Graph Descriptions

This repository holds information about individual Theme 1 graphs based on the data provided for those graphs in FRINK's LakeFS repository.

It is generated first by assembling a LinkML schema, compiling information about the graph through iteration over its triples, and then using a modification of LinkML's Markdown documentation generator to produce readable pages with class diagrams from that schema.

Improving graph descriptions

If you wish to improve the descriptions of your graph's entity types and predicates, then you may introduce certain information (in the form of triples) to the data you submit to LakeFS. This information will then update any indicators of absent information that you may encounter in the generated graph documentation.

All CURIEs below are defined through the URLs of the hyperlinks when those CURIEs are first introduced.

IRI prefixes

We have observed the following IRI prefixes, and thus they will be appropriately substituted wherever they occur in the generated graph documentation:

Click here to view the list of prefixes, along with notes about some of them

prefix	IRI	notes
dc:	http://purl.org/dc/elements/1.1/
dct:	http://purl.org/dc/terms/
geo:	http://www.opengis.net/ont/geosparql#
owl:	http://www.w3.org/2002/07/owl#
prov:	http://www.w3.org/ns/prov#
rdf:	http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs:	http://www.w3.org/2000/01/rdf-schema#
schema:	https://schema.org/
skos:	http://www.w3.org/2004/02/skos/core#
sosa:	http://www.w3.org/ns/sosa/
xsd:	http://www.w3.org/2001/XMLSchema#
kwg:	https://stko-kwg.geog.ucsb.edu/lod/ontology	KnowWhereGraph
niem50:	http://release.niem.gov/niem/niem-core/5.0/	NIEM Core 5.0
jxdm72:	http://release.niem.gov/niem/domains/jxdm/7.2/#	NIEM Justice 7.2
obo:	http://purl.obolibrary.org/obo/	OBO Foundry (general)
cheminf:	http://purl.obolibrary.org/obo/CHEMINF_	Chemical Information Ontology
bao:	http://www.bioassayontology.org/bao#BAO_	Bioassay Ontology
edam:	http://edamontology.org/	EDAM ontology
semsci:	http://semanticscience.org/resource/SIO_	Semanticscience Integrated Ontology
niehs:	https://ice.ntp.niehs.nih.gov/property/	Integrated Chemical Environment
umls:	https://identifiers.org/umls:	Unified Medical Language System
hyf:	https://www.opengis.net/def/schema/hy_features/hyf	OGC ontology
sf:	http://www.opengis.net/ont/sf	OGC ontology
gwml22:	http://www.opengis.net/gwml-main/2.2/	OGC ontology
hyfo:	https://www.opengis.net/def/hy_features/ontology/hyf/	OGC ontology
hyfa:	https://www.opengis.net/def/appschema/hy_features/hyf/	OGC ontology
phila:	https://metadata.phila.gov/	City of Philadelphia
qudt:	http://qudt.org/schema/qudt/	QUDT ontology
wdp:	http://www.wikidata.org/prop/	Wikidata-related (from https://w.wiki/4Byv)
wdpq:	http://www.wikidata.org/prop/qualifier/	Wikidata-related (from https://w.wiki/4Byv)
wdpqn:	http://www.wikidata.org/prop/qualifier/value-normalized/	Wikidata-related (from https://w.wiki/4Byv)
wdpqv:	http://www.wikidata.org/prop/qualifier/value/	Wikidata-related (from https://w.wiki/4Byv)
wdpr:	http://www.wikidata.org/prop/reference/	Wikidata-related (from https://w.wiki/4Byv)
wdprn:	http://www.wikidata.org/prop/reference/value-normalized/	Wikidata-related (from https://w.wiki/4Byv)
wdprv:	http://www.wikidata.org/prop/reference/value/	Wikidata-related (from https://w.wiki/4Byv)
wdpsv:	http://www.wikidata.org/prop/statement/value/	Wikidata-related (from https://w.wiki/4Byv)
wdps:	http://www.wikidata.org/prop/statement/	Wikidata-related (from https://w.wiki/4Byv)
wdpsn:	http://www.wikidata.org/prop/statement/value-normalized/	Wikidata-related (from https://w.wiki/4Byv)
wd:	http://www.wikidata.org/entity/	Wikidata-related (from https://w.wiki/4Byv)
