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Test RSC SureChembl linksets #32

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stain opened this issue Jan 21, 2016 · 9 comments
Open

Test RSC SureChembl linksets #32

stain opened this issue Jan 21, 2016 · 9 comments
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@stain

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@stain
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stain commented Jan 21, 2016

@nicklynch said

RSC have created a linkset for a 100 K mini dataset for SureChMBL
Linkset download for 100K http://ops.rsc.org/download/RDF-2016.01.12.zip

There is properties in this but we should not load ttl file that for now as not sure of licensing of the ACD/Labs for this
Would it be possible to load this into Dev IMS so we can start some testing on this and the API calls?

I've made https://github.com/openphacts/ops-rsc-surechembl-dataset that captures this and produces the linksets only at http://repository.mygrid.org.uk/artifactory/ops/org/openphacts/data/ops-rsc-linksets/0.20151104.0-SNAPSHOT/

I've validated these with IMS, and found that they all load, except SURE_CHEMBL/LINKSET_EXACT_SURE_CHEMBL20160112.ttl, e.g.

<http://ops.rsc.org/OPS1931331> skos:exactMatch <http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL170241> .
<http://ops.rsc.org/OPS1931518> skos:exactMatch <http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL167446> .
<http://ops.rsc.org/OPS1931950> skos:exactMatch <http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL175877> .

This is the most important one as it links the SCHEMBL identifiers to the OPS identifiers - thus linking SureChembl to the rest.

The DataSources.txt in IMS needs to be modified to support the new URI pattern for SureChembl. Nothing is currently resolved from those URIs - @agaulton - are they going to remain as those URIs?
@stain stain self-assigned this Jan 21, 2016
@agaulton
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The URIs used in the SureChEMBL RDF should be like: http://rdf.ebi.ac.uk/resource/surechembl/molecule/SCHEMBL175877 rather than resource/chembl/molecule. So looks like there is an issue in the linkset? We have no plans to change our URIs in the foreseeable future though.
Anna

On 21 Jan 2016, at 14:59, Stian Soiland-Reyes [email protected] wrote:

@nicklynch said

RSC have created a linkset for a 100 K mini dataset for SureChMBL
Linkset download for 100K http://ops.rsc.org/download/RDF-2016.01.12.zip

There is properties in this but we should not load ttl file that for now as not sure of licensing of the ACD/Labs for this
Would it be possible to load this into Dev IMS so we can start some testing on this and the API calls?

I've made https://github.com/openphacts/ops-rsc-surechembl-dataset that captures this and produces the linksets only at http://repository.mygrid.org.uk/artifactory/ops/org/openphacts/data/ops-rsc-linksets/0.20151104.0-SNAPSHOT/

I've validated these with IMS, and found that they all load, except SURE_CHEMBL/LINKSET_EXACT_SURE_CHEMBL20160112.ttl, e.g.

http://ops.rsc.org/OPS1931331 skos:exactMatch http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL170241 .
http://ops.rsc.org/OPS1931518 skos:exactMatch http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL167446 .
http://ops.rsc.org/OPS1931950 skos:exactMatch http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL175877 .
This is the most important one as it links the SCHEMBL identifiers to the OPS identifiers - thus linking SureChembl to the rest.

The DataSources.txt in IMS needs to be modified to support the new URI pattern for SureChembl. Nothing is currently resolved from those URIs - @agaulton - are they going to remain as those URIs?

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@nicklynch
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@batchelorc Any thoughts on linkset comments here?

@stain
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stain commented Jan 22, 2016

Thanks, @agaulton - I'll add the pattern http://rdf.ebi.ac.uk/resource/surechembl/molecule/SCHEMBL(\d+) (still 404) together with https://www.surechembl.org/chemical/SCHEMBL(\d)+

BTW, if I do

curl -v -H "Accept: application/rdf+xml" https://www.surechembl.org/chemical/SCHEMBL175877

.. I get a 500 Internal Server error :-( (I guess it should redirect to the rdf.ebi.ac.uk resource, even if it's still 404 Not Found)

@batchelorc
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Hello chaps,

Well spotted! We need to fix this, so I’ll put a JIRA item in before we generate the RDF.

