I am really excited abot the state of current chemical ontological development – there are now 3-4 groups including ours and I’ll expand later. But first I want to set the scene – looking at my ontological roots.
The first conscious involvement with ontology was with crystallography – the CIF dictionary project. This was – and is – a splendid example of a community building its ontological infrastructure. It gave me – naively – the view that it should be possible to define everything in the world and link it together. A colleague at Glaxo, Lesley West, cam to hear Henry Rzepa speak and – I can’t quite remember how – we found we had a lot in common about hypermedia and annotation. Lesley had been in regulatory affairs in Glaxo and she introduced me to the world of disease dictionaries – such as ICD-10 (more later) a compendium of 10,000 terms of “morbidity and mortality”. I know it by heart. Together we had the vision – in ca. 1994 of a world of namespaced (we didn’t know the term) hyperlinked (we knew that) ontologies (we didn’t know that). We cam up with the concept of “The Virtual Hyperglossary” (VHG) and had all sorts of experiences including setting up a company under its name.
For a brief while the VHG caught a few people’s attention and I was invited to meetings of InterCOCTA – a UNESCO project to try to harmonize the world through defining terminology. Simply – if we don’t understand each other we are likely to come to blows or worse. The doyen of the group was Fred Riggs – a distu=inguished professor of political sience from Hawaii. He showed me the relationship between terms and concepts (I was very stupid and he was very patient). For example there are many meanings of the word “bureaucracy” which varies from pejorative to neutral to positive in different cultures. Fred also created a terminology of conflict – “Turmoil among Nations” where he analysed or foresaw the asymmetric struggkes of today. And that is one of the many reasons why an understanding of language is essential for peace in the world. (A practical example – one of the delegates was from Iceland and she was compiling a glossary of fish. Since fish are (or were) important to Iceland’d economy, the precise meaning of a term is important. A sardine in the UK is different from a sardine in the Mediterranean.
Over these years I realised that ontologies touch our deepest being. Everyone has a world view built up over the years. When we try to communicate in words we always fail to agree on the entirety. Everyone is different and has a different view. If uncontrolled this leads to conflict and I have seen these and been part of them. So whenever anyone talks about creating ontologies I warn them that they will – inevitably come into conflict and must be prepraed to work out how to resolve this – it might be a compromise – it might be an agreement to differ.
This is reflected in the Upper ontology page which specifically warns
Upper ontologies are also commercially valuable, creating competition to define them. Peter Murray-Rust has claimed that this leads to “semantic and ontological warfare due to competing standards” , and accordingly any standard foundation ontology is likely to be contested among commercial or political parties, each with their own idea of ‘what exists’.
No one upper ontology has yet gained widespread acceptance as a de facto standard. Different organizations are attempting to define standards for specific domains. The ‘Process Specification Language’ (PSL) created by the National Institute for Standards and Technology (NIST) is one example.
There is debate over whether the concept of using a single, shared upper ontology is even feasible or practical at all. There is further debate over whether the debates are valid – often leading to outright censorship and boosterism of particular approaches in supposedly neutral sources including this one. Some of these arguments are outlined below, with no attempt to be comprehensive. Please do not censor them because you promote some ontology. [WP italics]
My quote was actually made when XML was at the peak of the Garner curve and I could see companies wishing to stake out territory in an ontological gold rush. Ontologies will cause enough conflict without being protected walled gardens. The world needs ontologies for its survival – we need to understand ourselves and we need to understand the laws of nature.