wdata:	http://www.wikidata.org/wiki/Special:EntityData/	Wikidata-related (from https://w.wiki/4Byv)
wdno:	http://www.wikidata.org/prop/novalue/	Wikidata-related (from https://w.wiki/4Byv)
wdref:	http://www.wikidata.org/reference/	Wikidata-related (from https://w.wiki/4Byv)
wds:	http://www.wikidata.org/entity/statement/	Wikidata-related (from https://w.wiki/4Byv)
wdt:	http://www.wikidata.org/prop/direct/	Wikidata-related (from https://w.wiki/4Byv)
wdtn:	http://www.wikidata.org/prop/direct-normalized/	Wikidata-related (from https://w.wiki/4Byv)
wdv:	http://www.wikidata.org/value/	Wikidata-related (from https://w.wiki/4Byv)
wikibase:	http://wikiba.se/ontology#	Wikidata-related (from https://w.wiki/4Byv)
hsdo:	http://schema.org/	This prefix should be substituted with schema: wherever it occurs.
neo4j:	neo4j://graph.schema#	Not a real prefix; should be substituted wherever it occurs.
example:	http://example.org/	Not a real prefix; should be substituted wherever it occurs.
attribute:	http://attribute.org/	Not a real prefix; should be substituted wherever it occurs.
relation:	http://relation.org/	Not a real prefix; should be substituted wherever it occurs.
badwdt:	https://www.wikidata.org/wiki/Property:	Not a real RDF prefix; should be substituted wherever it occurs.
dreamkg:	http://www.semanticweb.org/dreamkg/ijcai/	from DREAM-KG; should be substituted with a working IRI prefix.
scales:	http://schemas.scales-okn.org/rdf/scales#	from SCALES; should be substituted with a working IRI prefix.
sockg:	http://www.semanticweb.org/zzy/ontologies/2024/0/soil-carbon-ontology/	from SOC-KG; should be substituted with a working IRI prefix.
securechain:	https://w3id.org/secure-chain/	from Secure Chain-KG
rural:	http://sail.ua.edu/ruralkg/	from RURAL-KG; should be substituted with a working IRI prefix.
contaminoso:	http://sawgraph.spatialai.org/v1/contaminoso#	from SAWGRAPH; should be substituted with a working IRI prefix.
usfrs:	http://sawgraph.spatialai.org/v1/us-frs#	from SAWGRAPH; should be substituted with a working IRI prefix.
usfrsdata:	http://sawgraph.spatialai.org/v1/us-frs-data#	from SAWGRAPH; should be substituted with a working IRI prefix.
naics:	http://sawgraph.spatialai.org/v1/fio/naics#	from SAWGRAPH; should be substituted with a working IRI prefix.
ilisgs:	http://sawgraph.spatialai.org/v1/il-isgs#	from SAWGRAPH; should be substituted with a working IRI prefix.
meegad:	http://sawgraph.spatialai.org/v1/me-egad#	from SAWGRAPH; should be substituted with a working IRI prefix.
memgs:	http://sawgraph.spatialai.org/v1/me-mgs#	from SAWGRAPH; should be substituted with a working IRI prefix.
memgs2:	http://sawgraph.spatialai.org/v1/me_mgs#	from SAWGRAPH; should be substituted with a working IRI prefix.
ussdwis:	http://sawgraph.spatialai.org/v1/us-sdwis#	from SAWGRAPH; should be substituted with a working IRI prefix.
pfas:	http://sawgraph.spatialai.org/v1/pfas#	from SAWGRAPH; should be substituted with a working IRI prefix.
sawwater:	http://sawgraph.spatialai.org/v1/saw_water#	from SAWGRAPH; should be substituted with a working IRI prefix.
fio:	http://sawgraph.spatialai.org/v1/fio#	from SAWGRAPH; should be substituted with a working IRI prefix.
psys:	http://proton.semanticweb.org/protonsys#	from SAWGRAPH; should be substituted with a working IRI prefix.
io:	https://spec.industrialontologies.org/ontology/core/Core/	Industrial Ontologies Foundry
iosc:	https://spec.industrialontologies.org/ontology/supplychain/SupplyChain/	Industrial Ontologies Foundry
sudokn:	http://asu.edu/semantics/SUDOKN/	from SUDOKN: should be substituted with a working IRI prefix.
sudokn2:	Utilities:communication/	Not a real prefix; should be substituted wherever it occurs.
sudokn3:	Utilities:water/	Not a real prefix; should be substituted wherever it occurs.

