diff --git a/changelog-detailed.md b/changelog-detailed.md index 4638c75..194cd52 100644 --- a/changelog-detailed.md +++ b/changelog-detailed.md @@ -1,6 +1,251 @@ # Detailed Changelog for EDAM Data were generated using the [Bubastis](http://www.ebi.ac.uk/efo/bubastis/) ontology-diff tool. +# EDAM\_1.15.owl + +## Classes modified: + +Class: http://edamontology.org/data_0886 +Label: Structure alignment +- 'Structure alignment' SubClassOf 'has topic' some 'Structure comparison' ++ 'Structure alignment' SubClassOf 'has topic' some 'Structure analysis' + +Class: http://edamontology.org/format_2197 +Label: OWL format +- 'OWL format' SubClassOf 'XML' ++ 'OWL format' SubClassOf 'Ontology format' ++ 'OWL format' SubClassOf 'RDF format' + +Class: http://edamontology.org/format_3655 +Label: pepXML ++ 'pepXML' SubClassOf 'XML' + +Class: http://edamontology.org/data_0863 +Label: Sequence alignment +- 'Sequence alignment' SubClassOf 'has topic' some 'Sequence comparison' ++ 'Sequence alignment' SubClassOf 'has topic' some 'Sequence analysis' + +Class: http://edamontology.org/data_1364 +Label: Hidden Markov model ++ 'Hidden Markov model' SubClassOf 'Mathematical model' + +Class: http://edamontology.org/format_2376 +Label: RDF format +- 'RDF format' SubClassOf 'XML' ++ 'RDF format' SubClassOf 'Format' ++ 'RDF format' SubClassOf http://edamontology.org/format_3748 + +Class: http://edamontology.org/format_3464 +Label: JSON +- 'JSON' SubClassOf 'Textual format' ++ 'JSON' SubClassOf 'Format' ++ 'JSON' SubClassOf http://edamontology.org/format_3750 + +Class: http://edamontology.org/operation_0569 +Label: Protein secondary structure rendering +Label: Protein secondary structure visualisation +- 'Protein secondary structure visualisation' SubClassOf 'has topic' some 'Protein structure analysis' +- 'Protein secondary structure visualisation' SubClassOf 'Visualisation' ++ 'Protein secondary structure visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass + +Class: http://edamontology.org/operation_0568 +Label: RNA secondary structure visualisation +- 'RNA secondary structure visualisation' SubClassOf 'RNA secondary structure analysis' +- 'RNA secondary structure visualisation' SubClassOf 'Visualisation' +- 'RNA secondary structure visualisation' SubClassOf 'has input' some 'RNA secondary structure' ++ 'RNA secondary structure visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass + +Class: http://edamontology.org/operation_0565 +Label: Sequence alignment visualisation +- 'Sequence alignment visualisation' SubClassOf 'has output' some 'Sequence alignment image' +- 'Sequence alignment visualisation' SubClassOf 'has input' some 'Sequence alignment' +- 'Sequence alignment visualisation' SubClassOf 'Visualisation' +- 'Sequence alignment visualisation' SubClassOf 'Sequence analysis' ++ 'Sequence alignment visualisation' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass + +Class: http://edamontology.org/data_2106 +Label: Reaction ID (BioCyc) +- 'Reaction ID (BioCyc)' SubClassOf 'has topic' some 'Peptides and amino acids' ++ 'Reaction ID (BioCyc)' SubClassOf 'has topic' some 'Small molecules' + +Class: http://edamontology.org/operation_2241 +Label: Transmembrane protein visualisation +- 'Transmembrane protein visualisation' SubClassOf 'Protein secondary structure visualisation' ++ 'Transmembrane protein visualisation' SubClassOf 'Structure visualisation' + +Class: http://edamontology.org/data_3707 +Label: Biodiversity report ++ 'Biodiversity report' SubClassOf http://edamontology.org/data_3736 + +Class: http://edamontology.org/operation_1781 +Label: Gene regulatory network