ComPlat / ChemistryKnowledgeBase

a project based on semantic media wiki - enriched with chemistry toolkits
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Integration of ontologies #54

Closed IllDepence closed 1 year ago

IllDepence commented 1 year ago

My current understanding based on this paper (see Table 1 and 2):

Open questions

IllDepence commented 1 year ago

tested with export of

Category:Investigation
Carbon_dioxide_reduction_via_light_activation_of_a_ruthenium–Ni(cyclam)_complex/Table_1

but didn’t result in a same_as relation properly resulted in <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/> in the export

(Side note: @kkthek , the addition of the equivalent URI was yet another victim of the WikiImport-Script)

IllDepence commented 1 year ago

note: same_as for instance level, on schema level:

https://www.w3.org/TR/owl-ref/#equivalentClass-def https://www.w3.org/TR/owl-ref/#equivalentProperty-def

IllDepence commented 1 year ago

Tested for column headers (with demo purl URLs)

Investigation properties are defined:

Photocatalytic_CO2_conversion_experiments {{{field|catalyst|property=Catalyst [...] {{{field|pH|property=PH value [...]

Properties have equivalent URLs set:

Property:Catalyst [[equivalent URI:=https://purl.org/tema/000893]]

Property:PH_value [[equivalent URI:=https://purl.org/tema/000124]]

tested with

Category:Investigation
http://chemwiki.scc.kit.edu/main/mediawiki/Property:Catalyst
http://chemwiki.scc.kit.edu/main/mediawiki/Property:PH_value
http://chemwiki.scc.kit.edu/main/mediawiki/Category:Photocatalytic_CO2_conversion_experiments
Carbon_dioxide_reduction_via_light_activation_of_a_ruthenium–Ni(cyclam)_complex/Table_1

but equivalentProperty relations don’t show up in RDF exports

kkthek commented 1 year ago

The special property needed to be activated first in LocalSettings.php. It's called "Equivalent URI", try again with:

[[Equivalent URI::https://purl.org/tema/000124]]

IllDepence commented 1 year ago

for Categories it already worked with := and equivalent (see comment above)

tested now for properties with

but didn’t work

tested by putting

Category:Investigation
http://chemwiki.scc.kit.edu/main/mediawiki/Property:Catalyst
http://chemwiki.scc.kit.edu/main/mediawiki/Property:PH_value
http://chemwiki.scc.kit.edu/main/mediawiki/Category:Photocatalytic_CO2_conversion_experiments
Carbon_dioxide_reduction_via_light_activation_of_a_ruthenium–Ni(cyclam)_complex/Table_1

in the export field and looking for the purl URLs in the output

IllDepence commented 1 year ago

Meeting notes:

not supported in SMW: Domain and range restrictions

kkthek commented 1 year ago

@IllDepence: update: we can use the special property "Imported from" to have the desired behaviour.

  1. Create a page with name: MediaWiki:Smwimport<kürzel> where <kürzel> is the abbreviation for the namespace. with this content:
http://some.url.org/|[http://some.url.org/ Friendly name of this vocabulary]
 trivialname|Type:Text

[[Category:Imported vocabulary]]
  1. Add on the property page "Property:Trivialname" the following annotation:

[[Imported from::<kürzel>:trivialname]]

  1. Do an RDF Export of a page using this property.
IllDepence commented 1 year ago

Added

Chebi with content

http://purl.obolibrary.org/obo/chebi.owl|http://purl.obolibrary.org/obo/chebi.owl Chemical Entities of Biological Interest]
 catalyst|Type:Page

[[Category:Imported vocabulary]]

and to Catalyst

[[Imported from::chebi:catalyst]]

results in RDF export with test input from here

<chebi:catalyst rdf:resource="http://chemwiki.scc.kit.edu/main/mediawiki/Special:URIResolver/Molecule-3A100630"/>
[...]
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/chebi.owlcatalyst"/>
IllDepence commented 1 year ago

since in the output above http://purl.obolibrary.org/obo/chebi.owlcatalyst doesn’t make sense, I changed the URL from

http://purl.obolibrary.org/obo/chebi.owl

to

http://purl.obolibrary.org/obo/

and the catalyst to CHEBI_35223, s.t. in the RDF the URL ends up being

http://purl.obolibrary.org/obo/CHEBI_35223

which properly redirects to https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35223

side note: https://www.ebi.ac.uk/chebi/searchId.do?chebiId= and CHEBI:35223 as URL and property name can’t be used b/c a colon followed by a number leads to an error in the RDF export

kkthek commented 1 year ago

I added the page for the vocabulary "chebi", "MediaWiki:Smw import chebi" to the repo

CNChem commented 1 year ago

Vocabularies chmo and ncit were added to the wiki, "MediaWiki:Smw import chmo", "MediaWiki:Smw import ncit"

kkthek commented 1 year ago

updated the pages in the repo. Added two categories: "Molecular process" and "Assay" which are used in investigations. @CNChem: pls add the required "imported from"-annotations to these 2 categories.

CNChem commented 1 year ago

Added two more vocabularies: MOP OBI

Added imported from to Molecular Process Assay Investigation

Set type for those categories to page, is this correct?

kkthek commented 1 year ago

yes. added it also to the repository.