goobograph

Overview ¶

Package go-obograph is a golang library for handling OBO Graphs https://github.com/geneontology/obographs . It provides API for the following...

• Read JSON formatted OBO Graph file.
• Build an in memory and read only graph structure for extracting information.
• Persist the graph structure in arangodb database.

Example of a command line application to store OBO Graph in arangodb database

import (
	"bufio"
	"context"
	"errors"
	"fmt"
	"log"
	"os"

	oboaction "github.com/dictyBase/go-obograph/command/action"
	oboflag "github.com/dictyBase/go-obograph/command/flag"
	"github.com/urfave/cli"
)

func main() {
	app := cli.NewApp()
	app.Name = "test cli for load obojson format file in arangodb"
	app.Flags = []cli.Flag{
		cli.StringFlag{
			Name:  "log-format",
			Usage: "format of the logging out, either of json or text.",
			Value: "json",
		},
		cli.StringFlag{
			Name:  "log-level",
			Usage: "log level for the application",
			Value: "error",
		},
		oboflag.OntologyFlags()...,
	}
	app.Action = oboaction.LoadOntologies
	if err := app.Run(os.Args); err != nil {
		log.Fatalf("error in running command %s", err)
	}
}