All the best,
Colin.

From: Stian Soiland-Reyes [mailto:[email protected]]
Sent: 21 January 2016 14:59
To: openphacts/IdentityMappingService
Subject: [IdentityMappingService] Test RSC SureChembl linksets (#32)

@nicklynchhttps://github.com/nicklynch said

RSC have created a linkset for a 100 K mini dataset for SureChMBL
Linkset download for 100K http://ops.rsc.org/download/RDF-2016.01.12.zip

There is properties in this but we should not load ttl file that for now as not sure of licensing of the ACD/Labs for this
Would it be possible to load this into Dev IMS so we can start some testing on this and the API calls?

I've made https://github.com/openphacts/ops-rsc-surechembl-dataset that captures this and produces the linksets only at http://repository.mygrid.org.uk/artifactory/ops/org/openphacts/data/ops-rsc-linksets/0.20151104.0-SNAPSHOT/

I've validated these with IMS, and found that they all load, except SURE_CHEMBL/LINKSET_EXACT_SURE_CHEMBL20160112.ttl, e.g.

http://ops.rsc.org/OPS1931331 skos:exactMatch http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL170241 .

http://ops.rsc.org/OPS1931518 skos:exactMatch http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL167446 .

http://ops.rsc.org/OPS1931950 skos:exactMatch http://rdf.ebi.ac.uk/resource/chembl/molecule/SCHEMBL175877 .

This is the most important one as it links the SCHEMBL identifiers to the OPS identifiers - thus linking SureChembl to the rest.

The DataSources.txt in IMS needs to be modified to support the new URI pattern for SureChembl. Nothing is currently resolved from those URIs - @agaultonhttps://github.com/agaulton - are they going to remain as those URIs?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/32.

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@agaulton
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Yep, we don’t have the SureChembl RDF in the EBI RDF platform yet, so the URIs won’t resolve at present.

Are we using the SureChEMBL interface URLs somewhere in the RDF/Open PHACTS (e.g. https://www.surechembl.org/chemical/SCHEMBL175877)? I.e., is there a reason we should expect this to resolve to RDF?

Cheers
Anna

On 22 Jan 2016, at 10:04, Stian Soiland-Reyes [email protected] wrote:

Thanks, @agaulton - I'll add http://rdf.ebi.ac.uk/resource/surechembl/molecule/SCHEMBL175877 (still 404) together with https://www.surechembl.org/chemical/SCHEMBL175877

BTW, if I do

curl -v -H "Accept: application/rdf+xml" https://www.surechembl.org/chemical/SCHEMBL175877
.. I get a 500 Internal Server error :-( (I guess it should redirect to the rdf.ebi.ac.uk resource, even if it's still 404 Not Found)

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@danidi
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danidi commented Jan 22, 2016

From a user perspective, adding the interface URL to the IMS helps to retrieve data from the API. E.g. you could search on the SureChEMBL page and the use this URL directly in the API.

@agaulton
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OK that makes sense, I just wasn’t sure if it came from our side...
A

On 22 Jan 2016, at 10:55, danidi [email protected] wrote:

From a user perspective, adding the interface URL to the IMS helps to retrieve data from the API. E.g. you could search on the SureChEMBL page and the use this URL directly in the API.

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@madgpap
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madgpap commented Jan 22, 2016

👍

@stain
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stain commented Jan 22, 2016

Agree on @danidi - also the www URI will be coming back from IMS as part of the response when looking up any of the URIs that lead to it through the RSC linkset; which could be useful for users to click on in a browser.

The redirect from www to rdf is just about being good web citizen (once) you have the RDF live. I expect it fails with a 500 (rather than 406 Not Acceptable) is because you have partially got the redirection functionality there?

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@danidi @stain @batchelorc @madgpap @nicklynch @agaulton