From 47e67b788bbd007aec77a6b68b961787133ab18b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C5=81ukasz=20Szeremeta?= Date: Sat, 17 Apr 2021 23:26:13 +0200 Subject: [PATCH] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 54334e7..7f83984 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![Codacy Badge](https://app.codacy.com/project/badge/Grade/3602c4be20d14be1b750db5a1875263a)](https://www.codacy.com/gh/lszeremeta/molstruct/dashboard?utm_source=github.com&utm_medium=referral&utm_content=lszeremeta/molstruct&utm_campaign=Badge_Grade) [![PyPI](https://img.shields.io/pypi/v/molstruct)](https://pypi.org/project/molstruct/) [![Docker Image Size (latest by date)](https://img.shields.io/docker/image-size/lszeremeta/molstruct?label=Docker%20image%20size)](https://hub.docker.com/r/lszeremeta/molstruct) -Molstruct is a lightweight Python CLI tool that converts chemical molecule data [Comma Separated Values (CSV)](https://en.wikipedia.org/wiki/Comma-separated_values) files to structured data formats - [JSON-LD](https://json-ld.org/), [RDFa](http://rdfa.info/), and [Microdata](https://schema.org/docs/gs.html). Molstruct has a lot of customization options that you can but don't have to use. Python 3.2+ is supported and no dependencies are required. Sounds good so far? What would you say to a really tiny [Molstruct Docker container](https://hub.docker.com/r/lszeremeta/molstruct)? Just try Molstruct! +Molstruct is a lightweight Python CLI tool that converts chemical molecule data [Comma Separated Values (CSV)](https://en.wikipedia.org/wiki/Comma-separated_values) files to structured data formats - [JSON-LD](https://json-ld.org/), [RDFa](http://rdfa.info/), and [Microdata](https://schema.org/docs/gs.html). Molstruct has a lot of customization options that you can, but don't have to use. Python 3.2+ is supported and no dependencies are required. Sounds good so far? What would you say to a really tiny [Molstruct Docker container](https://hub.docker.com/r/lszeremeta/molstruct)? Just try Molstruct! ## What is structured data @@ -24,7 +24,7 @@ You can install the Molstruct from [PyPI](https://pypi.org/project/molstruct/): pip install molstruct ``` -Molstruct is also available as a [Docker image](#docker-image). In most cases, installing Molstruct from PyPI or using Docker should be sufficient and convenient but you may want to [run Molstruct from sources or build a Docker image yourself](https://github.com/lszeremeta/molstruct/wiki/Run-from-sources-and-manual-Docker-build). +Molstruct is also available as a [Docker image](#docker-image). In most cases, installing Molstruct from PyPI or using Docker should be sufficient and convenient, but you may want to [run Molstruct from sources or build a Docker image yourself](https://github.com/lszeremeta/molstruct/wiki/Run-from-sources-and-manual-Docker-build). 2. Download [DrugBank open dataset](https://go.drugbank.com/releases/latest/downloads/all-drugbank-vocabulary) in CSV format and unzip downloaded archive. 3. Molstruct has a [predefined preset](#predefined-presets) for this dataset. You just need to select the output format and enter the path to the CSV file. Assuming the `drugbank vocabulary.csv` file is in the current directory and the output format you're interested in is RDFa, the command will be as follows: @@ -113,7 +113,7 @@ Available options may vary depending on the version. To display all available op ## Predefined presets -To make your work easier, Molstruct has built-in preset support. Thanks to this, you do not have to set everything manually, you just select the appropriate preset and it's ready. The presets are flexible. If you want to change e.g. the column names selected for a preset, you can do so. At the moment you can use the [DrugBank open](https://www.drugbank.ca/releases/latest#open-data) preset. There are plans to add more in the future. Any suggestions are welcome! +To make your work easier, Molstruct has built-in preset support. Thanks to this, you do not have to set everything manually, you just select the appropriate preset and it's ready. The presets are flexible. If you want to change, e.g. the column names selected for a preset, you can do so. At the moment you can use the [DrugBank open](https://www.drugbank.ca/releases/latest#open-data) preset. There are plans to add more in the future. Any suggestions are welcome! ### `drugbank-open` @@ -149,7 +149,7 @@ Returns simple HTML with added Microdata. When generating a file, only selected molstruct -f microdata --columns --id "CAS" --name "Common name" --inChIKey "Standard InChI Key" --limit 50 "drugbank vocabulary.csv" > output.html ``` -Does the same as the example above but save results to `output.html`. +Does the same as the example above but saves results to `output.html`. ```shell docker run -it --rm --name molstruct-app --mount type=bind,source=/home/user/input,target=/app/input,readonly lszeremeta/molstruct:latest -f microdata --columns --id "CAS" --name "Common name" --inChIKey "Standard InChI Key" --limit 50 "input/drugbank vocabulary.csv" > output.html