dgidb

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Rails frontend to The Genome Institute's drug gene interaction database.

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- - tests.yml
- - news_filter.rb
  - tour_filter.rb
- - application_controller.rb
  - downloads_controller.rb
  - drug_claims_controller.rb
  - drugs_controller.rb
  - gene_claim_categories_controller.rb
  - gene_claims_controller.rb
  - genes_controller.rb
  - interaction_claims_controller.rb
  - interaction_types_controller.rb
  - interactions_controller.rb
  - search_controller.rb
  - services_v1_controller.rb
  - services_v2_controller.rb
  - sources_controller.rb
  - static_controller.rb
  - utilities_controller.rb
- - anti_neoplastic.rb
  - approved_drug.rb
  - category_source_db_name.rb
  - category_source_trust_level.rb
  - clinically_actionable.rb
  - drug_claim_type.rb
  - drug_resistance.rb
  - druggable_genome.rb
  - filter.rb
  - filter_chain.rb
  - filter_helper.rb
  - gene_claim_category.rb
  - gene_claim_category_interaction.rb
  - identity_filter.rb
  - immunotherapy.rb
  - interaction_claim_type.rb
  - source_db_name.rb
  - source_trust_level.rb
- - application_helper.rb
- - api_updater.rb
  - application_job.rb
  - create_monthly_tsvs.rb
  - grouper.rb
  - post_grouper.rb
  - pre_grouper.rb
  - send_api_analytics.rb
  - tsv_updater.rb
  - update_cgi.rb
  - update_civic.rb
  - update_ckb.rb
  - update_docm.rb
  - update_drug_bank.rb
  - update_dtc.rb
  - update_ensembl.rb
  - update_entrez.rb
  - update_go.rb
  - update_guide_to_pharmacology.rb
  - update_oncokb.rb
  - update_pharmgkb.rb
  - update_pharos.rb
  - updater.rb
- - .gitkeep
- - .gitkeep
  - application_record.rb
  - gene_category_search_result.rb
  - interaction_search_result.rb
  - tour.rb
- - attribute_presenter.rb
  - claim_attribute_presenter.rb
  - drug_claim_presenter.rb
  - drug_detail_presenter.rb
  - drug_presenter.rb
  - druggable_gene_category_presenter.rb
  - gene_category_search_result_presenter.rb
  - gene_category_search_results_presenter.rb
  - gene_claim_presenter.rb
  - gene_detail_presenter.rb
  - gene_id_mapping_presenter.rb
  - gene_name_presenter.rb
  - gene_presenter.rb
  - interaction_claim_presenter.rb
  - interaction_detail_presenter.rb
  - interaction_presenter.rb
  - interaction_search_result_api_v1_presenter.rb
  - interaction_search_result_api_v2_presenter.rb
  - interaction_search_results_api_v1_presenter.rb
  - interaction_search_results_api_v2_presenter.rb
  - interaction_search_results_presenter.rb
  - news_presenter.rb
  - paginated_collection_presenter.rb
  - pagination_presenter.rb
  - related_drug_presenter.rb
  - search_result_presenter.rb
  - source_presenter.rb
  - trust_level_presenter.rb
- - lookup_categories.rb
  - lookup_drugs.rb
  - lookup_genes.rb
  - lookup_interactions.rb
  - lookup_related_genes.rb
  - search.rb
- - category_result_sort_order.rb
  - drug_claim_sort_order.rb
  - gene_claim_sort_order.rb
  - interaction_result_sort_order.rb
- delayed_job
- rails
- - production.rb
  - sidekiq.rb
  - staging.rb
- - development.rb
  - production.rb
  - test.rb
- - airbrake.rb
  - assets.rb
  - backtrace_silencers.rb
  - external_strings.rb
  - genome.rb
  - inflections.rb
  - mime_types.rb
  - mini_profiler.rb
  - secret_token.rb
  - session_store.rb
  - sidekiq.rb
  - tours.rb
  - version_string.rb
  - wrap_parameters.rb
- - en.yml
- application.rb
- boot.rb
- database.yml
- deploy.rb
- environment.rb
- routes.rb
- scheduled_tasks.yml
- secrets.yml
- - 20121212223401_normalize_interactions_for_filtering.rb
  - 20121213151709_normalize_gene_categories.rb
  - 20121214160809_further_normalization.rb
  - 20121214161439_add_fulltext_indexes.rb
  - 20121214191000_rename_display_name_column.rb
  - 20121218184952_add_indexes_for_names.rb
  - 20121218224238_primary_drug_name_for_drug_claims.rb
  - 20130103214307_normalize_drug_types.rb
  - 20130214204650_add_source_counters.rb
  - 20130305165700_add_source_type_table.rb
  - 20130307160126_add_case_insensitive_indexes.rb
  - 20130424183200_add_display_name_to_source_type.rb
  - 20130712222803_add_gene_gene_interaction_table.rb
  - 20130712225648_add_inter_gene_interaction_count_to_sources.rb
  - 20130906013631_add_lower_indexes.rb
  - 20170216144343_add_drug_id_to_drug_claims.rb
  - 20170216165933_add_gene_id_to_gene_claims.rb
  - 20170217172327_drop_drug_claims_drugs.rb
  - 20170217184303_drop_gene_claims_genes.rb
  - 20170222165433_add_interactions_table.rb
  - 20170302155212_add_drug_aliases_table.rb
  - 20170303162418_add_drug_attributes_table.rb
  - 20170314140736_add_gene_aliases_table.rb
  - 20170314161924_add_gene_attributes_table.rb
