biointerchange 0.2.2 → 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/Gemfile +1 -0
- data/README.md +269 -19
- data/VERSION +1 -1
- data/examples/bininda_emonds_mammals.new +1 -0
- data/examples/rdfization.rb +17 -0
- data/examples/tree1.new +1 -0
- data/examples/tree2.new +1 -0
- data/examples/vocabulary.rb +26 -5
- data/generators/javaify.rb +12 -18
- data/generators/make_supplement_releases.rb +2 -0
- data/generators/pythonify.rb +21 -8
- data/generators/rdfxml.rb +15 -1
- data/lib/biointerchange/cdao.rb +2014 -0
- data/lib/biointerchange/core.rb +70 -77
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +16 -0
- data/lib/biointerchange/genomics/gff3_reader.rb +18 -4
- data/lib/biointerchange/genomics/gvf_reader.rb +14 -0
- data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +108 -0
- data/lib/biointerchange/phylogenetics/newick_reader.rb +81 -0
- data/lib/biointerchange/phylogenetics/tree_set.rb +50 -0
- data/lib/biointerchange/registry.rb +50 -8
- data/lib/biointerchange/so.rb +150 -0
- data/lib/biointerchange/textmining/pdfx_xml_reader.rb +21 -2
- data/lib/biointerchange/textmining/pubannos_json_reader.rb +24 -1
- data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +9 -0
- data/lib/biointerchange/textmining/text_mining_reader.rb +5 -5
- data/spec/phylogenetics_spec.rb +79 -0
- data/supplemental/java/biointerchange/pom.xml +1 -1
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java +2602 -0
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +30 -28
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +136 -104
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +367 -278
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4388 -3127
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +5970 -4351
- data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +733 -544
- data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +3 -1
- data/supplemental/python/biointerchange/cdao.py +2021 -0
- data/supplemental/python/biointerchange/faldo.py +37 -38
- data/supplemental/python/biointerchange/gff3o.py +156 -157
- data/supplemental/python/biointerchange/goxref.py +172 -172
- data/supplemental/python/biointerchange/gvf1o.py +428 -429
- data/supplemental/python/biointerchange/sio.py +3133 -3134
- data/supplemental/python/biointerchange/so.py +6626 -6527
- data/supplemental/python/biointerchange/sofa.py +790 -791
- data/supplemental/python/example.py +23 -5
- data/supplemental/python/setup.py +2 -2
- data/web/about.html +1 -0
- data/web/api.html +223 -15
- data/web/biointerchange.js +27 -6
- data/web/cli.html +8 -3
- data/web/index.html +6 -2
- data/web/ontologies.html +3 -0
- data/web/service/rdfizer.fcgi +7 -15
- data/web/webservices.html +6 -2
- metadata +30 -3
data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java
CHANGED
@@ -18,7 +18,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0004)
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*/
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public static Resource seqid() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0004");
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}
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/**
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@@ -30,7 +30,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0045)
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*/
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public static Set<Resource> strand() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0010"), _namespace_GFF3O("GFF3_0045") }));
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}
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/**
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@@ -38,7 +38,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0012)
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*/
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public static Resource attributes() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0012");
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}
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/**
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@@ -46,7 +46,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0014)
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*/
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public static Resource parent() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0014");
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}
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/**
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@@ -54,7 +54,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0015)
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*/
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public static Resource contains() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0015");
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}
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/**
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@@ -66,7 +66,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0050)
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*/
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public static Set<Resource> region() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0021"), _namespace_GFF3O("GFF3_0050") }));
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}
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/**
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@@ -74,7 +74,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0023)
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*/
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public static Resource species() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0023");
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}
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/**
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@@ -86,7 +86,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0027)
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*/
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public static Set<Resource> set_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0025"), _namespace_GFF3O("GFF3_0027") }));
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}
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/**
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@@ -98,7 +98,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0028)
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*/
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public static Set<Resource> feature_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0026"), _namespace_GFF3O("GFF3_0028") }));
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}
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/**
