Really cool! :)

If anyone has eg student project possibilities, it would be great to see some work on Wikidata SPARQL query portability- eg working through the list at query.wikidata.org, which tend to look like this:

SELECT ?item ?itemLabel WHERE { ?item wdt:P31 wd:Q146. # Must be of a cat SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } # Helps get the label in your language, if not, then en language }

which won’t work as-is outside of the current Wikidata SPARQL Blazegraph endpoint.

Something like this is needed (with a filter for lang too):

SELECT ?item ?itemLabel WHERE { ?item wdt:P31 wd:Q146; rdfs:label ?itemLabel }

I don’t recall where the Wikidata sample queries live (github? Wiki somewhere) but it would be lovely to hear if they could all run on an alternative backend…

Dan

On Wed, 11 Jan 2023 at 15:52, Kingsley Idehen via Wikidata < wikidata@lists.wikimedia.org> wrote:

All,

We are pleased to announce immediate availability of an new Virtuoso-hosted Wikidata instance based on the most recent datasets. This instance comprises 17 billion+ RDF triples.

Host Machine Info: Item Value

CPU

2x Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz

Cores

24

Memory

378 GB

SSD

4x Crucial M4 SSD 500 GB

Cloud related costs for a self-hosted variant, assuming:

dedicated machine for 1 year without upfront costs

128 GiB memory

16 cores or more

512GB SSD for the database

3T outgoing internet traffic (based on our DBpedia statistics)

vendor machine type memory vCPUs monthly machine monthly disk monthly network monthly total

Amazon

r5a.4xlarge

128 GiB

16

$479.61

$55.96

$276.48

$812.05

Google

e2highmem-16

128 GiB

16

$594.55

$95.74

$255.00

$945.30

Azure

D32a

128 GiB

32

$769.16

$38.40

$252.30

$1,060.06

SPARQL Query and Full Text Search service endpoints:

https://wikidata.demo.openlinksw.com/sparql -- SPARQL Query Services Endpoint

https://wikidata.demo.openlinksw.com/fct -- Faceted Search & Browsing

Additional Information

Loading the Wikidata dataset 2022/12 into Virtuoso Open Source - Announcements - OpenLink Software Community (openlinksw.com) https://community.openlinksw.com/t/loading-the-wikidata-dataset-2022-12-into-virtuoso-open-source/3580

Happy New Year!

-- Regards,

Kingsley Idehen Founder & CEO OpenLink Software Home Page: http://www.openlinksw.com Community Support: https://community.openlinksw.com Weblogs (Blogs): Company Blog: https://medium.com/openlink-software-blog Virtuoso Blog: https://medium.com/virtuoso-blog Data Access Drivers Blog: https://medium.com/openlink-odbc-jdbc-ado-net-data-access-drivers

Personal Weblogs (Blogs): Medium Blog: https://medium.com/@kidehen Legacy Blogs: http://www.openlinksw.com/blog/~kidehen/ http://kidehen.blogspot.com

Profile Pages: Pinterest: https://www.pinterest.com/kidehen/ Quora: https://www.quora.com/profile/Kingsley-Uyi-Idehen Twitter: https://twitter.com/kidehen Google+: https://plus.google.com/+KingsleyIdehen/about LinkedIn: http://www.linkedin.com/in/kidehen

Web Identities (WebID): Personal: http://kingsley.idehen.net/public_home/kidehen/profile.ttl#i : http://id.myopenlink.net/DAV/home/KingsleyUyiIdehen/Public/kingsley.ttl#this

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On 1/12/23 3:39 AM, Larry Gonzalez wrote:

Dear Kingsley,

Let me start saying that I appreciate and thank the effort of loading complete wikidata over a graph database and make and sparql endpoint available. I know it is not an easy task to do

I just tried out the new virtuoso-hosted sparql endpoint with some queries. My experiments are not exhaustive at all, but I just wanted to raise two concern that I detected

Considering a (very simple) query that count all humans:

''' SELECT (count(?human) as ?c) WHERE {   ?human wdt:P31 wd:Q5 . } '''

I get a result of 10396057, which is ok considering the dataset that you are using

But if we try to export all instances of human (on a tsv file) with the following query:

''' SELECT ?human WHERE {   ?human wdt:P31 wd:Q5 . } '''

Then I only get 100000 results. Is there a limit over the number of results that a query can have?

Yes, because these services are primarily for ad-hoc querying rather than wholesale data exports. If you want to export massive amounts of data then you can do so using OFFSET and LIMIT.

Alternatively, you can instantiate your own instance in the Azure or AWS cloud and use as you see fit.

Like what we provide regarding DBpedia, there's a server side configuration in place for enforcing a "fair use" policy :)

Furthermore, if we want to get all humans ordered by id, then the endpoint times out. The following is the query:

''' SELECT ?human WHERE {   ?human wdt:P31 wd:Q5 . } ORDER BY DESC(?human) '''

If you set the query timeout to a value over 1000 msecs, the Virtuoso Anytime Query feature will provide you with a partial solution which you can use in conjunction with OFFSET and LIMIT to creative an interactive cursor (or scrollable cursor). Beyond that, its back to the "fair use" policy and option to instantiate your own service-specific instance using our cloud offerings.

