From 4ab40bd018423e2f684886fdc786b17432df9bcf Mon Sep 17 00:00:00 2001 From: Jon Ison Date: Fri, 13 May 2016 11:52:37 +0100 Subject: [PATCH 01/17] Improved changelog.md there were some errors - check out the new one --- changelog.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/changelog.md b/changelog.md index fd0112c..2b5ebaa 100644 --- a/changelog.md +++ b/changelog.md @@ -11,18 +11,19 @@ Description of changes are grouped as follows: 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 +* new terms requested by the community, including for metagenomics and biodiversity +* requests for structural improvements and fixes, including a clean-up of synonyms (automation of this in the pipeline) ## Added -* 24 concepts changed +* 20 concepts added (9 Data, 6 Operation, 5 Format) ## Changed -* 20 concepts added, mainly formats. +* 24 concepts changed (simplifying the "Visualisation" operation concepts) ## 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. From fc42cb0b294b43a64dfa79d62c23d7a586e92754 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mat=C3=BA=C5=A1=20Kala=C5=A1?= Date: Sat, 14 May 2016 14:38:57 +0200 Subject: [PATCH 02/17] Updated changelog.md with release 1.15 details --- changelog.md | 37 +++++++++++++++++++++++++------------ 1 file changed, 25 insertions(+), 12 deletions(-) diff --git a/changelog.md b/changelog.md index 2b5ebaa..48ecaf2 100644 --- a/changelog.md +++ b/changelog.md @@ -1,27 +1,40 @@ # 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 requested by the community, including for metagenomics and biodiversity -* requests for structural improvements and fixes, including a clean-up of synonyms (automation of this in the pipeline) +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 * 20 concepts added (9 Data, 6 Operation, 5 Format) ## Changed -* 24 concepts changed (simplifying the "Visualisation" operation concepts) +* 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 synonymys 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 From ead0a936dd090e42e4549458bc99afe54c778df2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mat=C3=BA=C5=A1=20Kala=C5=A1?= Date: Sat, 14 May 2016 15:01:15 +0200 Subject: [PATCH 03/17] Update page_1.15.html --- web/page_1.15.html | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/web/page_1.15.html b/web/page_1.15.html index f8c73f2..534ce0c 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)


From 1db71965bedad7416575b20ea32f376e0d358dcb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mat=C3=BA=C5=A1=20Kala=C5=A1?= Date: Sat, 14 May 2016 15:01:51 +0200 Subject: [PATCH 04/17] Update page_1.15.html --- web/page_1.15.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/page_1.15.html b/web/page_1.15.html index 534ce0c..08646f9 100644 --- a/web/page_1.15.html +++ b/web/page_1.15.html @@ -1850,6 +1850,6 @@

