Merge pull request #120 from glosis-ld/develop

Develop
glosis-ld · Oct 11, 2023 · 239d6ea · 239d6ea
2 parents 05ec51f + 48d9bf5
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diff --git a/csv_codelists/glosis_cl.csv b/csv_codelists/glosis_cl.csv
diff --git a/csv_codelists/glosis_procedure.csv b/csv_codelists/glosis_procedure.csv
diff --git a/docs/README.md b/docs/README.md
@@ -36,6 +36,9 @@ As example: codelist of physiochemical properties:
 
 One of them: [http://w3id.org/glosis/model/codelists/physioChemicalPropertyCode-Nittot](http://w3id.org/glosis/model/codelists/physioChemicalPropertyCode-Nittot)
 
+### Sources
+All the ontology modules, code lists and scripts can be found at the [GloSIS GitHub respository](https://github.com/glosis-ld/glosis)
+
 ## Citing
 
 Cite as:

diff --git a/glosis_cl.ttl b/glosis_cl.ttl
diff --git a/glosis_common.ttl b/glosis_common.ttl
@@ -19,8 +19,8 @@
 <http://w3id.org/glosis/model/common>
         a                owl:Ontology ;
         owl:imports      ssn: , sosa: ;
-        owl:versionIRI   <http://w3id.org/glosis/model/common/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/common/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                       foaf:name "Raul Palma"

diff --git a/glosis_layer_horizon.ttl b/glosis_layer_horizon.ttl
@@ -24,8 +24,8 @@
 <http://w3id.org/glosis/model/layerhorizon>
         a                owl:Ontology ;
         owl:imports      ssn: , sosa: , glosis_cl: , glosis_cm: , iso28258: , glosis_u: ;
-        owl:versionIRI   <http://w3id.org/glosis/model/layerhorizon/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/layerhorizon/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                       foaf:name "Raul Palma"

diff --git a/glosis_main.ttl b/glosis_main.ttl
@@ -26,8 +26,8 @@
 
 <http://w3id.org/glosis/model>
         a                owl:Ontology ;
-        owl:versionIRI   <http://w3id.org/glosis/model/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ;
                                            rdfs:seeAlso <https://www.psnc.pl/> ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;

diff --git a/glosis_observation.ttl b/glosis_observation.ttl
@@ -17,8 +17,8 @@
 <http://w3id.org/glosis/model/observation>
         a                owl:Ontology ;
         owl:imports      ssn: , sosa: , iso28258: ;
-        owl:versionIRI   <http://w3id.org/glosis/model/observation/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/observation/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                       foaf:name "Raul Palma"

diff --git a/glosis_procedure.ttl b/glosis_procedure.ttl
@@ -22,8 +22,8 @@
     dct:source "Data model for the Global Soil Information System (GloSIS) v1.0, edited by Tomas Reznik and Katharina Schleidt and Africa Soil Profile Database"@en ;
     dct:title "GLOSIS Procedures code list"@en ;
     rdfs:comment "This module contains the code lists identifying laboratory processes employed to assess physio-chemical soil properties."@en ;    
-    owl:versionIRI <http://w3id.org/glosis/model/procedure/1.2.1> ;
-    owl:versionInfo "1.2.1" .
+    owl:versionIRI <http://w3id.org/glosis/model/procedure/1.3.0> ;
+    owl:versionInfo "1.3.0" .
 
 glosis_proc:acidityExchangeableProcedure a skos:ConceptScheme ;
     rdfs:label "Code list for acidityExchangeable analysis procedures - codelist scheme"@en ;

diff --git a/glosis_profile.ttl b/glosis_profile.ttl
@@ -20,8 +20,8 @@
 <http://w3id.org/glosis/model/profile>
         a                owl:Ontology ;
         owl:imports      ssn: , sosa: , glosis_cl: , glosis_cm: , iso28258: ;
-        owl:versionIRI   <http://w3id.org/glosis/model/profile/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/profile/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                       foaf:name "Raul Palma"

diff --git a/glosis_siteplot.ttl b/glosis_siteplot.ttl
@@ -23,8 +23,8 @@
 <http://w3id.org/glosis/model/siteplot>
         a                owl:Ontology ;
         owl:imports      ssn: , sosa: , glosis_cl: , glosis_cm: , iso28258: ;
-        owl:versionIRI   <http://w3id.org/glosis/model/siteplot/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/siteplot/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                       foaf:name "Raul Palma"

diff --git a/glosis_surface.ttl b/glosis_surface.ttl
@@ -20,8 +20,8 @@
 <http://w3id.org/glosis/model/surface>
         a                owl:Ontology ;
         owl:imports      ssn: , sosa: , glosis_cl: , glosis_cm: , iso28258: ;
-        owl:versionIRI   <http://w3id.org/glosis/model/surface/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/surface/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                       foaf:name "Raul Palma"