Regards,

Kingsley

Thank you again for all your efforts. I am looking forward to see how this new endpoint work, :)

Are you planning to update regularly the dataset?

All the best! Larry

https://iccl.inf.tu-dresden.de/web/Larry_Gonzalez

On 11.01.23 21:51, Kingsley Idehen via Wikidata wrote:

...

All,

We are pleased to announce immediate availability of an new Virtuoso-hosted Wikidata instance based on the most recent datasets. This instance comprises 17 billion+ RDF triples.

Host Machine Info:

Item     Value

CPU

|2x Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz|

Cores

|24|

Memory

|378 GB|

SSD

|4x Crucial M4 SSD 500 GB|

Cloud related costs for a self-hosted variant, assuming:

*

dedicated machine for 1 year without upfront costs

*

128 GiB memory

*

16 cores or more

*

512GB SSD for the database

*

3T outgoing internet traffic (based on our DBpedia statistics)

vendor     machine type     memory     vCPUs     monthly machine     monthly disk monthly network     monthly total

Amazon

r5a.4xlarge

128 GiB

16

$479.61

$55.96

$276.48

$812.05

Google

e2highmem-16

128 GiB

16

$594.55

$95.74

$255.00

$945.30

Azure

D32a

128 GiB

32

$769.16

$38.40

$252.30

$1,060.06

SPARQL Query and Full Text Search service endpoints:

*

https://wikidata.demo.openlinksw.com/sparql -- SPARQL Query Services     Endpoint

*

https://wikidata.demo.openlinksw.com/fct -- Faceted Search & Browsing

Additional Information

*

Loading the Wikidata dataset 2022/12 into Virtuoso Open Source -     Announcements - OpenLink Software Community (openlinksw.com) https://community.openlinksw.com/t/loading-the-wikidata-dataset-2022-12-into-virtuoso-open-source/3580

Happy New Year!

-- Regards,

Kingsley Idehen Founder & CEO OpenLink Software Home Page:http://www.openlinksw.com Community Support:https://community.openlinksw.com Weblogs (Blogs): Company Blog:https://medium.com/openlink-software-blog Virtuoso Blog:https://medium.com/virtuoso-blog Data Access Drivers Blog:https://medium.com/openlink-odbc-jdbc-ado-net-data-access-drivers

Personal Weblogs (Blogs): Medium Blog:https://medium.com/@kidehen Legacy Blogs:http://www.openlinksw.com/blog/~kidehen/                http://kidehen.blogspot.com

Profile Pages: Pinterest:https://www.pinterest.com/kidehen/ Quora:https://www.quora.com/profile/Kingsley-Uyi-Idehen Twitter:https://twitter.com/kidehen Google+:https://plus.google.com/+KingsleyIdehen/about LinkedIn:http://www.linkedin.com/in/kidehen

Web Identities (WebID): Personal:http://kingsley.idehen.net/public_home/kidehen/profile.ttl#i :http://id.myopenlink.net/DAV/home/KingsleyUyiIdehen/Public/kingsley.ttl#this

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Hi Samuel,

The current approach is not great and could be improved a lot. So we just set a very high server side http timeout. This helps some but not all clients. We don't predict anything we just let it happen. Virtuoso can predict these kind of timeouts but like all query planning this is not perfect and we found it more helpful to just try to run the queries and see how for we get. This is because sparql.uniprot.org is aimed to help people answer hard analytical style queries and these just take time and resources to run. Also we can't predict load as demand is external so a simple query might timeout because a different complicated query is using to many of the resources in the server.

What we would like to do instead is more complicated.

We should take the query send it to a queue for running generating a query-id. Then send a 303 redirect to the new location with the query-id. Where the query results are paged to disk/named pipe. Then just do the same with retry-after 10second headers, then increasing to one minute. Then we would know if people are actually interested in waiting. Once we have results we can reply with a 200 ok and start sending results. For us this involves a lot of engineering work so we never went that way. But it is the optimal solution, of not doing work that is not wanted. Because if the client stopped asking for the new location within the time limit plus a margin we know they went away and we can stop the query. This can also play nice with a http cache layer.

The main limitation here was the requirement for a distributed key-value store to store these query-id's and results/named-pipes and the need for in between sparql server communication.

We did not have time to implement this in the past, but maybe in the future :)

Regards,

Jerven

On 1/18/23 19:55, Samuel Klein wrote:

Ah, thanks Jerven.  How do you deal with http-layer query timeouts?  Are you able to predict them for certain common queries rather than waiting for the timeout to hit?  S

On Fri, Jan 13, 2023 at 4:02 AM Jerven Tjalling Bolleman jerven.bolleman@sib.swiss wrote:

Hi All,

Regarding these FAIR use settings. They are tuneable and maybe
turned off, so the specific
values that Openlink uses may or may not be used if wikidata would
host itself a virtuoso instance.

e.g. for sparql.uniprot.org <http://sparql.uniprot.org> you are
unlikely to run into these limits (as the values are set very high
indeed)
and are more likely to suffer from settings around the http layer
that limit query run time due to connection issues.

