Witvilet Connectome linking

[wrgr]

Would it be possible to add links to connectomes hosted externally to boss or to mirror them in a standardized format? I think it would be a great asset for reusability. We are running into challenges in doing secondary data analysis in an academic class. Thanks!!

For example: Witvilet 2020 has graph data, but is hosted externally. Would be nice to have it more accessible and clearly linked. (E.g., a connectome block with a pointer to the paper supplementary files. Thanks!!!

https://www.nature.com/articles/s41586-021-03778-8

[j6k4m8]

@wrgr Definitely! This is on our roadmap as the metadata service converges on complete; in the meantime we host these data (immutably) in a standardized form in Motif Studio. Exhaustive API docs here, but here's a short Python script to download the latest:

import requests
hosts = requests.get("https://api.motifstudio.bossdb.org/providers/hostlist").json()['hosts']

Each graph has a name and an ID:

>>> hosts[0]
{'name': 'Witvliet et al. 2020, Dataset 1', 'id': 'Witvliet_1'}

You can request graphs in a few different formats like graphml or gexf:

graph_raw = requests.post(
    "https://api.motifstudio.bossdb.org/queries/graph/download", 
    json={"host_id": hosts[0]['id'], "format": "graphml"}
)

This can be written to a file,

with open(f"{hosts[0]['id']}.graphml", "wb") as f:
    f.write(graph_raw.content)

...or materialized in, say, a graph library like NetworkX:

import io
import networkx as nx

G = nx.read_graphml(io.BytesIO(graph.content))