From 0bcc80527508ac9cb15c2c4020c7806707c4135f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C5=81ukasz=20Szeremeta?= Date: Thu, 18 Jul 2019 16:50:44 +0200 Subject: [PATCH] Update README --- LICENSE.txt | 4 ++-- README.md | 9 ++++++++- src/main/java/pl/edu/uwb/ii/sdfeater/Compound.java | 4 ++-- src/main/java/pl/edu/uwb/ii/sdfeater/File.java | 2 +- 4 files changed, 13 insertions(+), 6 deletions(-) diff --git a/LICENSE.txt b/LICENSE.txt index d12d54c..a4d19d9 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,7 +1,7 @@ MIT License -Copyright (c) 2017-2018 Łukasz Szeremeta -Copyright (c) 2018 Dominik Tomaszuk +Copyright (c) 2017-2019 Łukasz Szeremeta +Copyright (c) 2018-2019 Dominik Tomaszuk Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 01642c8..6ab9032 100644 --- a/README.md +++ b/README.md @@ -54,11 +54,18 @@ You can specify the output format using `-f,--format`. Available output formats: * `cvme` - [CVME](http://cs.aalto.fi/en/current/events/2017-09-22-002/) file format based on SKOS, * `smiles` - plain text SMILES (if available in the compound property) * `inchi` - plain text InChI (if available in the compound property) +* `bioschemas` - [Bioschemas](https://bioschemas.org/) +* `turtle` - [Terse RDF Triple Language](https://www.w3.org/TR/turtle/) +* `ntriples` - [N-Triples](https://www.w3.org/TR/n-triples/) +* `jsonld` - [JSON-LD](https://json-ld.org/) +* `rdfxml` - [RDF/XML](https://www.w3.org/TR/rdf-syntax-grammar/) +* `rdfthrift` - [RDF Binary encoding using Thrift](https://afs.github.io/rdf-thrift/rdf-binary-thrift.html) ## Used open source projects - [Apache Commons CLI](https://github.com/apache/commons-cli) as CLI controller ([Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)), - [Gson](https://github.com/google/gson) as periodic table JSON parser ([Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)), -- [periodic-table](https://github.com/andrejewski/periodic-table) - base JSON periodic table file ([ISC License](https://choosealicense.com/licenses/isc/)). +- [periodic-table](https://github.com/andrejewski/periodic-table) - base JSON periodic table file ([ISC License](https://choosealicense.com/licenses/isc/)), +- [Apache Jena](https://jena.apache.org/) - for some output formats. The sample SDF files in the examples directory are based on data from [ChEBI](https://www.ebi.ac.uk/chebi/init.do) ([CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)) and [DrugBank](https://www.drugbank.ca/releases/latest#open-data) open structures ([CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/)) databases. diff --git a/src/main/java/pl/edu/uwb/ii/sdfeater/Compound.java b/src/main/java/pl/edu/uwb/ii/sdfeater/Compound.java index 488a32e..7ec6682 100644 --- a/src/main/java/pl/edu/uwb/ii/sdfeater/Compound.java +++ b/src/main/java/pl/edu/uwb/ii/sdfeater/Compound.java @@ -378,10 +378,10 @@ void addToJenaModel() { } /** - * Print main compound data in Schema.org + * Print main compound data in Schema.org (BioSchemas) * */ - void printSchema() { + void printBioSchemas() { String val_tmp = ""; String query_str = "@prefix schema: .\n\n"; diff --git a/src/main/java/pl/edu/uwb/ii/sdfeater/File.java b/src/main/java/pl/edu/uwb/ii/sdfeater/File.java index fa174c8..dfbfcd6 100644 --- a/src/main/java/pl/edu/uwb/ii/sdfeater/File.java +++ b/src/main/java/pl/edu/uwb/ii/sdfeater/File.java @@ -121,7 +121,7 @@ void parse(Compound c, char format, boolean urls, boolean periodic) { c.printInChI(); break; case 'b': - c.printSchema(); + c.printBioSchemas(); break; case 't': case 'n':