make release 1.18 ready for launch

edamontology · Jul 4, 2017 · ea76fdd · ea76fdd
1 parent c694ce0
commit ea76fdd
Show file tree

Hide file tree

Showing 4 changed files with 54,999 additions and 10 deletions.
diff --git a/EDAM_dev.owl b/EDAM_dev.owl
@@ -43,11 +43,11 @@
         <oboOther:idspace>EDAM http://edamontology.org/ &quot;EDAM relations and concept properties&quot;</oboOther:idspace>
         <dc:format>application/rdf+xml</dc:format>
         <next_id>3805</next_id>
-        <oboOther:date>27.04.2017 21:47 GMT</oboOther:date>
+        <oboOther:date>04.07.2017 12:47 GMT</oboOther:date>
         <oboOther:idspace>EDAM_data http://edamontology.org/data_ &quot;EDAM types of data&quot;</oboOther:idspace>
         <oboInOwl:hasSubset>concept_properties &quot;EDAM concept properties&quot;</oboInOwl:hasSubset>
         <oboOther:remark>EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources.  EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.</oboOther:remark>
-        <doap:Version>1.18_dev</doap:Version>
+        <doap:Version>1.19_dev</doap:Version>
         <dc:creator>Jon Ison</dc:creator>
         <dc:creator>Matúš Kalaš</dc:creator>
         <oboOther:idspace>EDAM_format http://edamontology.org/format_ &quot;EDAM data formats&quot;</oboOther:idspace>

diff --git a/changelog-detailed.md b/changelog-detailed.md
@@ -1,6 +1,297 @@
 # Detailed Changelog for EDAM
 Data were generated using the [Bubastis](http://www.ebi.ac.uk/efo/bubastis/) ontology-diff tool.
 
