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Diffstat (limited to 'api_readme.md')
| -rw-r--r-- | api_readme.md | 36 |
1 files changed, 18 insertions, 18 deletions
diff --git a/api_readme.md b/api_readme.md index 96e8b246..1588db66 100644 --- a/api_readme.md +++ b/api_readme.md @@ -6,17 +6,17 @@ 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 +curl https://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 +curl https://genenetwork.org/api/v_pre1/species/mouse ``` OR ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json +curl https://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* @@ -26,34 +26,34 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json This query can optionally filter by species: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species) +curl https://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) +curl https://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 Genotypes for Group/RISet ## ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD +curl https://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 +curl https://genenetwork.org/api/v_pre1/datasets/bxd ``` OR ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd +curl https://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) ## Fetch Sample Data for Dataset ## ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +curl https://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 @@ -62,11 +62,11 @@ Returns a CSV file with sample/strain names as the columns and trait IDs as rows ### For mRNA Assay/"ProbeSet" ### ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +curl https://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``` +curl https://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) @@ -74,20 +74,20 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` ### 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 +curl https://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 +curl https://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 +curl https://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" } ``` @@ -96,7 +96,7 @@ For phenotypes this just gets the max LRS, its location, and additive effect (a 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 +curl https://genenetwork.org/api/v_pre1/trait/BXD/10001 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } ``` @@ -116,7 +116,7 @@ Each method's query takes the following parameters respectively (more will be ad Example query: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +curl https://genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true ``` ### R/qtl ### @@ -132,7 +132,7 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPub 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 +curl https://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) @@ -150,6 +150,6 @@ This query currently takes the following parameters (though more will be added): 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 +curl https://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 }, ... ] ``` |