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commit 83a8863
Merge: b124dfb f4e4003
Author: beasleyjonm <[email protected]>
Date:   Wed Sep 11 12:27:06 2024 -0400

    Merge pull request #256 from RobokopU24/PHAROS_target_for_edges

    Add "target_for" edges from loadPHAROS.py

commit f4e4003
Author: beasleyjonm <[email protected]>
Date:   Fri Aug 23 13:47:54 2024 -0400

    Add "target_for" edges from loadPHAROS.py

commit b124dfb
Merge: 74ea571 0a22609
Author: beasleyjonm <[email protected]>
Date:   Tue Aug 13 11:24:52 2024 -0400

    Merge pull request #252 from RobokopU24/neo4j_5

    Neo4j 5

commit 74ea571
Merge: 6836058 eeacd0b
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:58:48 2024 -0400

    Merge pull request #245 from RobokopU24/DnlRKorn-patch-7

    Set filenames to be based on object settings in all functions loadHistoneMap.py

commit 6836058
Merge: 0f389ab 2f0d2e7
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:57:17 2024 -0400

    Merge pull request #239 from RobokopU24/DnlRKorn-patch-1

    Update loadFDB.py

commit 0f389ab
Merge: 9f75017 f83234c
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:54:42 2024 -0400

    Merge pull request #241 from RobokopU24/DnlRKorn-patch-3

    Added TODO to loadGTEx.py

commit 9f75017
Merge: 0cf45a0 a45698f
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:50:59 2024 -0400

    Merge pull request #243 from RobokopU24/DnlRKorn-patch-5

    Update loadIA.py

commit 0cf45a0
Merge: 8db9527 827751d
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:50:14 2024 -0400

    Merge pull request #244 from RobokopU24/DnlRKorn-patch-6

    Added TODO to loadPanther.py

commit 8db9527
Merge: e94d556 40cad6f
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:49:25 2024 -0400

    Merge pull request #246 from RobokopU24/DnlRKorn-patch-8

    Added TODO to loadUniRef.py

commit 0a22609
Merge: 77c92b3 e94d556
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:47:12 2024 -0400

    Merge branch 'master' into neo4j_5

commit 77c92b3
Author: Evan Morris <[email protected]>
Date:   Tue Aug 13 10:45:36 2024 -0400

    changed bd_file_name in accordance with changes in BINDING (no more version in file name), also reverting some changes see description

    I had made a change that would store the downloaded files with consistent names so that get_latest_version would be called fewer times, but it's not really worth it because it's slow to recompress the archive and it doesn't prevent all calls to latest version.. there are better ways to do this

commit 5acb052
Author: Evan Morris <[email protected]>
Date:   Mon Aug 12 19:05:43 2024 -0400

    removing import, not in use (yet)

commit 17ff6ae
Author: Evan Morris <[email protected]>
Date:   Mon Aug 12 18:48:39 2024 -0400

    making quote usage consistent

commit 487863b
Author: Evan Morris <[email protected]>
Date:   Mon Aug 12 18:14:03 2024 -0400

    upgrading Reactome to neo4j 5, adding 4 to 5 migration step

commit 6af1635
Author: Evan Morris <[email protected]>
Date:   Mon Aug 12 17:18:22 2024 -0400

    commenting these out so they are truly optional by default

commit 7540dde
Author: Evan Morris <[email protected]>
Date:   Mon Aug 12 17:17:35 2024 -0400

    adding edge id

commit daa90bc
Author: Evan Morris <[email protected]>
Date:   Thu Aug 8 16:29:08 2024 -0400

    fixing literal comparison

commit 7268385
Author: Evan Morris <[email protected]>
Date:   Thu Aug 8 14:45:17 2024 -0400

    oops, fixing source id

commit 222db0c
Author: Evan Morris <[email protected]>
Date:   Thu Aug 8 14:22:49 2024 -0400

    adding a spec for ctkp and changing source id to ClinicalTrialsKP in the mappings

commit e94d556
Merge: 8d8b643 f369559
Author: Evan Morris <[email protected]>
Date:   Thu Aug 8 14:13:16 2024 -0400

    Merge pull request #250 from RobokopU24/docs-fix

    fixing remnants of data_services

commit f369559
Author: Evan Morris <[email protected]>
Date:   Thu Aug 8 14:06:17 2024 -0400

    fixing remnants of data_services

commit db4c548
Author: Evan Morris <[email protected]>
Date:   Thu Aug 8 13:51:37 2024 -0400

    adding CTKP

commit 5bf7bda
Author: Evan Morris <[email protected]>
Date:   Tue Aug 6 16:10:06 2024 -0400

    merging of properties more robust, avoid failure when there are properties to merge where only one is a list

commit 265e4e8
Author: Evan Morris <[email protected]>
Date:   Fri Aug 2 02:08:54 2024 -0400

    bumping bl versions

commit 8422572
Author: Evan Morris <[email protected]>
Date:   Fri Aug 2 01:36:37 2024 -0400

    allowing nodes with no names, with the condition they get their id set as the name

commit 669de09
Author: Evan Morris <[email protected]>
Date:   Wed Jul 31 12:29:23 2024 -0400

    fixing load argument from-path for neo4j 5

commit 40cad6f
Author: DnlRKorn <[email protected]>
Date:   Tue Jul 30 16:52:44 2024 -0400

