diff --git a/.hermit_ok b/.hermit_ok new file mode 100644 index 0000000..7763f6a --- /dev/null +++ b/.hermit_ok @@ -0,0 +1,2 @@ +Classes equivalent to 'owl:Nothing': + owl:Nothing diff --git a/.travis.yml b/.travis.yml index c91c8f2..9f48af3 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,5 +3,13 @@ python: - "2.7" # command to install dependencies install: "pip install git+https://github.com/edamontology/edamxpathvalidator.git" +addons: + apt: + packages: + - oracle-java8-installer +# install dependencies for owltools checker +before_script: + - sudo update-java-alternatives -s java-8-oracle + - wget http://www.hermit-reasoner.com/download/current/HermiT.zip && unzip -o -d . HermiT.zip HermiT.jar # command to run tests -script: "edamxpathvalidator EDAM_dev.owl" +script: "edamxpathvalidator EDAM_dev.owl && java -jar HermiT.jar -U EDAM_dev.owl | diff .hermit_ok -" diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 9ec137d..b790669 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -942,7 +942,6 @@ - http://semanticscience.org/resource/SIO_000115 beta12orEarlier ID @@ -31941,10 +31940,10 @@ hdf5 - An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax. + An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. 1.11 h5 - Binary format used by Galaxy for hierarchical data. + HDF5 is a generic hierarchical data file format used to store and organize large amounts of data. @@ -32433,7 +32432,7 @@ - SQLite + SQLite format https://www.sqlite.org/fileformat2.html Data format used by the SQLite database. @@ -32447,8 +32446,9 @@ - GeminiSQLite - + Gemini SQLite format + + https://gemini.readthedocs.org/en/latest/content/quick_start.html 1.11 Data format used by the SQLite database conformant to the Gemini schema. @@ -44017,7 +44017,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Community profiling - Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. 1.1 diff --git a/changelog.md b/changelog.md index fd0112c..a0b1bba 100644 --- a/changelog.md +++ b/changelog.md @@ -1,28 +1,42 @@ # Changelog for EDAM -Description of changes are grouped as follows: -* **Added:** new features -* **Changed:** changes to existing functionality -* **Deprecated:** a once-stable feature that has been removed -* **Removed:** a deprecated feature that has been removed -* **Fixed:** a bug fix -* **Misc:** some miscellaneous other change +Descriptions of changes are grouped as follows: +* **Added:** new concepts or features +* **Changed:** changes to existing concepts and features +* **Deprecated:** once-stable concepts or features that became obsolete +* **Removed:** deprecated concepts or features that have been removed +* **Fixed:** fixed bugs, issues, corrected concepts and features +* **Misc:** miscellaneous other changes # 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 +EDAM\_1.15 includes: +* new concepts and terms requested by the community, including ones for environmental omics and biodiversity +* structural improvements and fixes, including a clean-up of synonyms (automation of this in the pipeline), updates of formats, and simplification of _Visualisation_ concepts ## Added -* 24 concepts changed +* 20 concepts added (9 Data, 6 Operation, 5 Format) ## Changed -* 20 concepts added, mainly formats. +* 24 concepts changed (9 Data, 5 Format, 9 Operation, 1 Topic) +* Added citations, media types, and/or file extensions of some Format concepts +* Added and/or cleaned-up synonyms of various concepts ## Deprecated -* 5 concepts deprecated +* 5 concepts deprecated (2 Data, 3 Operation) +## Fixed +* 26 issues fixed and closed (#119, #121, #130, #131, #132, #133, #134, #135, #136, #141, #142, #144, #145, #146, #150, #151, #152, #156, #157, #158, #159, #160, #165, #168, #169, #172) +* 3 issues fixed and left open for eventual further discussion (#120, #143, #166) + +## Misc +* 1 invalid issue closed (#149) +* 2 issues closed, wrong project (#153, #154) +* 4 issues closed, won't fix (#125, #147, #148, #155) +* 2 other issues closed (#124, #140) + + + # EDAM\_1.14.owl See the [detailed change log](https://github.com/edamontology/edamontology/blob/master/changelog-detailed.md) for exact details of changes. diff --git a/web/page_1.15.html b/web/page_1.15.html index f8c73f2..08646f9 100644 --- a/web/page_1.15.html +++ b/web/page_1.15.html @@ -246,7 +246,9 @@

Bioinformatics operations, types of data, formats,


Download and Status

-

Version 1.15 of EDAM has been released. Contributions and suggestions are welcome!


+

Version 1.15 of EDAM has been released:

+

http://edamontology.org/EDAM_1.15.owl

+

Contributions and suggestions are welcome!


Locations for download in OWL format:

http://edamontology.org/EDAM.owl (Always points to the last stable version)


@@ -1848,6 +1850,6 @@

Bioinformatics operations, types of data, formats,


-

Last update: 2016-May-13

+

Last update: 2016-May-14