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Update README
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lszeremeta committed Jul 18, 2019
1 parent 8ac2000 commit 0bcc805
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4 changes: 2 additions & 2 deletions LICENSE.txt
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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
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9 changes: 8 additions & 1 deletion README.md
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Expand Up @@ -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.

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4 changes: 2 additions & 2 deletions src/main/java/pl/edu/uwb/ii/sdfeater/Compound.java
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Expand Up @@ -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: <http://schema.org/> .\n\n";

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2 changes: 1 addition & 1 deletion src/main/java/pl/edu/uwb/ii/sdfeater/File.java
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Expand Up @@ -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':
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