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@@ -106,7 +106,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0039)
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*/
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public static Resource target() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0039");
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}
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/**
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@@ -118,7 +118,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0040)
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*/
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public static Set<Resource> target_properties() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0044"), _namespace_GFF3O("GFF3_0040") }));
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}
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/**
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@@ -126,7 +126,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0047)
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*/
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public static Resource derives_from() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0047");
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}
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/**
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@@ -134,7 +134,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0056)
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*/
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public static Resource feature_ontology() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0056");
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}
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/**
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@@ -142,7 +142,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0005)
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*/
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public static Resource source() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0005");
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}
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/**
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* (http://www.biointerchange.org/gff3o#GFF3_0006)
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public static Resource type() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0006");
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}
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/**
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* (http://www.biointerchange.org/gff3o#GFF3_0054)
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public static Set<Resource> start() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0007"), _namespace_GFF3O("GFF3_0042"), _namespace_GFF3O("GFF3_0054") }));
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}
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/**
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* (http://www.biointerchange.org/gff3o#GFF3_0055)
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public static Set<Resource> end() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0008"), _namespace_GFF3O("GFF3_0043"), _namespace_GFF3O("GFF3_0055") }));
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}
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/**
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* (http://www.biointerchange.org/gff3o#GFF3_0009)
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public static Resource score() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0009");
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}
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* (http://www.biointerchange.org/gff3o#GFF3_0011)
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public static Resource phase() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0011");
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}
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* (http://www.biointerchange.org/gff3o#GFF3_0013)
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public static Resource tag() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0013");
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}
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* (http://www.biointerchange.org/gff3o#GFF3_0022)
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public static Resource version() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0022");
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}
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* (http://www.biointerchange.org/gff3o#GFF3_0024)
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public static Resource build() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0024");
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}
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/**
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* (http://www.biointerchange.org/gff3o#GFF3_0029)
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public static Resource attribute_properties() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0029");
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* (http://www.biointerchange.org/gff3o#GFF3_0034)
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public static Resource dbxref() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0034");
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public static Resource ontology_term() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0035");
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* (http://www.biointerchange.org/gff3o#GFF3_0036)
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public static Resource name() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0036");
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}
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public static Resource alias() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0037");
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* (http://www.biointerchange.org/gff3o#GFF3_0041)
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public static Resource target_id() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0041");
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* (http://www.biointerchange.org/gff3o#GFF3_0046)
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public static Resource gap() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0046");
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* (http://www.biointerchange.org/gff3o#GFF3_0048)
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public static Resource note() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0048");
