Merge commit '4de5735b970be03fa9d99f7529f582f5a75723d9'

LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
+                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,10 +1,12 @@
 # goslin
-
+<img src="./goslin.svg" align="right">
 
 Goslin is the **G**rammar **o**n **s**uccinct **li**pid **n**omenclature.
 
 Goslin defines multiple grammers compatible with ANTLRv4 for different sources of shorthand lipid nomenclature. This allows to generate parsers based on the defined grammars, which provide immediate feedback whether a processed lipid shorthand notation string is compliant with a particular grammar, or not.
 
+[Overview of Goslin and Tutorials](docs/README.adoc)
+
 ## References
 * [D. Kopczynski et al., Biorxiv, April 20th, 2020](https://doi.org/10.1101/2020.04.17.046656)
 
@@ -17,47 +19,13 @@ Goslin defines multiple grammers compatible with ANTLRv4 for different sources o
 - [R implementation](https://github.com/lifs-tools/rgoslin)
 - [Webapplication and REST API](https://github.com/lifs-tools/goslin-webapp)
 
-## Adding goslin as a Git subtree
-
-In the root of your git project, run the git subtree command, with `<PREFIX>` replaced by the subdirectory path where you want the subtree to live:
-
-~~~~
-git subtree add --prefix=<PREFIX> https://github.com/lifs-tools/goslin.git master
-~~~~
-
-Instead of `master`, you can choose any other branch or tag to clone.
-For more information on git subtree, see [Git Subtree](https://github.com/git/git/blob/master/contrib/subtree/git-subtree.txt) or [this article](https://blog.developer.atlassian.com/the-power-of-git-subtree/).
-
-
-## Pulling and pushing of a Git subtree
-For pulling and pushing, you have to change into the root directory of the host repository and execute the following commands:
-
-### Pulling
-~~~~
-git subtree pull --prefix=<PREFIX> https://github.com/lifs-tools/goslin.git master
-~~~~
-
-### Pushing
-~~~~
-git subtree push --prefix=<PREFIX> https://github.com/lifs-tools/goslin.git master
-~~~~
-
-Alternatively, you can create shortcuts/aliases in your repository's `.git/config` file:
-
-~~~~
-[alias]
-    # the acronym stands for "subtree pull"
-    goslin-pull = "!f() { git subtree pull --prefix <PREFIX> https://github.com/lifs-tools/goslin.git master; }; f"
-    # the acronym stands for "subtree push"
-    goslin-push = "!f() { git subtree push --prefix <PREFIX> https://github.com/lifs-tools/goslin.git master; }; f"
-~~~~
-
-Make sure to replace `<PREFIX>` with the proper path from your repository root directory to the directory where you placed your subtree in!
+## Test data
 
-This allows you to run `git goslin-pull` to pull the latest master version, or `git goslin-push` to push your latest local commits on the goslin subtree to the upstream repository.
+1. lipidmaps-names-Feb-10-2020.tsv - generated from [LipidMAPS LMSDB](https://www.lipidmaps.org/) export on Feb. 10th, 2020. Filtered all entries without an abbreviation.
+2. swisslipids-names-Feb-10-2020.tsv - generated from [Swiss Lipids](https://www.swisslipids.org) (lipids table) export on Feb. 10th ,2020.
 
+Short samples of lipid names used for testing of the implementations are available from the [testfiles directory](testfiles/).
 
-## Test data
+## License
 
-1. lipidmaps-names-Feb-10-2020.tsv - generated from LipidMAPS LMSDB export on Feb. 10th, 2020. Filtered all entries without an abbreviation.
-2. swisslipids-names-Feb-10-2020.tsv - generated from Swiss Lipids (lipids table) export on Feb. 10th ,2020.
+The Goslin grammars are licensed under the terms of the MIT license (see [LICENSE](LICENSE)).