navocab

navocab implements tooling for navigating SKOS vocabulary definitions used in the iSamples project.

Install

Checkout this repository:

git clone https://github.com/isamplesorg/navocab.git

Then run poetry install:

cd navocab
poetry install

Operation

$ 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.

load

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.

Navigating

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": []
}