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* (http://www.biointerchange.org/gff3o#GFF3_0049)
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public static Resource is_circular() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0049");
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}
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/**
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* (http://www.biointerchange.org/gff3o#GFF3_0052)
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public static Resource landmark_properties() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0052");
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* (http://www.biointerchange.org/gff3o#GFF3_0053)
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public static Resource id() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0053");
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}
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/**
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* (http://www.biointerchange.org/gff3o#GFF3_0058)
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public static Set<Resource> sequence() {
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("
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return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0057"), _namespace_GFF3O("GFF3_0058") }));
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@@ -328,7 +328,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0001)
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*/
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public static Resource Set() {
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return _namespace_GFF3O("
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return _namespace_GFF3O("GFF3_0001");
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}
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@@ -336,7 +336,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0002)
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*/
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public static Resource Feature() {
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return _namespace_GFF3O("
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+
return _namespace_GFF3O("GFF3_0002");
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}
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@@ -344,7 +344,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0003)
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*/
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public static Resource Attribute() {
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return _namespace_GFF3O("
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+
return _namespace_GFF3O("GFF3_0003");
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}
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@@ -352,7 +352,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0016)
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*/
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public static Resource Strand() {
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-
return _namespace_GFF3O("
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+
return _namespace_GFF3O("GFF3_0016");
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}
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/**
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@@ -360,7 +360,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0038)
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*/
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public static Resource Target() {
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-
return _namespace_GFF3O("
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+
return _namespace_GFF3O("GFF3_0038");
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}
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/**
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@@ -368,7 +368,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0051)
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*/
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public static Resource Landmark() {
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-
return _namespace_GFF3O("
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+
return _namespace_GFF3O("GFF3_0051");
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}
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@@ -376,7 +376,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0017)
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*/
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|
public static Resource Positive() {
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-
return _namespace_GFF3O("
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+
return _namespace_GFF3O("GFF3_0017");
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}
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/**
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@@ -384,7 +384,7 @@ public class GFF3O {
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* (http://www.biointerchange.org/gff3o#GFF3_0018)
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|
*/
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|
public static Resource Negative() {
|
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|
-
return _namespace_GFF3O("
|
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|
+
return _namespace_GFF3O("GFF3_0018");
|
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|
}
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/**
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@@ -392,7 +392,7 @@ public class GFF3O {
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|
* (http://www.biointerchange.org/gff3o#GFF3_0019)
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|
*/
|
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|
public static Resource UnknownStrand() {
|
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|
-
return _namespace_GFF3O("
|
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|
+
return _namespace_GFF3O("GFF3_0019");
|
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|
}
|
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|
|
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398
|
/**
|
@@ -400,7 +400,7 @@ public class GFF3O {
|
|
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|
* (http://www.biointerchange.org/gff3o#GFF3_0020)
|
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|
*/
|
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|
public static Resource NotStranded() {
|
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|
-
return _namespace_GFF3O("
|
