Hi Samuel, All,

I am the software engineer responsible for sparql.uniprot.org.
I already offered to help in https://phabricator.wikimedia.org/T206561.
So no need to ask Andra or Egon ;)

While we are good users of virtuoso, and strongly suggest it is
evaluated. As it is in general a good product that does scale.[1]

One of the things we did differently than WDQS is to introduce a
controlled layer between the "public" and the "database".
To allow things like query rewriting/redirection upon data model
changes, as well as rewriting some schema rediscovery queries to a known
faster query. We also parse the queries with RDF4J before handing them
to virtuoso. This makes sure that the queries that we accept are only
valid SPARQL 1.1. Avoiding users getting used to almost SPARQL dialects
(i.e. retain the flexiblity to move to a different endpoint). We are in
the process of updating this code and contributing it to RDF4J, with the
first contribution in the develop/4.0.0 branch

I think a number of current customizations in WDQS can be moved to a
front RDF4J layer. Then the RDF4J sail/repository layer can be used to
preserve flexibility. So that WDQS can more easily switch between
backend databases in the future.

One large difference between UniProt and WDQS is that WikiData is
continually updated while UniProt is batch released a few times a year.
WDQS is somewhat easier in some areas and more difficult in others
because of that.

Regards,
Jerven

[1] No Database is perfect, but it does scale a lot better than
Blazegraph did. Which we also evaluated in the past. There is still a
lot of potential in Virtuoso to scale even better in the future.





