Litcoin bagel 7

litcoin-test-13

adding env to gitignore

Litcoin bagel 6

litcoin-test-12

making error catching more broad for all bagel methods

Litcoin Bagel 5

litcoin-test-11

refactoring and fixing bagel cache

Litcoin bagel 3

litcoin-test-9

failing gracefully for failed sapbert or name res calls

Litcoin bagel 2

litcoin-test-8

switching gpt model, making 429s hard stop

Litcoin bagel 4

litcoin-test-10

adding error checking for taxon normalization

Litcoin bagel testing

Squashed commit of the following:

commit d136e055266c6d80dc722b115aaa1a5a9d54cc1b
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Mon Oct 21 23:50:53 2024 -0400

    trying to clean up weird logger stuff

neo4j 5 8

neo4j-5-testing-8

reverting to sequential node norm calls

neo4j 5 7

neo4j-5-testing-7

fixing pool size and making backoff factor slower for node norm

neo4j 5 6

Squashed commit of the following:

commit 8d8b643284e70e23c6bb5e2bb48425c9bc949ee4
Merge: 1f01b43 b0cf278
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Tue Jul 23 15:01:08 2024 -0400

    Merge pull request #230 from RobokopU24/drugcentral_treats_refactor

    Refactored treats edges for DrugCentral to differentiate between indi…

commit b0cf278e02ffffd2b64834a8f57894dcd7adc72e
Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com>
Date:   Tue Jul 23 12:04:39 2024 -0400

    Update loaddrugcentral.py kathleen modifications

    changed the mapping of symptomatic treatment to RO:0002606 (instead of RO:0003307)

    changed the mapping of diagnosis to DrugCentral:5271

commit 1f01b43a842706e9cb5723c88c3bbd8371ff505a
Merge: ec6b7d8 734cc6e
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:38:15 2024 -0400

    Merge pull request #232 from RobokopU24/binding-predicate-update

    Modified predicates affected by biolink:binds

commit 734cc6e4c42e2315b217e762bb481aff867835e7
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:32:02 2024 -0400

    bumping parsing versions for binds refactor parsers

commit ec6b7d8a7bfdfd17ec6b95354b21f17ce9079c75
Merge: e44cae6 00c6627
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:28:50 2024 -0400

    Merge pull request #233 from RobokopU24/pharos_KL/AT

    Improving the KL/AT in Pharos

commit 00c6627485c2866d7bbfc301db55ce428bcdcf1f
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Fri Jul 19 14:26:48 2024 -0400

    bumping parsing version

commit 766c5b75dff428030bb2820547c1a3fb1521d248
Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com>
Date:   Tue Jul 16 12:42:45 2024 -0400

    Update predicates.py

    forgot to revert changes for interacts_with. Will keep it unmodified until further clarification.

commit 4cb0188743f17168cf5e5166196bf61e52ffd82d
Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com>
Date:   Tue Jul 16 12:41:36 2024 -0400

    Update predicates.py after comments

    Made changes to reflect comments by Chris:

    1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from.
    "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?"

    2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor

    3. Do not modify "interacts_with"  until we know where this predicate comes from.
    I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss.

    (but I'd be tempted to put 2436 for this one)"

    Main take away: where do these predicates come from? Can we track down how this was generated?

commit 711ac5af9d19ae6bdeb7c24c1b54dd836db3cfa5
Author: Kathleen <ekcarter@renci.org>
Date:   Wed Jul 10 15:10:28 2024 -0400

    Improving the KL/AT in Phaors

commit a687f3066bd7a1fb8a17897d2b7805f546f9aa57
Author: Kathleen <ekcarter@renci.org>
Date:   Wed Jul 10 12:32:26 2024 -0400

    Modified predicates affected by biolink:binds

commit e44cae6e8ff2bcff2ce08a57a8749997241107a1
Merge: 7ba9538 fa8ebf0
Author: Evan Morris <evandietzmorris@gmail.com>
Date:   Wed Jun 26 16:38:02 2024 -0400

    Merge pull request #231 from RobokopU24/requirements.txt-patch

    Update requirements.txt

commit fa8ebf05e3761cb0d563818928857d0c8af3a2d2
Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com>
Date:   Wed Jun 26 16:37:03 2024 -0400

    Update requirements.txt

    Updated requests 2.32.0 -> 2.32.3

commit ef231fcf2be790bab0ff3360ee39796c27859d7f
Author: beasleyjonm <beasleyjonm@gmail.com>
Date:   Fri May 24 14:01:06 2024 -0400

    Refactored treats edges for DrugCentral to differentiate between indications, off-label use, prevention, and treatment of symptoms.