Developing anatomy ontologies in the context of others

Melissa Haendel, Chris Mungall, Carlo Torniai, Matt Yoder

lung

lung

respiratory gaseous exchange

lobular organ

parenchymatous organ

solid organ

pleural sac

thoracic cavity organ

thoracic cavity

multicellular organismal process

abnormal lung morphology

abnormal respiratory system morphology

GO

MPO

MA

FMA

abnormal pulmonary acinus morphology

abnormal pulmonary alveolus morphology

lungalveolus

respiratory system process

organ system

respiratory system

Lower respiratory

tract

alveolar sac

pulmonary acinus

organ system

respiratory system

EHDAA2

lung

lung bud

respiratory primordium

pharyngeal region

develops_frompart_of

is_a (SubClassOf)

surrounded_by

The problem: Data Silos

Differences in bone and bone tissue representation

Ontology alignment

How to synchronize anatomy ontologies

“mapping”

Xref strategy imports/MIREOT

Three approaches:

There are issues with mappingsClass A Class B In Bioportal? Useful?

FMA extensor retinaculum of wrist

MA retina Yes No

FMA portion of blood MA blood No Yes

ZFA Macula MA macula Yes No

ZFA aortic arch MA arch of aorta Yes Dubious

ZFA hypophysis MA pitiuitary No Yes

FMA tibia FBbt tibia Yes No

FMA colon GAZ Colón, Panama Yes No

PATO male Chebi maleate 2(-) Yes No

Zebrafish terms are is_a subtypes of teleost terms

is_a

Zebrafish Anatomy Teleost Anatomy Ontology

Reconciliation and linking between TAO and ZFA

Logic implemented via Xrefs- difficult to keep synchronized

OBO relations between ontologies

treat-xrefs-as-equivalent: CAROtreat-xrefs-as-equivalent: GOtreat-xrefs-as-equivalent: VSAOtreat-xrefs-as-is_a: VHOGtreat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10088

These are some assertions in UBERON, and relate the Xrefs in Uberon to classes in other ontologies using specificied semantics. This allows merging of ontologies in taxonomically appropriate ways

Zebrafish terms are is_a subtypes of teleost terms

is_a

Zebrafish Anatomy Teleost Anatomy Ontology

Reconciliation and linking between TAO and ZFA

Logic implemented via Xrefs- difficult to keep synchronized

X

Using Uberon for alignment facilitates identification of missing classes

Ontology alignment

anatomical structure

endoderm of forgut

lung bud

lung

respiration organ

organ

foregut

alveolus

alveolus of lung

organ part

FMA:lung

MA:lung

endoderm

GO: respiratory gaseous exchange

MA:lung alveolus

FMA: pulmonary

alveolus

is_a (taxon equivalent)

develops_frompart_of

is_a (SubClassOf)

capable_of

NCBITaxon: Mammalia

EHDAA:lung bud

only_in_taxon

pulmonary acinus

alveolar sac

lung primordium

swim bladder

respiratory primordium

NCBITaxon:Actinopterygii

Uberon classes connect to other ontologies via a variety of relations

Uberonclasses

Synchronization by import across ontologies

One can import a whole ontology or just portions of another ontologyMIREOT: Minimum information to reference an external ontology term

CARO

VSAO

Present TAO Modularized ontology

zebrafish

caro / uberon/allcell tissue

metazoa

muscletissue

vertebrata

mesonephros

limb

arthropoda

antenna

teleost

weberian ossicle

mammalia

mammary gland

nervous system

mollusca

foot

cephalopod

tentacle

mantle

drosophila

neuron types XYZ

mushroom body

brachial lobe

NO pons

vertebravertebralcolumn

circulatory system

appendage

mesoderm

gut

tibia

gland

bone

skeletaltissue

parietalbone

fin

gonad

trachea

respiratoryairway

cross-ontologylink (sample)

amphibia

tibiafibula

larva

shellcuticle

skeleton

import

mouse human

Leveraging an integrated set of ontologies

Proposed model moving forward

Maintain series of ontologies at different taxonomic levels- euk, plant, metazoan, vertebrate, mollusc, arthropod,

insect, mammal, human, drosophila Each ontology imports/MIREOTs relevant subset of

ontology “above” it- this is recursive

Subtypes are only introduced as needed Work together on commonalities at appropriate

level above your ontology

• To get the imports working well• To have distributed social responsibility assigned• Design patterns to ensure we are all doing the same thing• To check for consistency and errors across multiple ontologies using reasoners to get correct results for all users

-These ontologies are supposed to be orthogonal but aren’t always

• Visualization tools that can aid non-ontology experts in identifying errors across multiple ontologies

Modularizing ontologies – We need:

Modularizing ontologies

Identify key points of integration between ontologies Invest energy in understanding what is out there, i.e. seek to import and reuse, rather than “aligning” later

Modularize based on domain or taxon

Let the reasoner help do the work

Work together to distribute work

Idealized protocol for new AOs

1. Collect draft list of classes, build design documents

2. Subdivide into anatomical domains, taxonomic levels, and/or differentiating characteristics

3. Request new classes from existing AOs, stub in in your own ontology, make annotations to this effect (e.g. include tracker IDs)

4. Import pre-reasoned subset from other ontologies

5. Build your ontology

More about using ontologies together-post-composition

(seta and 'is bearer of' some White) and (part_of some head)RO/BFO

HAO PATO HAO

RO/BFO

Ontologies can help reconcile annotation inconsistencies