Evidence parsers for the 24.12 Platform release

What's Changed

• chore: prepare 24.06 release by @ireneisdoomed in #200
• feat: updating validation lab parser for the new data by @DSuveges in #192
• feat: integrate pharmacogenetics data by @ireneisdoomed in #185
• chore(deps): bump tqdm from 4.66.2 to 4.66.3 by @dependabot in #201
• chore(deps): bump certifi from 2024.2.2 to 2024.7.4 by @dependabot in #203
• chore(deps): bump urllib3 from 2.2.0 to 2.2.2 by @dependabot in #202
• fix: change variant field to geneticVariation in cancerBiomarkers parser by @vivienho in #204
• fix: update ValidationLab parser to split assessment field by newline by @vivienho in #205
• feat: added function to add variantId column to pharmagenetics dataset by @vivienho in #206
• fix(burden): minor bugs for data validation by @ireneisdoomed in #210
• feat(safety): add evidence from 38773351 by @ireneisdoomed in #208
• Changes made before running parsers for 24.09 release by @vivienho in #207
• fix(chembl): update stopReasonCategories file by @ireneisdoomed in #212
• revert(safety): revert 4773244 by @ireneisdoomed in #213
• fix(ppp): integrating PPP rules into snakemake pipeline by @DSuveges in #215
• Changes made to enable running parsers for 24.12 release by @vivienho in #217

New Contributors

• @vivienho made their first contribution in #204

Full Changelog: 2.3.1...2.4.0

Evidence parsers for the 24.06 Platform release

What's Changed

New features:

• feat: import_trait_mappings reads disease curation from configIl 2907 by @ireneisdoomed in #178
• Feature: Updating Project score datasource by @DSuveges in #186
• feat: updating ot crispr parser to handle replicate screens by @DSuveges in #187
• feat(burden): drop evidence on categorical traits by @ireneisdoomed in #196
• feat(burden): update AZ config to newer release + include associations from synonymous models by @ireneisdoomed in #195
• feat: add links to the AZ evidence + other release things by @ireneisdoomed in #199
• Adding gene essentiality parser by @DSuveges in #159

Fixes and refactors:

• chore(safety): remove human applicability flag by @ireneisdoomed in #189
• refactor (genetics parser): changing logic how QTLs processed by @DSuveges in #190
• refactor(Gene2Phenotype): making code agnostic about the number of panels provided by @DSuveges in #194
• chore(configuration): adding new panelapp file to configuration by @DSuveges in #197

Updated dependencies:

• build(deps): bump aiohttp from 3.8.5 to 3.9.0 by @dependabot in #177
• build(deps): bump gitpython from 3.1.36 to 3.1.37 by @dependabot in #173
• build(deps): bump urllib3 from 1.26.16 to 1.26.18 by @dependabot in #174
• build(deps): bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in #182
• build(deps): bump aiohttp from 3.9.0 to 3.9.2 by @dependabot in #184
• build(deps): bump gitpython from 3.1.36 to 3.1.41 by @dependabot in #183
• build(deps): bump requests from 2.31.0 to 2.32.0 by @dependabot in #198
• build(deps): bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in #193

Full Changelog: 2.3.0...2.3.1

Evidence parsers for the 23.12 release

What's Changed

• New parser: Direct ingestion of GTEx V8 for preparation of baseline expression data by @tskir in #172
• Changes for Platform release 23.12 by @tskir in #175

Full Changelog: 2.2.0...2.3.0

Evidence parsers for the 23.09 release

What's Changed

• Accommodate "Uncategorised" ChEMBL label by @ireneisdoomed in #154
• Update dependency versions to resolve security issues by @tskir in #155
• Adding parser for ot_crispr dataset by @DSuveges in #117
• Adding validation lab parser + parameter file. by @DSuveges in #115
• Adding parser and parameter files for encore by @DSuveges in #116
• Ds 2911 ppp snakemake by @DSuveges in #157
• Adding parsers to generate evidence based on publicly available CRISPR screens by @DSuveges in #158
• Updates of the parsers for the 23.06 release by @DSuveges in #160
• build(deps): bump requests from 2.27.1 to 2.31.0 by @dependabot in #161
• Updating parser for 2023.05 Intogen release. by @DSuveges in #162
• Update crispr parser by @DSuveges in #163
• build(deps): bump certifi from 2022.12.7 to 2023.7.22 by @dependabot in #164
• Add literature reference to Genebass and Finngen evidence by @ireneisdoomed in #165
• build(deps): bump gitpython from 3.1.30 to 3.1.32 by @dependabot in #168
• P&Ds tables parser by @ireneisdoomed in #166
• Changes related 23.09 by @ireneisdoomed in #167
• Changes for release 23.09 by @tskir in #170