Bioinformatics operations, types of data, formats,

-

Last update: 2016-May-13

+

Last update: 2016-May-14

From dc97ea0432825fdb932080bfda0813f3791f3571 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mat=C3=BA=C5=A1=20Kala=C5=A1?= Date: Sat, 14 May 2016 15:08:57 +0200 Subject: [PATCH 05/17] Update changelog.md --- changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/changelog.md b/changelog.md index 48ecaf2..a0b1bba 100644 --- a/changelog.md +++ b/changelog.md @@ -20,7 +20,7 @@ EDAM\_1.15 includes: ## Changed * 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 synonymys of various concepts +* Added and/or cleaned-up synonyms of various concepts ## Deprecated * 5 concepts deprecated (2 Data, 3 Operation) From 570c53c6cdf11c154b6c6f4db2c8a049e73d6dde Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Thu, 26 May 2016 09:27:37 +0200 Subject: [PATCH 06/17] correct HDF5 description, fix #179. --- EDAM_dev.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 9ec137d..b94da6b 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -31941,10 +31941,10 @@ 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. From 67859cf926d8c7094bd2522cbe7798892d050c31 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Thu, 26 May 2016 09:42:55 +0200 Subject: [PATCH 07/17] Gemini SQLite is_a SQLite, not Binary (fix #180). --- EDAM_dev.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EDAM_dev.owl b/EDAM_dev.owl index b94da6b..1b763d4 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -32448,7 +32448,7 @@ GeminiSQLite - + https://gemini.readthedocs.org/en/latest/content/quick_start.html 1.11 Data format used by the SQLite database conformant to the Gemini schema. From bd062d4fc9748c1c2da52a70db7fcf83327e661b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Thu, 26 May 2016 16:12:35 +0200 Subject: [PATCH 08/17] Gemini SQLite format is a Sequence variation annotation format fix #181 --- EDAM_dev.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 1b763d4..c2d73f2 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -32449,6 +32449,7 @@ GeminiSQLite + https://gemini.readthedocs.org/en/latest/content/quick_start.html 1.11 Data format used by the SQLite database conformant to the Gemini schema. From 686753ce8c2d4c8c91d0773c0cf11bc083ac0972 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Thu, 26 May 2016 16:13:39 +0200 Subject: [PATCH 09/17] fix SQLite formats labels, fix #180 --- EDAM_dev.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/EDAM_dev.owl b/EDAM_dev.owl index c2d73f2..32a50ab 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -32433,7 +32433,7 @@ - SQLite + SQLite format https://www.sqlite.org/fileformat2.html Data format used by the SQLite database. @@ -32447,7 +32447,7 @@ - GeminiSQLite + Gemini SQLite format https://gemini.readthedocs.org/en/latest/content/quick_start.html From f97047098e601269c108b589b5ea2009ad4d97fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 11:05:36 +0200 Subject: [PATCH 10/17] Community profiling is not a data concept As reported by @simonjupp in #178 --- EDAM_dev.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 32a50ab..190daa0 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -44018,7 +44018,6 @@ 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 From 4d19132ad359e0ed9c59dcc250e8f0217faf27cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 11:43:06 +0200 Subject: [PATCH 11/17] Identifier and Parameter concepts are not disjoint this last commit fixes #178. And makes ELK and Hermit happy! --- EDAM_dev.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 190daa0..b790669 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -942,7 +942,6 @@ - http://semanticscience.org/resource/SIO_000115 beta12orEarlier ID From 599e05a417f2479215a599b00c6114f7bbb6c42d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 14:30:30 +0200 Subject: [PATCH 12/17] start configuring owltools to check consistency in CI this (and subsequent commits on the same subject) is mostly a copy-paste from work done by @cmungall, as a solution to a issues like #178. --- .travis.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index c91c8f2..93aa267 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,5 +3,11 @@ python: - "2.7" # command to install dependencies install: "pip install git+https://github.com/edamontology/edamxpathvalidator.git" +# install dependencies for owltools checker +before_script: + - mkdir -p bin + - export PATH=$PATH:$PWD/bin + - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools + - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar # command to run tests -script: "edamxpathvalidator EDAM_dev.owl" +script: "edamxpathvalidator EDAM_dev.owl && owltools --log-error EDAM_dev.owl --reasoner hermit --run-reasoner" From 766019e93144b583869227f7fc1ab6dc8d2845df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 14:37:56 +0200 Subject: [PATCH 13/17] make owltools executable --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 93aa267..86bef10 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,5 +9,6 @@ before_script: - export PATH=$PATH:$PWD/bin - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar + - chmod +x bin/* # command to run tests script: "edamxpathvalidator EDAM_dev.owl && owltools --log-error EDAM_dev.owl --reasoner hermit --run-reasoner" From 406df18b3469dade0fb9df617801637f38bef1ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 14:50:24 +0200 Subject: [PATCH 14/17] install java 8, required by owltools --- .travis.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.travis.yml b/.travis.yml index 86bef10..2f1c2f2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,6 +3,10 @@ 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: - mkdir -p bin From e4f28d9c9d54a9c2080db9bd9b0f38d47345d9aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 14:57:52 +0200 Subject: [PATCH 15/17] test java version on Travis --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 2f1c2f2..a1b9ab1 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,4 +15,4 @@ before_script: - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar - chmod +x bin/* # command to run tests -script: "edamxpathvalidator EDAM_dev.owl && owltools --log-error EDAM_dev.owl --reasoner hermit --run-reasoner" +script: "java -version && edamxpathvalidator EDAM_dev.owl && owltools --log-error EDAM_dev.owl --reasoner hermit --run-reasoner" From 3446430d270d541688550f1b8a0b99716049371b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 15:07:22 +0200 Subject: [PATCH 16/17] switch to java 8 using java-alternatives --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index a1b9ab1..15d5359 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,6 +9,7 @@ addons: - oracle-java8-installer # install dependencies for owltools checker before_script: + - sudo update-java-alternatives -s java-8-oracle - mkdir -p bin - export PATH=$PATH:$PWD/bin - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools From 8eb1a36c6a8b046b3a1709a9972330cfdd94d024 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= Date: Fri, 27 May 2016 16:42:41 +0200 Subject: [PATCH 17/17] switch to simple HermiT solution to check EDAM for consistency in CI related to #178 --- .hermit_ok | 2 ++ .travis.yml | 8 ++------ 2 files changed, 4 insertions(+), 6 deletions(-) create mode 100644 .hermit_ok 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 15d5359..9f48af3 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,10 +10,6 @@ addons: # install dependencies for owltools checker before_script: - sudo update-java-alternatives -s java-8-oracle - - mkdir -p bin - - export PATH=$PATH:$PWD/bin - - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools - - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar - - chmod +x bin/* + - wget http://www.hermit-reasoner.com/download/current/HermiT.zip && unzip -o -d . HermiT.zip HermiT.jar # command to run tests -script: "java -version && edamxpathvalidator EDAM_dev.owl && owltools --log-error EDAM_dev.owl --reasoner hermit --run-reasoner" +script: "edamxpathvalidator EDAM_dev.owl && java -jar HermiT.jar -U EDAM_dev.owl | diff .hermit_ok -"