    Added TODO to loadUniRef.py

commit eeacd0b
Author: DnlRKorn <[email protected]>
Date:   Fri Jul 26 16:41:36 2024 -0400

    Set filenames to be based on object settings in all functions loadHistoneMap.py

commit 827751d
Author: DnlRKorn <[email protected]>
Date:   Fri Jul 26 10:19:57 2024 -0400

    Added TODO to loadPanther.py

commit a45698f
Author: DnlRKorn <[email protected]>
Date:   Fri Jul 26 10:11:53 2024 -0400

    Update loadIA.py

    Changed hardcoded URLs to class variables.

commit 350f7b6
Author: Evan Morris <[email protected]>
Date:   Thu Jul 25 14:50:44 2024 -0400

    reverting to sequential node norm calls

commit f83234c
Author: DnlRKorn <[email protected]>
Date:   Thu Jul 25 12:08:30 2024 -0400

    Added TODO to loadGTEx.py

commit 2f0d2e7
Author: DnlRKorn <[email protected]>
Date:   Thu Jul 25 11:21:21 2024 -0400

    Update loadFDB.py

    Added small safety check in get_data.

commit 1613f62
Author: Evan Morris <[email protected]>
Date:   Wed Jul 24 15:04:45 2024 -0400

    fixing pool size and making backoff factor slower for node norm

commit 3302b5a
Author: Evan Morris <[email protected]>
Date:   Tue Jul 23 15:28:25 2024 -0400

    Squashed commit of the following:

    commit 8d8b643
    Merge: 1f01b43 b0cf278
    Author: Evan Morris <[email protected]>
    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 b0cf278
    Author: eKathleenCarter <[email protected]>
    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 1f01b43
    Merge: ec6b7d8 734cc6e
    Author: Evan Morris <[email protected]>
    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 734cc6e
    Author: Evan Morris <[email protected]>
    Date:   Fri Jul 19 14:32:02 2024 -0400

        bumping parsing versions for binds refactor parsers

    commit ec6b7d8
    Merge: e44cae6 00c6627
    Author: Evan Morris <[email protected]>
    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 00c6627
    Author: Evan Morris <[email protected]>
    Date:   Fri Jul 19 14:26:48 2024 -0400

        bumping parsing version

    commit 766c5b7
    Author: eKathleenCarter <[email protected]>
    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 4cb0188
    Author: eKathleenCarter <[email protected]>
    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 711ac5a
    Author: Kathleen <[email protected]>
    Date:   Wed Jul 10 15:10:28 2024 -0400

        Improving the KL/AT in Phaors

    commit a687f30
    Author: Kathleen <[email protected]>
    Date:   Wed Jul 10 12:32:26 2024 -0400

        Modified predicates affected by biolink:binds

    commit e44cae6
    Merge: 7ba9538 fa8ebf0
    Author: Evan Morris <[email protected]>
    Date:   Wed Jun 26 16:38:02 2024 -0400

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

        Update requirements.txt

    commit fa8ebf0
    Author: beasleyjonm <[email protected]>
    Date:   Wed Jun 26 16:37:03 2024 -0400

        Update requirements.txt

        Updated requests 2.32.0 -> 2.32.3

    commit ef231fc
    Author: beasleyjonm <[email protected]>
    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.

commit ccd0e57
Author: Evan Morris <[email protected]>
Date:   Tue Jul 23 15:27:07 2024 -0400

    increasing connection pool size and retry attempts for node norm

commit 8d8b643
Merge: 1f01b43 b0cf278
Author: Evan Morris <[email protected]>
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 b0cf278
Author: eKathleenCarter <[email protected]>
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 9f19660
Author: Evan Morris <[email protected]>
Date:   Tue Jul 23 11:36:10 2024 -0400

    improving error catching and logging for node normalization

commit 7731c4a
Author: Evan Morris <[email protected]>
Date:   Tue Jul 23 01:48:49 2024 -0400

    implemented concurrent calls to node normalizer for performance, using requests sessions for retries and performance,  cleaned up comments

commit 4bdeb7d
Author: Evan Morris <[email protected]>
Date:   Tue Jul 23 01:37:56 2024 -0400

    implemented better timeouts, retries, and failure for determining latest version, changed so that downloaded data files wont have version in their name

commit 6bc0270
Author: Evan Morris <[email protected]>
Date:   Fri Jul 19 16:44:32 2024 -0400

