Accessing metadata

This page explains everything there is to know about accessing metadata from PhyloData.

What is metadata?

Every experiment has a bunch of metadata associated with it. You can explore almost everything about an experiment by looking at its page on this website. However, you can also access the metadata using the PhyloData Python library.

Every load_experiment function returns a PaperWithExperiment object. It has the following structure:

class PaperWithExperiment:
    paper: Paper
    experiment: Experiment
    files: list[File]
    samples: list[Sample]
    trees: Optional[Trees]
    evolutionary_model: list[EvolutionaryModelComponent]
    metadata: Metadata

As you can see, the structure closely matches the experiment pages on the website.

Paper metadata

from phylodata import load_experiment

experiment = load_experiment("munro-2019-climate-6tvf", version=1)

print(experiment.paper.title)
print(experiment.paper.year)
print(experiment.paper.authors)
print(experiment.paper.abstract)
print(experiment.paper.bibtex)
print(experiment.paper.doi)

Experiment metadata

from phylodata import load_experiment

experiment = load_experiment("munro-2019-climate-6tvf", version=1)

print(experiment.experiment.type)
print(experiment.experiment.human_readable_id)
print(experiment.experiment.upload_date)
print(experiment.experiment.version)

File metadata

from phylodata import load_experiment

experiment = load_experiment("munro-2019-climate-6tvf", version=1)

for file in experiment.files:
    print(file.name)
    print(file.type)
    print(file.size_bytes)
    print(file.md5)
    print(file.is_preview)
    print(file.local_path)

files returns all files, including preview files and files that haven’t been downloaded. get_files and the like only return the files that have been downloaded and respect the preview preferences.

Sample metadata

from phylodata import load_experiment

experiment = load_experiment("munro-2019-climate-6tvf", version=1)

for sample in experiment.samples:
    print(sample.sample_id)
    print(sample.scientific_name)
    print(sample.classification)
    print(sample.sample_data)
    print(sample.common_name)

Trees metadata

from phylodata import load_experiment

experiment = load_experiment("munro-2019-climate-6tvf", version=1)

print(experiment.trees.number_of_trees)
print(experiment.trees.number_of_tips)
print(experiment.trees.ultrametric)
print(experiment.trees.time_tree)
print(experiment.trees.rooted)
print(experiment.trees.average_root_age)

Evolutionary model metadata

from phylodata import load_experiment

experiment = load_experiment("munro-2019-climate-6tvf", version=1)

for model in experiment.evolutionary_model:
    print(model.name)
    print(model.type)