## This file is a list of things to be downloaded using the command:

# run.py download

# To add a new item to be download, add a block like this - must have 'url',

# 'local_name' is optional, use to avoid name collisions

# #

# # Description of source

# #

# -

# # brief comment about file, and optionally a local_name:

# url: http://curefordisease.org/some_data.txt

# local_name: some_data_more_chars_prevent_name_collision.pdf

#

# For downloading from S3 buckets, see here for information about what URL to use:

# https://docs.aws.amazon.com/AmazonS3/latest/dev/UsingBucket.html#access-bucket-intro

# Amazon S3 virtual hosted style URLs follow the format shown below:

# https://bucket-name.s3.Region.amazonaws.com/key_name

#

---

#

# **** ROBOT ****

#

-

url: https://github.com/ontodev/robot/releases/download/v1.9.5/robot.jar

local_name: robot.jar

-

url: https://raw.githubusercontent.com/ontodev/robot/master/bin/robot

local_name: robot

# **** Ontology files ****

#

# ENVO

#

-

url: http://purl.obolibrary.org/obo/envo.json

local_name: envo.json

# NCBITaxon

#

-

url: http://purl.obolibrary.org/obo/ncbitaxon.owl.gz

local_name: ncbitaxon.owl.gz

#

# ChEBI

#

-

url: http://purl.obolibrary.org/obo/chebi.owl.gz

local_name: chebi.owl.gz

#

# GO

#

-

url: http://purl.obolibrary.org/obo/go.json

local_name: go.json

#

# GO

#

-

url: http://purl.obolibrary.org/obo/go.owl

local_name: go.owl

#

# MONDO

#

-

url: https://purl.obolibrary.org/obo/mondo/mondo.json

local_name: mondo.json

#

# HP

#

-

url: https://purl.obolibrary.org/obo/hp/hp.json

local_name: hp.json

# **** Data sources ****

# BacDive

# Explore Bacterial Diversity

-

url: gdrive:1dOquB0M6H5Vxu6cBPa4kJ7F9v44medoV

local_name: bacdive_strains.json

# MediaDive

# Explore MediaDive data

-

url: https://mediadive.dsmz.de/rest/media

local_name: mediadive.json

# Madin et al Condensed-traits

-

url: https://github.com/bacteria-archaea-traits/bacteria-archaea-traits/blob/master/output/condensed_traits_NCBI.csv?raw=true

local_name: madin_etal.csv

# # # ****Conversion Tables****

#

# Environment

#

-

url: https://raw.githubusercontent.com/bacteria-archaea-traits/bacteria-archaea-traits/master/data/conversion_tables/environments.csv

local_name: environments.csv

#

# EPM JSON for curies package

#

-

url: https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/obo.epm.json

local_name: epm.json

#

# Uniprot Functional Microbes

#

-

url: https://kghub.io/frozen_incoming_data/uniprot/uniprot_proteomes.tar.gz

local_name: uniprot_proteomes.tar.gz

#

# Uniprot Human

#

-

url: https://kghub.io/frozen_incoming_data/uniprot/uniprot_human.tar.gz

local_name: uniprot_human.tar.gz

#

# Unipathways

#

-

url: https://github.com/geneontology/unipathway/raw/master/upa.owl

local_name: upa.owl

# RHEA mappings

-

url: https://ftp.expasy.org/databases/rhea/tsv/rhea2go.tsv

local_name: rhea2go.tsv

-

url: https://ftp.expasy.org/databases/rhea/tsv/rhea2ec.tsv

local_name: rhea2ec.tsv

#

# EC

#

-

url: https://w3id.org/biopragmatics/resources/eccode/eccode.json

local_name: ec.json

#

# EC OWL

#

-

url: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz

local_name: ec.owl.gz

#

# BactoTraits

#

-

url: https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv

local_name: BactoTraits_databaseV2_Jun2022.csv

#

# CTD

#

-

url: https://ctdbase.org/reports/CTD_chemicals_diseases.tsv.gz

local_name: CTD_chemicals_diseases.tsv.gz

#

# Fermentation explorer

#

-

url: https://raw.githubusercontent.com/thackmann/FermentationExplorer/main/Shiny/FermentationExplorer/data/database.csv

local_name: fermentation_explorer.csv

#

# Disbiome

#

-

url: https://disbiome.ugent.be:8080/experiment

local_name: disbiome.json

#

# Wallen et al

#

-

url: https://static-content.springer.com/esm/art:10.1038/s41467-022-34667-x/MediaObjects/41467_2022_34667_MOESM4_ESM.xlsx

local_name: wallen_etal.xlsx