From 3302b5a5ab784fbf2c2c04dd92297e779f8214c2 Mon Sep 17 00:00:00 2001 From: Evan Morris Date: Tue, 23 Jul 2024 15:28:25 -0400 Subject: [PATCH] Squashed commit of the following: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit commit 8d8b643284e70e23c6bb5e2bb48425c9bc949ee4 Merge: 1f01b43 b0cf278 Author: Evan Morris 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 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 Date: Fri Jul 19 14:32:02 2024 -0400 bumping parsing versions for binds refactor parsers commit ec6b7d8a7bfdfd17ec6b95354b21f17ce9079c75 Merge: e44cae6 00c6627 Author: Evan Morris 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 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 Date: Wed Jul 10 15:10:28 2024 -0400 Improving the KL/AT in Phaors commit a687f3066bd7a1fb8a17897d2b7805f546f9aa57 Author: Kathleen Date: Wed Jul 10 12:32:26 2024 -0400 Modified predicates affected by biolink:binds commit e44cae6e8ff2bcff2ce08a57a8749997241107a1 Merge: 7ba9538 fa8ebf0 Author: Evan Morris 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 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. --- parsers/drugcentral/src/loaddrugcentral.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/parsers/drugcentral/src/loaddrugcentral.py b/parsers/drugcentral/src/loaddrugcentral.py index 4a008760..bd828a85 100644 --- a/parsers/drugcentral/src/loaddrugcentral.py +++ b/parsers/drugcentral/src/loaddrugcentral.py @@ -24,12 +24,12 @@ class DrugCentralLoader(SourceDataLoader): attribution = "https://drugcentral.org/about" parsing_version: str = '1.5' - omop_relationmap = {'off-label use': 'RO:0002606', # is substance that treats - 'reduce risk': 'RO:0002606', # is substance that treats + omop_relationmap = {'off-label use': 'biolink:applied_to_treat', # is substance that treats + 'reduce risk': 'biolink:preventative_for_condition', # is substance that treats 'contraindication': 'NCIT:C37933', # contraindication 'symptomatic treatment': 'RO:0002606', # is substance that treats 'indication': 'RO:0002606', # is substance that treats - 'diagnosis': 'RO:0002606'} # there's only one row like this. + 'diagnosis': 'DrugCentral:5271'} # there's only one row like this. act_type_to_knowledge_source_map = {'IUPHAR': 'infores:gtopdb', 'KEGG DRUG': 'infores:kegg',