RDF serialization
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General structure
The XML document is a serialization of RDF triples that describe two types of data: a hierarchical structure expressed using the "OWL DL 2" standard, and additional information about the classes and instances in that hierarchy.
The root tag of the document contains a list of namespace prefixes and their aliases, followed by tags describing unique RDF subjects (in the form of alphanumeric IDs if they are blank nodes, or URIs).
Example of a blank node subject:
<rdf:Description rdf:nodeID="TncAyrlD2310">
...
</rdf:Description>
Example of an URI subject:
<rdf:Description rdf:about="http://brancusi1.usc.edu/brain_parts/abducens-nerve-1/">
...
</rdf:Description>
Inside each tag describing the subject we use one or more tags to describe the corresponding pairs of predicates and objects that form with the subject an RDF triple.
The predicates are URIs and make heavy use of namespace prefixes. The objects can be of any type (BNode, URI, Literal).
Example of a URI predicate and a Literal object:
<bams:name>Abducens nerve</bams:name>
Example of a URI predicate and a URI object:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/reference"/>
Example of a URI predicate and a BNode (blank node) object:
<bams:reference rdf:nodeID="TncAyrlD324"/>
Sections
The subjects and their corresponding predicate-object pairs are listed in the following sections:
Brain PartsIdentified using the rdf:type predicate like that:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/brainPart"/>
The other predicates used in this section and their meaning:
- bams:name - brain part name
- bams:abbreviation - brain part abbreviation
- bams:description - brain part description
- bams:grossConstituent - a URI pointing to one of the gross constituents: gray matter, fiber tract, ventricle
- bams:species - brain part species
- bams:nomenclature - the ID of the nomenclature Bnode that this brain part belongs to
- bams:collationDate - collation date in YYYY-MM-DD format
- bams:collator - the numeric ID of the collator
- bams:endorsed - true if the approach used by the collator was approved by the nomenclature's author, false otherwise
- bams:collatorArgument - a note added by the collator and associated brain part's position in the hierarchy
- bams:collatorInvolvement - refers to the mode of hierarhcy construction, and can take one of the following values:
-- bams:directInsertion - when the data was provided in a digital format and inserted without any alteration
-- bams:directCollation - when the data was collated directly from the reference material
-- bams:expertiseAndCollationNomenclatureCitedReferences - when the collator used his/her personal expertise in addition to the reference material
-- bams:expertiseAndCollationOtherReferences - when the collator used his/her own expertise without any cited references
Identified using the rdf:type predicate like that:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/grossConstituent"/>
The other predicates used in this section and their meaning:
- bams:name - one of: gray matter, fiber tract, ventricle
Identified using the rdf:type predicate like that:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/nomenclature"/>
The other predicates used in this section and their meaning:
- bams:name - nomenclature name and (if available) year
Identified using the rdf:type predicate like that:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/hierarchy"/>
- bams:class1 - the parent's URI
- bams:class2 - the child's URI
- owl:OntologyProperty - bams:hasPart. It means that the parent from bams:class1 has the part in bams:class2 Topological Relations
Identified using the rdf:type predicate like that:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/topologicalRelation"/>
The other predicates used in this section and their meaning:
- bams:collator - the numeric ID of the collator
- bams:reference - ID of the reference
- bams:annotation - an annotation done by the collator
- bams:class1 and bams:class2 - classes referring to brain regions, defined above. We used this denomination to avoid ontological commitment.
- owl:OntologyProperty - the property that links bams:class1 to bams:class2 (in that order). The object can be one of:
-- owl.disjointWith - when it has been established that the two classes are disjoint
-- bams.meet - when the two classes come in direct contact at their borders
-- bams.overlap - when there is overlap
-- bams.covers - when bams:class1 covers bams:class2
-- rdfs.subClassOf - when bams:class1 is a subclass of bams:class2
-- owl.equivalentClass - when the two classes are equivalent
-- bams.unspecified - when there is a topological relation that remains unspecified
Identified using the rdf:type predicate like that:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/reference"/>
The other predicates used in this section and their meaning:
- bams:type - reference type ( one of: bams.book, bams.bookChapter, bams.article)
- bams:author - author
- bams:title - title
- bams:year - year of apparition
- bams.month - month of apparition
- bams:volume - volume
- bams:number - number
- bams:pages - range of pages relevant for this reference
- bams:booktitle - book title
- bams:publisher - publisher
- bams:editor - editor
- bams:series - the series of which this reference is a part of
- bams:chapter - book chapter
- bams:edition - edition
- bams:institution - institution
- bams:url - URL
Identified using the rdf:type predicate like that:
<rdf:type rdf:resource="http://brancusi1.usc.edu/RDF/collator"/>
The other predicates used in this section and their meaning:
- bams:collatorId - a numeric ID identifying each collator
- bams:firstName - first name
- bams:middleName - middle name
- bams:lastName - last name
