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| -rw-r--r-- | api/GN2-REST-API.md | 41 | ||||
| -rw-r--r-- | story-boards/fetch-phenotype-data/index.md | 39 |
2 files changed, 79 insertions, 1 deletions
diff --git a/api/GN2-REST-API.md b/api/GN2-REST-API.md index fb6a691..17401f7 100644 --- a/api/GN2-REST-API.md +++ b/api/GN2-REST-API.md @@ -2,6 +2,29 @@ This document describes fetching data from GeneNetwork using the REST API. +Karl Broman wrote the [GNapi](https://github.com/kbroman/GNapi/blob/master/README.md) R package for accessing the GN API which allows convenient access: + +- `check_gn()` - Check connection. +- `list_species()` - List available species. +- `list_groups("drosophila")` - List available groups of datasets +- `list_datasets("BXD")` - List available datasets for a given group (here, `"BXD"`). +- `info_dataset("CB_M_1004_P")` - Get meta information about a data set. +- `info_datasets("B6D2F2")` - Get meta information about all data sets for a group. +- `info_pheno("BXD", "10038")` - Get summary information for a phenotype +- `get_pheno("BXD", "10646")` - Get phenotype values for a classical trait. +- `get_geno("BXD")` - Get genotypes for a group. +- `run_gemma("BXDPublish", "10015")` - Perform a genome scan with [gemma](https://github.com/genetics-statistics/GEMMA) +- `run_rqtl("BXDPublish", "10015")` - Perform a genome scan with [R/qtl](https://rqtl.org) +- `run_correlation("HC_M2_0606_P", "BXDPublish", "1427571_at")` - Finds traits that are correlated with a given trait. + +For further examples, see the [online +vignette](https://kbroman.org/GNapi/GNapi.html), which is also +available from within R: + +```r +vignette("GNapi") +``` + --- # Fetching Dataset/Trait info/data # --- @@ -24,7 +47,10 @@ curl http://genenetwork.org/api/v_pre1/species/mouse.json *For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* -## Fetch Groups/RISets ## +## Groups + +The data is organised by group (also a drop down menu on the GN search page). General information on groups can be found [here](http://gn1.genenetwork.org/mouseCross.html). + This query can optionally filter by species: @@ -87,6 +113,19 @@ curl http://genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv Returns a CSV file with sample/strain names as the columns and trait IDs as rows +## Phenotype matrix + +``` +curl https://genenetwork.org/api/v_pre1/sample_data/BXDPublish.csv > BXDPublish.csv +``` + +You should query the API to get more information. Something like this +for the BXD + +``` +curl https://genenetwork.org/api/v_pre1/datasets/mouse/bxd > bxd_datasets.json +``` + ## Fetch Sample Data for Single Trait ## ``` curl http://genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at diff --git a/story-boards/fetch-phenotype-data/index.md b/story-boards/fetch-phenotype-data/index.md new file mode 100644 index 0000000..bd0b8d1 --- /dev/null +++ b/story-boards/fetch-phenotype-data/index.md @@ -0,0 +1,39 @@ +# Storyboard: fetch phenotype data from GeneNetwork + +GeneNetwork contains data on thousands of experiments. +How do you fetch data from the database so it can be used in R, Python or a spreadsheet? + +# Using the REST API + +GeneNetwork comes with a flexible REST API which allows fetching standard datatypes from the database. Much of the output is in JSON format which can be parsed from R, Python etc. There is also the excellent jq tool which allows viewing output in color. E.g. + +```sh +curl https://genenetwork.org/api/v_pre1/datasets/bxd > bxd.json +jq -C -S . bxd.json |less -R +``` + +shows for example + +```js + { + "AvgID": 3, + "CreateTime": "Tue, 02 Nov 2021 00:00:00 GMT", + "DataScale": "log2", + "FullName": "UTHSC BXD Hippocampus Postnatal Day 7 Ethanol Both Sexes Affy Clarion S (Nov21) RMA", + "Id": 1041, + "Long_Abbreviation": "UTHSC_BXD_Hip_PostD7EtohBS_Nov21", + "ProbeFreezeId": 432, + "ShortName": "UTHSC BXD Hippocampus Postnatal Day 7 Ethanol Both Sexes Affy Clarion S (Nov21) RMA", + "Short_Abbreviation": "UTHSC_BXD_Hip_PostD7EtohBS_1121", + "confidentiality": 0, + "public": 1 + } +``` + +curl is a tool for fetching API data. You can also use wget or download with R or Python. + +Karl Broman wrote the [GNapi](https://github.com/kbroman/GNapi) R package for accessing the GN API. + +# Reading the API tutorial + +In the next step check out the [documentation](../../api/GN2-REST-API.md). |