navocab implements tooling for navigating SKOS vocabulary definitions used in the iSamples project.
Checkout this repository:
git clone https://github.com/isamplesorg/navocab.git
Then run poetry install:
cd navocab
poetry install
$ navocab --help
Usage: navocab [OPTIONS] COMMAND [ARGS]...
Options:
-s, --store TEXT SQLite db for vocabularies
--verbosity TEXT Logging level
--help Show this message and exit.
Commands:
broader Perform a depth first traversal of the vocabulary starting...
concept Print out a concept in JSON format.
concepts List the skos:Concept entities in the selected vocabulary.
load Load RDF from the provided local or remote URI.
match Perform a full text search against literal values in the...
namespaces List available namespaces and their prefixes.
narrower Perform a depth first traversal of the vocabulary starting...
roots Retrieve the vocabulary root term(s).
vocabs List the vocabulary URIs in the store.
navocab keeps loaded vocabularies in an sqlite cache. To load a vocabulary, provide the local or remote address of the vocabulary turtle file. The default database name is vocabularies.db in the current directory.
navocab load https://raw.githubusercontent.com/isamplesorg/metadata/develop/src/vocabularies/sampledFeature.ttl
...
2022-10-07 10:58:30,435 navocab:INFO: Graph now has 180 statements.
Note: load currently issues a bunch of SQLAlchemy.bind() warnings. This is due to a pending update in one of the rdflib libraries.
To load all the current (2022-10-07) vocabularies and extensions:
navocab load known
...
2022-10-07 11:25:56,212 navocab:INFO: Graph now has 1414 statements.
To list the available vocabularies (namespace abbreviations can be listed with the namespaces operation):
$ navocab vocabs
sf:sampledfeaturevocabulary
mat:materialsvocabulary
spec:specimentypevocabulary
ming:mineralgroupvocabulary
gmat:geomaterialsvocabulary
Or with full namespaces:
navocab vocabs -f
https://w3id.org/isample/vocabulary/sampledfeature/0.9/sampledfeaturevocabulary
https://w3id.org/isample/vocabulary/material/0.9/materialsvocabulary
https://w3id.org/isample/vocabulary/specimentype/0.9/specimentypevocabulary
https://w3id.org/isample/vocabulary/mingroup/0.9/mineralgroupvocabulary
https://w3id.org/isample/vocabulary/geomaterial/0.9/geomaterialsvocabulary
The vocabulary root terms:
$ navocab roots
sf:sampledfeaturevocabulary
sf:anysampledfeature
mat:materialsvocabulary
mat:material
spec:specimentypevocabulary
spec:physicalspecimen
ming:mineralgroupvocabulary
No root terms in this vocabulary.
gmat:geomaterialsvocabulary
No root terms in this vocabulary.
Narrower terms of spec:physicalspecimen:
$ navocab narrower spec:physicalspecimen
spec:anyaggregation
spec:anthropogenicaggregation
spec:biomeaggregation
spec:bundlebiomeaggregation
spec:slurrybiomeaggregation
spec:genericaggregation
spec:artifact
spec:biologicalspecimen
spec:biomeaggregation
spec:bundlebiomeaggregation
spec:slurrybiomeaggregation
spec:organismpart
spec:organismproduct
spec:wholeorganism
spec:fluidincontainer
spec:fossil
spec:othersolidobject
spec:researchproduct
spec:analyticalpreparation
spec:experimentalproduct
Finding concepts (-c to just list the concepts uri):
navocab match oxide -c
ming:oxidemineral
ocmat:faience
mat:liquidwater
mat:anyanthropogenicmaterial
Matching strings in specific predicate:
navocab match oxide -c -p skos:prefLabel
ming:oxidemineral
Full results:
navocab match oxide -p skos:prefLabel
{
"uri": "https://w3id.org/isample/vocabulary/mingroup/0.9/oxidemineral",
"name": "oxidemineral",
"label": [
"Mineral-Oxide"
],
"definition": "Includes class oxides, hydroxides, and arsenties. Oxides are
minerals in which the oxide anion is bonded to one or more metal alloys. The
hydroxide-bearing minerals are typically included in the oxide class. Arsenite
minerals are very rare oxygen-bearing arsenic minerals.",
"broader": [
"https://w3id.org/isample/vocabulary/material/0.9/mineral"
],
"narrower": []
}