biointerchange 0.2.2 → 1.0.0
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- 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
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: biointerchange
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.
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4
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+
version: 1.0.0
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5
5
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prerelease:
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6
6
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platform: ruby
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7
7
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authors:
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@@ -13,7 +13,7 @@ authors:
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13
13
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autorequire:
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14
14
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bindir: bin
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15
15
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cert_chain: []
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16
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-
date: 2013-
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16
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+
date: 2013-06-08 00:00:00.000000000 Z
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17
17
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dependencies:
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18
18
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- !ruby/object:Gem::Dependency
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19
19
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name: rdf
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@@ -79,6 +79,22 @@ dependencies:
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79
79
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- - ! '>='
|
80
80
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- !ruby/object:Gem::Version
|
81
81
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version: 2.3.2
|
82
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+
- !ruby/object:Gem::Dependency
|
83
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+
name: bio
|
84
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+
requirement: !ruby/object:Gem::Requirement
|
85
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+
none: false
|
86
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+
requirements:
|
87
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+
- - ! '>='
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88
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+
- !ruby/object:Gem::Version
|
89
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+
version: 1.4.2
|
90
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+
type: :runtime
|
91
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+
prerelease: false
|
92
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+
version_requirements: !ruby/object:Gem::Requirement
|
93
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+
none: false
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94
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+
requirements:
|
95
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+
- - ! '>='
|
96
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+
- !ruby/object:Gem::Version
|
97
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+
version: 1.4.2
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82
98
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- !ruby/object:Gem::Dependency
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83
99
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name: rspec
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84
100
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requirement: !ruby/object:Gem::Requirement
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@@ -180,12 +196,16 @@ files:
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180
196
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- bin/biointerchange
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181
197
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- examples/BovineGenomeChrX.gff3.gz
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182
198
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- examples/Saccharomyces_cerevisiae_incl_consequences.gvf.gz
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199
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+
- examples/bininda_emonds_mammals.new
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183
200
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- examples/chromosome_BF.gff
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184
201
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- examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
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185
202
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- examples/gb-2007-8-3-R40.xml
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186
203
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- examples/pubannotation.10096561.json
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187
204
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- examples/pubannotation.10096561.json.old
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188
205
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- examples/pubannotation.2626671.json
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206
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+
- examples/rdfization.rb
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207
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+
- examples/tree1.new
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208
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+
- examples/tree2.new
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189
209
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- examples/vocabulary.rb
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190
210
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- examples/webservice_example.json
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191
211
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- generators/GOxrefify.rb
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@@ -194,6 +214,7 @@ files:
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194
214
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- generators/pythonify.rb
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195
215
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- generators/rdfxml.rb
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196
216
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- lib/biointerchange.rb
|
217
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+
- lib/biointerchange/cdao.rb
|
197
218
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- lib/biointerchange/core.rb
|
198
219
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- lib/biointerchange/exceptions.rb
|
199
220
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- lib/biointerchange/faldo.rb
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@@ -210,6 +231,9 @@ files:
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210
231
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- lib/biointerchange/goxref.rb
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211
232
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- lib/biointerchange/gvf1o.rb
|
212
233
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- lib/biointerchange/model.rb
|
234
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+
- lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb
|
235
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+
- lib/biointerchange/phylogenetics/newick_reader.rb
|
236
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+
- lib/biointerchange/phylogenetics/tree_set.rb
|
213
237
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- lib/biointerchange/reader.rb
|
214
238
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- lib/biointerchange/registry.rb
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215
239
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- lib/biointerchange/sio.rb
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@@ -227,12 +251,14 @@ files:
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227
251
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- spec/exceptions_spec.rb
|
228
252
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- spec/gff3_rdfwriter_spec.rb
|
229
253
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- spec/gvf_rdfwriter_spec.rb
|
254
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+
- spec/phylogenetics_spec.rb
|
230
255
|
- spec/text_mining_pdfx_xml_reader_spec.rb
|
231
256
|
- spec/text_mining_pubannos_json_reader_spec.rb
|
232
257
|
- spec/text_mining_rdfwriter_spec.rb
|
233
258
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- supplemental/java/biointerchange/pom.xml
|
234
259
|
- supplemental/java/biointerchange/src/main/java/org/biointerchange/App.java
|
235
260
|
- supplemental/java/biointerchange/src/main/java/org/biointerchange/AppSIO.java
|
261
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+
- supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java
|
236
262
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- supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java
|
237
263
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- supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java
|
238
264
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- supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java
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@@ -242,6 +268,7 @@ files:
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242
268
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- supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java
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243
269
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- supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java
|
244
270
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- supplemental/python/biointerchange/__init__.py
|
271
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+
- supplemental/python/biointerchange/cdao.py
|
245
272
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- supplemental/python/biointerchange/faldo.py
|
246
273
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- supplemental/python/biointerchange/gff3o.py
|
247
274
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- supplemental/python/biointerchange/goxref.py
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@@ -286,7 +313,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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|
286
313
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version: '0'
|
287
314
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segments:
|
288
315
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- 0
|
289
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-
hash:
|
316
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+
hash: 3715660603784796436
|
290
317
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
291
318
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none: false
|
292
319
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requirements:
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