  - 20170315152806_add_interaction_attributes_table.rb
  - 20170317143034_delete_description_columns.rb
  - 20170317175150_add_gene_categories_genes_table.rb
  - 20170414213904_create_publications.rb
  - 20170417192246_create_interactions_publications_table.rb
  - 20170417192258_create_interaction_claims_publications_table.rb
  - 20170424175208_add_entrez_id_to_gene.rb
  - 20170503192632_add_indexes_on_new_gene_fields.rb
  - 20170512141234_remove_nomenclature_from_groups.rb
  - 20170512150855_add_unique_contraints.rb
  - 20170605204001_create_chembl_molecules.rb
  - 20170616211809_create_delayed_jobs.rb
  - 20170619174047_add_search_flags_to_drugs.rb
  - 20170619191811_add_chembl_id_to_drugs.rb
  - 20170619204652_create_chembl_molecule_synonyms.rb
  - 20170619205542_remove_timestamps_from_chembl_molecules.rb
  - 20170622142108_add_syn_type_to_chembl_molecule_synonyms.rb
  - 20170628044755_require_drugs_to_have_molecules.rb
  - 20170629024912_change_chembl_molecule_drug_foreign_key_type.rb
  - 20170630203634_add_not_null_constraints_to_drugs.rb
  - 20170705222429_create_join_table_interaction_source.rb
  - 20170706215825_drop_known_action_type.rb
  - 20170727025111_interaction_attributes_cascade_delete.rb
  - 20170727192237_add_index_to_molregno.rb
  - 20170728015708_add_indices_for_drug_grouper.rb
  - 20170728023124_add_indices_for_gene_grouper.rb
  - 20170729004221_add_indices_to_drug_attributes_for_drug_grouper.rb
  - 20170808210937_add_constraints_to_chembl_molecules.rb
  - 20170824182356_revise_constraints_of_chembl_molecules.rb
  - 20170913202927_create_drug_alias_blacklists.rb
  - 20170914145053_add_clean_function.rb
  - 20191016180948_add_directionality_to_interaction_claim_type.rb
  - 20191107152512_add_definition_to_interaction_claim_type.rb
  - 20200608185423_add_license_to_source.rb
  - 20200615173440_add_interaction_claim_linkout.rb
  - 20200620144029_allow_multiple_source_types.rb
  - 20200811160413_add_column_reference_to_interaction_claim_type.rb
  - 20200901140610_changes_for_new_drug_grouper.rb
  - 20200904144705_rename_drug_fda_approved.rb
- seeds.rb
- structure.sql
- - flowchart.png
- perl_example.pl
- python_example.py
- ruby_example.rb
- shell_example.sh
- - .gitkeep
- - online_updater.rb
- - .gitkeep
  - db_bootstrapping.rake
  - generators.rake
  - groupers.rake
  - importers.rake
  - normalizers.rake
  - updaters.rake
- - database.rb
  - grouper.rb
  - logging.rb
  - pmid.rb
  - snapshot_helpers.rb
  - tsv.rb
  - uniquify_claims.rb
  - updater.rb
- .gitkeep
- 404.html
- 422.html
- 500.html
- favicon.ico
- robots.txt
- - drug_fabricator.rb
  - gene_fabricator.rb
  - gene_publication_fabricator.rb
  - interaction_fabricator.rb
  - publication_fabricator.rb
  - source_fabricator.rb
- - about_spec.rb
  - api_spec.rb
  - contact_spec.rb
  - druggable_gene_categories_spec.rb
  - druggable_gene_category_spec.rb
  - drugs_spec.rb
  - faq_spec.rb
  - genes_spec.rb
  - interactions_spec.rb
  - news_spec.rb
  - search_categories_spec.rb
  - search_interactions_spec.rb
  - sources_spec.rb
- - application_helper_spec.rb
- - null_object_spec.rb
- - lookup_categories_spec.rb
  - lookup_genes_spec.rb
  - search_spec.rb
- - cookie_helper.rb
- - database_spec.rb
  - logging_spec.rb
- spec_helper.rb
- about.yml
- api.yml
- categories_search_results.yml
- contact.yml
- data_clients.yml
- druggable_gene_categories.yml
- druggable_gene_category.yml
- faq.yml
- index.yml
- interaction_search_results.yml
- news.yml
- publications.yml
- score.yml
- search.yml
- search_categories.yml
- search_interactions.yml
- search_results.yml
- sources.yml
- restart.txt
- search_categories.yml
- search_interactions.yml
.gitignore
.rspec
.ruby-version
Capfile
config.ru
data
erd.pdf
Gemfile
Gemfile.lock
INSTALL-LINUX
INSTALL-OSX
LICENSE
Rakefile
README.md
VERSION

# Installation Guide

1. Get the code

git clone https://github.com/dgidb/dgidb

Downloads the entire project code from GitHub to your computer.

cd dgidb

Moves into the project folder you just downloaded.

2. Ruby

Easy Recommended

Prerequisites

Git Needed to download the project code from GitHub.
Ruby Ruby is required to use the bundle command.

bundle install

Installs the Ruby libraries listed in the Gemfile.

✅ If bundle install finishes without errors, continue with the run command from the README (e.g. rails server).

dgidb

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# Installation Guide

2. Ruby

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dgidb

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# Installation Guide

2. Ruby

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