Building Biomedical Ontologies Jennifer Clark, GO Editorial Office.

Building Biomedical Ontologies

Jennifer Clark, GO Editorial Office

Clark et al., 2005

part_of

is_a

Clark et al., 2005

"encyclopaedia of Flemish children's games“ BRUEGEL

classes

GO terms, types, kinds, universals

instances

annotated gene product attributes,

tokens, individuals, particulars

Domain of Ontology

• biological process

• Loggerhead nesting

• evidence codes

• NCBI organismal classification

• is_a

• part_of

• develops_from

Relationships

part_of

• no necessity

• necessarily is part

• necessarily has part

• necessarily is part and necessarily has part

How to define A is_a B

A is_a B =def.

1. A and B are names of universals (natural kinds, types) in reality

2. all instances of A are as a matter of biological science also instances of B

Easy term request:

Please add

• leucophore differentiation,

• erythrophore differentiation

• cyanophore differentiation

• neuron differentiation

cellular process

cell differentiation

Is_a

part_of

cell fate cell

specification development

cell differentiation

osteoblast neuron keratinocyte differentiation differentiation differentiation

adipocyte garland celldifferentiation differentiation

‘X cell differentiation’

is_a

Essence = Genus + Differentiae

Genus: differentiation

Differentiae: a neuron (or x cell)

X cell differentiation


Differentiation of an x cell.


The process whereby

a relatively unspecialized cell

acquires specialized features

of an x cell.

[List characteristics of x cell.]

[Term]id: GO:0030182name: neuron differentiationnamespace: biological_process

def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuron." [GO:mah]

is_a: GO:0030154 ! cell differentiationrelationship: part_of GO:0048699 ! neurogenesis

[Term]id: CL:0000540name: neuron

def: "The basic cellular unit of nervous tissue. Each neuronconsists of a body\, an axon\, and dendrites. Their purposeis to receive\, conduct\, and transmit impulses in the nervous system." [MESH:A.08.663]

xref_analog: FBbt:00005106xref_analog: FBbt:00005146is_a: CL:0000393 ! electrically responsive cellis_a: CL:0000404 ! electrically signaling cellrelationship: develops_from CL:0000031 ! neuroblast

http://cancerweb.ncl.ac.uk

• neuron• An excitable cell specialised for the transmission of

electrical signals over long distances. Neurons receive input from sensory cells or other neurons and send output to muscles or other neurons. Neurons with sensory input are called sensory neurons, neurons with muscle outputs are called motoneurons, neurons that connect only with other neurons are called interneurons. Neurons connect with each other via synapses. Neurons can be the longest cells known, a single axon can be several metres in length. Although signals are usually sent via action potentials, some neurons are nonspiking.

http://cancerweb.ncl.ac.uk/cgi-bin/omd?excitable+cell

http://cancerweb.ncl.ac.uk/cgi-bin/omd?transmission

http://cancerweb.ncl.ac.uk/cgi-bin/omd?electrical

http://cancerweb.ncl.ac.uk/cgi-bin/omd?signals

http://cancerweb.ncl.ac.uk/cgi-bin/omd?long

http://cancerweb.ncl.ac.uk/cgi-bin/omd?distances

http://cancerweb.ncl.ac.uk/cgi-bin/omd?Neurons

http://cancerweb.ncl.ac.uk/cgi-bin/omd?receive

http://cancerweb.ncl.ac.uk/cgi-bin/omd?sensory

http://cancerweb.ncl.ac.uk/cgi-bin/omd?cells

Stedman's Online Medical Dictionary

• neuron (noor on)

• The morphologic and functional unit of the nervous system, consisting of the nerve cell body, the dendrites, and the axon. Syn: neurone Syn: neurocyte, nerve cell


def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuron. The basic cellular unit of nervous tissue. Each neuron consists of a body\, an axon\, and dendrites. Their purpose is to receive\, conduct\, and transmit impulses in the nervous system." [MESH:A.08.663, GO:mah]

is_a: GO:0030154 ! cell differentiationrelationship: part_of GO:0048699 ! neurogenesis


def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuron. The basic cellular unit of nervous tissue. Each neuron consists of a body\, an axon\, and dendrites. Their purpose is to receive\, conduct\, and transmit impulses in the nervous system." [MESH:A.08.663, GO:mah]

is_a: GO:0030154 ! cell differentiationrelationship: part_of GO:0048699 ! neurogenesisintersection_of: is_a GO:0030154 ! cell differentiationintersection_of: has_participant CL:0000540 ! neuron

Difficult term request

• Reconcile plant trichomes and insect trichomes.

