Releases: RobokopU24/ORION
Releases · RobokopU24/ORION
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.
neo4j 5 5
neo4j-5-testing-5 improving error catching and logging for node normalization
neo4j 5 4
implemented concurrent calls to node normalizer for performance, usin… …g requests sessions for retries and performance, cleaned up comments
Release v1.0.14b
Merge pull request #232 from RobokopU24/binding-predicate-update Modified predicates affected by biolink:binds
neo4j 5 3
Squashed commit of the following:
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
LitCoin Pipeline 10
litcoin-pipeline-10 making retries slower and nameres timeout longer
LitCoin Pipeline 9
litcoin-pipeline-9 fixing typo
neo4j 5 2
neo4j-5-testing-2 switching to pypi version of robokop-genetics