@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix htswlib: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .

# I'm still learning how to do modeling & validation
# this version is just using rdfs:Literal for
# any literal node.

<http://jumpgate.caltech.edu/wiki/LibraryOntology#>
    dc:title "HTS-Workflow ontology" ;
    a owl:Ontology .

htswlib:Class a rdfs:Class .

htswlib:IlluminaFlowcell
    a rdfs:Class, htswlib:Class ;
    rdfs:comment "information about a illumina flowcell" ;
    rdfs:label "Flowcell" .

htswlib:IlluminaLane
    a rdfs:Class, htswlib:Class ;
    rdfs:comment "information specific to a lane in a flowcell" ;
    rdfs:label "Lane" .

htswlib:Library
    a rdfs:Class, htswlib:Class ;
    rdfs:comment "a biological library that can be run on a flowcell" ;
    rdfs:label "library" .

htswlib:Sequencer
    a rdfs:Class, htswlib:Class;
    rdfs:comment "an instrument that converts libraries into sequence reads" ;
    rdfs:label "Sequencer" .

htswlib:Species
    a rdfs:Class, htswlib:Class ;
    rdfs:comment "What 'species' was our sample created from." ;
    rdfs:label "Species" .

htswlib:MappedCount
    a rdfs:Class, htswlib:Class ;
    rdfs:comment "Count of reads with locations" ;
    rdfs:label "Mapped locations" .

# reused properties?
htswlib:flowcell
    a rdf:Property ;
    rdfs:comment "link to our source flowcell" ;
    rdfs:label "Flowcell" ;
    rdfs:domain htswlib:IlluminaLane ;
    rdfs:range htswlib:IlluminaFlowcell .

htswlib:has_lane
    a rdf:Property ;
    rdfs:comment "which lanes are attached to a flowcell" ;
    rdfs:label "lanes" ;
    # cheating, only flowcells & libraries can have lanes
    rdfs:domain htswlib:Library ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range htswlib:IlluminaLane .

htswlib:date
    a rdf:Property ;
    rdfs:comment "Date thing was constructed" ;
    rdfs:label "made on" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:total_unique_locations
    a rdf:Property ;
    rdfs:comment "How many reads mapped uniquely" ;
    rdfs:label "Unique locations" ;
    rdfs:domain htswlib:Library ;
    rdfs:domain htswlib:IlluminaLane ;
    rdfs:range rdfs:Literal .

htswlib:has_mappings
    a rdf:Property ;
    rdfs:comment "collection of counts against sequence collections" ;
    rdfs:label "Has mapping" ;
    rdfs:domain htswlib:Library ;
    rdfs:domain htswlib:IlluminaLane ;
    rdfs:range htswlib:MappedCount .

# flowcell properties
htswlib:flowcell_id
    a rdf:Property ;
    rdfs:comment "Serial number of a flowcell, used as unique key" ;
    rdfs:label "Flowcell ID" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:flowcell_notes
    a rdf:Property ;
    rdfs:comment "Comments about flowcell" ;
    rdfs:label "Notes" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:control_lane
    a rdf:Property ;
    rdfs:comment "Control lane used for image analysis/base calling" ;
    rdfs:label "Control Lane" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:read_length
    a rdf:Property ;
    rdfs:comment "How many cycles did we run the sequencer for" ;
    rdfs:label "Read length" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:flowcell_type
    a rdf:Property ;
    rdfs:comment "What kind of flowcell, e.g. single, paired." ;
    rdfs:label "Flowcell Type" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:image_software
    a rdf:Property ;
    rdfs:comment "Image analysis software name." ;
    rdfs:label "Image processor" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:image_version
    a rdf:Property ;
    rdfs:comment "Image analysis software version identifier." ;
    rdfs:label "Image processor version" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:basecall_software
    a rdf:Property ;
    rdfs:comment "Base caller software name." ;
    rdfs:label "Basecaller" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:basecall_version
    a rdf:Property ;
    rdfs:comment "Base caller software version identifier." ;
    rdfs:label "Basecaller Version" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:alignment_software
    a rdf:Property ;
    rdfs:comment "Alignment software name." ;
    rdfs:label "Alignment software" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:alignment_version
    a rdf:Property ;
    rdfs:comment "Alignment software version identifier." ;
    rdfs:label "Aligner" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range rdfs:Literal .

htswlib:sequenced_by
    a rdf:Property ;
    rdfs:comment "Which sequencer sequenced this flowcell" ;
    rdfs:label "Sequenced By" ;
    rdfs:domain htswlib:IlluminaFlowcell ;
    rdfs:range htswlib:Sequencer .

htswlib:sequencer_model
    a rdf:Property ;
    rdfs:comment "What model of sequencer was this flowcell run on." ;
    rdfs:label "Sequencer model" ;
    rdfs:domain htswlib:Sequencer ;
    rdfs:range rdfs:Literal .

htswlib:sequencer_instrument
    a rdf:Property ;
    rdfs:comment "Sequencer instrument identifier." ;
    rdfs:label "Instrument ID " ;
    rdfs:domain htswlib:Sequencer ;
    rdfs:range rdfs:Literal .

htswlib:sequencer_name
    a rdf:Property ;
    rdfs:comment "Local name for sequencer." ;
    rdfs:label "Sequencer name " ;
    rdfs:domain htswlib:Sequencer ;
    rdfs:range rdfs:Literal .

