Initialised objects of study taxonomy as skos taxonomy (#140)

taxonomies/best-practices/name-annotation.md

@@ -0,0 +1,85 @@
+# Introduction
+
+This document gathers best practices for lightweight ontology and taxonomy design and edition. 
+It should be considered as a collection of guidelines to follow when contributing to Neuroshapes ontologies and taxonomies. 
+Note that the term 'ontology' in this document is used to refer to both ontologies as well as taxonomies.
+
+## Namespaces
+The following table shows the set of prefix names and their corresponding namespaces used in this document.
+
+
+## Best practices on lightweight ontology and taxonomy edition
+
+### Documentation best practices
+
+#### Topic and provenance
+An ontology should be annotated with its purpose as well as its provenance.  The authorative vocabulary for doing this is the dublin core one.
+Its official prefix name is **dc** and the corresponding namespace is **<http://purl.org/dc/elements/1.1/>**.
+The following annotation should be provided: 
+* dc:title
+* dc:creator and/or dc:contributor
+* dc:subject
+
+#### Versioning
+
+owl:versionInfo is used to provide version information. Its value should match the semantic versioning pattern. 
+For example "0.1.0" is a valid value for owl:versionInfo whereas "version_1" is not.
+
+
+### Entity naming
+
+An ontology as well as entities it defines (called here ontology terms) have a [URI](https://www.w3.org/TR/uri-clarification) as identifier.
+For example "http://purl.obolibrary.org/obo/NCBITaxon_10090" is the URI of the term "Mus musculus". 
+The previous URI can have a short form which is called prefix (a stable string) for the ontology and a [CURIE](https://www.w3.org/TR/curie) for the ontology entities. 
+Let's take the previous example again. The prefix name of (i.e. the short form of) "http://purl.obolibrary.org/obo/NCBITaxon_10090" can be "obo", resulting in a curie of the form "obo:NCBITaxon_10090". 
+Given the curie "obo:NCBITaxon_10090", "obo" is the prefix name and "NCBITaxon_10090" the fragment.
+
+How to write a good CURIE:
+
+ - No underscores (for example **activ**:0000001 instead of **BBP_ACT**:0000001). 
+ - Lower case prefix names (for example "activ" instead of "ACTIV").
+ - Words instead of numbers as fragment (for example **activ:activity** instead of **activ:0000001**) if the number of ontology entities is small. 
+
+#### Ontology term name as single noun
+A term name refers to its curie's fragment. 
+
+- Use [camel case](https://en.wikipedia.org/wiki/Camel_case) notation:
+    * concept name should start with a capital letter
+    * no space is allowed
+    * good example **"damo:ChannelDistribution"**
+    * bad examples  **"damo:channelDistribution"** or **"damo:channel_Distribution"**
+
+
+#### Ontology term Annotations: minimal fields
+
+Here are some annotation properties that can be attached to a concept to describe it.
+
+ * rdfs:label: a short label that can be used to name the concept. At least a label in English should be provided (using @en as language tag). Note that only one label per language is allowed.
+ * skos:prefLabel: a preferred label for an ontology term. The rdfs:label value can be reused here. Note that a skos:prefLabel is a rdfs:label.
+ * Link each term with the ontology which defines it through a rdfs:isDefinedBy assertion.
+
+ #### Ontology property name as verb sense
+
+A property name refers to its curie's fragment. 
+
+- Use a verb as property name so that a triple (a statement: (term, property, term)) can be easily read.
+    * for example: "file:aSpecificFile **prop:hasFileExtension** ext:csv" instead of "file:aSpecificFile **prop:fileExtension** ext:csv"
+- Use mixed case notation:
+    * the property name should start with lower case and be capitalized thereafter
+    * no space is allowed
+    * good example **"prop:hasFileExtension"**
+    * bad example  **"BBP_PROP:has_file_extension"**
+- Link each property with the ontology which defines it through a rdfs:isDefinedBy assertion
+
+
+
+ ### Use of authorative vocabulary
+
+ Authorative vocabulary list:
+
+  * skos: http://www.w3.org/2004/02/skos/core#
+  * dc:	http://purl.org/dc/elements/1.1/
+
+### Frequent errors
+
+ * rdfs:isDefinedBy is not for providing a textual definition for a term or a property but for indicating a resource within which the concept or the property is defined.

taxonomies/data-types.ttl

@@ -1,3 +1,4 @@
+
 @prefix : <http://bbp.epfl.ch/neurosciencegraph/ontologies/datatypes/> .
 @prefix dc: <http://purl.org/dc/elements/1.1/> .
 @prefix dt: <http://bbp.epfl.ch/neurosciencegraph/ontologies/datatypes/> .
@@ -14,6 +15,7 @@
 @prefix vann: <http://purl.org/vocab/vann/> .
 @prefix schema: <http://schema.org/> .
 @prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix datatypes: <http://bbp.epfl.ch/neurosciencegraph/taxonomies/datatypes/> .
 @base <http://bbp.epfl.ch/neurosciencegraph/ontologies/datatypes/> .
 
