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 cell 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.

X cell differentiation The process whereby a relatively unspecialized cell acquires specialized features of an x cell. [List characteristics of x cell.]

[Term] id: GO: name: neuron differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuron." [GO:mah] is_a: GO: ! cell differentiation relationship: part_of GO: ! neurogenesis

[Term] id: CL: name: neuron def: "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 ] xref_analog: FBbt: xref_analog: FBbt: is_a: CL: ! electrically responsive cell is_a: CL: ! electrically signaling cell relationship: develops_from CL: ! neuroblast

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.excitable celltransmission electricalsignalslongdistancesNeuronsreceivesensorycells outputmusclessensory neuronsmotoneuronsinterneuronssynapsescellssingleaxonmetreslength

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 cellneuroneneurocytenerve cell

[Term] id: GO: name: neuron differentiation namespace: biological_process 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 , GO:mah] is_a: GO: ! cell differentiation relationship: part_of GO: ! neurogenesis

[Term] id: GO: name: neuron differentiation namespace: biological_process 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 , GO:mah] is_a: GO: ! cell differentiation relationship: part_of GO: ! neurogenesis intersection_of: is_a GO: ! cell differentiation intersection_of: has_participant CL: ! neuron

Difficult term request Reconcile plant trichomes and insect trichomes.

Plant trichome image/ _trichome_arabidopsis.jpg image/ _trichome_arabidopsis.jpg

Insect trichome

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

Discussion… 5000 words 25 A4 pages. [ ] hair/trichome formation =956691&group_id=36855&atid=440764

Difficult term request All the metamorphosis terms should be changed to morphogenesis terms.

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: 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.

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 words 53 A4 pages [ ] metamorphosis terms = &group_id=36855&atid=440764

Some more ontology thoughts…

Basis in Reality: When building or maintaining an ontology, always think carefully about how classes relate to instances in reality

molecular function binding tetrapyrrole bindingcofactor binding chlorophyll heme coenzyme quinone binding binding is_a PSBI Annotations Ontology PSBI

superman strength flight x-ray vision leaps over tall buildings in a single bound Catwoman strength, speed, agility and ultra-keen senses of a cat.

cartoon character super power ontology super sensessuper physical powers x-ray cat super super vision senses leaping strength is_a Annotations Ontology

cartoon character super power ontology super sensessuper physical powers x-ray cat super super vision senses leaping strength is_a Catwoman Annotations Ontology Superman

cartoon character super power ontology super sensessuper physical powers x-ray cat super super vision senses leaping strength is_a Catwoman’s cat senses Catwoman’s super strength Annotations Ontology Superman’s X-ray vision Superman’s super leaping

cartoon character super power ontology super sensessuper physical powers is_a Catwoman’s cat senses Catwoman’s super strength Annotations Ontology Superman’s X-ray vision Superman’s super leaping

molecular function binding tetrapyrrole bindingcofactor binding chlorophyll heme coenzyme quinone binding binding is_a PSBI Annotations Ontology PSBI

molecular function binding tetrapyrrole bindingcofactor binding chlorophyll heme coenzyme quinone binding binding is_a PSBI’s quinone binding function Annotations Ontology PSBI’s chlorophyll binding function

3 Objectivity: The existence of classes is not dependent on our biological knowledge.

do not designate biological natural kinds. ‘unlocalised’ ‘unknown’ ‘unclassified’

Task: Annotate molecular function of 10-4, a gene from Drosophila melanogaster

molecular function unknown is_a 10-4 Molecular function ontologyAnnotations

molecular function unknown is_a 10-4 Molecular function ontologyAnnotations

molecular function unknown is_a 10-4 Molecular function ontologyAnnotations

With thanks… For slides: Barry Smith David Hill For everything: The Gene Ontology Consortium