# lane properties
htswlib:status
   a rdf:Proprety ;
   rdfs:comment "Operators opinion of lane status, e.g. were there spots in the pictures" ;
   rdfs:label "Status" ;
   rdfs:domain htswlib:IlluminaLane ;
   rdfs:range htswlib:Literal .

htswlib:cluster_estimate
   a rdf:Proprety ;
   rdfs:comment "Estimate of clusters per tile" ;
   rdfs:label "Cluster Estimate" ;
   rdfs:domain htswlib:IlluminaLane ;
   rdfs:range htswlib:Literal .

htswlib:pM
   a rdf:Proprety ;
   rdfs:comment "picoMolarity" ;
   rdfs:label "picoMolarity" ;
   rdfs:domain htswlib:IlluminaLane ;
   rdfs:range htswlib:Literal .


# library only properties
htswlib:library_id
    a rdf:Property ;
    rdfs:comment "Library unique identifier" ;
    rdfs:label "Library ID" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:name
    a rdf:Property ;
    rdfs:comment "human readable name" ;
    rdfs:label "Name" ;
    rdfs:range rdfs:Literal .

htswlib:library_type
    a rdf:Property ;
    rdfs:comment """what type of library are we, which is primarily
                 determined by the type of adaptors ligated onto
                 sequence fragments.""" ;
    rdfs:label "Library Type" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:condition
   a rdf:Property ;
   rdfs:comment "Describes what treatment has been applied to the cells" ;
   rdfs:label "Condition" ;
   rdfs:domain htswlib:Library ;
   rdfs:range rdfs:Literal .

htswlib:stopping_point
    a rdf:Property ;
    rdfs:comment "Protocol stopping point" ;
    rdfs:label "Stopping Point" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:concentration
    a rdf:Property ;
    rdfs:comment "Concentration of sample in nanograms per microliter" ;
    rdfs:label "Concentration" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:insert_size
    a rdf:Property ;
    rdfs:comment "The expected size of the sample sequence" ;
    rdfs:label "Insert Size" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:gel_cut
    a rdf:Property ;
    rdfs:comment "The estimated fragment sizes cut from gel";
    rdfs:label "Gel Cut" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:made_by
    a rdf:Property ;
    rdfs:comment "Name of person who created library" ;
    rdfs:label "Made by" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:multiplex_index
    a rdf:Property ;
    rdfs:comment "multiplex sequence" ;
    rdfs:label "index" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:cell_line
    a rdf:Property ;
    rdfs:comment "Description of source material" ;
    rdfs:label "cell line" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:experiment_type
    a rdf:Property ;
    rdfs:comment "What type of sequencing is this. e.g. RNA-Seq, DeNovo etc." ;
    rdfs:label "Experiment Type" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:affiliation
    a rdf:Property ;
    rdfs:comment "Entity associated with this sample" ;
    rdfs:label "affiliation" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

htswlib:species
    a rdf:Property ;
    rdfs:comment "Scientific name of sample species" ;
    rdfs:label "Species" ;
    rdfs:domain htswlib:Library ;
    #rdfs:domain htswlib:IlluminaLane;
    rdfs:range htswlib:Species .

htswlib:replicate
    a rdf:Property ;
    rdfs:comment "Which replicate this was" ;
    rdfs:label "replicate" ;
    rdfs:domain htswlib:Library ;
    rdfs:range rdfs:Literal .

# lane only properties
htswlib:lane_number
    a rdf:Property ;
    rdfs:comment "Which lane were we run in" ;
    rdfs:label "lane id" ;
    rdfs:domain htswlib:IlluminaLane ;
    rdfs:range rdfs:Literal .

# FIXME: should this be note?
htswlib:comment
    a rdf:Property ;
    rdfs:comment "Comment about an object" ;
    rdfs:range rdfs:Literal .

htswlib:library
     a rdf:Property ;
     rdfs:comment "which library was run on this lane." ;
     rdfs:label "Library" ;
     rdfs:domain htswlib:IlluminaLane ;
     rdfs:range htswlib:Library .

# species properites
htswlib:species_name
     a rdf:Property ;
     rdfs:comment "Scientific name of species" ;
     rdfs:label "Species" ;
     rdfs:domain htswlib:Species ;
     rdfs:range rdfs:Literal .

# mapped count properties
htswlib:mapped_to
     a rdf:Property ;
     rdfs:comment "A sequence collection, genome, chromosome, spike in, etc.";
     rdfs:label "Mapped to" ;
     rdfs:domain htswlib:MappedCount ;
     rdfs:range rdfs:Literal .

htswlib:reads
     a rdf:Property ;
     rdfs:comment "Number of read locations" ;
     rdfs:label "Reads" ;
     rdfs:domain htswlib:MappedCount ;
     rdfs:range rdfs:Literal .