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|
+
return _namespace_GFF3O("GFF3_0020");
|
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404
|
}
|
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405
|
|
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406
|
/**
|
@@ -409,49 +409,49 @@ public class GFF3O {
|
|
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|
* @param uri URI that is tested for being an object property
|
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410
|
*/
|
411
411
|
public static boolean isObjectProperty(Resource uri) {
|
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|
-
if (uri
|
412
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0004"))) {
|
413
413
|
return true;
|
414
414
|
}
|
415
|
-
if (uri
|
415
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0010"))) {
|
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416
|
return true;
|
417
417
|
}
|
418
|
-
if (uri
|
418
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0012"))) {
|
419
419
|
return true;
|
420
420
|
}
|
421
|
-
if (uri
|
421
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0014"))) {
|
422
422
|
return true;
|
423
423
|
}
|
424
|
-
if (uri
|
424
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0015"))) {
|
425
425
|
return true;
|
426
426
|
}
|
427
|
-
if (uri
|
427
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0021"))) {
|
428
428
|
return true;
|
429
429
|
}
|
430
|
-
if (uri
|
430
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0023"))) {
|
431
431
|
return true;
|
432
432
|
}
|
433
|
-
if (uri
|
433
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0025"))) {
|
434
434
|
return true;
|
435
435
|
}
|
436
|
-
if (uri
|
436
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0026"))) {
|
437
437
|
return true;
|
438
438
|
}
|
439
|
-
if (uri
|
439
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0039"))) {
|
440
440
|
return true;
|
441
441
|
}
|
442
|
-
if (uri
|
442
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0044"))) {
|
443
443
|
return true;
|
444
444
|
}
|
445
|
-
if (uri
|
445
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0045"))) {
|
446
446
|
return true;
|
447
447
|
}
|
448
|
-
if (uri
|
448
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0047"))) {
|
449
449
|
return true;
|
450
450
|
}
|
451
|
-
if (uri
|
451
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0050"))) {
|
452
452
|
return true;
|
453
453
|
}
|
454
|
-
if (uri
|
454
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0056"))) {
|
455
455
|
return true;
|
456
456
|
}
|
457
457
|
return false;
|
@@ -463,91 +463,91 @@ public class GFF3O {
|
|
463
463
|
* @param uri URI that is tested for being a datatype property
|
464
464
|
*/
|
465
465
|
public static boolean isDatatypeProperty(Resource uri) {
|
466
|
-
if (uri
|
466
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0005"))) {
|
467
467
|
return true;
|
468
468
|
}
|
469
|
-
if (uri
|
469
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0006"))) {
|
470
470
|
return true;
|
471
471
|
}
|
472
|
-
if (uri
|
472
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0007"))) {
|
473
473
|
return true;
|
474
474
|
}
|
475
|
-
if (uri
|
475
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0008"))) {
|
476
476
|
return true;
|
477
477
|
}
|
478
|
-
if (uri
|
478
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0009"))) {
|
479
479
|
return true;
|
480
480
|
}
|
481
|
-
if (uri
|
481
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0011"))) {
|
482
482
|
return true;
|
483
483
|
}
|
484
|
-
if (uri
|
484
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0013"))) {
|
485
485
|
return true;
|
486
486
|
}
|
487
|
-
if (uri
|
487
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0022"))) {
|
488
488
|
return true;
|
489
489
|
}
|
490
|
-
if (uri
|
490
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0024"))) {
|
491
491
|
return true;
|
492
492
|
}
|
493
|
-
if (uri
|
493
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0027"))) {
|
494
494
|
return true;
|
495
495
|
}
|
496
|
-
if (uri
|
496
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0028"))) {
|
497
497
|
return true;
|
498
498
|
}
|
499
|
-
if (uri
|
499
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0029"))) {
|
500
500
|
return true;
|
501
501
|
}
|
502
|
-
if (uri
|
502
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0034"))) {
|
503
503
|
return true;
|
504
504
|
}
|
505
|
-
if (uri
|
505
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0035"))) {
|
506
506
|
return true;
|
507
507
|
}
|
508
|
-
if (uri
|
508
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0036"))) {
|
509
509
|
return true;
|
510
510
|
}
|
511
|
-
if (uri
|
511
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0037"))) {
|
512
512
|
return true;
|
513
513
|
}
|
514
|
-
if (uri
|
514
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0040"))) {
|
515
515
|
return true;
|
516
516
|
}
|
517
|
-
if (uri
|
517
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0041"))) {
|
518
518
|
return true;
|
519
519
|
}
|
520
|
-
if (uri
|
520
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0042"))) {
|
521
521
|
return true;
|
522
522
|
}
|
523
|
-
if (uri
|
523
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0043"))) {
|
524
524
|
return true;
|
525
525
|
}
|
526
|
-
if (uri
|
526
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0046"))) {
|
527
527
|
return true;
|
528
528
|
}
|
529
|
-
if (uri
|
529
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0048"))) {
|
530
530
|
return true;
|
531
531
|
}
|
532
|
-
if (uri
|
532
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0049"))) {
|
533
533
|
return true;
|
534
534
|
}
|
535
|
-
if (uri
|
535
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0052"))) {
|
536
536
|
return true;
|
537
537
|
}
|
538
|
-
if (uri
|
538
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0053"))) {
|
539
539
|
return true;
|
540
540
|
}
|
541
|
-
if (uri
|
541
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0054"))) {
|
542
542
|
return true;
|
543
543
|
}
|
544
|
-
if (uri
|
544
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0055"))) {
|
545
545
|
return true;
|
546
546
|
}
|
547
|
-
if (uri
|
547
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0057"))) {
|
548
548
|
return true;
|
549
549
|
}
|
550
|
-
if (uri
|
550
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0058"))) {
|
551
551
|
return true;
|
552
552
|
}
|
553
553
|
return false;
|
@@ -559,22 +559,22 @@ public class GFF3O {
|
|
559
559
|
* @param uri URI that is tested for being a class
|
560
560
|
*/
|
561
561
|
public static boolean isClass(Resource uri) {
|
562
|
-
if (uri
|
562
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0001"))) {
|
563
563
|
return true;
|
564
564
|
}
|
565
|
-
if (uri
|
565