analysis +- 'Gene regulatory network analysis' SubClassOf 'has topic' some 'Gene regulatory networks' ++ 'Gene regulatory network analysis' SubClassOf 'has topic' some 'Molecular interactions, pathways and networks' + +Class: http://edamontology.org/data_0956 +Label: Data index report +- 'Data index report' SubClassOf 'has topic' some 'Document, record and content management' ++ 'Data index report' SubClassOf 'has topic' some 'Database management' + +Class: http://edamontology.org/data_0955 +Label: Data index +- 'Data index' SubClassOf 'has topic' some 'Document, record and content management' ++ 'Data index' SubClassOf 'has topic' some 'Database management' + +Class: http://edamontology.org/operation_3223 +Label: Differential expression analysis +- 'Differential expression analysis' SubClassOf 'Gene expression profile comparison' ++ 'Differential expression analysis' SubClassOf 'Nucleic acid comparison' ++ 'Differential expression analysis' SubClassOf http://edamontology.org/operation_3742 + +Class: http://edamontology.org/data_3107 +Label: Sequence feature name +- 'Sequence feature name' SubClassOf 'Sequence feature identifier' +- 'Sequence feature name' SubClassOf 'Name' ++ 'Sequence feature name' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass + +Class: http://edamontology.org/operation_2486 +Label: Topology diagram drawing +- 'Topology diagram drawing' SubClassOf 'Protein secondary structure visualisation' ++ 'Topology diagram drawing' SubClassOf 'Structure visualisation' + +Class: http://edamontology.org/operation_2485 +Label: Helical wheel drawing +- 'Helical wheel drawing' SubClassOf 'Protein secondary structure visualisation' ++ 'Helical wheel drawing' SubClassOf 'Structure visualisation' + +Class: http://edamontology.org/format_3261 +Label: RDF/XML +- 'RDF/XML' SubClassOf 'OWL format' + +Class: http://edamontology.org/operation_2437 +Label: Gene regulatory network prediction +- 'Gene regulatory network prediction' SubClassOf 'has topic' some 'Gene regulatory networks' ++ 'Gene regulatory network prediction' SubClassOf 'has topic' some 'Molecular interactions, pathways and networks' + +Class: http://edamontology.org/operation_2409 +Label: Data handling +- 'Data handling' SubClassOf 'has topic' some 'Document, record and content management' ++ 'Data handling' SubClassOf 'has topic' some 'Database management' + +Class: http://edamontology.org/topic_3301 +Label: Microbiology +- 'Microbiology' SubClassOf 'Biomedical science' ++ 'Microbiology' SubClassOf 'Biology' + +Class: http://edamontology.org/data_1022 +Label: Sequence feature label ++ 'Sequence feature label' SubClassOf 'Sequence feature identifier' ++ 'Sequence feature label' SubClassOf 'Name' + +Class: http://edamontology.org/operation_0490 +Label: Dotplot plotting +- 'Dotplot plotting' SubClassOf 'Sequence alignment visualisation' ++ 'Dotplot plotting' SubClassOf 'Sequence visualisation' + +Class: http://edamontology.org/data_3356 +Label: Hidden Markov model +- 'Hidden Markov model' SubClassOf 'Mathematical model' ++ 'Hidden Markov model' SubClassOf http://www.w3.org/2002/07/owl#DeprecatedClass + +Class: http://edamontology.org/data_1696 +Label: Drug report +- 'Drug report' SubClassOf 'has topic' some 'Drugs and target structures' ++ 'Drug report' SubClassOf 'has topic' some 'Small molecules' + +Class: http://edamontology.org/operation_0224 +Label: Query and retrieval +- 'Query and retrieval' SubClassOf 'has topic' some 'Information retrieval' ++ 'Query and retrieval' SubClassOf 'has topic' some 'Data management' + +## New classes: + +Class: http://edamontology.org/format_3750 +Label: YAML ++ 