Ontology: when philosophy meets science

A analyzable web of accusation exists successful subject and medicine.

To untangle nan web, scientists must explicate this accusation to computers. How do they do this and guarantee nan accusation represents everyone?

Ontologies whitethorn clasp nan answer.

To be, aliases not to be?

In philosophy, ontology is nan study of reality and existence.

When philosophers specified arsenic Descartes and Plato wrote connected gods, nan beingness and life, they were proposing their ontologies.

In science, an ontology is simply a room of descriptions. Ontologies thief categorize concepts and their relationships to each other.

Caption: Ontology and neural web papers each year
Credit: Digital Science

Let’s usage nan quality bosom arsenic an example.

Matters of nan heart

The bosom successful nan FMA ontology is “an organ pinch cavitated organ parts” and related to veins and arteries.

The Gene Ontology links circumstantial genes to bosom maturation and function. The Human Disease Ontology describes diseases for illustration bosom sarcoma.

A interrogator tin stack and nexus these ontologies. These links tin foretell which genes summation nan consequence of bosom sarcoma and which different organs bosom sarcoma affects.

Ontologies are much than method devices – they’re maps of meaning.

The measurement researchers tie those maps determines whose knowledge is included and whose isn’t.

Building meaning

Professor Gareth Baynam is simply a objective geneticist, argumentation advisor and nan Medical Director of nan Rare Care Centre. 

Gareth is besides a co-founder of the cosmopolitan Indigenous aesculapian translator Lyfe Languages.

He’s portion of nan International Rare Disease Research Consortium (IRDRC), which intends to amended nan test of uncommon diseases successful Indigenous people. 

Alongside colleagues, Gareth is moving to build Indigenous ontologies for health.

This includes Aboriginal ontologies present successful Australia. These ontologies whitethorn thief to adjacent nan First Nations wellness gap by combining ancient knowledge and caller technology.

Caption: An creator practice of nan Rare Care Centre Model of Care Ontology
Credit: Ronda Clarke

Combining ancient and cutting-edge

The IRDRC identified nan request to nexus world Indigenous ontologies to nan Mondo Disease Ontology.

Mondo unifies genetic, beingness traits and illness ontologies. It assesses different traits successful some humans and animals to amended illness test and care.

Most of Mondo’s quality ontologies are based connected European genetics and Western ideas. This intends captious accusation from different cultures and ancestries whitethorn beryllium missing.

“You tin deliberation of Mondo arsenic for illustration an atlas,” says Gareth. It’s a group of maps and really those maps connect, arsenic if you drilled holes done nan book of maps and connected those maps successful different ways.”

Ontologies are particularly useful successful instrumentality learning. Because computers are very literal, they tin struggle to construe quality descriptions of objects and their relationships.

But computers understand ontologies. They tin find relationships betwixt genes, diseases and objects. There tin beryllium millions of links, excessively analyzable for a quality to activity retired alone.

Artificial ontology

Researchers are utilizing ontologies to train artificial intelligence models.

These models are being utilized to foretell breast cancer, future diseases and patient triage.

“As a doctor, erstwhile I return a family history, I inquire really different group successful your family subordinate – your parents, grandparents, aunts, uncles, cousins,” says Gareth.  

“As a Western concept, that’s acquainted to galore people. But successful different cultures, what group picture arsenic an auntie, uncle aliases grandparent whitethorn beryllium different.

“An auntie aliases uncle whitethorn conscionable picture group older than you. We request a measurement to correspond those sorts of specifications successful maps.”

Overlooking aliases misinterpreting these relationships tin person real, measurable impacts connected healthcare.

Caption: An illustration of nan cistron ontology. Here are nan ontology position to specify a biochemical pathway to create sugars.
Credit: National Human Genome Research Institute

A healthier WA

The WA Department of Health assessed our wellness strategy successful nan 2019 Sustainable Health Review. It mapped nan challenges and goals of WA wellness to 2029. 

One of nan findings was that objective attraction only counted 16% towards diligent wellness outcomes, while socioeconomic factors and wellness behaviours contributed 40%.

“Look astatine nan National Aboriginal Community Controlled Health Organisation ways of improving wellness and wellbeing. There’s belief health, relationship to Country, language, family, societal and affectional wellbeing,” says Gareth.

“We want a wellness ontology that’s inclusive and holistic. If we’re missing these elements successful our maps, past location are full segments of wellness we’re ne'er moreover going to address.

“The Indigenous ontologies already exist. They person been transmitted done nan spoken connection for tens of thousands of years.

“We’re trying to link them to caller devices successful a measurement that includes spot and layers of permission. You can’t conscionable extract that knowledge retired of personification and usage it without permission.”

If Indigenous ontologies don’t go digital, they will stay invisible to caller exertion and nan literal-minded computers. 

But location are ethical issues astir making this knowledge publically available.  

“There are immoderate cardinal principles successful Indigenous information sovereignty – custodianship, access, respect and support of use,” says Gareth. 

“We activity pinch nan Elders to make judge we’re utilizing nan correct words successful nan correct settings. [We’re building] thing that is sufficiently trustworthy from an Indigenous wellness perspective.”