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src=\"https://sbrg.github.io/lifelike-website/images/cfb_logo.png\" alt=\"CFB\" border=\"0\" /\u003e \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003cimg src=\"https://sbrg.github.io/lifelike-website/images/dtu_logo.png\" alt=\"DTU\" border=\"0\" /\u003e \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003cimg src=\"https://sbrg.github.io/lifelike-website/images/ucsd_logo.png\" alt=\"UCSD\" border=\"0\" /\u003e\n\nLifelike is an open-source project that aims to provide a simple, yet powerful platform for turning structured and unstructured data from a variety of sources into a single, coherent and explorable knowledge graph.\n\n[![DOI](https://zenodo.org/badge/437040913.svg)](https://zenodo.org/badge/latestdoi/437040913)\n\n## Quick start\n\nThe easiest way to get started and run a fully functional development environment of Lifelike is to clone this repository and run the `make up` command:\n\n```shell\ngit clone https://github.com/SBRG/lifelike.git\ncd lifelike\n\nmake up\n```\n\nThis will take a few minutes to complete, after which you can start using Lifelike by pointing your browser to [http://localhost:8080](http://localhost:8080).\n\nYou can log in using the default admin user `admin@example.com` and password `password`.\n\n## Other installation methods\n\nYou can see more details about how to deploy lifelike in a production environment,\nor customize the development installation in the following sections.\n\n1. [Docker with Docker Compose](docker)\n2. [Kubernetes with Helm chart](helm/lifelike)\n\n## Lifelike main concepts\n\n### Projects\n\nLifelike organizes content into projects. A project is a filesystem-like collection of resources either uploaded by users or generated by Lifelike based on other resources. Those resources can be all kinds of data, including structured data like spreadsheets, unstructured data like PDF files, images, or text documents.\n\n### Knowledge Domains\n\nLifelike structures knowledge around domains. A domain is a collection of semantically related entities belonging to a field of study.\n\n### Annotations\n\nAnnotations are a powerful way to attach context to your data in knowledge Domains, Lifelike automatically annotates all your data with Domain known entities as well as lets you define your own custom annotations.\n\n### Knowledge Graph\n\nDomain data sources are annotated and stored in a graph database. A knowledge graph consists of nodes and edges. Nodes are domain entities and edges are relations between entities.\n\n### Visualizations\n\nVisualizations are a powerful way to help you to understand the relationships between entities as well as a powerful tool to find new relationships as new data comes in.\n\nLifelike currently provides the following built-in visualization types:\n\n-   Maps\n-   Enrichment tables\n-   Sankey diagrams\n-   Pathway Browser\n\n### Other features\n\n-   Multi-user collaborative workbench\n-   Powerful search engine\n\n## Common development operations\n\nYou can run `make help` to see a list of available commands.\n\n```text\n$ make help\n\nusage: make [target]\n\ndevelopment:\n  githooks                        Set up Git commit hooks for linting and code formatting\n\ndocker:\n  up                              Build and run container(s) for development. [c=\u003cnames\u003e]\n  images                          Build container(s) for distribution.\n  status                          Show container(s) status. [c=\u003cnames\u003e]\n  logs                            Show container(s) logs. [c=\u003cnames\u003e]\n  restart                         Restart container(s). [c=\u003cnames\u003e]\n  stop                            Stop containers(s). [c=\u003cnames\u003e]\n  exec                            Execute a command inside a container. [c=\u003cname\u003e, cmd=\u003ccommand\u003e]\n  test                            Execute test suite\n  down                            Destroy all containers and volumes\n  reset                           Destroy and recreate all containers and volumes\n  diagram                         Generate an architecture diagram from the Docker Compose files\n\nhelm:\n  helm-lint                       Run helm lint on Lifelike chart\n  helm-dependency-update          Install or update chart dependencies\n  helm-schema-gen                 Generate Helm chart values JSON schema\n  helm-docs                       Generate Helm chart README docs\n  helm-package                    Generate Lifelike helm chart package\n  helm-install                    Install or upgrade Lifelike chart\n  helm-install-single-node        Install or upgrade Lifelike chart using the single-node example values\n\nother:\n  help                            Show this help.\n```\n\n## Architecture\n\nLifelike is a distributed system comprised of the following components:\n\n![Architecture diagram](docker/diagram.svg)\n\n### Core services\n\n-   **[Appserver](appserver)**. Backend API service, written in Python using the the Flask framework.\n-   **[Client](client)**. Frontend Single Page Application, written in Typescript using the Angular framework.\n-   **[Statistical enrichment](statistical-enrichment)**. Statistics generation microservice, written in Python using the the Flask framework.\n-   **[Cache invalidator](cache-invalidator)**. Recurrent task runner for bulk large computations and cache data management, written in Python.\n-   **[Graph data migrator](graph-db)**. Utility service for migrating and versioning knowledge graph database, using the Liquibase database migration tool.\n\n### Backing services\n\n-   **PostgreSQL** as a RDBMS.\n-   **ArangoDB** as a graph database.\n-   **Elasticsearch** as a full-text search engine.\n-   **Redis** as a key-value cache store.\n-   **PDFParser** as a document parsing library.\n-   **Sendgrid** as an email messaging service.\n\n## License\n\nLifelike is distributed under a [modified MIT license](LICENSE).\n\n![Lifelike](appserver/assets/lifelike.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Flifelike","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosustain%2Flifelike","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Flifelike/lists"}