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0002"))) {
|
566
566
|
return true;
|
567
567
|
}
|
568
|
-
if (uri
|
568
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0003"))) {
|
569
569
|
return true;
|
570
570
|
}
|
571
|
-
if (uri
|
571
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0016"))) {
|
572
572
|
return true;
|
573
573
|
}
|
574
|
-
if (uri
|
574
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0038"))) {
|
575
575
|
return true;
|
576
576
|
}
|
577
|
-
if (uri
|
577
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0051"))) {
|
578
578
|
return true;
|
579
579
|
}
|
580
580
|
return false;
|
@@ -586,16 +586,16 @@ public class GFF3O {
|
|
586
586
|
* @param uri URI that is tested for being a named individual
|
587
587
|
*/
|
588
588
|
public static boolean isNamedIndividual(Resource uri) {
|
589
|
-
if (uri
|
589
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0017"))) {
|
590
590
|
return true;
|
591
591
|
}
|
592
|
-
if (uri
|
592
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0018"))) {
|
593
593
|
return true;
|
594
594
|
}
|
595
|
-
if (uri
|
595
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0019"))) {
|
596
596
|
return true;
|
597
597
|
}
|
598
|
-
if (uri
|
598
|
+
if (uri.equals(_namespace_GFF3O("GFF3_0020"))) {
|
599
599
|
return true;
|
600
600
|
}
|
601
601
|
return false;
|
@@ -619,7 +619,7 @@ public class GFF3O {
|
|
619
619
|
*/
|
620
620
|
public static boolean hasParent(Resource uri, Resource parent) {
|
621
621
|
if (__parent_properties.containsKey(uri)) {
|
622
|
-
if (__parent_properties.get(uri)
|
622
|
+
if (__parent_properties.get(uri).equals(parent)) {
|
623
623
|
return true;
|
624
624
|
}
|
625
625
|
return hasParent((Resource)__parent_properties.get(uri), parent);
|
@@ -628,11 +628,7 @@ public class GFF3O {
|
|
628
628
|
}
|
629
629
|
|
630
630
|
private static Resource _namespace_GFF3O(String accession) {
|
631
|
-
|
632
|
-
return ResourceFactory.createResource("http://www.biointerchange.org/gff3o#" + accession);
|
633
|
-
} else {
|
634
|
-
return ResourceFactory.createProperty("http://www.biointerchange.org/gff3o#" + accession);
|
635
|
-
}
|
631
|
+
return ResourceFactory.createResource("http://www.biointerchange.org/gff3o#" + accession);
|
636
632
|
}
|
637
633
|
|
638
634
|
|
@@ -641,6 +637,42 @@ public class GFF3O {
|
|
641
637
|
private static Map<Resource, Resource> _init___parent_properties() {
|
642
638
|
Map<Resource, Resource> map = new HashMap<Resource, Resource>();
|
643
639
|
|
640
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0004"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
|
641
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0010"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
|
642
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0012"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
|
643
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0014"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
|
644
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0015"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0025"));
|
645
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0021"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
|
646
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0023"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0025"));
|
647
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0039"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
|
648
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0045"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0044"));
|
649
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0047"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
|
650
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0050"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0044"));
|
651
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0056"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0025"));
|
652
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0005"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
653
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0006"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
654
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0007"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
655
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0008"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
656
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0009"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
657
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0011"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
658
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0013"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0029"));
|
659
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0022"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0027"));
|
660
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0024"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0027"));
|
661
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0034"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
662
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0035"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
663
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0036"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
664
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0037"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
665
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0041"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0040"));
|
666
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0042"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0040"));
|
667
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0043"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0040"));
|
668
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0046"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
669
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0048"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
670
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0049"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
671
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0053"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
|
672
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0054"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
|
673
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0055"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
|
674
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0057"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
|
675
|
+
map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0058"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
|
644
676
|
|
645
677
|
return map;
|
646
678
|
}
|