+# EDAM\_1.18.owl
+
+## Classes modified:
+
+Class changed: IRI http://edamontology.org/operation_0334
+label: Enzyme kinetics calculation
++ 'Enzyme kinetics calculation' SubClassOf 'Protein property calculation'
+- 'Enzyme kinetics calculation' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_0333
+label: Zinc finger prediction
++ 'Zinc finger prediction' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Zinc finger prediction' SubClassOf 'has topic' some 'Protein folding, stability and design'
+- 'Zinc finger prediction' SubClassOf 'has output' some 'Protein interaction report'
+- 'Zinc finger prediction' SubClassOf 'Protein-nucleic acid binding prediction'
+
+Class changed: IRI http://edamontology.org/operation_0386
+label: Protein dipole moment calculation
++ 'Protein dipole moment calculation' SubClassOf 'Protein property calculation'
+- 'Protein dipole moment calculation' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_0398
+label: Protein molecular weight calculation
++ 'Protein molecular weight calculation' SubClassOf 'Protein property calculation'
+- 'Protein molecular weight calculation' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_0399
+label: Protein extinction coefficient calculation
++ 'Protein extinction coefficient calculation' SubClassOf 'Protein property calculation'
+- 'Protein extinction coefficient calculation' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_0366
+label: Protein sequence cleavage
++ 'Protein sequence cleavage' SubClassOf 'Protein property calculation'
+- 'Protein sequence cleavage' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_3441
+label: Plotting
++ 'Plotting' SubClassOf 'Visualisation'
+- 'Plotting' SubClassOf 'Operation'
+
+Class changed: IRI http://edamontology.org/operation_3471
+label: Nucleic acid folding prediction (alignment-based)
++ 'Nucleic acid folding prediction (alignment-based)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Nucleic acid folding prediction (alignment-based)' SubClassOf 'Nucleic acid folding analysis'
+
+Class changed: IRI http://edamontology.org/operation_3470
+label: RNA secondary structure prediction (shape-based)
++ 'RNA secondary structure prediction (shape-based)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'RNA secondary structure prediction (shape-based)' SubClassOf 'RNA secondary structure prediction'
+
+Class changed: IRI http://edamontology.org/operation_2931
+label: Secondary structure comparison
++ 'Secondary structure comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Secondary structure comparison' SubClassOf 'Comparison'
+- 'Secondary structure comparison' SubClassOf 'has topic' some 'Structure analysis'
+
+Class changed: IRI http://edamontology.org/operation_2935
+label: Microarray wave graph plotting
++ 'Microarray wave graph plotting' SubClassOf 'Plotting'
+- 'Microarray wave graph plotting' SubClassOf 'Microarray data rendering'
+
+Class changed: IRI http://edamontology.org/operation_2934
+label: Microarray cluster textual view generation
++ 'Microarray cluster textual view generation' SubClassOf 'Plotting'
+- 'Microarray cluster textual view generation' SubClassOf 'Microarray data rendering'
+
+Class changed: IRI http://edamontology.org/operation_2941
+label: Whole microarray graph plotting
++ 'Whole microarray graph plotting' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Whole microarray graph plotting' SubClassOf 'Microarray data rendering'
+
+Class changed: IRI http://edamontology.org/operation_2940
+label: Microarray scatter plot plotting
++ 'Microarray scatter plot plotting' SubClassOf 'Plotting'
+- 'Microarray scatter plot plotting' SubClassOf 'Microarray data rendering'
+
+Class changed: IRI http://edamontology.org/operation_2943
+label: Microarray Box-Whisker plot plotting
++ 'Microarray Box-Whisker plot plotting' SubClassOf 'Plotting'
+- 'Microarray Box-Whisker plot plotting' SubClassOf 'Microarray data rendering'
+
+Class changed: IRI http://edamontology.org/operation_2939
+label: Microarray principal component plotting
++ 'Microarray principal component plotting' SubClassOf 'Plotting'
+- 'Microarray principal component plotting' SubClassOf 'Microarray data rendering'
+
+Class changed: IRI http://edamontology.org/operation_0467
+label: Protein secondary structure prediction (integrated)
++ 'Protein secondary structure prediction (integrated)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein secondary structure prediction (integrated)' SubClassOf 'Protein secondary structure prediction'
+
+Class changed: IRI http://edamontology.org/operation_0471
+label: Protein secondary structure prediction (disulfide bonds)
++ 'Protein secondary structure prediction (disulfide bonds)' SubClassOf 'Protein feature detection'
+- 'Protein secondary structure prediction (disulfide bonds)' SubClassOf 'Protein secondary structure prediction'
+
+Class changed: IRI http://edamontology.org/operation_0451
+label: Recombination detection
++ 'Recombination detection' SubClassOf 'Nucleic acid sequence analysis'
+- 'Recombination detection' SubClassOf 'Nucleic acid sequence alignment analysis'
+
+Class changed: IRI http://edamontology.org/operation_0452
+label: Indel detection
++ 'Indel detection' SubClassOf 'Nucleic acid sequence analysis'
+- 'Indel detection' SubClassOf 'Nucleic acid sequence alignment analysis'
+
+Class changed: IRI http://edamontology.org/operation_0450
+label: Chimeric sequence detection
++ 'Chimeric sequence detection' SubClassOf 'Nucleic acid sequence analysis'
+- 'Chimeric sequence detection' SubClassOf 'Nucleic acid sequence alignment analysis'