Please let Mahir know if you introduce any new IRI prefixes not in the above list that should also be substituted.

Documentation triples for any object

For any class or predicate that your graph uses, you can add any of the following triples to it and they will be reflected in the documentation appropriately. All of the following example triples document an entity with the CURIE "example:myClass", and it is hoped that the example object values will help indicate what the triples are intended for.

In the following table, only one triple of each type will be reflected in the documentation. For example, if multiple "skos:definition" triples are defined for an object, only one of those "skos:definition" triples for that object will have its information shown.

Subject	Predicate	Object	Notes
example:myClass	dct:description	"Description of the class"	✅ Required (either this, skos:definition, or rdfs:comment)
example:myClass	skos:definition	"Description of the class"	✅ Required (either this, dct:description, or rdfs:comment)
example:myClass	rdfs:comment	"Description of the class"	✅ Required (either this, dct:description, or skos:definition)
example:myClass	dct:title	"Title of the class"	✅ Required (either this or rdfs:label)
example:myClass	rdfs:label	"Title of the class"	✅ Required (either this or dct:title)
example:myClass	owl:deprecated	"This element has been deprecated since ... because ..."
example:myClass	rdfs:isDefinedBy	https://path.to/where/this/class/is/defined	Object must be a URI.
example:myClass	dct:language	"English"
example:myClass	dct:isReplacedBy	https://path.to/the/class/which/replaces/myClass/if/myClass/is/deprecated	Object must be a URI.
example:myClass	dct:creator	http://github.com/frink-okn	Object must be a URI.
example:myClass	dct:created	"2024-10-30T00:00:00Z"^^xsd:dateTime
example:myClass	dct:modified	"2024-11-30T00:00:00Z"^^xsd:dateTime

In the following table, multiple triples of each type will be reflected in the documentation. For example, if multiple "dct:contributor" triples are defined for an object, all of them will have their information shown.

Subject	Predicate	Object	Notes
example:myClass	prov:todo	"This class has this issue..."
example:myClass	skos:note	"Here's a general note about this class..."	1
example:myClass	skos:changeNote	"Here's a note describing a change to this class..."	1
example:myClass	skos:editorialNote	"Here's an editorial note about this class..."	1
example:myClass	skos:historyNote	"Here's a note about the history of this class..."	1
example:myClass	skos:scopeNote	"Here's a note about the scope of this class..."	1
example:myClass	rdfs:seeAlso	https://path.to/another/relevant/uri/of/some/kind
example:myClass	skos:altLabel	"Alternate name for this class"
example:myClass	skos:mappingRelation	https://path.to/uri/that/maps/to/myClass	Object must be a URI.
example:myClass	skos:exactMatch	https://path.to/uri/that/exactly/matches/myClass	Object must be a URI.
example:myClass	skos:closeMatch	https://path.to/uri/that/is/a/close/match/to/myClass	Object must be a URI.
example:myClass	skos:relatedMatch	https://path.to/uri/that/is/related/to/myClass	Object must be a URI.
example:myClass	skos:narrowMatch	https://path.to/uri/that/narrowly/matches/myClass	Object must be a URI.
example:myClass	skos:broadMatch	https://path.to/uri/that/broadly/matches/myClass	Object must be a URI.
example:myClass	dct:contributor	http://github.com/nsf-open	Object must be a URI.
example:myClass	dcat:theme	https://path.to/category/in/some/scheme	Object must be a URI.
example:myClass	dcat:keyword	"exemplary class"
example:myClass	schema:keywords	"exemplary class"

