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.
Files changed (55) hide show
  1. data/Gemfile +1 -0
  2. data/README.md +269 -19
  3. data/VERSION +1 -1
  4. data/examples/bininda_emonds_mammals.new +1 -0
  5. data/examples/rdfization.rb +17 -0
  6. data/examples/tree1.new +1 -0
  7. data/examples/tree2.new +1 -0
  8. data/examples/vocabulary.rb +26 -5
  9. data/generators/javaify.rb +12 -18
  10. data/generators/make_supplement_releases.rb +2 -0
  11. data/generators/pythonify.rb +21 -8
  12. data/generators/rdfxml.rb +15 -1
  13. data/lib/biointerchange/cdao.rb +2014 -0
  14. data/lib/biointerchange/core.rb +70 -77
  15. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +16 -0
  16. data/lib/biointerchange/genomics/gff3_reader.rb +18 -4
  17. data/lib/biointerchange/genomics/gvf_reader.rb +14 -0
  18. data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +108 -0
  19. data/lib/biointerchange/phylogenetics/newick_reader.rb +81 -0
  20. data/lib/biointerchange/phylogenetics/tree_set.rb +50 -0
  21. data/lib/biointerchange/registry.rb +50 -8
  22. data/lib/biointerchange/so.rb +150 -0
  23. data/lib/biointerchange/textmining/pdfx_xml_reader.rb +21 -2
  24. data/lib/biointerchange/textmining/pubannos_json_reader.rb +24 -1
  25. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +9 -0
  26. data/lib/biointerchange/textmining/text_mining_reader.rb +5 -5
  27. data/spec/phylogenetics_spec.rb +79 -0
  28. data/supplemental/java/biointerchange/pom.xml +1 -1
  29. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java +2602 -0
  30. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +30 -28
  31. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +136 -104
  32. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +367 -278
  33. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4388 -3127
  34. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +5970 -4351
  35. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +733 -544
  36. data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +3 -1
  37. data/supplemental/python/biointerchange/cdao.py +2021 -0
  38. data/supplemental/python/biointerchange/faldo.py +37 -38
  39. data/supplemental/python/biointerchange/gff3o.py +156 -157
  40. data/supplemental/python/biointerchange/goxref.py +172 -172
  41. data/supplemental/python/biointerchange/gvf1o.py +428 -429
  42. data/supplemental/python/biointerchange/sio.py +3133 -3134
  43. data/supplemental/python/biointerchange/so.py +6626 -6527
  44. data/supplemental/python/biointerchange/sofa.py +790 -791
  45. data/supplemental/python/example.py +23 -5
  46. data/supplemental/python/setup.py +2 -2
  47. data/web/about.html +1 -0
  48. data/web/api.html +223 -15
  49. data/web/biointerchange.js +27 -6
  50. data/web/cli.html +8 -3
  51. data/web/index.html +6 -2
  52. data/web/ontologies.html +3 -0
  53. data/web/service/rdfizer.fcgi +7 -15
  54. data/web/webservices.html +6 -2
  55. metadata +30 -3
data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java CHANGED
@@ -18,7 +18,7 @@ public class FALDO {
18
18
  * (http://biohackathon.org/resource/faldo#InBetweenPosition)
19
19
  */
20
20
  public static Resource In_between_positions() {
21
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#InBetweenPosition");
21
+ return _namespace_FALDO("InBetweenPosition");
22
22
  }
23
23
 
24
24
  /**
@@ -26,7 +26,7 @@ public class FALDO {
26
26
  * (http://biohackathon.org/resource/faldo#Position)
27
27
  */
28
28
  public static Resource Position() {
29
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#Position");
29
+ return _namespace_FALDO("Position");
30
30
  }
31
31
 
32
32
  /**
@@ -34,7 +34,7 @@ public class FALDO {
34
34
  * (http://biohackathon.org/resource/faldo#ExactPosition)
35
35
  */
36
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  public static Resource Exact_position() {
37
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#ExactPosition");
37
+ return _namespace_FALDO("ExactPosition");
38
38
  }
39
39
 