    Squashed commit of the following:

    commit 1f01b43
    Merge: ec6b7d8 734cc6e
    Author: Evan Morris <[email protected]>
    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 734cc6e
    Author: Evan Morris <[email protected]>
    Date:   Fri Jul 19 14:32:02 2024 -0400

        bumping parsing versions for binds refactor parsers

    commit ec6b7d8
    Merge: e44cae6 00c6627
    Author: Evan Morris <[email protected]>
    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 00c6627
    Author: Evan Morris <[email protected]>
    Date:   Fri Jul 19 14:26:48 2024 -0400

        bumping parsing version

    commit 766c5b7
    Author: eKathleenCarter <[email protected]>
    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 4cb0188
    Author: eKathleenCarter <[email protected]>
    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 711ac5a
    Author: Kathleen <[email protected]>
    Date:   Wed Jul 10 15:10:28 2024 -0400

        Improving the KL/AT in Phaors

    commit a687f30
    Author: Kathleen <[email protected]>
    Date:   Wed Jul 10 12:32:26 2024 -0400

        Modified predicates affected by biolink:binds

    commit e44cae6
    Merge: 7ba9538 fa8ebf0
    Author: Evan Morris <[email protected]>
    Date:   Wed Jun 26 16:38:02 2024 -0400

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

        Update requirements.txt

    commit fa8ebf0
    Author: beasleyjonm <[email protected]>
    Date:   Wed Jun 26 16:37:03 2024 -0400

        Update requirements.txt

        Updated requests 2.32.0 -> 2.32.3

commit 1f01b43
Merge: ec6b7d8 734cc6e
Author: Evan Morris <[email protected]>
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 734cc6e
Author: Evan Morris <[email protected]>
Date:   Fri Jul 19 14:32:02 2024 -0400

    bumping parsing versions for binds refactor parsers

commit ec6b7d8
Merge: e44cae6 00c6627
Author: Evan Morris <[email protected]>
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 00c6627
Author: Evan Morris <[email protected]>
Date:   Fri Jul 19 14:26:48 2024 -0400

    bumping parsing version

commit 766c5b7
Author: eKathleenCarter <[email protected]>
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 4cb0188
Author: eKathleenCarter <[email protected]>
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 711ac5a
Author: Kathleen <[email protected]>
Date:   Wed Jul 10 15:10:28 2024 -0400

    Improving the KL/AT in Phaors

commit a687f30
Author: Kathleen <[email protected]>
Date:   Wed Jul 10 12:32:26 2024 -0400

    Modified predicates affected by biolink:binds

commit e44cae6
Merge: 7ba9538 fa8ebf0
Author: Evan Morris <[email protected]>
Date:   Wed Jun 26 16:38:02 2024 -0400

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

    Update requirements.txt

commit fa8ebf0
Author: beasleyjonm <[email protected]>
Date:   Wed Jun 26 16:37:03 2024 -0400

    Update requirements.txt

    Updated requests 2.32.0 -> 2.32.3

commit 8ea9ecb
Author: Evan Morris <[email protected]>
Date:   Wed Jun 5 15:01:41 2024 -0400

    switching to pypi version of robokop-genetics

commit 86cf66a
Author: Evan Morris <[email protected]>
Date:   Tue Jun 4 12:46:18 2024 -0400

    updating bl version

commit 0d72f7c
Author: Evan Morris <[email protected]>
Date:   Tue May 28 12:02:05 2024 -0400

    updating release actions to new versions

commit 5678229
Author: Evan Morris <[email protected]>
Date:   Tue May 28 12:00:17 2024 -0400

    updating dockerfile and docker compose for neo4j 5, making docker platform an env var instead of hard coded

commit 905d6f7
Author: Evan Morris <[email protected]>
Date:   Tue May 28 11:09:30 2024 -0400

    updating neo4j tools for neo4j 5

commit 2bad6d3
Author: Evan Morris <[email protected]>
Date:   Tue May 28 11:08:47 2024 -0400

    making it so that specific subgraph sources matter for determining whether on-disk merge is needed

commit 1a2a5fb
Author: Evan Morris <[email protected]>
Date:   Tue May 28 11:06:03 2024 -0400

    moved NormalizationScheme into normalization file, altered subgraph metadata to be a metadata object not just dict

commit ef231fc
Author: beasleyjonm <[email protected]>
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.

commit cc81717
Author: Evan Morris <[email protected]>
Date:   Tue May 21 15:29:50 2024 -0400

    bumping versions of all dependencies

commit 7ba9538
Merge: 69a9d5c 4a0236e
Author: Evan Morris <[email protected]>
Date:   Tue May 21 14:46:17 2024 -0400

    Merge pull request #229 from RobokopU24/dependabot/pip/requests-2.32.0

    Bump requests from 2.31.0 to 2.32.0

commit 4a0236e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue May 21 08:27:19 2024 +0000

    ---
    updated-dependencies:
    - dependency-name: requests
      dependency-type: direct:production
    ...

