Merge pull request #11 from opentargets/il-2701

New burden curation, improved documentation and bug fixes
opentargets · Sep 8, 2022 · 412f207 · 412f207
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diff --git a/README.md b/README.md
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 This repository contains a collection of different manual annotations produced within the [Open Targets organisation](https://www.opentargets.org).
 
-## Content
-- **Mappings**. Label to ontology mappings of different nature:
-  - [biosystem](mappings/biosystem).
-    - Labels of anatomical structures such as tissues, organs or systems are mapped to the [UBERON ontology](https://uberon.github.io).
-    - Labels of cell lines are mapped to the [Cell Line Ontology](http://www.clo-ontology.org).
-  - [disease](mappings/disease). Labels of diseases mapped to the [EFO ontology](https://www.ebi.ac.uk/efo/). This directory is pending to be harmonised under a common file (see [#1400](https://github.com/opentargets/platform/issues/1400) for context).
-
-- **Target Safety annotation**. 
-  Manual curation of experimental data and insights from publications and other well-known sources of target safety and toxicity data, including the Tox21 database.
-
-  The annotation related to `safety_risks.tsv` and `adverse_effects.tsv` is currently being fed to the Platform's pipelines, whereas `experimental_toxicity.tsv` has been discontinued in favour of a new pipeline that processes [ToxCast data files](https://www.epa.gov/chemical-research/toxcast-data-accessing-toxcast-data-and-scenarios-exploring-data).
-
-- **Gene Burden annotation**.
-  Manual curation of burden tests from key publications and resources.
-
-  - Schizophrenia Consortium. Associations of 9 genes with schizophrenia. The data is pulled from their downloads page (https://schema.broadinstitute.org/downloads).
-  - Epi25 Consortium. Associations of 2 genes with epilepsy. The data is pulled from their downloads page (https://epi25.broadinstitute.org/downloads).
-  - OTAR022 Metabolomics study. Associations of 21 genes with different metabolomics measurements. The data is pulled from 2 sites:
-    - Table 1 of their manuscript provides the key metrics.
-    - The sheet named "strongest gene/metabolite" in the Supplementary Table 5 provides annotation of nº samples.
-  - CKD Publication. Associations of 3 genes with chronic kidney disease. The data is pulled from 2 sites:
-    - Table 2 of their publication (https://jasn.asnjournals.org/content/jnephrol/30/6/1109.full.pdf?with-ds=yes).
-    - Supplementary Table 5 provides annotation of nº samples.
-  - Autism Sequencing Consortium. Associations of 102 genes with autism. The data is pulled from the Supplementary Table 2 in their publication (https://www.sciencedirect.com/science/article/pii/S0092867419313984#mmc2).
-  - REGENERON. Associations of 497 genes with traits from the UK Biobank. The data has been parsed from the Supplementary Table 2, 3, and 4 of their publication (https://www.nature.com/articles/s41586-021-04103-z) + the mappings done by GWAS Catalog.
+See instructions for:
+- [Mappings](docs/mappings.md)
+- [Gene Burden annotation](docs/gene_burden.md)
+- [Target Safety annotation](docs/target_safety.md)
diff --git a/docs/gene_burden.md b/docs/gene_burden.md
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+## Gene Burden annotation
+
+Manual curation of burden tests from key publications and resources.
+
+### Schizophrenia Consortium
+Associations of 9 genes with schizophrenia. The data is pulled from their downloads page (https://schema.broadinstitute.org/downloads).
+
+### Epi25 Consortium
+Associations of 2 genes with epilepsy. The data is pulled from their downloads page (https://epi25.broadinstitute.org/downloads).
+
+
+### OTAR022 Metabolomics study
+Associations of 21 genes with different metabolomics measurements. The data is pulled from 2 sites:
+    - Table 1 of their manuscript provides the key metrics.
+    - The sheet named "strongest gene/metabolite" in the Supplementary Table 5 provides annotation of nº samples.
+
+### CKD Publication
+Associations of 3 genes with chronic kidney disease. The data is pulled from 2 locations:
+    - Table 2 of their publication (https://jasn.asnjournals.org/content/jnephrol/30/6/1109.full.pdf?with-ds=yes).
+    - Supplementary Table 5 provides annotation of nº samples.
+### Autism Sequencing Consortium
+Associations of 102 genes with autism. The data is pulled from the Supplementary Table 2 in their publication (https://www.sciencedirect.com/science/article/pii/S0092867419313984#mmc2).
+
+### REGENERON
+Associations of 497 genes with traits from the UK Biobank. The data has been parsed from the Supplementary Table 2, 3, and 4 of their publication (https://www.nature.com/articles/s41586-021-04103-z) + the mappings done by GWAS Catalog.
+
+### Autism Publication from the SPARK cohort
+Associations of 60 genes with autism were identified by analyzing de novo and rare inherited variants from WES and WGS data. The data is pulled from the results of the meta analysis described in the Supplementary Table 9 of their publication (https://www.nature.com/articles/s41588-022-01148-2). Only associations with a p-value < 2.5 × 10−6 are included.
+
+### Fat distributionn Publication
+16 genes associated with fat distribution (BMI-adjusted WHR) were identified by analysing missense variants from WES data. Most of them with a protective direction of effect. The data is pulled from the Table 1 of their publication (https://www.nature.com/articles/s41467-022-32398-7.pdf). Only associations with a p-value < 3.6 × 10−7 are included.
diff --git a/docs/mappings.md b/docs/mappings.md
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+## Mappings
+
+Label to ontology mappings of different nature:
+  - [biosystem](../mappings/biosystem).
+    - Labels of anatomical structures such as tissues, organs or systems are mapped to the [UBERON ontology](https://uberon.github.io).
+    - Labels of cell lines are mapped to the [Cell Line Ontology](http://www.clo-ontology.org).
+  - [disease](../mappings/disease). Labels of diseases mapped to the [EFO ontology](https://www.ebi.ac.uk/efo/). This directory is pending to be harmonised under a common file (see [#1400](https://github.com/opentargets/platform/issues/1400) for context).
diff --git a/docs/target_safety.md b/docs/target_safety.md
@@ -0,0 +1,5 @@
+## Target Safety annotation 
+
+Manual curation of experimental data and insights from publications and other well-known sources of target safety and toxicity data, including the Tox21 database.
+
+The annotation related to `safety_risks.tsv` and `adverse_effects.tsv` is currently being fed to the Platform's pipelines, whereas `experimental_toxicity.tsv` has been discontinued in favour of a new pipeline that processes [ToxCast data files](https://www.epa.gov/chemical-research/toxcast-data-accessing-toxcast-data-and-scenarios-exploring-data).