 <http://bbp.epfl.ch/neurosciencegraph/ontologies/datatypes/> rdf:type owl:Ontology ;
@@ -211,3 +213,4 @@ dt:InVitroSliceWholeCellPatchClampElectrophysiologyTrace rdfs:isDefinedBy <http:
 
 
 ###  Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi
+

taxonomies/licenses.ttl

@@ -0,0 +1,22 @@
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix nsg: <https://bbp-nexus.epfl.ch/vocabs/bbp/neurosciencegraph/core/v0.1.0/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix licenses: <http://bbp.epfl.ch/neurosciencegraph/taxonomies/licenses/> .
+
+licenses: a skos:ConceptScheme ;
+    rdfs:label "License taxonomy"@en ;
+    dc:creator "Sy Mohameth Francois <[email protected]>" ;
+    dc:publisher "Blue Brain Project, EPFL" ;
+    dc:rights "This work is distributed under a Creative Commons Attribution 4.0 (CC-BY-4.0) Public License <https://creativecommons.org/licenses/by/4.0/>"@en ;
+    dcterms:license <https://creativecommons.org/licenses/by/4.0/> ;
+    owl:versionInfo "0.1.0" .

taxonomies/objects-of-study.ttl

@@ -0,0 +1,90 @@
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix nsg: <https://bbp-nexus.epfl.ch/vocabs/bbp/neurosciencegraph/core/v0.1.0/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix objectsofstudy: <http://bbp.epfl.ch/neurosciencegraph/taxonomies/objectsofstudy/> .
+
+objectsofstudy: a skos:ConceptScheme, owl:Ontology ;
+    rdfs:label "Categorization of objects of studies"@en ;
+    dc:creator "Sy Mohameth Francois <[email protected]>" ;
+    dc:subject "Categorization of objects of studies"@en ;
+    dc:publisher "Blue Brain Project, EPFL" ;
+    dc:rights "This work is distributed under a Creative Commons Attribution 4.0 (CC-BY-4.0) Public License <https://creativecommons.org/licenses/by/4.0/>"@en ;
+    dcterms:license <https://creativecommons.org/licenses/by/4.0/> ;
+    owl:versionInfo "0.1.0" ;
+    skos:hasTopConcept objectsofstudy:wholebrain,objectsofstudy:ionchannels,objectsofstudy:reactions,objectsofstudy:proteins.
+
+objectsofstudy:wholebrain a skos:Concept;
+    rdfs:label "Whole Brain"@en;
+    skos:preflabel "Whole Brain"@en;
+    skos:definition "Whole Brain"@en;
+    skos:inScheme objectsofstudy:;
+    skos:topConceptOf objectsofstudy: .
+
+objectsofstudy:slice a skos:Concept;
+    rdfs:label "Slice"@en;
+    skos:preflabel "Slice"@en;
+    skos:broader objectsofstudy:wholebrain;
+    skos:inScheme objectsofstudy:;
+
+
+objectsofstudy:brainregion a skos:Concept;
+    rdfs:label "Brain Region"@en;
+    skos:preflabel "Brain Region"@en;
+    skos:definition "Area of the brain that can be anatomically defined."@en;
+    skos:broader objectsofstudy:slice;
+    skos:inScheme objectsofstudy:;
+
+
+objectsofstudy:circuits a skos:Concept;
+    rdfs:label "Circuit"@en;
+    skos:preflabel "Circuit"@en;
+    skos:definition "A circuit is a specific pattern of connectivity between neurons within a region, it carries out the specific kinds of processing of a region."@en;
+    skos:broader objectsofstudy:brainregion;
+    skos:inScheme objectsofstudy:;
+
+
+objectsofstudy:singlecells a skos:Concept;
+    rdfs:label "Single Cell"@en;
+    skos:preflabel "Single Cell"@en;
+    skos:broader objectsofstudy:circuits;
+    skos:inScheme objectsofstudy:;
+
+
+
+objectsofstudy:synapses a skos:Concept;
+    rdfs:label "Synapse"@en;
+    skos:preflabel "Synapse"@en;
+    skos:broader objectsofstudy:singlecells;
+    skos:inScheme objectsofstudy:;
+
+
+
+objectsofstudy:ionchannels a skos:Concept;
+    rdfs:label "Ion Channel"@en;
+    skos:preflabel "Ion Channel"@en;
+    skos:inScheme objectsofstudy:;
+    skos:topConceptOf objectsofstudy: .
+
+
+objectsofstudy:reactions a skos:Concept;
+    rdfs:label "Reactions"@en;
+    skos:preflabel "Reactions"@en;
+    skos:inScheme objectsofstudy:;
+    skos:topConceptOf objectsofstudy: .
+
+
+objectsofstudy:proteins a skos:Concept;
+    rdfs:label "Proteins"@en;
+    skos:preflabel "Proteins"@en;
+    skos:inScheme objectsofstudy:;
+    skos:topConceptOf objectsofstudy: .

taxonomies/protocol-types.ttl

@@ -1,3 +1,4 @@
+
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@@ -31,4 +32,4 @@ protocol-types:fixationstainingmounting a skos:Concept ;
 
 protocol-types:activity a skos:Concept, nsg:ProtocolType ;
     skos:topConceptOf protocol-types: ;
-    skos:inScheme protocol-types: .
+    skos:inScheme protocol-types: .

taxonomies/roles.ttl

@@ -0,0 +1,24 @@
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix nsg: <https://bbp-nexus.epfl.ch/vocabs/bbp/neurosciencegraph/core/v0.1.0/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix roles: <http://bbp.epfl.ch/neurosciencegraph/taxonomies/roles/> .
+
+roles: a skos:ConceptScheme ;
+    rdfs:label "Categorization of roles of contributors involved in activities"@en ;
+    dc:creator "Sy Mohameth Francois <[email protected]>" ;
+    dc:contributor "Anna-Kristin Kaufmann <[email protected]>" ;
+    dc:contributor "Lu Huanxiang <[email protected]>" ;
+    dc:publisher "Blue Brain Project, EPFL" ;
+    dc:rights "This work is distributed under a Creative Commons Attribution 4.0 (CC-BY-4.0) Public License <https://creativecommons.org/licenses/by/4.0/>"@en ;
+    dcterms:license <https://creativecommons.org/licenses/by/4.0/> ;
+    owl:versionInfo "0.1.0" .