40
40
  /**
@@ -42,7 +42,7 @@ public class FALDO {
42
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  * (http://biohackathon.org/resource/faldo#OneOfPosition)
43
43
  */
44
44
  public static Resource One_of_positions() {
45
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#OneOfPosition");
45
+ return _namespace_FALDO("OneOfPosition");
46
46
  }
47
47
 
48
48
  /**
@@ -50,7 +50,7 @@ public class FALDO {
50
50
  * (http://biohackathon.org/resource/faldo#InRangePosition)
51
51
  */
52
52
  public static Resource Indeterminate_position_within_a_range() {
53
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#InRangePosition");
53
+ return _namespace_FALDO("InRangePosition");
54
54
  }
55
55
 
56
56
  /**
@@ -58,7 +58,7 @@ public class FALDO {
58
58
  * (http://biohackathon.org/resource/faldo#StrandedPosition)
59
59
  */
60
60
  public static Resource Stranded_position() {
61
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#StrandedPosition");
61
+ return _namespace_FALDO("StrandedPosition");
62
62
  }
63
63
 
64
64
  /**
@@ -66,7 +66,7 @@ public class FALDO {
66
66
  * (http://biohackathon.org/resource/faldo#FuzzyPosition)
67
67
  */
68
68
  public static Resource Fuzzy_position() {
69
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#FuzzyPosition");
69
+ return _namespace_FALDO("FuzzyPosition");
70
70
  }
71
71
 
72
72
  /**
@@ -74,7 +74,7 @@ public class FALDO {
74
74
  * (http://biohackathon.org/resource/faldo#ForwardStrandPosition)
75
75
  */
76
76
  public static Resource Positive_strand() {
77
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#ForwardStrandPosition");
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+ return _namespace_FALDO("ForwardStrandPosition");
78
78
  }
79
79
 
80
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  /**
@@ -82,7 +82,7 @@ public class FALDO {
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  * (http://biohackathon.org/resource/faldo#BothStrandsPosition)
83
83
  */
84
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  public static Resource Both_strands() {
85
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#BothStrandsPosition");
85
+ return _namespace_FALDO("BothStrandsPosition");
86
86
  }
87
87
 
88
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  /**
@@ -90,7 +90,7 @@ public class FALDO {
90
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  * (http://biohackathon.org/resource/faldo#ReverseStrandPosition)
91
91
  */
92
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  public static Resource Negative_strand() {
93
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#ReverseStrandPosition");
93
+ return _namespace_FALDO("ReverseStrandPosition");
94
94
  }
95
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96
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  /**
@@ -98,7 +98,7 @@ public class FALDO {
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  * (http://biohackathon.org/resource/faldo#Region)
99
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  */
100
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  public static Resource Region() {
101
- return _namespace_FALDO("http://biohackathon.org/resource/faldo#Region");
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+ return _namespace_FALDO("Region");
102
102
  }
103
103
 