    Signed-off-by: dependabot[bot] <[email protected]>

commit 69a9d5c
Merge: 67a5dbf 3cfa692
Author: Evan Morris <[email protected]>
Date:   Fri May 17 10:11:55 2024 -0400

    Merge pull request #228 from RobokopU24/deployment-updates

    Deployment updates

commit 3cfa692
Author: Evan Morris <[email protected]>
Date:   Tue May 14 13:11:21 2024 -0400

    adding error checking for output_format==None

commit 3af2ee2
Author: Evan Morris <[email protected]>
Date:   Tue May 14 12:48:01 2024 -0400

    improving output_format parsing

commit 2bf5721
Author: Evan Morris <[email protected]>
Date:   Tue May 14 12:46:29 2024 -0400

    removing jsonl which does nothing

commit bc3779b
Author: Evan Morris <[email protected]>
Date:   Tue May 14 12:45:22 2024 -0400

    fixing ubergraph source id

commit 55b48c3
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:34:48 2024 -0400

    adding redundant jsonl output

commit d0cf880
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:31:49 2024 -0400

    adding option for redundant edge kg file output to the graph spec

commit aa8125b
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:23:55 2024 -0400

    moving redundant kg generation into Common

commit 132221a
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:13:45 2024 -0400

    bail before generating dumps on QC failures, but don't fail based on infores identifiers

commit 0458291
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:54:59 2024 -0400

    adding rule mining kg

commit a26349f
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:51:13 2024 -0400

    pinning pharos version in the parser instead of graph specs

commit fac5c00
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:37:49 2024 -0400

    adding dug graph spec

commit d1a3612
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:37:41 2024 -0400

    adding a slim resources values option

commit 26aabc3
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:36:59 2024 -0400

    updating image and biolink versions

commit 67a5dbf
Merge: 63f33bd adf4b0f
Author: Evan Morris <[email protected]>
Date:   Fri May 10 15:59:41 2024 -0400

    Merge pull request #225 from RobokopU24/subclass_loops

    Subclass loops and qualifier merging

commit 63f33bd
Merge: 16b24ca 78eb0e0
Author: Evan Morris <[email protected]>
Date:   Fri May 10 15:59:19 2024 -0400

    Merge pull request #224 from RobokopU24/yobokop_go2gene_fix

    Fixed broken link for SGD Gene2GOTerm download file.

commit 78eb0e0
Author: Evan Morris <[email protected]>
Date:   Fri May 10 15:49:01 2024 -0400

    adding drugmechdb to baseline in yobokop

commit 0de4d26
Author: beasleyjonm <[email protected]>
Date:   Thu May 9 13:29:23 2024 -0400

    Fixed broken link for SGD Gene2GOTerm download file.

commit adf4b0f
Author: Evan Morris <[email protected]>
Date:   Fri May 3 15:53:24 2024 -0400

    added knowledge level and agent type to pharos

commit 5f3e996
Author: Evan Morris <[email protected]>
Date:   Fri May 3 14:32:12 2024 -0400

    added test for edge merging with qualifiers

commit 20220ec
Author: Evan Morris <[email protected]>
Date:   Fri May 3 13:33:50 2024 -0400

    implementation for having edge merging include qualifiers in matching key

commit c54edc8
Author: Evan Morris <[email protected]>
Date:   Fri May 3 13:28:18 2024 -0400

    implementing removal of subclass_of loop edges

commit 45d6ced
Author: Evan Morris <[email protected]>
Date:   Fri May 3 12:55:01 2024 -0400

    making public instance of drugcentral the default in the helm chart

commit 16b24ca
Merge: 6149183 1aec57c
Author: Evan Morris <[email protected]>
Date:   Fri May 3 12:34:32 2024 -0400

    Merge pull request #221 from RobokopU24/molepro

    A PR with way too many things in it

commit 1aec57c
Author: Evan Morris <[email protected]>
Date:   Thu May 2 14:20:38 2024 -0400

    removing specific version from logging error which conflicted with the actual default

commit 8168864
Author: Evan Morris <[email protected]>
Date:   Wed May 1 16:14:39 2024 -0400

    fixed missing prefix bug

commit df44bc6
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 15:15:03 2024 -0400

    bumping parsing version

commit 5968f3e
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 15:14:38 2024 -0400

    fixing agent type typo

commit 55b99b5
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 00:44:36 2024 -0400

    removing biolink prefix from edge and node properties, removing properties with no values from headers, improved comments

commit 759c513
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 00:23:52 2024 -0400

    adding some new env vars to the docker-compose

commit 335b91c
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 00:13:42 2024 -0400

    changing args for neo4j_dump so that the output directory and sources can be in different places

commit 26c4aa6
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 11:25:45 2024 -0400

    bumping vp parsing version

commit 81d790f
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 11:22:28 2024 -0400

    moving get_goa_edge_properties back outside of the class (to fix viral proteome)

commit fd9033a
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 10:08:14 2024 -0400

    fixing leftover staticmethod declaration

commit d3d5739
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:11:20 2024 -0400

    added publication nodes and edges

commit 4eca7be
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:10:30 2024 -0400

    added knowledge level and agent type, commented out extra gene groups file download

