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https://github.com/greenelab/annotation-refinery

A python package that consists of functions that process publicly available annotated sets of genes
https://github.com/greenelab/annotation-refinery

gene-sets ontology package script tool

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A python package that consists of functions that process publicly available annotated sets of genes

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README 

        
===================

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 ``.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.



.. code-block::



    [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.



.. code-block::



    # 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//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.



.. code-block::



    [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