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bridgedb / BridgeDb

The BridgeDb Library source code
https://bridgedb.org/
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Where is the BridgeDB ontology? #13

Closed stain closed 9 years ago

stain commented 9 years ago

Two namespaces:

.. used for terms like linksetJustification, subjectsDatatype and more BridgeDb-specific like hasIdentifiersOrgPattern and systemCode.

I don't know if these two namespaces are the same or not. But the fact is that none of them resolve (both give 404), yet they are used here:

Which one should it be? Has there been any attempt to create the ontology? Did vocabularies.bridgedb.org use to resolve to something else than an empty Drupal site?

brenninc commented 9 years ago

Hi Stain,

That was an issue that was not fully resolved.

Ideally they should be merged/changed into a single URL There is no reason to have these different.

We originally started using: http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl# as we had control of that

http://vocabularies.bridgedb.org/ops# fits more with the bridgedb branding but that is not a Manchester controlled site.

Christian

PS. I leave it to the current project team to pick the best way to clean what is agreeably a mess up.

stain commented 9 years ago

My draft - in case it doesn't exist:

I assume there that the 'datasource' ontology is separate.. yet there are things in the constants that sounds like they should are also be in bdb, e.g. fullfillsLens

stain commented 9 years ago

Thanks for the details, @brenninc.

OK, I'll complete the above ontology with the remaining datasource terms, and then we can call it the "Bridge DB ontology" - which match how it is described as "bdb" now. I might fix the odd spelling mistake.

I'll add support to the BridgeDB RDF code for both the old and new namespaces - probably some kind of warning for old ones?

@egonw - would you be the right person to (eventually) modify what the http://vocabularies.bridgedb.org/ops# points to - or who should I ask?

vocabularies.bridgedb.org. 7200 IN  A   137.120.17.33
33.17.120.137.in-addr.arpa. 28800 IN    PTR vocabularies.bigcat.maastrichtuniversity.nl.
ariutta commented 9 years ago

Great work! @stain, here's one more file with terms to check for consistency with the ontology: datasources_headers.txt. You probably know better than me what these terms should be, but let me know if I can help update the file to be consistent with the BridgeDb ontology.

My current mappings from datasources_headers.txt to ontology terms can be seen here: https://github.com/bridgedb/bridgedbjs/blob/master/lib/dataset.js#L29

Christian-B commented 9 years ago

While you are looking at this one thing to consider is the use of bridgeDB:hasUrlPattern and bridgeDB:hasUriPattern The difference was because a classic BridgeDb DataSource only has one UrlPattern.

May be worth considering a better clearer naming here,

as in bridgeDB:DataSource_Chembl_Target a bridgeDB:DataSource ; bridgeDB:fullName "Chembl Target" ; bridgeDB:systemCode "ChemblTarget" ; ...... bridgeDB:hasUrlPattern http://data.kasabi.com/dataset/chembl-rdf/target/t$id ; bridgeDB:hasUriPattern http://chem2bio2rdf.org/chembl/resource/chembl_targets/$id ; bridgeDB:hasUriPattern http://linkedchemistry.info/chembl/target/t$id ; bridgeDB:hasUriPattern http://rdf.ebi.ac.uk/resource/chembl/target/$id . bridgeDB:hasUrlPattern http://data.kasabi.com/dataset/chembl-rdf/target/t$id ; bridgeDB:hasUriPattern http://chem2bio2rdf.org/chembl/resource/chembl_targets/$id ; bridgeDB:hasUriPattern http://linkedchemistry.info/chembl/target/t$id ;

See:https://github.com/bridgedb/BridgeDb/blob/OpenPHACTS/master/org.bridgedb.rdf/resources/DataSource.ttl

stain commented 9 years ago

Thanks, I was a bit confused of hasUrlPattern vs hasUriPattern - is there still a need for the first one?

Perhaps the primary property on a pattern should be changed to a hasPrimaryUriPattern subproperty of hasUriPattern?

stain commented 9 years ago

My draft for the BridgeDb DataSource ontology: https://github.com/bridgedb/BridgeDb/blob/OpenPHACTS/develop/org.bridgedb.rdf/resources/ontology.ttl

Visualized: http://www.essepuntato.it/lode/owlapi/https://rawgit.com/bridgedb/BridgeDb/OpenPHACTS/develop/org.bridgedb.rdf/resources/ontology.ttl

@AlasdairGray - perhaps you could have a brief look? For the terms from datadesc spec I included the documentation as is, but added the friendly skos:Concept as range on hasDataType, linksetJustification, objectsDatatype and subjectsDatatype - as a kind of soft OWL/Full preventor as those would typically go towards other Classes and Properties.

TODO: rdfs:comment for the terms that are not in http://www.openphacts.org/specs/2013/WD-datadesc-20130912/#bridgedb (but then I would need to understand them all.. :-)

Christian-B commented 9 years ago

@stain Said "Perhaps the primary property on a pattern should be changed to a hasPrimaryUriPattern subproperty of hasUriPattern?"

That would have my vote if I still had one.

stain commented 9 years ago

So I changed hasUrlPattern to hasPrimaryUriPattern, a subproperty of hasUriPattern.

The primary property is something different, that I'll leave as is.

Christian-B commented 9 years ago

The "primary" property was not used by OPS but included for backward comparability and to ensure that the OPS version still implemented the existing BridgeDb API's

stain commented 9 years ago

Assigned to @egonw who said he would have a look at publishing this at http://vocabularies.bridgedb.org/ops#

egonw commented 9 years ago

The result is online at the requested link. I started with the data source TTL files but in the end also included @stain's ontology.ttl terms.

@stain, is there anything left in the http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl# namespace that was not in your ontology.ttl yet? If so, please reopen and let me know.

egonw commented 9 years ago

@ariutta, you want to use the ontology, you can perhaps use the https://github.com/alexmilowski/green-turtle HTML+RDFa parser in JavaScript?

ariutta commented 9 years ago

Thanks, Egon. I will use that. On Sep 27, 2015 11:27 AM, "Egon Willighagen" notifications@github.com wrote:

@ariutta https://github.com/ariutta, you want to use the ontology, you can perhaps use the https://github.com/alexmilowski/green-turtle HTML+RDFa parser in JavaScript?

— Reply to this email directly or view it on GitHub https://github.com/bridgedb/BridgeDb/issues/13#issuecomment-143582731.