Regards,
Jerven

On 1/12/23 11:45 PM, Kingsley Idehen via Wikidata wrote:

...

On 1/12/23 3:39 AM, Larry Gonzalez wrote:

...

Dear Kingsley,

Let me start saying that I appreciate and thank the effort of
loading complete wikidata over a graph database and make and
sparql endpoint available. I know it is not an easy task to do

I just tried out the new virtuoso-hosted sparql endpoint with
some queries. My experiments are not exhaustive at all, but I
just wanted to raise two concern that I detected

Considering a (very simple) query that count all humans:

'''
SELECT (count(?human) as ?c)
WHERE
{
  ?human wdt:P31 wd:Q5 .
}
'''

I get a result of 10396057, which is ok considering the dataset
that you are using

But if we try to export all instances of human (on a tsv file)
with the following query:

'''
SELECT ?human
WHERE
{
  ?human wdt:P31 wd:Q5 .
}
'''

Then I only get 100000 results. Is there a limit over the number
of results that a query can have?

Yes, because these services are primarily for ad-hoc querying
rather than wholesale data exports. If you want to export massive
amounts of data then you can do so using OFFSET and LIMIT.

Alternatively, you can instantiate your own instance in the Azure
or AWS cloud and use as you see fit.

Like what we provide regarding DBpedia, there's a server side
configuration in place for enforcing a "fair use" policy :)

...

Furthermore, if we want to get all humans ordered by id, then
the endpoint times out. The following is the query:

'''
SELECT ?human
WHERE
{
  ?human wdt:P31 wd:Q5 .
}
ORDER BY DESC(?human)
'''

If you set the query timeout to a value over 1000 msecs, the
Virtuoso Anytime Query feature will provide you with a partial
solution which you can use in conjunction with OFFSET and LIMIT
to creative an interactive cursor (or scrollable cursor). Beyond
that, its back to the "fair use" policy and option to instantiate
your own service-specific instance using our cloud offerings.


Regards,

Kingsley

...

Thank you again for all your efforts. I am looking forward to
see how this new endpoint work, :)

Are you planning to update regularly the dataset?

All the best!
Larry

https://iccl.inf.tu-dresden.de/web/Larry_Gonzalez



On 11.01.23 21:51, Kingsley Idehen via Wikidata wrote:

...

All,

We are pleased to announce immediate availability of an new
Virtuoso-hosted Wikidata instance based on the most recent
datasets. This instance comprises 17 billion+ RDF triples.

Host Machine Info:

Item     Value

CPU



|2x Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz|

Cores



|24|

Memory



|378 GB|

SSD



|4x Crucial M4 SSD 500 GB|


Cloud related costs for a self-hosted variant, assuming:

  *

    dedicated machine for 1 year without upfront costs

  *

    128 GiB memory

  *

    16 cores or more

  *

    512GB SSD for the database

  *

    3T outgoing internet traffic (based on our DBpedia statistics)


vendor     machine type     memory     vCPUs monthly
machine     monthly disk monthly network monthly total

Amazon



r5a.4xlarge



128 GiB



16



$479.61



$55.96



$276.48



$812.05

Google



e2highmem-16



128 GiB



16



$594.55



$95.74



$255.00



$945.30

Azure



D32a



128 GiB



32



$769.16



$38.40



$252.30



$1,060.06


SPARQL Query and Full Text Search service endpoints:

  *

https://wikidata.demo.openlinksw.com/sparql -- SPARQL Query
Services
    Endpoint

  *

https://wikidata.demo.openlinksw.com/fct -- Faceted Search &
Browsing


Additional Information

  *

    Loading the Wikidata dataset 2022/12 into Virtuoso Open
Source -
    Announcements - OpenLink Software Community (openlinksw.com
<http://openlinksw.com>)
<https://community.openlinksw.com/t/loading-the-wikidata-dataset-2022-12-into-virtuoso-open-source/3580>
<https://community.openlinksw.com/t/loading-the-wikidata-dataset-2022-12-into-virtuoso-open-source/3580>



Happy New Year!

-- 
Regards,

Kingsley Idehen
Founder & CEO
OpenLink Software
Home Page:http://www.openlinksw.com
Community Support:https://community.openlinksw.com
Weblogs (Blogs):
Company Blog:https://medium.com/openlink-software-blog
Virtuoso Blog:https://medium.com/virtuoso-blog
Data Access Drivers
Blog:https://medium.com/openlink-odbc-jdbc-ado-net-data-access-drivers


Personal Weblogs (Blogs):
Medium Blog:https://medium.com/@kidehen
Legacy Blogs:http://www.openlinksw.com/blog/~kidehen/
http://kidehen.blogspot.com

Profile Pages:
Pinterest:https://www.pinterest.com/kidehen/
Quora:https://www.quora.com/profile/Kingsley-Uyi-Idehen
Twitter:https://twitter.com/kidehen
Google+:https://plus.google.com/+KingsleyIdehen/about
LinkedIn:http://www.linkedin.com/in/kidehen

Web Identities (WebID):
Personal:http://kingsley.idehen.net/public_home/kidehen/profile.ttl#i

: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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