commit 24cebab
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:09:57 2024 -0400

    fixed bug with backwards increases_transport_of edges, added knowledge level and agent type

commit 555fb00
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:09:27 2024 -0400

    fixed missing publications and qualified_predicate bug, added knowledge level and agent type

commit b62a969
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:08:46 2024 -0400

    adding knowledge level and agent type, using some more constants

commit 214b104
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:08:20 2024 -0400

    adding knowledge level and agent type

commit 00503f9
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:06:29 2024 -0400

    added evidence code to knowledge level and agent type mapping

commit 2359a69
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:06:03 2024 -0400

    adding knowledge level and agent type, switching to use some constants

commit 08faa26
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:05:34 2024 -0400

    adding ability to fetch data from public DB, bumping source data version, adding knowledge level and agent type, adding drugbank knowledge source mapping and logging unmapped ks

commit 3e12154
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:04:05 2024 -0400

    adding knowledge level and agent type, general clean up

commit b9b07a8
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:03:04 2024 -0400

    adding knowledge level and agent type

commit 7785179
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:00:49 2024 -0400

    adding knowledge level and agent type, a bit of general clean up

commit b679768
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 03:59:19 2024 -0400

    fixing extra quote and commenting out drugmechdb until we decide to put it on automat

commit e16628d
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 03:56:25 2024 -0400

    adding predicate counts organized by knowledge source to metadata

commit 8df1571
Merge: cb3c2d2 fc1786e
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 01:35:51 2024 -0400

    Merge remote-tracking branch 'origin/DrugMechDBfulldataparser' into molepro

commit fc1786e
Author: beasleyjonm <[email protected]>
Date:   Wed Apr 10 15:08:49 2024 -0400

    Update loadDrugMechDB.py

    Changed "qualifier_predicate" to "qualified_predicate"

commit a9be99f
Author: beasleyjonm <[email protected]>
Date:   Wed Apr 10 15:08:04 2024 -0400

    Update drugmechdb_predicate_map.json

    Changed "qualifier_predicate" to "qualified_predicate"

commit cb3c2d2
Author: Evan Morris <[email protected]>
Date:   Mon Apr 8 15:53:47 2024 -0400

    moving biolink prefix mapping to bl_utils, removing some obsolete workarounds for biolink prefix / IRI mappings

commit 2f295b3
Author: Evan Morris <[email protected]>
Date:   Mon Apr 8 11:08:54 2024 -0400

    fixed data_services env var

commit 63aac81
Author: beasleyjonm <[email protected]>
Date:   Mon Apr 8 00:56:02 2024 -0400

    Updated parser to consolidate all relevant drugmechdb path ids into list on unique edges.

commit c16aa70
Author: beasleyjonm <[email protected]>
Date:   Sun Apr 7 01:04:17 2024 -0400

    Updated parser to parse every edge in the original db. Manually mapped un-normalized ids.

commit 632db5c
Author: Evan Morris <[email protected]>
Date:   Fri Apr 5 17:35:49 2024 -0400

    adding knowledge level and agent type

commit 51881ad
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 15:08:57 2024 -0400

    updating some requirement versions and changing everything to specific pinned versions

commit 2a00d29
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 15:08:27 2024 -0400

    adding bl_version to helm charts and removing unnecessary neo4j password

commit 9c0ea2b
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 15:06:54 2024 -0400

    adding error checking and fallback for ssl issues

commit f3b1d37
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 14:19:09 2024 -0400

    switching to http due to ssl errors with the https

commit a83c7a8
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 11:50:32 2024 -0400

    bumping parsing versions

commit 5923994
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 11:49:30 2024 -0400

    adding error checking for fields coming from llm that aren't strings

commit 2730218
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 23:19:46 2024 -0400

    updating latest image

commit 88bf8fd
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 23:18:59 2024 -0400

    removing extra entity extractor graph

commit 0c245f9
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 23:18:08 2024 -0400

    updated for new data, added abstract id to entity extractor and changed over to csv format output

commit 3ee028a
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 22:34:49 2024 -0400

    making a couple env vars optional, adding name res endpoint as an env var

commit cde0bce
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 22:28:57 2024 -0400

    fixing bug where fetch retry didn't try to fetch for the same version as it tried

commit 996e8e4
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 22:28:00 2024 -0400

    adding litcoin from litcoin branches - merge was messy so new commits

commit fcaa439
Author: Evan Morris <[email protected]>
Date:   Thu Mar 21 16:07:58 2024 -0400

    updating version for monarch kg

commit 27d338b
Author: Evan Morris <[email protected]>
Date:   Thu Mar 21 16:06:25 2024 -0400

    adding aggregator knowledge source for cam kp

commit 54b8cc2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 15:11:16 2024 -0400

    forcing just one primary knowledge source instead of splitting

commit 837c339
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:56:22 2024 -0400

    updating with better defaults for sterling

commit 0aa6a2e
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:55:25 2024 -0400