'YAML' SubClassOf 'Format' + +Class: http://edamontology.org/format_3749 +Label: JSON-LD ++ 'JSON-LD' SubClassOf 'JSON' ++ 'JSON-LD' SubClassOf 'Linked data format' ++ 'JSON-LD' SubClassOf 'RDF format' + +Class: http://edamontology.org/format_3748 +Label: Linked data format ++ 'Linked data format' SubClassOf 'Format (typed)' + +Class: http://edamontology.org/format_3747 +Label: protXML ++ 'protXML' SubClassOf 'Mass spectrometry data format' ++ 'protXML' SubClassOf 'XML' + +Class: http://edamontology.org/format_3746 +Label: BIOM format ++ 'BIOM format' SubClassOf 'Biodiversity data format' ++ 'BIOM format' SubClassOf 'Textual format' + +Class: http://edamontology.org/data_3735 +Label: Run number ++ 'Run number' SubClassOf 'Sequencing metadata name' + +Class: http://edamontology.org/data_3734 +Label: Lane identifier ++ 'Lane identifier' SubClassOf 'Sequencing metadata name' + +Class: http://edamontology.org/data_3737 +Label: Alpha diversity data ++ 'Alpha diversity data' SubClassOf 'Biodiversity report' + +Class: http://edamontology.org/data_3736 +Label: Ecological data ++ 'Ecological data' SubClassOf 'Data' + +Class: http://edamontology.org/data_3739 +Label: Gamma diversity data ++ 'Gamma diversity data' SubClassOf 'Biodiversity report' + +Class: http://edamontology.org/data_3738 +Label: Beta diversity data ++ 'Beta diversity data' SubClassOf 'Biodiversity report' + +Class: http://edamontology.org/data_3733 +Label: Flow cell identifier ++ 'Flow cell identifier' SubClassOf 'Sequencing metadata name' + +Class: http://edamontology.org/data_3732 +Label: Sequencing metadata name ++ 'Sequencing metadata name' SubClassOf 'Name' + +Class: http://edamontology.org/data_3743 +Label: Ordination plot ++ 'Ordination plot' SubClassOf 'Plot' ++ 'Ordination plot' SubClassOf 'Protein property' + +Class: http://edamontology.org/operation_3741 +Label: Differential protein expression analysis ++ 'Differential protein expression analysis' SubClassOf 'Protein comparison' ++ 'Differential protein expression analysis' SubClassOf 'Differential expression analysis' + +Class: http://edamontology.org/operation_3744 +Label: Multiple sample visualisation ++ 'Multiple sample visualisation' SubClassOf 'Visualisation' + +Class: http://edamontology.org/operation_3745 +Label: Ancestral reconstruction ++ 'Ancestral reconstruction' SubClassOf 'Phylogenetic tree analysis' + +Class: http://edamontology.org/operation_3742 +Label: Differential expression analysis ++ 'Differential expression analysis' SubClassOf 'Comparison' + +Class: http://edamontology.org/operation_3730 +Label: Cross-assembly ++ 'Cross-assembly' SubClassOf 'Sequence assembly' + +Class: http://edamontology.org/operation_3731 +Label: Sample comparison ++ 'Sample comparison' SubClassOf 'Comparison' + # EDAM\_1.14.owl ## Classes modified: diff --git a/changelog.md b/changelog.md index 9827092..fd0112c 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,22 @@ Description of changes are grouped as follows: * **Fixed:** a bug fix * **Misc:** some miscellaneous other change +# EDAM\_1.15.owl +See the [detailed change log](https://github.com/edamontology/edamontology/blob/master/changelog-detailed.md) for exact details of changes. + +EDAM\_15 includes: +* new terms or corrections requested by the community, especially to add new formats + and synonym cleanups + +## Added +* 24 concepts changed + +## Changed +* 20 concepts added, mainly formats. + +## Deprecated +* 5 concepts deprecated + # EDAM\_1.14.owl See the [detailed change log](https://github.com/edamontology/edamontology/blob/master/changelog-detailed.md) for exact details of changes.