Improve README

README.md

@@ -5,6 +5,7 @@
 [SDF](https://pubs.acs.org/doi/abs/10.1021/ci00007a012) parser written in Java running from command-line interface (CLI). SDFEater not only ~~eats~~ parse your SDF files, but also can add additional data to the output.
 
 ## Publications and resources
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 If you need more detailed information, take a look at these publications and resources. There you will find detailed description of the parser, performance tests and example Cypher outputs.
 
 1. Ł. Szeremeta, "SDFEater: A Parser for Chemoinformatics Formats"
@@ -15,32 +16,38 @@ Information Systems, M. Ganzha, L. Maciaszek, and M. Paprzycki, Eds., vol. 15. I
 4. D. Tomaszuk, “chemskos”. figshare, 29-Aug-2018 [Online]. Available: https://doi.org/10.6084/m9.figshare.7022144.
 
 ## How to start?
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 Simply download one of the [ready to use JAR file](https://github.com/lszeremeta/SDFEater/releases) from project releases. You can also [clone this repository](https://help.github.com/articles/cloning-a-repository/) and build the project yourself.
 
 ### Build project yourself
 
 1. Clone this repository:
-```
+
+```shell
 git clone https://github.com/lszeremeta/SDFEater.git
 ```
 
 2. Build SDFEater using [Apache Maven](https://maven.apache.org/):
-```
+
+```shell
 cd SDFEater
 mvn clean package
 ```
 
 Built JAR files can be found in the _target_ directory.
 
 ## Example usage
-```
+
+```shell
 java -jar SDFEater-version-jar-with-dependencies.jar -i ../examples/chebi_special_char_test.sdf -f cypher -up
 ```
+
 Example above reads SDF input file, adds periodic table data for atoms, try to replace chemical database IDs with URL and give [Cypher](https://neo4j.com/developer/cypher-query-language/) file in the output.
 
 In _examples_ directory you can find example SDF files 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  open structures](https://www.drugbank.ca/releases/latest#open-data) ([CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/)) databases.
 
 ## CLI options
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 Running SDFEater without parameters displays help.
 
 * `-i,--input <arg>` - input SDF file path (required)
@@ -49,7 +56,9 @@ Running SDFEater without parameters displays help.
 * `-u,--urls` - try to generate full database URLs instead of IDs (enabled in `cvme`)
 
 ## Output formats
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 You can specify the output format using `-f,--format`. Available output formats:
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 * `cypher` - [Cypher](https://neo4j.com/developer/cypher-query-language/) molecule, atoms, bonds and relation ready to [import to the Neo4j graph database](https://neo4j.com/developer/kb/export-sub-graph-to-cypher-and-import/),
 * `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 molecule property)
@@ -64,16 +73,19 @@ You can specify the output format using `-f,--format`. Available output formats:
 * `microdata` - Simple HTML with [Microdata](https://www.w3.org/TR/microdata/) (based on [MolecularEntitly](https://bioschemas.org/types/MolecularEntity/) type)
 
 ## 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/)),
-- [Apache Jena](https://jena.apache.org/) - for some output formats ([Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)),
-- [Apache Commons Text](https://commons.apache.org/proper/commons-text/) - to HTML escape for RDFa and Microdata formats ([Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)).
+
+* [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/)),
+* [Apache Jena](https://jena.apache.org/) - for some output formats ([Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)),
+* [Apache Commons Text](https://commons.apache.org/proper/commons-text/) - to HTML escape for RDFa and Microdata formats ([Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)).
 
 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.
 
 ## Contribution
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 Would you like to improve the SDFEater? Great! We are waiting for your help and suggestions. If you are new in open source contributions, read [How to Contribute to Open Source](https://opensource.guide/how-to-contribute/).
 
 ## License
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 Distributed under [MIT license](https://github.com/lszeremeta/chebi-sdf-parser/blob/master/LICENSE.txt).