    bumping requirements for bmt and jsonlines

commit e2c462a
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:54:42 2024 -0400

    making neo4j logs write to same scratch directory (hoping to solve permissions issues)

commit 19423b2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:53:33 2024 -0400

    improving neo4j dump generation options and logging from cli entrypoint

commit be5ba67
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:27:35 2024 -0400

    cleaning up qualifier value ancestors and making sure the edge with no qualifiers gets written

commit 859a9eb
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 06:10:38 2024 -0400

    making BL_VERSION configurable with an env var and enforced with bmt

commit 49e55d1
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 06:02:09 2024 -0400

    refactoring for performance and cleanup, now handles cases with direction but no aspect, using constants for qualifiers, make tqdm optional

commit 5574f28
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 05:58:09 2024 -0400

    removing extra empty properties, handling multiple primary knowledge sources

commit cf541c2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 05:55:13 2024 -0400

    making it so that invalid infores ids don't crash normalization again

commit 74f0b02
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:27:08 2024 -0400

    Squashed commit of the following:

    commit 28fe0f5
    Author: james0032 <[email protected]>
    Date:   Fri Mar 8 21:44:56 2024 +0000

        predicate format corrected

    commit b0ba22d
    Merge: 9bf375c 421a9a1
    Author: James Chung <[email protected]>
    Date:   Wed Nov 22 10:55:22 2023 -0500

        merge for snakify curie

    commit 9bf375c
    Author: James Chung <[email protected]>
    Date:   Wed Nov 22 10:43:25 2023 -0500

        QUALIFIED_PREDICATE

    commit 421a9a1
    Author: Evan Morris <[email protected]>
    Date:   Fri Nov 17 14:15:27 2023 -0500

        converting predicates from bmt get_ancestors to snakified biolink curies

    commit e92b623
    Author: James Chung <[email protected]>
    Date:   Fri Aug 25 14:56:27 2023 -0400

        First version of redundant graph generator

commit 1ae25c9
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:14:32 2024 -0400

    first pass at molepro parser, really the first implementation of a generic parser

commit 36b8463
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:13:05 2024 -0400

    adding the other form of synonym property

commit 373af9c
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:12:38 2024 -0400

    adding a way to write just one normalized node

commit 6a16c0e
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:12:07 2024 -0400

    adding more groupings

commit a0dffb3
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:41:59 2024 -0400

    adding more node constants and rearranging some, removing biolink from knowledge source attributes

commit 53b3375
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:14:02 2024 -0400

    cleaning up unnecessary defaults for nodes, this is functionally equivalent

commit fda2bf2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:13:22 2024 -0400

    updating binding to use appropriate edge property constants

commit 1f0e6f4
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:12:25 2024 -0400

    removing obsolete imports

commit 5d0e150
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:11:50 2024 -0400

    reorganized constants: moved node_types.py into biolink_constants.py, added lots of edge properties, changed from using ROOT_ENTITY to just NAMED_THING
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EvanDietzMorris committed Sep 11, 2024
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20 changes: 10 additions & 10 deletions .github/workflows/release.yml
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Expand Up @@ -13,27 +13,27 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out the repo
uses: actions/checkout@v2
uses: actions/checkout@v4
- name: Get the version
id: get_version
run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\//}
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
with:
images:
ghcr.io/${{ github.repository }}
- name: Login to ghcr
uses: docker/login-action@v1
uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
with:
images:
ghcr.io/${{ github.repository }}
- name: Push to GitHub Packages
uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
with:
context: .
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
build-args: VERSION=${{ steps.get_version.outputs.VERSION }}
build-args: VERSION=${{ steps.get_version.outputs.VERSION }}
3 changes: 3 additions & 0 deletions .gitignore
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@@ -0,0 +1,3 @@
# pycache
**/__pycache__
*.pycache
192 changes: 192 additions & 0 deletions Common/biolink_constants.py
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@@ -0,0 +1,192 @@
# A collection of constants for biolink variable names and types
# TODO it would be nice to verify these with bmt
NAMED_THING = 'biolink:NamedThing'
BIOLOGICAL_ENTITY = 'biolink:BiologicalEntity'
DISEASE_OR_PHENOTYPIC_FEATURE = 'biolink:DiseaseOrPhenotypicFeature'
DISEASE = 'biolink:Disease'
PHENOTYPIC_FEATURE = 'biolink:PhenotypicFeature'
MOLECULAR_ENTITY = 'biolink:MolecularEntity'
CHEMICAL_SUBSTANCE = 'biolink:ChemicalSubstance'
DRUG = 'biolink:Drug'
METABOLITE = 'biolink:Metabolite'
ANATOMICAL_ENTITY = 'biolink:AnatomicalEntity'
GENE = 'biolink:Gene'
GENE_PRODUCT = 'biolink:GeneProduct'
GENE_OR_GENE_PRODUCT = 'biolink:GeneOrGeneProduct'
SEQUENCE_VARIANT = 'biolink:SequenceVariant'
BIOLOGICAL_PROCESS_OR_ACTIVITY = 'biolink:BiologicalProcessOrActivity'
MOLECULAR_ACTIVITY = 'biolink:MolecularActivity'
BIOLOGICAL_PROCESS = 'biolink:BiologicalProcess'
PATHWAY = 'biolink:Pathway'
CELLULAR_COMPONENT = 'biolink:CellularComponent'
CELL = 'biolink:Cell'
GROSS_ANATOMICAL_STRUCTURE = 'biolink:GrossAnatomicalStructure'
GENETIC_CONDITION = 'biolink:GeneticCondition'
UNSPECIFIED = 'biolink:Unspecified'
GENE_FAMILY = 'biolink:GeneFamily'
GENOMIC_ENTITY = 'biolink:GenomicEntity'
FOOD = 'biolink:Food'
MACROMOLECULAR_COMPLEX = 'biolink:MacromolecularComplex'