Plant trichomehttp://bib18.ulb.ac.be/Botanique_I/image/6703873062005_trichome_arabidopsis.jpg

http://www.innovations-report.de/bilder_neu/40879_szymanski.trichomeLO.jpg

Insect trichomehttp://www.grisda.org/tstandish/images/animalia/arthropoda/Wildtype-D.-melanogaster-EM.jpg

• If a plant trichome is a hair cell, and an insect trichome is a cell hair, then plant trichome differentiation would be an is_a of hair cell differentiation. And insect trichome formation could be a part_of hair cell differentiation.

Becky Foulger 2004-08-04

Discussion…

5000 words25 A4 pages.

[ 956691 ] hair/trichome formation

https://sourceforge.net/tracker/index.php?func=detail&aid=956691&group_id=36855&atid=440764

Difficult term request

• All the metamorphosis terms should be changed to morphogenesis terms.

http://www.kellscraft.com/Butterflies/butter69.jpg

Standard structure

[i]x development

---[p] x morphogenesis

------[p] x formation

---------[p] y cell differentiation

------[p] x structural organization

---[p] x maturation

Standard definitions• x development • The process whose specific outcome is the progression of the x

over time, from its formation to the mature structure. • x morphogenesis • The process by which the anatomical structures of x are generated

and organized. Morphogenesis pertains to the creation of form. • x formation • The process that gives rise to x. This process pertains to the initial

formation of a structure from unspecified parts. • x structural organization • The process that contributes to creating the structural organization

of x. This process pertains to the physical shaping of a rudimentary structure.

morphogenesis terms

• x morphogenesis

• The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form.

metamorphosis terms

'leg disc metamorphosis' ; GO:0007478

def: The transformation of a leg imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into recognizable adult structures including the leg, coxa and ventral thoracic pleura.

Rules

Changes can be made to terms:

• Annotations must still be true afterwards.

• Name needs changed. Do it. • Definition wording needs changed. Do it.• Position in the graph needs changed. Do it.• Definition meaning needs changed. Obsolete the

term.

starting structure x mature structure

x morphogenesis

gene products act here

x metamorphosis multiple mature structures

gene products act here

x starting structure

The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form.

The transformation of a leg imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into recognizable adult structures including the leg, coxa and ventral thoracic pleura.

http://www.aardman.com

blob of plasticine Gromit

Gromit morphogenesis

‘gene products’ act here

Aardman plasticine metamorphosis

All the individual characters in the cast of Wallace and Gromit films

‘gene products’ act here

huge ball of plasticine Wallace

Gromit

Killer penguin

Shaun the sheep

before

after

Fixed metamorphosis terms

• leg disc morphogenesis

• Def: The process by which the anatomical structures derived from the leg disc are generated and organized. Morphogenesis pertains to the creation of form. [description]

• exact_synonym: leg disc metamorphosis

Discussion:

10,000 words53 A4 pages

[ 1228979 ] metamorphosis termshttps://sourceforge.net/tracker/index.php?func=detail&aid=1228979&group_id=36855&atid=440764

Some more ontology thoughts…

Basis in Reality:

When building or maintaining an ontology, always think carefullyabout how classes relate to instances in reality

molecular function

binding

tetrapyrrole binding cofactor binding

chlorophyll heme coenzyme quinonebinding binding binding binding

is_a

PSBI

Annotations

Ontology

PSBI

supermanstrengthflightx-ray visionleaps over tall buildings in a single bound

Catwomanstrength,speed,agilityand ultra-keen senses of a cat.

http://www.uncleodiescollectibles.com/doesnotcompute/2004-10-11/Actor%20Christoper%20Reeve.jpg

http://home.austarnet.com.au/davekimble/catwoman.jpg

cartoon character super power ontology

super senses super physical powers

x-ray cat super supervision senses leaping strength

is_a

Annotations

Ontology




is_a

Catwoman Catwoman

Annotations

Ontology

Superman

Superman




is_a

Catwoman’scat senses

Catwoman’ssuper strength

Annotations

Ontology

Superman’sX-ray vision

Superman’ssuper leaping

molecular function

binding



is_a

PSBI

Annotations

Ontology

PSBI

molecular function

binding



is_a

PSBI’s quinone binding function

Annotations

Ontology

PSBI’s chlorophyll binding function

3 Objectivity:

The existence of classesis not dependenton our biological knowledge.

do not designate biological natural kinds.

‘unlocalised’‘unknown’ ‘unclassified’

http://news.bbc.co.uk/1/hi/sci/tech/4501152.stm

Task:

Annotate

molecular function

of 10-4,

a gene from Drosophila melanogaster

molecular function

molecular function unknown

is_a

10-4

Molecular function ontology Annotations

With thanks…

For slides:

Barry SmithDavid Hill

For everything:

The Gene Ontology Consortium

Building Biomedical Ontologies Jennifer Clark, GO Editorial Office.

Documents

Transcript of Building Biomedical Ontologies Jennifer Clark, GO Editorial Office.