Summer recess is over ;) at least mine is

Hi All,

I hope everyone had a pleasant summer and is ready to dive in again to 
think about how to improve sparql.

For those who where around in the sparql 1.1 standardization days I have 
a special request. Can you remember why the path{1,200} syntax was 
dropped, if you implemented it anyway (and if it is still alive) in your 
code base. Please comment in issue 
https://github.com/w3c/sparql-12/issues/101)

I will continue with the xpath functions introduced since sparql 1.1 was 
out. And hope to have something that is implementable and comment ready 
for that specific item by October 23rd. If you want to join on gitter 
you are super welcome. My CG time will be on the wednesday afternoons 
between 15:15 and 16:45 central european time.

In the meantime, I would love to get feedback on the issue of query 
hints by people who use them. 
(https://github.com/w3c/sparql-12/issues/71)

For the curious about what we have been doing over summer in my office.

sparql.uniprot.org is larger than ever (56,748,717,377).
sparql.rhea-db.org has been updated as well.
sparql.hamap.expasy.org has joined the fray (A sparql endpoint filled 
with sparql queries ;) For why read 
https://www.biorxiv.org/content/10.1101/615294v1 )

My colleagues at SIB have of course updated and maintained

sparql.nextprot.org
sparql.omabrowser.org
sparql.orthodb.org
biosoda.expasy.org/rdf4j-server/repositories/bgeelight

And released for the first time

rdf.metanetx.org

We expect to have 2 more live sparql endpoints from different teams in 
our federated organization before the end of this year.

This really shows that sparql has become a key part of the SIB work. 
With 4 different sparqldb-engines in production we see that the standard 
part is critical for us.

This is not just the case for SIB. We see the same in Japan at the 
DBCLS/NDBC hackathon were sparql endpoints are very common and the whole 
discussion was about implementing visualisations of data retrieved via 
sparql queries. i.e. use our sparql endpoints as the single type of 
infrastructure for both analytical use cases and rest/visualization type 
work.

In the wider life-sciences custom engines are starting to pop more often 
e.g.
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0367-2
by the Czech elixir node. And I think improving the sparql standard to 
make that easier would be helpful.

Regards,
Jerven

-- 
Jerven Tjalling Bolleman
SIB | Swiss Institute of Bioinformatics
CMU - 1, rue Michel Servet - 1211 Geneva 4
t: +41 22 379 58 85 - f: +41 22 379 58 58
Jerven.Bolleman@sib.swiss - http://www.sib.swiss

Received on Wednesday, 18 September 2019 13:52:47 UTC