SPANG

Website: http://purl.org/spang

npm: https://www.npmjs.com/package/spang

Docker: https://hub.docker.com/r/sparqling/spang

Command line interface

$ npm install -g spang

A symbolic link to ./bin/spang.js will be created as spang2 in your path.

For the help message, just type the command

$ spang2

Install from GitHub

git clone https://github.com/sparqling/spang
cd spang
npm ci

Optional:

$ npm link

will make a symbolic link to ./bin/* in your path.

Installation of node

spang2 requires node (version >= 14).

node -v

If you do not have node, install it as follows.

Linux

If you do not have npm, install it.

sudo apt -y install npm

on Ubuntu, or

sudo yum -y install npm

on CentOS.

The defualt directories for installation of npm modules are under /usr/local/, which requires sudo.

You can change the directories as follows.

npm set prefix ~/.npm-global

The configuration is saved in ~/.npmrc, so you can also configure by editing it.

Install n to manage node version.

npm install -g n
n stable
node -v

Mac

If you do not have brew, install it.

brew -v

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install node or nodebrew using brew.

brew install node

brew install nodebrew
mkdir -p ~/.nodebrew/src
export PATH=$HOME/.nodebrew/current/bin:$PATH

Now you can use node. Check the version.

node -v

For maintainers

js/spang.js should be updated after modifying codes for those who call spang functions through their Web applications.

Update the js/spang.js by converting codes using browserify as follows.

npm run browserify

Requirements

• npm (>= 6.12.0)

Test

npm test

SPARQL specifications

Syntax

The EBNF notation of SPARQL is extracted from: https://www.w3.org/TR/sparql11-query/#sparqlGrammar

The PEG expression of SPARQL grammer was originally provided by: https://github.com/antoniogarrote/rdfstore-js/

PEG can be tested at: https://pegjs.org/online

Medadata

sparql-doc

# @title Get orthololog from MBGD
# @author Hirokazu Chiba
# @tag ortholog
# @endpoint http://sparql.nibb.ac.jp/sparql

extension

# @prefixes https://
# @input_class id:Taxon
# @output_class up:Protein
# @param gene=