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Got very intrigued by the "Biomedical Data Translator" and found this: https://ncats.nih.gov/translator https://ncats.nih.gov/translator ... and this paper:

Got very intrigued by the "Biomedical Data Translator" and found this: https://ncats.nih.gov/translator https://ncats.nih.gov/translator ... and this paper: https://ascpt.onlinelibrary.wiley.com/doi/full/10.1111/cts.13301 https://ascpt.onlinelibrary.wiley.com/doi/full/10.1111/cts.1... ... hoping it is the same thing. Have yet to find some usable code or published tool. Did anyone find any?

samuell 3y ago
They also mention mediKanren, apparently built on miniKanren (which is some language for logic programming). I personally saw a lot of potential for these approaches, and wrote some future outlook stuff as part of my thesis here: https://bionics.it/posts/linked-data-science https://bionics.it/posts/linked-data-science There is some cool new tech coming out here lately, including TypeDB, which is a little like a modern version of Prolog with proper data storage and less cryptic language: https://typedb.com/ https://typedb.com/ Unfortunately it seems to lack some of the expressive power that makes Prolog so well suited for integrating basically any outside data source on-the-fly :/
- sramsey 3y ago
  Hi, I'm the organizer of the DeclMed workshop. Yes, nearly all the code for the NCATS Biomedical Data Translator is on GitHub, in a variety of project areas. The best place to start is the Translator developer documentation: https://ncatstranslator.github.io/translator-developer-documentation/ https://ncatstranslator.github.io/translator-developer-docum... once you've got an overview, click on the "Developer Guide" tab on the aforementioned page. Please reach out if you have any questions (https://lab.saramsey.org https://lab.saramsey.org)
  - sramsey 3y ago
    I should have said, co-organizer of the workshop (with Will Byrd and Matt Might). Please also check out Tyler Beck's keynote (on Translator) at 5:24:35, and Sierra Moxon's talk on the Biolink semantic layer at 5:07:23, Chris Mungall's keynote on logic programming at 0:25:11, and Daniel Korn's presentation on drug repositioning at 6:58:01.
  - pfisherman 3y ago
    Hey sramsey. Glad to see the Translator is still going. I imagine that recent LLM mania has been a pretty big deal for the agent teams? Anyway, nice to see you around and say “Hi” to Noel and Christine for me ;)

samuell 3y ago

They also mention mediKanren, apparently built on miniKanren (which is some language for logic programming). I personally saw a lot of potential for these approaches, and wrote some future outlook stuff as part of my thesis here: https://bionics.it/posts/linked-data-science https://bionics.it/posts/linked-data-science There is some cool new tech coming out here lately, including TypeDB, which is a little like a modern version of Prolog with proper data storage and less cryptic language: https://typedb.com/ https://typedb.com/ Unfortunately it seems to lack some of the expressive power that makes Prolog so well suited for integrating basically any outside data source on-the-fly :/

sramsey 3y ago
Hi, I'm the organizer of the DeclMed workshop. Yes, nearly all the code for the NCATS Biomedical Data Translator is on GitHub, in a variety of project areas. The best place to start is the Translator developer documentation: https://ncatstranslator.github.io/translator-developer-documentation/ https://ncatstranslator.github.io/translator-developer-docum... once you've got an overview, click on the "Developer Guide" tab on the aforementioned page. Please reach out if you have any questions (https://lab.saramsey.org https://lab.saramsey.org)
- sramsey 3y ago
  I should have said, co-organizer of the workshop (with Will Byrd and Matt Might). Please also check out Tyler Beck's keynote (on Translator) at 5:24:35, and Sierra Moxon's talk on the Biolink semantic layer at 5:07:23, Chris Mungall's keynote on logic programming at 0:25:11, and Daniel Korn's presentation on drug repositioning at 6:58:01.
- pfisherman 3y ago
  Hey sramsey. Glad to see the Translator is still going. I imagine that recent LLM mania has been a pretty big deal for the agent teams? Anyway, nice to see you around and say “Hi” to Noel and Christine for me ;)