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Lincs #267

Merged
merged 6 commits into from
Dec 2, 2024
Merged

Lincs #267

merged 6 commits into from
Dec 2, 2024

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james0032
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Data stored on renci nfs. File path specified in parser.

Need review before completion of PR since no test ran for the new LICNS parser.

@beasleyjonm
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How did you obtain the LINCS files that are parsed here? I believe all of the LINCS data is dependent on cell line in which gene expression is measured, so I'm a little worried about saying a compound positively/negatively regulating some gene without providing the cell contexts in which it was measured.

@EvanDietzMorris
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The code looks great at a glance. I would probably delete some of the template comments, and it's also 2024 now ;)

But lets address JMs question before I start testing. Maybe we can use the anatomical context qualifier? The biolink docs actually mention a "experimental_context_qualifier" that has HeLa cells as the example, but I don't think that's actually in the model. I'm not sure if there is one for cell types otherwise.

@EvanDietzMorris
general clean up, fixing imports, removing template comments
46f8117
@EvanDietzMorris
fixing missing comma, making quote usage consistent
d2bead1
@EvanDietzMorris
fixing parser see commit description
3491e3f 
fixing several bugs and broken variable names
- fixing source data download location
- source data delimiter is comma not tab
- cleaning up properties (they need to be a dictionary, but node props were unnecessary anyway)

simplifying/fixing qualifier handling
- using predicates like RO:0002212 includes directionality and will normalize to qualified version, old implementation didn't work anyway, so this is better
@EvanDietzMorris
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We decided that addressing JM's concern was not possible with the source data provided, not going to include cell line information for now. The parser turned out to have several issues but I refactored it.

@EvanDietzMorris EvanDietzMorris merged commit 43874d9 into master Dec 2, 2024
1 check passed
@EvanDietzMorris EvanDietzMorris deleted the LINCS branch December 2, 2024 16:53
EvanDietzMorris added a commit that referenced this pull request Dec 19, 2024
@EvanDietzMorris
Squashed commit of the following:
40bbb95 
commit 502581d
Merge: 37ce60f 713f527
Author: Evan Morris <[email protected]>
Date:   Mon Dec 9 16:09:17 2024 -0500

    Merge pull request #265 from RobokopU24/add_GHaction

    Added a GitHub action...

commit 37ce60f
Merge: cd9a6c5 90c6231
Author: Evan Morris <[email protected]>
Date:   Mon Dec 9 16:07:41 2024 -0500

    Merge pull request #242 from RobokopU24/DnlRKorn-patch-4

    Fixed regex pattern issue in loadCTD.py

commit cd9a6c5
Merge: fcf6611 d63d4bb
Author: Evan Morris <[email protected]>
Date:   Mon Dec 9 16:04:50 2024 -0500

    Merge pull request #240 from RobokopU24/DnlRKorn-patch-2

    Dynamically load latest version of GenomeAlliance data

commit fcf6611
Merge: 43874d9 2a39e3a
Author: Evan Morris <[email protected]>
Date:   Mon Dec 9 16:00:09 2024 -0500

    Merge pull request #272 from RobokopU24/drugcentral-logscale-potencies

    Convert activity type mapping to log-scale.

commit 2a39e3a
Author: Evan Morris <[email protected]>
Date:   Tue Dec 3 12:18:36 2024 -0500

    making all instances of affinity/affinity parameter use the constants

commit 43874d9
Merge: 1867684 3491e3f
Author: Evan Morris <[email protected]>
Date:   Mon Dec 2 11:53:28 2024 -0500

    Merge pull request #267 from RobokopU24/LINCS

    Lincs

commit 3491e3f
Author: Evan Morris <[email protected]>
Date:   Mon Dec 2 11:51:21 2024 -0500

    fixing parser see commit description

    fixing several bugs and broken variable names
    - fixing source data download location
    - source data delimiter is comma not tab
    - cleaning up properties (they need to be a dictionary, but node props were unnecessary anyway)

    simplifying/fixing qualifier handling
    - using predicates like RO:0002212 includes directionality and will normalize to qualified version, old implementation didn't work anyway, so this is better

commit d2bead1
Author: Evan Morris <[email protected]>
Date:   Mon Dec 2 11:46:07 2024 -0500

    fixing missing comma, making quote usage consistent

commit 46f8117
Author: Evan Morris <[email protected]>
Date:   Tue Nov 26 10:56:15 2024 -0500

    general clean up, fixing imports, removing template comments

commit bc1e533
Author: beasleyjonm <[email protected]>
Date:   Mon Nov 25 16:38:44 2024 -0500

    Changed how activity parameters are described in log-scale.

commit 896e7af
Author: beasleyjonm <[email protected]>
Date:   Sat Nov 23 21:03:48 2024 -0500

    Convert activity type mapping to log-scale.

    The activity and potency types on Drug Central are log-scaled, so let's add the "p" in front of the activity types to reflect that.

commit 1867684
Merge: 52149ee 224d0b5
Author: beasleyjonm <[email protected]>
Date:   Thu Nov 21 12:19:08 2024 -0500

    Merge pull request #260 from RobokopU24/Issue257

    Add in all Monarch KG edge properties on ingest.

commit 52149ee
Merge: 6b8f389 7bbdc00
Author: beasleyjonm <[email protected]>
Date:   Thu Nov 21 12:14:21 2024 -0500

    Merge pull request #268 from RobokopU24/collapsed_qualifiers_kg

    Collapsed qualifiers kg

commit 7bbdc00
Author: beasleyjonm <[email protected]>
Date:   Thu Nov 7 12:35:08 2024 -0500