+
+Class changed: IRI http://edamontology.org/operation_0484
+label: SNP detection
++ 'SNP detection' SubClassOf 'Nucleic acid sequence analysis'
+- 'SNP detection' SubClassOf 'Nucleic acid sequence alignment analysis'
+
+Class changed: IRI http://edamontology.org/operation_2239
+label: 3D-1D scoring matrix generation
++ '3D-1D scoring matrix generation' SubClassOf 'Protein property calculation'
+- '3D-1D scoring matrix generation' SubClassOf 'Protein property calculation (from sequence)'
+- '3D-1D scoring matrix generation' SubClassOf 'Protein property calculation (from structure)'
+
+Class changed: IRI http://edamontology.org/operation_0400
+label: Protein pH-dependent property calculation
++ 'Protein pH-dependent property calculation' SubClassOf 'Protein property calculation'
+- 'Protein pH-dependent property calculation' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_3209
+label: Genome comparison
++ 'Genome comparison' SubClassOf 'Sequence comparison'
+- 'Genome comparison' SubClassOf 'Nucleic acid sequence comparison'
+
+Class changed: IRI http://edamontology.org/operation_3197
+label: Genetic variation analysis
+- 'Genetic variation analysis' SubClassOf 'Nucleic acid sequence comparison'
+
+Class changed: IRI http://edamontology.org/operation_3195
+label: Sequencing error detection
++ 'Sequencing error detection' SubClassOf 'Sequence comparison'
+- 'Sequencing error detection' SubClassOf 'Nucleic acid sequence comparison'
+
+Class changed: IRI http://edamontology.org/operation_0224
+label: Query and retrieval
++ 'Query and retrieval' SubClassOf 'Data handling'
+- 'Query and retrieval' SubClassOf 'Operation'
+
+Class changed: IRI http://edamontology.org/operation_0266
+label: Vector sequence detection
++ 'Vector sequence detection' SubClassOf 'Sequence comparison'
+- 'Vector sequence detection' SubClassOf 'Nucleic acid sequence comparison'
+
+Class changed: IRI http://edamontology.org/operation_0272
+label: Residue interaction prediction
++ 'Residue interaction prediction' SubClassOf 'Protein sequence analysis'
++ 'Residue interaction prediction' SubClassOf 'Protein property calculation'
+- 'Residue interaction prediction' SubClassOf 'Protein sequence alignment analysis'
+- 'Residue interaction prediction' SubClassOf 'Protein property calculation (from structure)'
+
+Class changed: IRI http://edamontology.org/operation_0244
+label: Protein flexibility and motion analysis
++ 'Protein flexibility and motion analysis' SubClassOf 'Protein property calculation'
+- 'Protein flexibility and motion analysis' SubClassOf 'Protein property calculation (from structure)'
+
+Class changed: IRI http://edamontology.org/operation_0248
+label: Residue interaction calculation
++ 'Residue interaction calculation' SubClassOf 'Protein property calculation'
+- 'Residue interaction calculation' SubClassOf 'Protein property calculation (from structure)'
+
+Class changed: IRI http://edamontology.org/operation_0249
+label: Protein geometry calculation
++ 'Protein geometry calculation' SubClassOf 'Protein property calculation'
+- 'Protein geometry calculation' SubClassOf 'Protein property calculation (from structure)'
+
+Class changed: IRI http://edamontology.org/operation_0243
+label: Protein property calculation (from structure)
++ 'Protein property calculation (from structure)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein property calculation (from structure)' SubClassOf 'Protein structure analysis'
+- 'Protein property calculation (from structure)' SubClassOf 'has topic' some 'Protein structure analysis'
+- 'Protein property calculation (from structure)' SubClassOf 'has output' some 'Protein property'
+- 'Protein property calculation (from structure)' SubClassOf 'Protein property calculation'
+
+Class changed: IRI http://edamontology.org/operation_0252
+label: Peptide immunogenicity prediction
++ 'Peptide immunogenicity prediction' SubClassOf 'Protein property calculation'
+- 'Peptide immunogenicity prediction' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_0284
+label: Codon usage table generation
++ 'Codon usage table generation' SubClassOf 'Codon usage analysis'
+- 'Codon usage table generation' SubClassOf 'Codon usage table processing'
+
+Class changed: IRI http://edamontology.org/operation_0285
+label: Codon usage table comparison
++ 'Codon usage table comparison' SubClassOf 'Codon usage analysis'
+- 'Codon usage table comparison' SubClassOf 'Codon usage table processing'
+
+Class changed: IRI http://edamontology.org/operation_2506
+label: Protein sequence alignment analysis
++ 'Protein sequence alignment analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein sequence alignment analysis' SubClassOf 'has input' some 'Sequence alignment (protein)'
+- 'Protein sequence alignment analysis' SubClassOf 'Sequence alignment analysis'
+- 'Protein sequence alignment analysis' SubClassOf 'Prediction and recognition (protein)'
+- 'Protein sequence alignment analysis' SubClassOf 'Protein analysis'
+
+Class changed: IRI http://edamontology.org/operation_2509
+label: Protein sequence comparison
++ 'Protein sequence comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein sequence comparison' SubClassOf 'Sequence comparison'
+- 'Protein sequence comparison' SubClassOf 'Protein comparison'
+- 'Protein sequence comparison' SubClassOf 'Protein sequence analysis'
+
+Class changed: IRI http://edamontology.org/operation_2508
+label: Nucleic acid sequence comparison
++ 'Nucleic acid sequence comparison' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Nucleic acid sequence comparison' SubClassOf 'Nucleic acid comparison'
