environmental Biology

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