Fish jelly, and linked data.

You can’t nail jelly to a tree. But you can put it in a bucket and slap a label on the bucket

Fish. Or, if you prefer, PISCES., in fact.

PISCES (as xml) (as json)
modified 2013-10-17
Complete PISCES
Nom. code Zoological
Uninomial PISCES
Taxonomic events
PISCES sensu AFD afd

Our new system has scientific names, with author, date, nomenclatural status – the whole thing. And, of course, these names all have URIs with id numbers. Which is ok from the POV of the semantic web, as URIs are opaque identifiers.

But, but wouldn’t it be nice if you actually could read the URI? Wouln’t it be nice to just use “Megalops cyprinoides” or “Herring” as an id? I mean – it’s that the whole point of naming things? The whole point of identifying things is that the name can be used as, well, an identifier. And indeed, it is used that way. All the time. When you go into the nursery and buy a rosebush, the label proudly displaying the scientific name as well as what most people actually call it, they don’t cite the author of the name. There’s no point saying “but without the author, it doesn’t mean anything” because it quite plainly and obviously does mean something. To lots of people.

So we support it. Eg

The main people to whom a name without author doesn’t mean anything are those people engaged in the work of managing names. The information-science aspect of keeping a nice clean set of identifiers available for the rest of the world to use. Taxonomists, and people at the pointy end of the job of working out what actually lives on this planet of ours. They’re the only ones who really care.

Thing is, our databases are built around that work – that’s the mission here. Within that space a bare scientific name actually is pretty much meaningless. But given that we do support these URIs, from a semweb perspective what does, or for that matter mean, exactly? What is it the URI of? What, in a word, is its referent?

I think that the referent of has got to be the word “Herring”. That’s all. Perhaps it’s even owl:sameAs text:Herring – if ‘text’ were a URI schema.

Our database does not have anything in it whose identifier is simply ‘Herring’. However, we do have a bunch of other stuff that might be of interest. In particular, we have a name whose URI is If you ask for Herring, which is an id that is not in our database, you will get that.

Is this a legit thing to do? The URI is kind of in a limbo. On the one hand, the URI exists – you don’t get a 404. On the other hand, we don’t serve up any data pertaining to the URI that you have referenced. You ask for ‘Herring’. You get something else that isn’t Herring (one of its fields is the text value ‘Herring’, but what does that mean?). Now, you and I understand this, but a semantic web engine isn’t going to. To put it another way, over the entire graph hosted at our server, sits on its own and isn’t connected to anything.

So. To address this, my plan is to create an object whose URI is It will have a type of – ooh, I dunno – boa-name:SimpleName, I’ll give it an rdf:value of ‘Herring’ and a number of predicates named – say – boa-name:isSimpleNameOf (or probably just do it in reverse: boa-name:hasSimpleName on the name object). There you go.

The situation is slightly different for The meaning of this is rather more specific. This URI is an alternative name – owl:sameAs – for the current APC or AFD concept for the valid or vernacular name whose simple name string is ‘Herring’. It’s the accepted taxon for the name at b.o.a .

That is, there is not a separate object. It’s an alternative URI for an object that we already host. And it may change over time: that’s the nature of semantic web data. Actually implementing this in d2r … I don’t know. I might need to build a few database views for the various ways this fact might be derived.

At least that’s the plan. If there are outright collisions of simple names in accepted taxa among our different domains, then, well – this will need to be re-thought a bit. It may very well be that is not usable as an id, but that might be.

In any event. The goal is to give these convenience URIs a home and maybe even make them mean something.


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