From 0d6c9ab0b34199e94aaf262f7a7eb7f6e0f77b72 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 29 Apr 2019 11:12:48 -0500 Subject: Started API readme file --- api_readme.md | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 api_readme.md diff --git a/api_readme.md b/api_readme.md new file mode 100644 index 00000000..eef0b2d7 --- /dev/null +++ b/api_readme.md @@ -0,0 +1,62 @@ +# API Command Documentation # + +## Fetch Species List ## + +To get a list of species with data available in GN (and their associated names and ids): +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species +[ + { + "FullName": "Mus musculus", + "Id": 1, + "Name": "mouse", + "TaxonomyId": 10090 + }, + ... + { + "FullName": "Populus trichocarpa", + "Id": 10, + "Name": "poplar", + "TaxonomyId": 3689 + } +] +``` + +Or to get a single species info: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse +``` +OR +``` +curl http://gn2-zach.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 ## + +This query can optionally filter by species: + +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species) +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse groups/RISets) +[ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] +``` + +## Fetch Datasets ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd +[ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ] +``` +(I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) + + + + -- cgit v1.2.3 From 7daf96560d0b1f945a0a5fd0aed4a9961b718635 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 29 Apr 2019 11:48:51 -0500 Subject: Added the rest of the currently existing commands --- api_readme.md | 72 ++++++++++++++++++++++++++++++++++++++++++++++------------- 1 file changed, 56 insertions(+), 16 deletions(-) diff --git a/api_readme.md b/api_readme.md index eef0b2d7..00ba25d7 100644 --- a/api_readme.md +++ b/api_readme.md @@ -1,25 +1,11 @@ -# API Command Documentation # +# API Query Documentation # ## Fetch Species List ## To get a list of species with data available in GN (and their associated names and ids): ``` curl http://gn2-zach.genenetwork.org/api/v_pre1/species -[ - { - "FullName": "Mus musculus", - "Id": 1, - "Name": "mouse", - "TaxonomyId": 10090 - }, - ... - { - "FullName": "Populus trichocarpa", - "Id": 10, - "Name": "poplar", - "TaxonomyId": 3689 - } -] +[ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ] ``` Or to get a single species info: @@ -57,6 +43,60 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd ``` (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) +## Fetch Individual Dataset Info ## +### For mRNA Assay/"ProbeSet" ### +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` +{ "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 } +``` +(This also has the option to specify group/riset) +### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ### +For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001 +{ "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } +``` +## Fetch Sample Data for Single Trait ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at +[ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] +``` + +## Fetch Trait Info (Name, Description, Location, etc) ## +### For mRNA Expression/"ProbeSet" ### +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at +{ "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" } +``` + +### For "Phenotypes" ### +For phenotypes this just gets the max LRS, its location, and additive effect (as calculated by qtlreaper) + +Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001 +{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } +``` + +## Calculate Correlation ## +Currently only Pearson Sample and Tissue correlations are implemented + +This query currently takes the following parameters (though more will be added): +* trait_id (*required*) - ID for trait used for correlation +* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets) +* target_db (*required*) - Target DB name to be correlated against +* type - Sample or Tissue (default = Sample) +* return - Number of results to return (default = 500) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 +[ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ] +``` -- cgit v1.2.3 From c39a7ca68c2584c49a86fac2d05144a1b32ccd56 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 3 May 2019 11:06:47 -0500 Subject: Added examples for fetching sample data & genotypes --- api_readme.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/api_readme.md b/api_readme.md index 00ba25d7..d0102d67 100644 --- a/api_readme.md +++ b/api_readme.md @@ -32,6 +32,12 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse gro [ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] ``` +## Fetch Genotypes for Group/RISet ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD +``` +Returns a CSV file with metadata in the first few rows, sample/strain names as columns, and markers as rows. Currently only works for genotypes we have stored in .geno files; I'll add the option to download BIMBAM files soon. + ## Fetch Datasets ## ``` curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd @@ -43,6 +49,13 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd ``` (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) +## Fetch Sample Data for Dataset ## +``` +curl http://gn2-zach.