104
104
  /**
@@ -125,37 +125,37 @@ public class FALDO {
125
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  * @param uri URI that is tested for being a class
126
126
  */
127
127
  public static boolean isClass(Resource uri) {
128
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#InBetweenPosition")) {
128
+ if (uri.equals(_namespace_FALDO("InBetweenPosition"))) {
129
129
  return true;
130
130
  }
131
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#Position")) {
131
+ if (uri.equals(_namespace_FALDO("Position"))) {
132
132
  return true;
133
133
  }
134
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#ExactPosition")) {
134
+ if (uri.equals(_namespace_FALDO("ExactPosition"))) {
135
135
  return true;
136
136
  }
137
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#OneOfPosition")) {
137
+ if (uri.equals(_namespace_FALDO("OneOfPosition"))) {
138
138
  return true;
139
139
  }
140
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#InRangePosition")) {
140
+ if (uri.equals(_namespace_FALDO("InRangePosition"))) {
141
141
  return true;
142
142
  }
143
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#StrandedPosition")) {
143
+ if (uri.equals(_namespace_FALDO("StrandedPosition"))) {
144
144
  return true;
145
145
  }
146
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#FuzzyPosition")) {
146
+ if (uri.equals(_namespace_FALDO("FuzzyPosition"))) {
147
147
  return true;
148
148
  }
149
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#ForwardStrandPosition")) {
149
+ if (uri.equals(_namespace_FALDO("ForwardStrandPosition"))) {
150
150
  return true;
151
151
  }
152
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#BothStrandsPosition")) {
152
+ if (uri.equals(_namespace_FALDO("BothStrandsPosition"))) {
153
153
  return true;
154
154
  }
155
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#ReverseStrandPosition")) {
155
+ if (uri.equals(_namespace_FALDO("ReverseStrandPosition"))) {
156
156
  return true;
157
157
  }
158
- if (uri == _namespace_FALDO("http://biohackathon.org/resource/faldo#Region")) {
158
+ if (uri.equals(_namespace_FALDO("Region"))) {
159
159
  return true;
160
160
  }
161
161
  return false;
@@ -188,7 +188,7 @@ public class FALDO {
188
188
  */
189
189
  public static boolean hasParent(Resource uri, Resource parent) {
190
190
  if (__parent_properties.containsKey(uri)) {
191
- if (__parent_properties.get(uri) == parent) {
191
+ if (__parent_properties.get(uri).equals(parent)) {
192
192
  return true;
193
193
  }
194
194
  return hasParent((Resource)__parent_properties.get(uri), parent);
@@ -197,11 +197,7 @@ public class FALDO {
197
197
  }
198
198
 
199
199
  private static Resource _namespace_FALDO(String accession) {
200
- if (isClass(ResourceFactory.createResource("http://biohackathon.org/resource/faldo#" + accession))) {
201
- return ResourceFactory.createResource("http://biohackathon.org/resource/faldo#" + accession);
202
- } else {
203
- return ResourceFactory.createProperty("http://biohackathon.org/resource/faldo#" + accession);
204
- }
200
+ return ResourceFactory.createResource("http://biohackathon.org/resource/faldo#" + accession);
205
201
  }
206
202
 
207
203
 
@@ -210,6 +206,12 @@ public class FALDO {
210
206
  private static Map<Resource, Resource> _init___parent_properties() {
211
207
  Map<Resource, Resource> map = new HashMap<Resource, Resource>();
212
208
 
209
+ map.put(ResourceFactory.createResource("http://biohackathon.org/resource/faldo#OneOfPosition"), ResourceFactory.createResource("http://biohackathon.org/resource/faldo#FuzzyPosition"));
210
+ map.put(ResourceFactory.createResource("http://biohackathon.org/resource/faldo#StrandedPosition"), ResourceFactory.createResource("http://biohackathon.org/resource/faldo#Position"));
211
+ map.put(ResourceFactory.createResource("http://biohackathon.org/resource/faldo#FuzzyPosition"), ResourceFactory.createResource("http://biohackathon.org/resource/faldo#Position"));
212
+ map.put(ResourceFactory.createResource("http://biohackathon.org/resource/faldo#ForwardStrandPosition"), ResourceFactory.createResource("http://biohackathon.org/resource/faldo#StrandedPosition"));
213
+ map.put(ResourceFactory.createResource("http://biohackathon.org/resource/faldo#BothStrandsPosition"), ResourceFactory.createResource("http://biohackathon.org/resource/faldo#StrandedPosition"));
214
+ map.put(ResourceFactory.createResource("http://biohackathon.org/resource/faldo#ReverseStrandPosition"), ResourceFactory.createResource("http://biohackathon.org/resource/faldo#StrandedPosition"));
213
215
 
214
216
  return map;
215
217
  }