Ontology (owl:Ontology)

At the moment, since a single HDT file is assumed to represent a whole unit of data modeled in a particular way, it is also assumed that there is exactly one entity of type owl:Ontology in your graph. Let us assume that the ontology entity has the CURIE "example:myOntology".

In addition to the triples described in the section "Documentation triples for any object" above, the following triples will have the following effects which it is hoped are understood from the examples given:

Subject	Predicate	Object	Notes
example:myOntology	dct:hasVersion	"0.0.1"

Please let Mahir know if the graph documentation generator should be aware of any other triples that characterize an ontology entity.

Classes (owl:Class or rdfs:Class)

Each entity type in your graph should have at least one of the following triples present. The example type in the following has the CURIE "example:myClass".

Subject	Predicate	Object	Notes
example:myClass	rdf:type	rdfs:Class	✅ Required (either this or owl:Class)
example:myClass	rdf:type	owl:Class	✅ Required (either this or rdfs:Class)
example:myClass	rdf:type	owl:DeprecatedClass	2

In addition to the triples described in the section "Documentation triples for any object" above, the following triples will have the following effects which it is hoped are understood from the examples given:

Subject	Predicate	Object	Notes
example:myClass	rdfs:subClassOf	example:mySuperClass

Please let Mahir know if the graph documentation generator should be aware of any other triples that characterize an entity type.

Predicates

Each predicate in your graph should be at least one of a number of possible types--that is, a predicate "example:myPredicate" should have at least one of the following triples defined as appropriate:

Subject	Predicate	Object	Notes
example:myPredicate	rdf:type	rdf:Property
example:myPredicate	rdf:type	rdfs:ContainerMembershipProperty
example:myPredicate	rdf:type	owl:DatatypeProperty
example:myPredicate	rdf:type	owl:AnnotationProperty
example:myPredicate	rdf:type	owl:ObjectProperty
example:myPredicate	rdf:type	owl:SymmetricProperty	3
example:myPredicate	rdf:type	owl:AsymmetricProperty	3
example:myPredicate	rdf:type	owl:IrreflexiveProperty	3
example:myPredicate	rdf:type	owl:ReflexiveProperty	3
example:myPredicate	rdf:type	owl:TransitiveProperty	3
example:myPredicate	rdf:type	owl:FunctionalProperty	3

The following triples will have the following effects which it is hoped are understood from the examples given:

Subject	Predicate	Object	Notes
example:myPredicate	rdfs:domain	example:oneDomainType	Multiple domain triples may be present to include multiple types.
example:myPredicate	rdfs:range	example:RangeType
example:myPredicate	rdfs:subPropertyOf	example:mySuperClass

Please let Mahir know if the graph documentation generator should be aware of any other triples that characterize a predicate.

Importing information from external ontologies

At the moment only auxiliary information from schema.org is introduced when a type or predicate from that ontology is encountered, so it is not strictly necessary to re-describe such a type/predicate if you use it in your own graph. Introducing such information from other external ontologies (including from those hosted on w3.org and the OBO foundry) is planned to be supported soon.

Footnotes

1. LinkML specifies that notes be intended either for internal consumption (e.g. for other ontology developers) or for external consumption (e.g. for end-users of the ontology). At the moment all skos: note triples are treated as internal notes; let Mahir know if you think they should be treated in some other way. ↩ ↩² ↩³ ↩⁴ ↩⁵

2. The named characteristic of the class type will be reflected in the class documentation. ↩

3. The named characteristic of the predicate type will be reflected in the predicate documentation. ↩ ↩² ↩³ ↩⁴ ↩⁵ ↩⁶