Full Changelog: 2.1.1...2.2.0

Evidence parsers for release 23.02

What's Changed

• Remove EPMC evidence generation by @ireneisdoomed in #139
• Bump protobuf from 4.21.5 to 4.21.6 by @dependabot in #140
• Remove duplicated evidence from IMPC by @tskir in #141
• ChEMBL parser by @ireneisdoomed in #142
• Bump pyspark from 3.1.3 to 3.2.2 by @dependabot in #143
• update curation and schema versions by @ireneisdoomed in #145
• Genebass effect sizes reported as betas by @ireneisdoomed in #146
• build(deps): bump certifi from 2022.6.15 to 2022.12.7 by @dependabot in #147
• Bump jupyter-core from 4.11.1 to 4.11.2 by @dependabot in #144
• feat: adding QTL effect size to genetics by @DSuveges in #148
• Include AOPWIKI datasource by @ireneisdoomed in #149
• Minor bug in the Genebass parser by @ireneisdoomed in #150
• feat: updating config for the 23.02 release by @DSuveges in #151
• Fixing panelapp parser to make sure it won't break if panel is retired by @DSuveges in #152
• Minor fixes on the Safety and Burden parsers by @ireneisdoomed in #153

Full Changelog: 2.1.0...2.1.1

Evidence parsers for release 22.09

Quite many smaller changes since the past release, however the gene burden parser is a new module.

What's Changed

• Update gene2phenotype parser for new field names. by @DSuveges in #107
• Updating the TEP parser by @DSuveges in #108
• Add safetyLiabilities module by @ireneisdoomed in #109
• Apply IMPC threshold in the evidence generation by @ireneisdoomed in #112
• New module: ChEMBL.py by @ireneisdoomed in #111
• Branch collecting code for parsing data for the partner preview. by @DSuveges in #110
• Add notebook that processes P&Ds dump and generates probes evidence by @ireneisdoomed in #113
• Remove the PheWAS Catalog data source by @tskir in #118
• Updating the logging design of the evidence generation pipeline by @tskir in #120
• Updating the pipeline to generate local files only by @tskir in #119
• 22.04 configuration by @ireneisdoomed in #122
• Parse AZ PheWAS Portal and Regeneron data for gene_burden by @ireneisdoomed in #121
• Gene2Phenotype updates by @DSuveges in #123
• Making EFO optional for evidence parsers by @DSuveges in #124
• Il 22.04 by @ireneisdoomed in #125
• Updated pathways to Reactome mappings by @ireneisdoomed in #126
• Import manual gene burden curation to the evidence generation by @ireneisdoomed in #127
• Remove REGENERON parsing by @ireneisdoomed in #129
• Fixes for the release 22.06 by @DSuveges in #128
• Add Genebass parser by @ireneisdoomed in #130
• Add year of publication to the EPMC evidence by @ireneisdoomed in #133
• Il-2687 by @ireneisdoomed in #132
• Get rid of Conda in favour of PIP by @tskir in #134
• Updating pyspark version. by @DSuveges in #136
• Il 2701 by @ireneisdoomed in #137
• 2209 data release by @DSuveges in #138

Full Changelog: 2.0.0...2.1.0

Support for new schema + Snakemake pipeline

Large number of significant changes were rolled out in this release.

• All parsers were re-written to support the slimmed-down evidence schema. The supported schema in this release: v.2.10
• New evidence parsers were added: Orphanet, CancerBiomarkers, EPMC
• New datatype: the phenodigm parser now generates the mouse model dataset for the target annotation as well
• New datatype: the target enabling packages (TEP) target annotation dataset
• All parsers were collated into a single Snakemake pipeline, that generates, validates the output against the schema then uploads to the storage location
• The running environment was cleaned to make the requirements more manageable and easier to reproduce
• The documentation of the repo now updated to reflect all these changes and now provides instructions on how to create a suitable VM instance and how to run the pipeline. Individual parsers are no longer described in the readme, to more information on those, please look for docstrings

1.0.1

Small changes to PhenoDigm parser and related files:

• gz extension added to output file as it is compressed.
• README update to explain that the last step in MouseModels.py (-w) may fail if the main step and the upload are run on different days because the date is automatically added to the file name.

1.0.0

Production version containing the necessary modules to parse the data from our internal datasources. This version corresponds to the usage of the JSON schema up to its version 1.7.5.