    Update collapse_qualifiers.py

commit 0839bcc
Author: Jon-Michael Beasley <[email protected]>
Date:   Thu Oct 31 13:42:46 2024 -0400

    Updated to fix code and add option to create collapsed qualifier Neo4j dump.

commit 0abf23c
Author: Jon-Michael Beasley <[email protected]>
Date:   Thu Oct 31 11:30:51 2024 -0400

    Added script to collapse object qualifier statements to the edge predicates.

commit 56e8b5b
Author: James Chung <[email protected]>
Date:   Thu Oct 31 08:14:15 2024 -0400

    return variable added

commit af3037a
Author: James Chung <[email protected]>
Date:   Wed Oct 30 23:35:18 2024 -0400

    LINCS parsers first try

commit b2eef57
Author: James Chung <[email protected]>
Date:   Wed Oct 30 23:34:52 2024 -0400

    LINCS parser first try

commit 713f527
Author: Kathleen Carter <[email protected]>
Date:   Tue Oct 29 10:51:47 2024 -0400

    setting environment variable

commit 26b1073
Author: Kathleen Carter <[email protected]>
Date:   Tue Oct 29 10:34:55 2024 -0400

    trying again with fresh eyes

commit 99fc5ee
Author: Kathleen Carter <[email protected]>
Date:   Tue Oct 29 10:29:49 2024 -0400

    trying again with fresh eyes

commit cc587c2
Author: Kathleen Carter <[email protected]>
Date:   Tue Oct 29 10:18:03 2024 -0400

    trying again with fresh eyes

commit 689d6e9
Author: Kathleen Carter <[email protected]>
Date:   Tue Oct 29 10:02:14 2024 -0400

    new script for action

commit ff79e6a
Author: Kathleen Carter <[email protected]>
Date:   Tue Oct 29 09:58:35 2024 -0400

    trying again with gresh eyes

commit 91d695e
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 17:23:43 2024 -0400

    error tracking/loggins

commit 7423a00
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 17:20:02 2024 -0400

    gitHub issues error

commit 24d3c91
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 17:16:19 2024 -0400

    split pull requests and issues

commit 736d185
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:58:49 2024 -0400

    split pull requests and issues

commit 55be1e5
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:50:50 2024 -0400

    lets try this with github-script@v6 instead...

commit 76bc6bb
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:44:57 2024 -0400

    fix double/single quote issue

commit 745d0c3
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:43:27 2024 -0400

    fix double/single quote issue

commit e887346
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:22:29 2024 -0400

    fix double/single quote issue

commit 979bc72
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:19:08 2024 -0400

    bump

commit ff0fc91
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:15:29 2024 -0400

    bump

commit 2ff1393
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:14:13 2024 -0400

    actually invoke python...

commit 3e95ae8
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:10:24 2024 -0400

    update to the latest versions of checkout and setup-python

commit e528db4
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:04:06 2024 -0400

    bump

commit 56e9918
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 15:01:21 2024 -0400

    Update requirements.txt

    Will need PyGithub for this...

commit 0d62da8
Author: Kathleen Carter <[email protected]>
Date:   Mon Oct 28 14:51:45 2024 -0400

    Added a GitHub action to automatically add the label "Biological Context QC" to issues and PRs that mention "predicate" or "biolink:"

    Automatically assign this event to Kathleen

commit 6b8f389
Merge: b5fcc32 f604791
Author: Evan Morris <[email protected]>
Date:   Thu Oct 24 15:40:23 2024 -0400

    Merge pull request #263 from RobokopU24/hgnc_fix

    updating HGNC file location and version date for new HGNC set up

commit f604791
Author: Evan Morris <[email protected]>
Date:   Thu Oct 24 13:23:43 2024 -0400

    updating HGNC file location and version date for new HGNC set up

commit b5fcc32
Merge: bc28a73 ff3099e
Author: Evan Morris <[email protected]>
Date:   Thu Oct 24 13:06:41 2024 -0400

    Merge pull request #262 from RobokopU24/dependabot/pip/mysql-connector-python-9.1.0

    Bump mysql-connector-python from 8.4.0 to 9.1.0

commit ff3099e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Oct 24 17:01:59 2024 +0000

    Bump mysql-connector-python from 8.4.0 to 9.1.0

    Bumps [mysql-connector-python](https://github.com/mysql/mysql-connector-python) from 8.4.0 to 9.1.0.
    - [Changelog](https://github.com/mysql/mysql-connector-python/blob/trunk/CHANGES.txt)
    - [Commits](mysql/mysql-connector-python@8.4.0...9.1.0)

    ---
    updated-dependencies:
    - dependency-name: mysql-connector-python
      dependency-type: direct:production
    ...

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

commit 224d0b5
Author: Daniel Korn <[email protected]>
Date:   Thu Sep 19 15:29:18 2024 -0400

    Added all available metadata present in Monarch KG to edge properties.

commit 5e9151b
Author: Daniel Korn <[email protected]>
Date:   Thu Sep 19 13:03:18 2024 -0400

    Changed Monarch KG ingest to automatically pull from the latest version. Also made process to check the metadata yaml file for the publishing date of the latest version.

commit 90c6231
Author: DnlRKorn <[email protected]>
Date:   Thu Jul 25 13:57:52 2024 -0400

    Fixed regex pattern issue in loadCTD.py

    Made the regex pattern a "raw" string.

commit d63d4bb
Author: DnlRKorn <[email protected]>
Date:   Thu Jul 25 11:48:15 2024 -0400

    Dynamically load latest version of GenomeAlliance data

    Previously genome alliance data was frozen to version 5.3.0; added some code to get the latest version instead.
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@james0032 @beasleyjonm @EvanDietzMorris