+- 'Nucleic acid sequence comparison' SubClassOf 'Nucleic acid sequence analysis'
+- 'Nucleic acid sequence comparison' SubClassOf 'Sequence comparison'
+
+Class changed: IRI http://edamontology.org/operation_2507
+label: Nucleic acid sequence alignment analysis
++ 'Nucleic acid sequence alignment analysis' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Nucleic acid sequence alignment analysis' SubClassOf 'Prediction and recognition (nucleic acid)'
+- 'Nucleic acid sequence alignment analysis' SubClassOf 'has input' some 'Sequence alignment (nucleic acid)'
+- 'Nucleic acid sequence alignment analysis' SubClassOf 'Nucleic acid analysis'
+- 'Nucleic acid sequence alignment analysis' SubClassOf 'Sequence alignment analysis'
+
+Class changed: IRI http://edamontology.org/operation_3088
+label: Protein property calculation (from sequence)
++ 'Protein property calculation (from sequence)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein property calculation (from sequence)' SubClassOf 'Protein property calculation'
+- 'Protein property calculation (from sequence)' SubClassOf 'Protein sequence analysis'
+
+Class changed: IRI http://edamontology.org/operation_0501
+label: Protein secondary structure alignment generation
++ 'Protein secondary structure alignment generation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein secondary structure alignment generation' SubClassOf 'Protein secondary structure comparison'
+- 'Protein secondary structure alignment generation' SubClassOf 'has output' some 'Secondary structure alignment (protein)'
+- 'Protein secondary structure alignment generation' SubClassOf 'Generation'
+
+Class changed: IRI http://edamontology.org/operation_0550
+label: DNA substitution modelling
++ 'DNA substitution modelling' SubClassOf 'Nucleic acid sequence analysis'
+- 'DNA substitution modelling' SubClassOf 'Nucleic acid sequence alignment analysis'
+
+Class changed: IRI http://edamontology.org/operation_1850
+label: Protein cysteine and disulfide bond assignment
++ 'Protein cysteine and disulfide bond assignment' SubClassOf 'Prediction and recognition (protein)'
+- 'Protein cysteine and disulfide bond assignment' SubClassOf 'Protein secondary structure assignment (from coordinate data)'
+
+Class changed: IRI http://edamontology.org/operation_0534
+label: Protein secondary structure assignment (from coordinate data)
++ 'Protein secondary structure assignment (from coordinate data)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein secondary structure assignment (from coordinate data)' SubClassOf 'Protein secondary structure assignment'
+- 'Protein secondary structure assignment (from coordinate data)' SubClassOf 'Protein structure analysis'
+
+Class changed: IRI http://edamontology.org/operation_0535
+label: Protein secondary structure assignment (from CD data)
++ 'Protein secondary structure assignment (from CD data)' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Protein secondary structure assignment (from CD data)' SubClassOf 'Protein secondary structure assignment'
+- 'Protein secondary structure assignment (from CD data)' SubClassOf 'has input' some 'Protein circular dichroism (CD) spectroscopic data'
+
+Class changed: IRI http://edamontology.org/operation_3778
+label: Text annotation
+- 'Text annotation' SubClassOf 'Analysis'
+
+Class changed: IRI http://edamontology.org/operation_2457
+label: GPCR coupling selectivity prediction
++ 'GPCR coupling selectivity prediction' SubClassOf 'Protein property calculation'
+- 'GPCR coupling selectivity prediction' SubClassOf 'Protein property calculation (from sequence)'
+
+Class changed: IRI http://edamontology.org/operation_2433
+label: Codon usage table processing
++ 'Codon usage table processing' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass
+- 'Codon usage table processing' SubClassOf 'Codon usage analysis'
+
+Class changed: IRI http://edamontology.org/operation_2488
+label: Protein secondary structure comparison
+- 'Protein secondary structure comparison' SubClassOf 'Secondary structure comparison'
+
+Class changed: IRI http://edamontology.org/operation_2499
+label: Splicing model analysis
++ 'Splicing model analysis' SubClassOf 'Sequence comparison'
+- 'Splicing model analysis' SubClassOf 'Nucleic acid sequence comparison'
+
+Class changed: IRI http://edamontology.org/operation_2474
+label: Protein architecture comparison
++ 'Protein architecture comparison' SubClassOf 'Protein comparison'
+- 'Protein architecture comparison' SubClassOf 'Protein secondary structure comparison'
+
+
 # EDAM\_1.17.owl
 
 ## Classes modified:

diff --git a/changelog.md b/changelog.md
@@ -17,19 +17,14 @@ EDAM\_1.18 includes:
 * various refactoring including concepts deprecations within the Operation branch to make this more simple and improve usability
 * new attribute to provide tips e.g. in bio.tools UI indicating "organisational classes", i.e. higher-level concepts which primarily structure the hierarchy and are not normally recommended for annotation.
 
-
-## Added
-
 ## Changed
-* 1 concept changed (1 Operation)
+* 37 concepts changed (37 Operations)
 
 ## Deprecated
+* 16 concepts deprecated (16 Operations)
 
 ## Fixed
-- 1 issue fixed (#276)
-
-## Misc
-- LICENSE.md file added for clarification (#273)
+- 1 issue fixed (#265, #269, #270, #277, #276)
 
 # EDAM\_1.17.owl
 See the [detailed change log](https://github.com/edamontology/edamontology/blob/master/changelog-detailed.md) for additions, deprecations, and changes in relations between concepts.