University of Glasgow

Roderic Page

OK, so the title is pure click bait, but here\'s the thing. It seems to
me that the Semantic Web as classically conceived (RDF/XML, SPARQL,
triple stores) has had relatively little impact outside academia,
whereas other technologies such as JSON, NoSQL (e.g., MongoDB, CouchDB)
and graph databases (e.g., Neo4J) have got a lot of developer mindshare.

In biodiversity informatics the Semantic Web has been a round for a
while. We\'ve been pumping out millions of RDF documents (mostly served
by LSIDs) since 2005 and, to a first approximation, nothing has
happened. I\'ve repeatedly blogged about why I think this is (see [this
post for a
summary](http://iphylo.blogspot.co.uk/2015/07/steve-baskauf-on-rdf-and-page-challenge.html)).

I was an early fan of RDF and the Semantic Web, but soon decided that it
was far more hassle than it was worth. The obsession with ontologies,
the problems of globally unique identifiers based on HTTP (http-14
range, anyone?), the need to get a lot of ducks in a row all mad it a
colossal pain. Then I discovered the NoSQL document database
[CouchDB](http://couchdb.apache.org), which is a JSON store that
features map-reduce views rather than on the fly queries. To somebody
with a relational database background this is a bit of a headfuck:

[![Fault
tolerance](https://lh3.googleusercontent.com/-i6RdZ9f7CsU/VnLWdz1uUEI/AAAAAAAAEF0/-BrevKnTYo0/fault-tolerance.png?imgmax=800 "fault-tolerance.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460"
height="230"}](http://insidebigdata.com/wp-content/uploads/2014/05/humor_mapreduce.png)

But CouchDB has a great interface, can be replicated to the cloud, and
is FUN (how many times can you say that about a database?). So I
starting playing with CouchDB for small projects, then used it to build
[BioNames](http://bionames.org) and more recently moved
[BioStor](http://biostor.org) to CouchDB hosted both locally and in the
[cloud](http://cloudant.com).

Then there are graph databases such as [Neo4J](http://neo4j.com), which
has some really cool things such as
[GraphGists](http://graphgist.neo4j.com/#!/gists) which is a playground
where you can create interactive graphs and query them ([here\'s an
example I
created](http://iphylo.blogspot.co.uk/2015/08/testing-gbif-taxonomy-with-graph.html)).
Once again, this is FUN.

Another big trend over the last decade is the flight from XML and its
hideous complexities (albeit coupled with great power) to the simplicity
of [JSON](http://json.org) (part of the [rise of
JavaScript](https://github.com/blog/2047-language-trends-on-github)).
JSON makes it very easy to pass around data in simple key-value
documents (with more complexity such as lists if you need them). Pretty
much any modern API will serve you data in JSON.

So, what happened to RDF? Well, along with a plethora of formats (XML,
triples, quads, etc., etc.) it adopted JSON in the form of JSON-LD (see
[JSON-LD and Why I Hate the Semantic
Web](http://manu.sporny.org/2014/json-ld-origins-2/) for background).
JSON-LD lets you have data in JSON (which both people and machines find
easy to understand) and all the complexity/clarity of having the data
clearly labelled using controlled vocabularies such as Dublin Core and
schema.org. This complexity is shunted off into a \"@context\" variable
where it can in many cases be safely ignored.

But what I find really interesting is that instead of JSON-LD being a
way to get developers interested in the rest of the Semantic Web stack
(e.g. HTTP URIs as identifiers, SPARQL, and triple stores), it seems
that what it is really going to do is enable well-described structured
to get access to all the cool things being developed around JSON. For
example, we have document databases such as CouchDB which speaks HTTP
and JSON, and search servers such as
[ElasticSearch](https://www.elastic.co) which make it easy to work with
large datasets. There are also some cool things happening with graph
databases and Javascript, such as
[Hexastore](https://github.com/crubier/Hexastore) (see also Weiss, C.,
Karras, P., & Bernstein, A. (2008, August 1). Hexastore. Proc. VLDB
Endow. VLDB Endowment. <http://doi.org/10.14778/1453856.1453965>, PDF
[here](http://karras.rutgers.edu/hexastore.pdf)) where we create the six
possible indexes of the classic RDF \[subject,predicate,object\] triple
(this is the sort of thing can also be done in CouchDB). Hence we can
have graph databases implemented in a web browser!

So, when we see large-scale \"Semantic Web\" applications that actually
exist and solve real problems, we may well be more likely to see
technologies other than the classic Semantic Web stack. As an example,
see the following paper:

> Szekely, P., Knoblock, C. A., Slepicka, J., Philpot, A., Singh, A.,
> Yin, C., ... Ferreira, L. (2015). Building and Using a Knowledge Graph
> to Combat Human Trafficking. The Semantic Web - ISWC 2015. Springer
> Science + Business Media.
> <http://doi.org/10.1007/978-3-319-25010-6_12>

There\'s a [free PDF
here](http://usc-isi-i2.github.io/papers/szekely15-iswc.pdf), and a
[talk
online](http://videolectures.net/iswc2015_szekely_human_trafficking/).
The consortium behind this project researchers did extensive text
mining, data cleaning and linking, creating a massive collection of
JSON-LD documents. Rather than use a triple store and SPARQL, they
indexed the JSON-LD using ElasticSearch (notice that they generated
graphs for each of the entities they care about, in a sense
denormalising the data).

I think this is likely to be the direction many large-scale projects are
going to be going. Use the Semantic Web ideas of explicit vocabularies
with HTTP URIs for definitions, encode the data in JSON-LD so it\'s
readable by developers (no developers, no projects), then use some of
the powerful (and fun) technologies that have been developed around
semi-structured data. And if you have JSON-LD, then you get SEO for free
by embedding that JSON-LD in your web pages.

In summary, if biodiversity informatics wants to play with the Semantic
Web/linked data then it seems obvious that some combination of JSON-LD
with NoSQL, graph databases, and search tools like ElasticSearch are the
way to go.


OK, so the title is pure click bait, but here's the thing. It seems to me that the Semantic Web as classically conceived (RDF/XML, SPARQL, triple stores) has had relatively little impact outside academia, whereas other technologies such as JSON, NoSQL (e.g., MongoDB, CouchDB) and graph databases (e.g., Neo4J) have got a lot of developer mindshare. In biodiversity informatics the Semantic Web has been a round for a while.

Messages de Rogue Scholar

Will JSON, NoSQL, and graph databases save the Semantic Web?