diff --git a/glosis_unit.ttl b/glosis_unit.ttl
@@ -8,8 +8,8 @@
 
 <http://w3id.org/glosis/model/unit>
     a                owl:Ontology ;
-    owl:versionIRI   <http://w3id.org/glosis/model/unit/1.2.1> ;
-    owl:versionInfo  "1.2.1" ;
+    owl:versionIRI   <http://w3id.org/glosis/model/unit/1.3.0> ;
+    owl:versionInfo  "1.3.0" ;
     dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                   rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                   foaf:name "Raul Palma"

diff --git a/iso28258.ttl b/iso28258.ttl
@@ -19,8 +19,8 @@
 
 <http://w3id.org/glosis/model/iso28258/2013>
         a                owl:Ontology ;
-        owl:versionIRI   <http://w3id.org/glosis/model/iso28258/2013/1.2.1> ;
-        owl:versionInfo  "1.2.1" ;
+        owl:versionIRI   <http://w3id.org/glosis/model/iso28258/2013/1.3.0> ;
+        owl:versionInfo  "1.3.0" ;
         dct:creator [ schema:affiliation [ foaf:name "PSNC" ] ;
                       rdfs:seeAlso <http://orcid.org/0000-0003-4289-4922> ;
                       foaf:name "Raul Palma"

diff --git a/utils/transformer_tool/README.md b/utils/transformer_tool/README.md
@@ -4,7 +4,7 @@
 
 One should perform the following steps before running the script:
 
-1. ``pip install - r requirements.txt``
+1. ``pip install -r requirements.txt``
 2. ``git clone https://github.com/Montanaz0r/pytarql.git``
 3. cd into cloned repository and run ``pip install .`` to activate setup.py
 
@@ -18,4 +18,4 @@ Script can transform in two ways:
 ```python transform_to_rdf.py data/test.csv data/myquery.rq output.ttl 1.1.1```
 
 ```python transform_to_csv.py input.ttl```
-(this creates a csv file with corresponding filename in the location of TURTLE file)
+(this creates a csv file with corresponding filename in the location of TURTLE file)
diff --git a/...l/examples/glosis_cl/glosis_cl_example.rq → ...tool/example_queries/glosis_cl_example.rq b/...l/examples/glosis_cl/glosis_cl_example.rq → ...tool/example_queries/glosis_cl_example.rq
@@ -3,6 +3,8 @@ PREFIX sosa:  <http://www.w3.org/ns/sosa/>
 PREFIX glosis_cl: <http://w3id.org/glosis/model/codelists/>
 PREFIX skos:  <http://www.w3.org/2004/02/skos/core#> 
 PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX dbo: <http://dbpedia.org/ontology/>
+PREFIX dbprop: <http://dbpedia.org/property/>
 
 
 CONSTRUCT {
@@ -28,7 +30,7 @@ CONSTRUCT {
    .  
 
 ### concepts
-  ?c_oneof a skos:Concept; a ?URI2 ;
+  ?c_oneof a skos:Concept; a ?URI2 ; a ?compoundURI ; a ?substanceURI ;
     skos:topConceptOf ?top_URI ;
     skos:prefLabel ?i_label ;
     skos:notation  ?i_notation ;
@@ -37,6 +39,11 @@ CONSTRUCT {
     skos:scopeNote ?i_citation ;
     skos:inScheme ?URI1 ;
     skos:broader ?broaderURI ;
+    # Chemical substances
+    dbo:pubchem ?pub_chem_code ;
+    dbo:inchi ?inchi_code ;
+    dbprop:inchikey ?inchi_key_code ;
+    rdfs:seeAlso ?pub_chem_URI ;
     .
 
   ?broaderURI skos:narrower ?c_oneof .
@@ -63,4 +70,10 @@ WHERE {
   BIND (IF(?parent_instance = '', ?URI1, ?nothing) AS ?top_URI)
   BIND (URI(CONCAT('http://w3id.org/glosis/model/codelists/', ?attribute, ?postfix, 'Code', '-', ?parent_instance)) AS ?parentURI)
   BIND (IF(?parent_instance != '', ?parentURI, ?nothing) AS ?broaderURI)
+  BIND (IF(?pub_chem != '', ?pub_chem, ?nothing) AS ?pub_chem_code)
+  BIND (IF(?pub_chem != '', URI(CONCAT('https://pubchem.ncbi.nlm.nih.gov/compound/', ?pub_chem)), ?nothing) AS ?pub_chem_URI)
+  BIND (IF(?pub_chem != '', dbo:ChemicalSubstance, ?nothing) AS ?substanceURI)
+  BIND (IF(?inchi_key != '', ?inchi_key, ?nothing) AS ?inchi_key_code)
+  BIND (IF(?inchi != '', ?inchi, ?nothing) AS ?inchi_code)
+  BIND (IF(?pub_chem != '', dbo:ChemicalCompound, ?nothing) AS ?compoundURI)
 }
diff --git a/...sis_procedure/glosis_procedure_example.rq → ...ample_queries/glosis_procedure_example.rq b/...sis_procedure/glosis_procedure_example.rq → ...ample_queries/glosis_procedure_example.rq