Computational biologist.
I use Python, C++, R, and AWS. Tinkering with Clojure. He/him.
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Oregon State University
- Corvallis, Oregon, United States
- http://lab.saramsey.org
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biolink-model
biolink-model PublicForked from biolink/biolink-model
Schema and generated objects for biolink data model and upper ontology
Python
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nippy
nippy PublicForked from taoensso/nippy
High-performance serialization library for Clojure
Clojure
467 contributions in the last year
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Contribution activity
July 2025
Created 114 commits in 2 repositories
Created a pull request in RTXteam/RTX that received 11 comments
Switching ARAX-Overlay FET to use ARAX-expand instead of DSL/ARAXQuery
See issue #2525. With this PR, Overlay/fisher_exact_test.py
no longer has to submit a DSL query via ARAXQuery in order to compute the number of nei…
+430
−463
lines changed
•
11
comments
Opened 8 other pull requests in 2 repositories
RTXteam/RTX
6
merged
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Issue 2548
This contribution was made on Jul 25
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#2540
This contribution was made on Jul 17
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Issue 2537 - fixing Flask startup deprecation warning about jsonencoder
This contribution was made on Jul 17
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Code cleanup of ARAX-expand and all of its dependencies
This contribution was made on Jul 15
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merge sundar's commit into issue-2455 branch, for testing
This contribution was made on Jul 10
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Issue 2455 (and also 2519 fixed in passing)
This contribution was made on Jul 10
Translator-CATRAX/stitch
2
merged
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updated hardware requirements
This contribution was made on Jul 30
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Issue 22
This contribution was made on Jul 30
Reviewed 1 pull request in 1 repository
RTXteam/RTX
1 pull request
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Code cleanup of ARAX-expand and all of its dependencies
This contribution was made on Jul 16
Created an issue in RTXteam/RTX that received 17 comments
upgrade version python used for ARAX
I know this was brought up at an ARAX AHM recently, but I am resurfacing the matter as an issue. Hi all, we're currently using python3.9 in ARAX's …
17
comments
Opened 32 other issues in 4 repositories
RTXteam/RTX
6
open
15
closed
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pathfinder queries via the ARAX UI seem to get a qnode property "fulltextname" that is not understood by ARS
This contribution was made on Jul 25
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xgboost glibc warning when I run pytest
This contribution was made on Jul 25
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Why is this event logged by Pathfinder as a "WARNING" and not an "ERROR"?
This contribution was made on Jul 25
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pytest test_ARAX_expand.py::test_kg2_version failing on arax.ncats.io/beta
This contribution was made on Jul 25
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fix wasteful JSON deserialization in query_controller.py
This contribution was made on Jul 25
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ARAX Query controller with
stream_progress=false
is now brokenThis contribution was made on Jul 24 -
can we get some of these "slow" FET unit tests working again?
This contribution was made on Jul 17
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install basic network troubleshooting tools in the ARAX container
This contribution was made on Jul 16
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ARAX_background_tasker.py will delete the node synonymizer sqlite file if it exists as a file (not a symlink)
This contribution was made on Jul 16
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ARAX startup warning about jsonencoder
This contribution was made on Jul 15
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connexion jsonschema format checker warning
This contribution was made on Jul 15
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SQLAlchemy feature deprecation warning
This contribution was made on Jul 15
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SSL warning in trapi_querier.py
This contribution was made on Jul 15
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Numpy warning from ARAX_ranker.py
This contribution was made on Jul 15
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add RTX/code/UI/OpenAPI/python-flask-server/RTX_OpenAPI_* to .gitignore
This contribution was made on Jul 14
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error with meta-kg when running ARAX pytest suite
This contribution was made on Jul 14
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apparent bug in ExplianableDTD_db.py
This contribution was made on Jul 14
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update conftest.py so that you can optionally skip running the ARAX_database_manager.py
This contribution was made on Jul 14
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explore whether the dependency of fisher_exact_test.py on ARAXQuery can be eliminated
This contribution was made on Jul 10
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clean up type hints in the ARAX-expand code so that it passes (mostly) mypy checks
This contribution was made on Jul 10
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Ugly exception if ARAX-expand is used and there is no pre-existing KP info cache
This contribution was made on Jul 9
Translator-CATRAX/stitch
3
open
6
closed
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add type hints for all the places where we use Callable in ingest_babel.py
This contribution was made on Jul 30
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switch all repositories of checked out "stitch" code to "main" and then delete "issue-22" branch
This contribution was made on Jul 30
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add Vulture "dead code" checks
This contribution was made on Jul 29
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error ingesting GeneProtein.txt conflation file
This contribution was made on Jul 29
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refactor ingest_babel.py to reduce code duplication
This contribution was made on Jul 29
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code cleanup on run-ingest-aws.sh
This contribution was made on Jul 27
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add pytest and ruff to the requirements.txt
This contribution was made on Jul 27
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we may be running ANALYZE a bit too frequently during ingests
This contribution was made on Jul 26
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add support for ingesting conflation files
This contribution was made on Jul 22
RTXteam/RTX-KG2
1
open
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Spanish language support
This contribution was made on Jul 29
RobokopU24/ORION
1
closed
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missing node bindings to query graph, in some Automat KP responses?
This contribution was made on Jul 9