# properties on nodes
NODE_ID = 'id'
NODE_TYPES = 'category'
NAME = 'name'
SYNONYM = 'synonym'
TRADE_NAME = 'trade_name'
CHEMICAL_ROLE = 'chemical_role'
HAS_CHEMICAL_FORMULA = 'has_chemical_formula'
IN_TAXON = 'in_taxon'
ROUTES_OF_DELIVERY = 'routes_of_delivery'
SYMBOL = 'symbol'


# properties on edges
EDGE_ID = 'id'
SUBJECT_ID = 'subject'
OBJECT_ID = 'object'
PREDICATE = 'predicate'
PRIMARY_KNOWLEDGE_SOURCE = 'primary_knowledge_source'
AGGREGATOR_KNOWLEDGE_SOURCES = 'aggregator_knowledge_source'
SUPPORTING_DATA_SOURCE = 'supporting_data_source'
P_VALUE = 'p_value'
ADJUSTED_P_VALUE = 'adjusted_p_value'
AGENT_TYPE = 'agent_type'
KNOWLEDGE_LEVEL = 'knowledge_level'
MAX_RESEARCH_PHASE = 'max_research_phase'
HAS_SUPPORTING_STUDY_RESULT = 'has_supporting_study_result'

# enums for knowledge level
KNOWLEDGE_ASSERTION = 'knowledge_assertion'
LOGICAL_ENTAILMENT = 'logical_entailment'
PREDICATION = 'prediction'
STATISTICAL_ASSOCIATION = 'statistical_association'
OBSERVATION = 'observation'
NOT_PROVIDED = 'not_provided'

# enums for agent type
MANUAL_AGENT = 'manual_agent'
AUTOMATED_AGENT = 'automated_agent'
DATA_PIPELINE = 'data_analysis_pipeline'
COMPUTATIONAL_MODEL = 'computational_model'
TEXT_MINING_AGENT = 'text_mining_agent'
IMAGE_PROCESSING_AGENT = 'image_processing_agent'
MANUAL_VALIDATION_OF_AUTOMATED_AGENT = 'manual_validation_of_automated_agent'

# properties that could be on edges or nodes (I think?)
DESCRIPTION = 'description'
PUBLICATIONS = 'publications'
XREFS = 'xref'

FDA_APPROVAL_STATUS = 'highest_FDA_approval_status'
MECHANISM_OF_ACTION = 'mechanism_of_action'

# these aren't in biolink, but we use them on edges
AFFINITY = 'affinity'
AFFINITY_PARAMETER = 'affinity_parameter'
INFORMATION_CONTENT = 'information_content'


# edge qualifier properties
ANATOMICAL_CONTEXT_QUALIFIER = 'anatomical_context_qualifier'
CAUSAL_MECHANISM_QUALIFIER = 'causal_mechanism_qualifier'
CONTEXT_QUALIFIER = 'context_qualifier'
DERIVATIVE_QUALIFIER = 'derivative_qualifier'
OBJECT_ASPECT_QUALIFIER = 'object_aspect_qualifier'
OBJECT_DERIVATIVE_QUALIFIER = 'object_derivative_qualifier'
OBJECT_DIRECTION_QUALIFIER = 'object_direction_qualifier'
OBJECT_FORM_OR_VARIANT_QUALIFIER = 'object_form_or_variant_qualifier'
OBJECT_PART_QUALIFIER = 'object_part_qualifier'
QUALIFIED_PREDICATE = 'qualified_predicate'
SPECIES_CONTEXT_QUALIFIER = 'species_context_qualifier'
SUBJECT_ASPECT_QUALIFIER = 'subject_aspect_qualifier'
SUBJECT_DERIVATIVE_QUALIFIER = 'subject_derivative_qualifier'
SUBJECT_DIRECTION_QUALIFIER = 'subject_direction_qualifier'
SUBJECT_FORM_OR_VARIANT_QUALIFIER = 'subject_form_or_variant_qualifier'
SUBJECT_PART_QUALIFIER = 'subject_part_qualifier'