On 23/08/2021 21:36, Samuel Klein wrote:
> Ah, that's lovely.  Thanks for the update, Kingsley!  Uniprot is a good
> parallel to keep in mind.
>
> For Egon, Andra, others who work with them: Is there someone you'd
> recommend chatting with at uniprot?
> "scaling alongside uniprot" or at least engaging them on how to solve
> shared + comparable issues (they also offer authentication-free SPARQL
> querying) sounds like a compelling option.
>
> S.
>
> On Thu, Aug 19, 2021 at 4:32 PM Kingsley Idehen via Wikidata
> <wikidata@lists.wikimedia.org <mailto:wikidata@lists.wikimedia.org>> wrote:
>
>     On 8/18/21 5:07 PM, Mike Pham wrote:
>>
>>     Wikidata community members,
>>
>>
>>     Thank you for all of your work helping Wikidata grow and improve
>>     over the years. In the spirit of better communication, we would
>>     like to take this opportunity to share some of the current
>>     challenges Wikidata Query Service (WDQS) is facing, and some
>>     strategies we have for dealing with them.
>>
>>
>>     WDQS currently risks failing to provide acceptable service quality
>>     due to the following reasons:
>>
>>     1.
>>
>>         Blazegraph scaling
>>
>>         1.
>>
>>             Graph size. WDQS uses Blazegraph as our graph backend.
>>             While Blazegraph can theoretically support 50 billion
>>             edges <https://blazegraph.com/>, in reality Wikidata is
>>             the largest graph we know of running on Blazegraph (~13
>>             billion triples
>>             <https://grafana.wikimedia.org/d/000000489/wikidata-query-service?viewPanel=7&orgId=1&refresh=1m>),
>>             and there is a risk that we will reach a size
>>             <https://www.w3.org/wiki/LargeTripleStores#Bigdata.28R.29_.2812.7B.29>limit
>>             of what it can realistically support
>>             <https://phabricator.wikimedia.org/T213210>. Once
>>             Blazegraph is maxed out, WDQS can no longer be updated.
>>             This will also break Wikidata tools that rely on WDQS.
>>
>>         2.
>>
>>             Software support. Blazegraph is end of life software,
>>             which is no longer actively maintained, making it an
>>             unsustainable backend to continue moving forward with long
>>             term.
>>
>>
>>     Blazegraph maxing out in size poses the greatest risk for
>>     catastrophic failure, as it would effectively prevent WDQS from
>>     being updated further, and inevitably fall out of date. Our long
>>     term strategy to address this is to move to a new graph backend
>>     that best meets our WDQS needs and is actively maintained, and
>>     begin the migration off of Blazegraph as soon as a viable
>>     alternative is identified
>>     <https://phabricator.wikimedia.org/T206560>.
>>
>
>     Hi Mike,
>
>     Do bear in mind that pre and post selection of Blazegraph for
>     Wikidata, we've always offered an RDF-based DBMS that can handle
>     current and future requirements for Wikidata, just as we do DBpedia.
>
>     At the time of our first rendezvous, handling 50 billion triples
>     would have typically required our Cluster Edition which is a
>     Commercial Only offering -- basically, that was the deal breaker
>     back then.
>
>     Anyway, in recent times, our Open Source Edition has evolved to
>     handle some 80 Billion+ triples (exemplified by the live Uniprot
>     instance) where performance and scale is primary a function of
>     available memory.
>
>     I hope this helps.
>
>     Related:
>
>     [1] https://wikidata.demo.openlinksw.com/sparql
>     <https://wikidata.demo.openlinksw.com/sparql>-- Our Live Wikidata
>     SPARQL Query Endpoint
>     [2]
>     https://docs.google.com/spreadsheets/d/15AXnxMgKyCvLPil_QeGC0DiXOP-Hu8Ln97fZ683ZQF0/edit#gid=0
>     <https://docs.google.com/spreadsheets/d/15AXnxMgKyCvLPil_QeGC0DiXOP-Hu8Ln97fZ683ZQF0/edit#gid=0>
>     -- Google Spreadsheet about various Virtuoso Configurations
>     associated with some well-known public endpoints
>     [3] https://t.co/EjAAO73wwE <https://t.co/EjAAO73wwE> -- this query
>     doesn't complete with the current Blazegraph-based Wikidata endpoint
>     [4] https://t.co/GTATPPJNBI <https://t.co/GTATPPJNBI> -- same query
>     completing when applied to the Virtuoso-based endpoint
>     [5] https://t.co/X7mLmcYC69 <https://t.co/X7mLmcYC69> -- about
>     loading Wikidata's datasets into a Virtuoso instance
>     [6]
>     https://twitter.com/search?q=%23Wikidata%20%23VirtuosoRDBMS%20%40kidehen&src=typed_query&f=live
>     <https://twitter.com/search?q=%2523Wikidata%20%2523VirtuosoRDBMS%20%2540kidehen&src=typed_query&f=live>
>     -- various demos shared via Twitter over the years regarding Wikidata
>
>     --
>     Regards,
>
>     Kingsley Idehen   
>     Founder & CEO
>     OpenLink Software
>     Home Page:http://www.openlinksw.com  <http://www.openlinksw.com>
>     Community Support:https://community.openlinksw.com  <https://community.openlinksw.com>
>     Weblogs (Blogs):
>     Company Blog:https://medium.com/openlink-software-blog  <https://medium.com/openlink-software-blog>
>     Virtuoso Blog:https://medium.com/virtuoso-blog  <https://medium.com/virtuoso-blog>
>     Data Access Drivers Blog:https://medium.com/openlink-odbc-jdbc-ado-net-data-access-drivers  <https://medium.com/openlink-odbc-jdbc-ado-net-data-access-drivers>
>
>     Personal Weblogs (Blogs):
>     Medium Blog:https://medium.com/@kidehen  <https://medium.com/@kidehen>
>     Legacy Blogs:http://www.openlinksw.com/blog/~kidehen/  <http://www.openlinksw.com/blog/~kidehen/>
>                    http://kidehen.blogspot.com  <http://kidehen.blogspot.com>
>
>     Profile Pages:
>     Pinterest:https://www.pinterest.com/kidehen/  <https://www.pinterest.com/kidehen/>
>     Quora:https://www.quora.com/profile/Kingsley-Uyi-Idehen  <https://www.quora.com/profile/Kingsley-Uyi-Idehen>
>     Twitter:https://twitter.com/kidehen  <https://twitter.com/kidehen>
>     Google+:https://plus.google.com/+KingsleyIdehen/about  <https://plus.google.com/+KingsleyIdehen/about>
>     LinkedIn:http://www.linkedin.com/in/kidehen  <http://www.linkedin.com/in/kidehen>
>
>     Web Identities (WebID):
>     Personal:http://kingsley.idehen.net/public_home/kidehen/profile.ttl#i  <http://kingsley.idehen.net/public_home/kidehen/profile.ttl#i>
>              :http://id.myopenlink.net/DAV/home/KingsleyUyiIdehen/Public/kingsley.ttl#this  <http://id.myopenlink.net/DAV/home/KingsleyUyiIdehen/Public/kingsley.ttl#this>
>
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>
>
> --
> Samuel Klein          @metasj           w:user:sj          +1 617 529 4266
>
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--

        *Jerven Tjalling Bolleman*
Principal Software Developer
*SIB | Swiss Institute of Bioinformatics*
1, rue Michel Servet - CH 1211 Geneva 4 - Switzerland
t +41 22 379 58 85
Jerven.Bolleman@sib.swiss - www.sib.swiss
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