Annotation Refinery

The Annotation Refinery python package consists of functions that process publicly available annotated sets of genes, such as Gene Ontology and Disease Ontology terms.

Requirements

Before you begin, make sure you have the required packages installed in your local Python environment.

`shell # Run this command from the root directory of this repository, where the # "requirements.txt" file is. pip install -r requirements.txt `

Configuration files

The Annotation Refinery requires at least two .ini configuration files in the main directory to run:

1. A main_config.ini file with the main configuration settings, and
2. At least one <species>.ini file, which will contain the locations of the desired annotation files for that species, among other things. Users can add configuration files in the main directory for as many species as they want the refinery to process.

Optionally, there can also be a secrets.ini file, which stores values like usernames and passwords for access to restricted URLs.

The Main Configuration File

The main configuration file includes settings like the location(s) of the species file(s), where the output of the refinery (the processed genesets) should be uploaded to, the name of the base directory for all the downloaded files, and optionally, the location of the secrets file.

[main]
SECRETS_FILE: secrets.ini
PROCESS_TO: Tribe


# All other download folders specified in the configuration files should
# be subdirectories of this folder.
[download_folder]
BASE_DOWNLOAD_FOLDER: download_files


[Tribe parameters]
TRIBE_URL: https://tribe.greenelab.com


[species files]
SPECIES_FILES: human.ini

The Species File(s)

Each species file should contain the URLs of the desired annotation files to be downloaded.

# File for human settings

[species_info]
SCIENTIFIC_NAME: Homo sapiens
TAXONOMY_ID: 9606

# *Note: This should be a subdirectory of the BASE_DOWNLOAD_FOLDER
# specified in the main_config.ini file.
SPECIES_DOWNLOAD_FOLDER: download_files/Human


# ***********************************************
# Below, add as sections the types of annotations
# that should be downloaded and processed
# ***********************************************

[GO]
DOWNLOAD: TRUE

GO_OBO_URL: ftp://ftp.geneontology.org/go/ontology/obo_format_1_2/gene_ontology.1_2.obo
ASSOC_FILE_URL: ftp://ftp.geneontology.org/go/gene-associations/gene_association.goa_human.gz

EVIDENCE_CODES: EXP, IDA, IPI, IMP, IGI, IEP

TAG_MAPPING_FILE: tag_mapping_files/brenda-gobp-all_mapping.dir.v2.txt
GO_ID_COLUMN: 2
GO_NAME_COLUMN: 3
TAG_COLUMN: 1
TAG_FILE_HEADER: TRUE


[KEGG]
DOWNLOAD: TRUE
KEGG_ROOT_URL: http://rest.kegg.jp
DB_INFO_URL: /info/kegg
SETS_TO_DOWNLOAD: /link/hsa/pathway, /link/hsa/module, /link/hsa/disease
SET_INFO_DIR: /get/

# This is the type of gene identifier used by KEGG for this species
XRDB: Entrez

[DO]
DOWNLOAD: TRUE
DO_OBO_URL: http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw
MIM2GENE_URL: http://omim.org/static/omim/data/mim2gene.txt
GENEMAP_URL: http://data.omim.org/downloads/<SecretKey>/genemap.txt

# This is the type of gene identifier used by DO
XRDB: Entrez

TAG_MAPPING_FILE: tag_mapping_files/tissue-disease_curated-associations.txt
DO_ID_COLUMN: 2
DO_NAME_COLUMN: 3
TAG_COLUMN: 1
TAG_FILE_HEADER: TRUE

The Secrets File

The secrets file contains things like usernames and passwords for databases, secret keys for APIs where annotation files will be downloaded from, etc.

[OMIM API secrets]
SECRET_KEY: ExampleSecretKey

[Tribe secrets]
TRIBE_ID: asdf1234
TRIBE_SECRET: qwerty1234

USERNAME: example_username
PASSWORD: password

Instructions for getting an OMIM API secret key can be found here: http://omim.org/downloads

Instructions for getting the Tribe secrets can be found here: http://tribe-greenelab.readthedocs.io/en/latest/api.html#creating-new-resources-through-tribe-s-api