# this should probably be changed to the valid biolink synonym property but don't want to break downstream tools yet
SYNONYMS = 'equivalent_identifiers'

BIOLINK_NODE_PROPERTIES = [
NODE_ID,
NODE_TYPES,
NAME,
DESCRIPTION,
PUBLICATIONS,
XREFS,
SYNONYM,
TRADE_NAME,
CHEMICAL_ROLE,
HAS_CHEMICAL_FORMULA,
FDA_APPROVAL_STATUS,
MECHANISM_OF_ACTION,
IN_TAXON,
ROUTES_OF_DELIVERY,
SYMBOL
]

REQUIRED_NODE_PROPERTIES = [
NODE_ID,
NODE_TYPES,
NAME
]

BIOLINK_EDGE_PROPERTIES = [
EDGE_ID,
SUBJECT_ID,
OBJECT_ID,
PREDICATE,
PRIMARY_KNOWLEDGE_SOURCE,
AGGREGATOR_KNOWLEDGE_SOURCES,
SUPPORTING_DATA_SOURCE,
PUBLICATIONS,
SYNONYMS,
DESCRIPTION,
XREFS,
P_VALUE,
ADJUSTED_P_VALUE,
AGENT_TYPE,
FDA_APPROVAL_STATUS,
KNOWLEDGE_LEVEL,
MECHANISM_OF_ACTION,
MAX_RESEARCH_PHASE,
HAS_SUPPORTING_STUDY_RESULT,
# qualifiers
ANATOMICAL_CONTEXT_QUALIFIER,
CAUSAL_MECHANISM_QUALIFIER,
CONTEXT_QUALIFIER,
DERIVATIVE_QUALIFIER,
OBJECT_ASPECT_QUALIFIER,
OBJECT_DERIVATIVE_QUALIFIER,
OBJECT_DIRECTION_QUALIFIER,
OBJECT_FORM_OR_VARIANT_QUALIFIER,
OBJECT_PART_QUALIFIER,
QUALIFIED_PREDICATE,
SPECIES_CONTEXT_QUALIFIER,
SUBJECT_ASPECT_QUALIFIER,
SUBJECT_DERIVATIVE_QUALIFIER,
SUBJECT_DIRECTION_QUALIFIER,
SUBJECT_FORM_OR_VARIANT_QUALIFIER,
SUBJECT_PART_QUALIFIER,
]

REQUIRED_EDGE_PROPERTIES = [
SUBJECT_ID,
OBJECT_ID,
PREDICATE,
PRIMARY_KNOWLEDGE_SOURCE
]

BIOLINK_PROPERTIES_THAT_ARE_LISTS = [
SYNONYMS,
SYNONYM,
NODE_TYPES,
AGGREGATOR_KNOWLEDGE_SOURCES,
PUBLICATIONS,
XREFS
]

# biolink compliant predicates
SUBCLASS_OF = 'biolink:subclass_of'
28 changes: 27 additions & 1 deletion Common/biolink_utils.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,19 @@
import requests
import yaml
import os

from bmt import Toolkit


BIOLINK_MODEL_VERSION = os.environ.get("BL_VERSION", "4.1.6")
BIOLINK_MODEL_SCHEMA_URL = f"https://raw.githubusercontent.com/biolink/biolink-model/v{BIOLINK_MODEL_VERSION}/biolink-model.yaml"
PREDICATE_MAP_URL = f"https://raw.githubusercontent.com/biolink/biolink-model/v{BIOLINK_MODEL_VERSION}/predicate_mapping.yaml"


def get_biolink_model_toolkit():
return Toolkit(schema=BIOLINK_MODEL_SCHEMA_URL, predicate_map=PREDICATE_MAP_URL)


map_data = {
"attribute_type_map": {
"`biolink:primary_knowledge_source`": "biolink:primary_knowledge_source",
Expand All @@ -26,7 +37,7 @@
class BiolinkUtils:

def __init__(self):
self.toolkit = Toolkit()
self.toolkit = get_biolink_model_toolkit()

def find_biolink_leaves(self, biolink_concepts: set):
"""
Expand Down Expand Up @@ -136,6 +147,21 @@ def predicate_has_qualifiers(self, predicate):
return False


BIOLINK_MAPPING_CHANGES = {
'KEGG': 'http://identifiers.org/kegg/',
'NCBIGene': 'https://identifiers.org/ncbigene/'
}


def get_biolink_prefix_map():
response = requests.get(f'https://raw.githubusercontent.com/biolink/biolink-model/v{BIOLINK_MODEL_VERSION}/project/prefixmap/biolink_model_prefix_map.json')
if response.status_code != 200:
response.raise_for_status()
biolink_prefix_map = response.json()
biolink_prefix_map.update(BIOLINK_MAPPING_CHANGES)
return biolink_prefix_map


INFORES_STATUS_INVALID = 'invalid'
INFORES_STATUS_DEPRECATED = 'deprecated'
INFORES_STATUS_VALID = 'valid'
Expand Down
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