Geneweaver Ortholog Normalizer

An application to aid in normalizing homology data.

See Aon: a service to augment Alliance Genome Resource data with additional species for more information.

Originally forked from this code repository.

Development Setup

This repository uses Poetry to manage dependencies and build packages.

To get started, clone the repository and install the dependencies:

git clone
cd geneweaver-ortholog-normalizer
poetry install

You can activate the virtual environment with:

poetry shell

Flask Server

The flask server can be started by running:

poetry run flask --app geneweaver.aon.app run

CLI

The application has a command-line interface for running certain management commands.

• gwaon: /gwɑːn/ (noun) - A command-line interface for the Geneweaver Ortholog Normalizer.

Loading The Database

You will need a postgresql database to load the ortholog data into. This has been tested on Postgres 12, but should work on Postgres > 12.

Create the database schema

The database schema can be created by running the following command:

poetry run gwaon create-schema

Load the ortholog data

The ortholog data can be loaded by running the following command:

poetry run gwaon load agr

Geneweaver Ortholog Normalizer Management

Current Development Usage

The service connects to the geneweaver database to access the tables gene, species, and genedb.

Update database URLS in:

• flask/src/config.py
• flask/alembic.ini

If an agr database does not exist, create an empty database to store the agr data.

If the AGR tables have not been created, create them with alembic from the flask directory:

cd flask
alembic upgrade head

Download the most recent ORTHO_FILE from https://www.alliancegenome.org/downloads#orthology as TSV. Make sure to set the ORTHO_FILE constant in flask/src/service.py to tell the module which file to load.

For now, database loading is achieved by calling the service.py module as a script. This will fill alg_algorithm, gn_gene, hom_homology, ora_ortholog_algorithms, ort_otholog, and sp_species.

python flask/src/service.py

The agr database should be filled. The following command runs the service:

python flask/app.py

Missing Information

If there is missing information, data can be added to the sp_species, gn_gene, and ort_ortholog tables by running the add_missing_info.py script.

Make sure you have set the correct file paths to the flask/missing_info/missing_genes.csv and flask/missing_info/missing_orthologs.csv files.

Then run the following script:

python flask/src/add_missing_info.py

Endpoint Migration Table

Old Endpoint	New Endpoint
agr_to_geneweaver_species/{sp_id}:	/species/{species_id}/geneweaver_id
all_algorithms:	/algorithms
all_genes:	/genes
all_homology:	/homologs
all_orthologs:	/orthologs
all_species:	/species
get_algorithm_by_name/{alg_name}:	/algorithms?name={name}
get_from_gene_of_ortholog_by_id/{ort_id}:	/orthologs/{ortholog_id}/genes
get_gene_species_name/{ode_ref_id}/{ode_gene_id}:	WIP
get_genes_by_ode_gene_id/{ode_ref_id}/{ode_gene_id}:	WIP
get_genes_by_prefix/{gn_prefix}:	/genes?prefix={prefix}
get_genes_by_species/{sp_name}:	/species/{species_id}/genes
get_homologous_ode_gene_ids_for_gene/{ode_ref_id}/{gdb_name}:	WIP
get_homology_by_gene/{gn_id}:	/homologs?gene_id={gene_id}
get_homology_by_gene_and_source/{gn_id}/{hom_source_name}:	/homologs?source={source}
get_homology_by_id/{hom_id}:	/homologs/{homolog_id}
get_homology_by_id_and_source/{hom_id}/{hom_source_name}:	/homologs/{homolog_id}?source={source}
get_homology_by_id_and_species/{hom_id}/{sp_id}:	/homologs/{homolog_id}?species={species}
get_homology_by_ode_gene_id/{ode_gene_id}:	WIP
get_homology_by_ode_gene_ids:	WIP
get_homology_by_species/{sp_id}:	/homologs?species={species}
get_intersect_by_homology:	WIP
get_ode_gene_by_gdb_id/{gdb_id}:	WIP
get_ode_gene_by_gene_id/{ode_gene_id}:	WIP
get_ode_gene_by_species/{ode_gene_id}/{sp_name}:	WIP
get_ode_genes_from_hom_id/{hom_id}/{target_gdb_id}:	WIP
get_ort_id_if_gene_is_ortholog/{ode_gene_id}/{ode_ref_id}:	WIP
get_ortholog_by_algorithm/{alg_name}:	/orthologs?algorithm={algorithm}
get_ortholog_by_from_gene_and_gdb/{from_ode_gene_id}/{gdb_id}:	WIP
get_ortholog_by_from_species/{sp_name}:	/orthologs?from_species={species_id}
get_ortholog_by_id/{ort_id}:	/orthologs/{ortholog_id}
get_ortholog_by_to_and_from_species/{to_sp_name}/{from_sp_name}:	/orthologs?to_species={species_id}&from_species={species_id}
get_ortholog_by_to_from_species_and_algorithm/{to_sp_name}/{from_sp_name}/{alg_name}:	/orthologs?to_species={species_id}&from_species={species_id}&algorithm={algorithm}
get_ortholog_by_to_species/{sp_name}:	/orthologs?to_species={species_id}
get_orthologous_species/{ode_gene_id}/{ode_ref_id}:	WIP
get_orthologs_by_from_gene/{ode_ref_id}/{ode_gene_id}:	WIP
get_orthologs_by_from_gene_and_best/{from_ode_ref_id}/{from_ode_gene_id}/{best}:	WIP
get_orthologs_by_from_to_gene_and_best/{from_ode_ref_id}/{from_ode_gene_id}/{to_ode_ref_id}/{to_ode_gene_id}/{best}:	WIP
get_orthologs_by_from_to_gene_and_revised/{from_ode_ref_id}/{from_ode_gene_id}/{to_ode_ref_id}/{to_ode_gene_id}/{ort_best_revised}:	WIP
get_orthologs_by_num_algorithms/{num}:	/orthologs?possible_match_algorithms={num_algorithms}
get_orthologs_by_symbol/{sym}/{orig_species}/{homologous_species}:	WIP
get_orthologs_by_to_and_from_gene/{from_ode_ref_id}/{from_ode_gene_id}/{to_ode_ref_id}/{to_ode_gene_id}:	WIP
get_orthologs_by_to_gene/{ode_ref_id}/{ode_gene_id}:	WIP
get_sp_id_by_hom_id/{hom_id}:	/homologs/{homolog_id}?species={species_id}
get_species_by_id/{sp_id}:	/species/{species_id}
get_species_homologs_list:	/species/{species_id}/homologs
get_to_gene_of_ortholog_by_id/{ort_id}:	WIP
id_convert_agr_to_ode/{gn_id}:	/genes/{gene_id}/geneweaver_id
id_convert_ode_to_agr/{ode_gene_id}/{ode_ref_id}:	/geneweaver/genes/{geneweaver_id}/aon_id
if_gene_has_homolog/{ode_gene_id}:	WIP
transpose_genes_by_species:	WIP