{"id":20772102,"url":"https://github.com/gyorilab/indra_db","last_synced_at":"2025-04-30T14:27:36.474Z","repository":{"id":33544313,"uuid":"149625204","full_name":"gyorilab/indra_db","owner":"gyorilab","description":"A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. 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This implementation is currently designed to work\nprimarily with Amazon Web Services RDS running Postrgres 9+. Used as a backend\nto INDRA, the INDRA Database provides a systematic way of scaling the knowledge\nacquired from other databases, reading, and manual input, and puts that\nknowledge at your fingertips through a direct Python client and a REST api.\n\n### REST API\n\nThe INDRA DB is available via a web UI at: https://db.indra.bio\n\nAt the same URL, a REST service is also available which allows for programmatic usage\nas documented here: https://github.com/gyorilab/indra_db/blob/master/indra_db_service/README.md\n\nA convenient way to query the INDRA DB is via INDRA's built-in client towards INDRA DB\nwhich is documented here: https://indra.readthedocs.io/en/latest/modules/sources/indra_db_rest/index.html.\n\n### Knowledge sources\n\nThe INDRA Database currently integrates and distills knowledge from several\ndifferent sources, both biology-focused natural language processing systems and\nother pre-existing databases\n\n#### Daily Readers\nWe have read all available content, and every day we run the following readers:\n- [REACH](https://github.com/clulab/reach)\n- [Sparser](https://github.com/ddmcdonald/sparser)\n\nwe read all new content with the following readers:\n- [Eidos](https://github.com/clulab/eidos)\n- [ISI](https://github.com/sgarg87/big_mech_isi_gg)\n- [MTI](https://ii.nlm.nih.gov/MTI/index.shtml) - used specifically to tag\ncontent with topic terms.\n\nwe read a limited subset of new content with the following readers:\n- [TRIPS](http://trips.ihmc.us/parser/cgi/drum)\n\non the latest content drawn from:\n- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/) - ~19 million abstracts and ~29 million titles\n- [PubMed Central](/www.ncbi.nlm.nih.gov/pmc/) - ~2.7 million fulltext\n- [Elsevier](https://www.elsevier.com/) - ~0.7 million fulltext \n(requires special access)\n\n#### Other Readers\nWe also include more or less static content extracted from the following readers:\n- [RLIMS-P](https://research.bioinformatics.udel.edu/rlimsp/)\n\n#### Other Databases\nWe include the information from these pre-existing databases:\n- [Pathway Commons database](http://pathwaycommons.org/)\n- [BEL Large Corpus](https://github.com/OpenBEL/)\n- [SIGNOR](https://signor.uniroma2.it/)\n- [BioGRID](https://thebiogrid.org/)\n- [TAS](https://www.biorxiv.org/content/10.1101/358978v1)\n- [TRRUST](https://omictools.com/trrust-tool)\n- [PhosphoSitePlus](https://www.phosphosite.org/)\n- [Causal Biological Networks Database](http://www.causalbionet.com/)\n- [VirHostNet](http://virhostnet.prabi.fr/)\n- [CTD](http://ctdbase.org/)\n- [Phospho.ELM](http://phospho.elm.eu.org/)\n- [DrugBank](https://www.drugbank.ca/)\n- [CONIB](https://pharmacome.github.io/conib/)\n- [CRoG](https://github.com/chemical-roles/chemical-roles)\n- [DGI](https://www.dgidb.org/)\n\nThese databases are retrieved primarily using the tools in `indra.sources`. The\nstatements extracted from all of these sources are stored and updated in the\ndatabase.\n\n### Knowledge Assembly\n\nThe INDRA Database uses the powerful internal assembly tools available in INDRA\nbut implemented for large-scale incremental assembly. The resulting corpus of\ncleaned and de-duplicated statements, each with fully maintained provenance, is\nthe primary product of the database.\n\nFor more details on the internal assembly process of INDRA, see the\n[INDRA documentation](http://indra.readthedocs.io/en/latest/modules/preassembler).\n\n### Access\n\nThe content in the database can be accessed by those that created it using the\n`indra_db.client` submodule. This repo also implements a REST API which can be\nused by those without direct acccess to the database. For access to our REST\nAPI, please contact the authors.\n\n## Installation\n\nThe INDRA database only works for Python 3.6+, though some parts are still compatible with 3.5.\n\nFirst, [install INDRA](http://indra.readthedocs.io/en/latest/installation.html),\nthen simply clone this repo, and make sure that it is visible in your\n`PYTHONPATH`.\n\n## Funding\nThe development of INDRA DB is funded under the DARPA Communicating with Computers program (ARO grant W911NF-15-1-0544).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgyorilab%2Findra_db","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgyorilab%2Findra_db","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgyorilab%2Findra_db/lists"}