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 + ## Fetch Individual Dataset Info ## ### For mRNA Assay/"ProbeSet" ### -- cgit v1.2.3 From 7749cec3336f5ecd3233be7f91cf5750a270c37d Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 21 May 2019 15:40:29 -0500 Subject: Added mapping and some other changes to readme --- api_readme.md | 46 +++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 43 insertions(+), 3 deletions(-) diff --git a/api_readme.md b/api_readme.md index d0102d67..96e8b246 100644 --- a/api_readme.md +++ b/api_readme.md @@ -1,5 +1,7 @@ # API Query Documentation # - +--- +# Fetching Dataset/Trait info/data # +--- ## Fetch Species List ## To get a list of species with data available in GN (and their associated names and ids): @@ -98,14 +100,52 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } ``` +--- + +# Analyses # +--- +## Mapping ## +Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper + +Each method's query takes the following parameters respectively (more will be added): +### GEMMA ### +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false) +* maf - minor allele frequency (default = 0.01) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +``` + +### R/qtl ### +(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf) +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function. +* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function +* num_perm - number of permutations; 0 by default +* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate +* interval_mapping - Whether to use interval mapping; "false" by default +* pair_scan - *NYI* + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +``` + +Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) + ## Calculate Correlation ## -Currently only Pearson Sample and Tissue correlations are implemented +Currently only Sample and Tissue correlations are implemented This query currently takes the following parameters (though more will be added): * trait_id (*required*) - ID for trait used for correlation * db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets) * target_db (*required*) - Target DB name to be correlated against -* type - Sample or Tissue (default = Sample) +* type - sample (default) | tissue +* method - pearson (default) | spearman * return - Number of results to return (default = 500) Example query: -- cgit v1.2.3 From 7dd9a3f8d232f3f747167de082eff22c30657ea0 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 21 Apr 2020 16:42:22 -0500 Subject: Testing --- wqflask/wqflask/templates/base.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index ec55ebeb..90be6111 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -4,7 +4,7 @@ - {% block title %}{% endblock %} GeneNetwork + {% block title %}{% endblock %} GeneNetwork2 -- cgit v1.2.3 From 1444f5618361a1c91bd792cfab8c8c53beb3421c Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 21 Apr 2020 16:43:11 -0500 Subject: Testing 2 --- wqflask/wqflask/templates/tutorials.html | 1 + 1 file changed, 1 insertion(+) create mode 100644 wqflask/wqflask/templates/tutorials.html diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html new file mode 100644 index 00000000..44e6a2c4 --- /dev/null +++ b/wqflask/wqflask/templates/tutorials.html @@ -0,0 +1 @@ +Testing123 -- cgit v1.2.3 From 657ab53bef4fc767fdc549f004153a7910b45bd0 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 10 Sep 2020 14:33:52 -0500 Subject: Fixed several sorting issues and moved orderDataType definitions into search_results.js since all the tables that use them import that file (that file's name needs to be changed, though) * wqflask/wqflask/static/new/javascript/search_results.js - Added the dom-checkbox and dom-inner-text order types into this file; they were previously duplicated across several template files * wqflask/wqflask/templates/gsearch_gene.html - Added dom-inner-text order type to relevant columns with hyperlink contents and disabled deferRender since it conflicted with use of both pagination and orderDataType for sorting * wqflask/wqflask/templates/gsearch_pheno.html - Same as above * wqflask/wqflask/templates/mapping_results.html - Added dom-inner-text for a few columns that have hyperlink values - still need to modify natural-minus-na to also include other "N/A"-equivalent values like "--" * wqflask/wqflask/templates/search_result_page.html Removed the dom-checkbox and dom-inner-text order types from this file since they were moved to search_results.js --- wqflask/wqflask/static/new/javascript/search_results.js | 14 ++++++++++++++ wqflask/wqflask/templates/gsearch_gene.html | 16 +--------------- wqflask/wqflask/templates/gsearch_pheno.html | 17 ++--------------- wqflask/wqflask/templates/mapping_results.html | 12 ++++++------ wqflask/wqflask/templates/search_result_page.html | 15 --------------- 5 files changed, 23 insertions(+), 51 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js index 4e87d67a..b696dc4d 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -281,4 +281,18 @@ $(function() { } }); + $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $('input', td).prop('checked') ? '1' : '0'; + } ); + }; + + $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $(td).text(); + } ); + } + }); \ No newline at end of file diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 478d6f5f..d2c78d65 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -59,20 +59,6 @@