RTXteam / RTX

Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)
https://arax.ncats.io/
MIT License
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upload KG2.8.3c TSV tarball to Knowledge Graph Exchange #2117

Closed saramsey closed 7 months ago

saramsey commented 1 year ago

The Knowledge Graph Exchange (KGE) still seems to be up and running. Team Unsecret Agent would like to have our KG2c TSV files archived if possible. So can we please archive the KG2.8.3c TSV tarball on the KGE?

Thanks, Steve

edeutsch commented 1 year ago

I'm curious what's in the knowledge graph exchange. What does it look like? I can't login. Maybe I should ask for a login..

saramsey commented 1 year ago

Different dump files for different large knowledge graphs. List of KGs available is:

Screenshot 2023-08-28 at 8 16 18 PM
saramsey commented 1 year ago

Not sure how frequently anyone is adding updates to KGs via the KGE. Last I heard from Richard it was now unsupported. On the other hand, we got a request to host a TSV tarball for KG2c and it beats hosting our own (due to licensing concerns).

sundareswarpullela commented 1 year ago

To do this, I am following the steps here but the file content_metadata.json is not getting generated when I run bash -x kgx-validation-and-metagraph.sh which uses the kgx module.

saramsey commented 1 year ago

@sundareswarpullela Did using the latest version of python help with this?

sundareswarpullela commented 1 year ago

The KGX code is currently running on buildkg2c.rtx.ai. I think it'll work now. Will update here.

saramsey commented 1 year ago

Thank you for the update, @sundareswarpullela !

sundareswarpullela commented 1 year ago

The content_metadata.json file is not getting generated by kgx package. Is it mandatory to have that?

saramsey commented 1 year ago

So... using the latest kgx package does not help?

saramsey commented 1 year ago

Does this command not work? [From this page.]

    kgx graph-summary --input-format tsv \
                      --output content_metadata.json \
                      --report-type meta-knowledge-graph \
                      --error-log graph_stats.err \
                      tests/resources/graph_nodes.tsv tests/resources/graph_edges.tsv
sundareswarpullela commented 1 year ago

content_metadata.json has been generated. The issue is with the kgx validate command that runs before the kgx graph-summary function in the kgx-validation-and-metagraph.sh file.

saramsey commented 1 year ago

Thank you @sundareswarpullela can you please update the issue template to reflect this updated information about how to generate the content_metadata.json file?

sundareswarpullela commented 1 year ago

KG2.8.4c has been updated, will generate content_metadata.json for KG2.8.3c within the week.

saramsey commented 1 year ago

Thanks, Sundar. We can discuss it on 10/27.

sundareswarpullela commented 1 year ago

content_metadata.json has been generated for KG2.8.3c. The files nodes.tsv, edges.tsv and content_metadata.json are present in the instance buildkg2c.rtx.ai in the directory ~/kg2.8.3_kgx. @sundareswarpullela and @saramsey will upload the files on 10/26/2023 at 10am PST during their one on one meeting.