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diff --git a/api/alternative-API-structure.md b/api/alternative-API-structure.md index df65b9b..5261e09 100644 --- a/api/alternative-API-structure.md +++ b/api/alternative-API-structure.md @@ -83,7 +83,118 @@ Suggested URLs for each query are given below. <hr> -## Fetch tests +## Mock-up API +Each level has two types of associated metadata: detailed information about the current level ('info') and a listing of options/endpoints at the next level ('index'). +One of these endpoints could/should be returned without a keyword---probably the 'info' is more useful and intuitive. + +### API version +For the highest level ('version'), the results might look like this: + +https://genenetwork.org/api/2.0/info + +or + +https://genenetwork.org/api/2.0 +``` +{ + "name": "GeneNetwork REST API", + "version": "2.0", + "comment": "This is the official REST API for the GeneNetwork service hosted at https://genenetwork.org/", + "license": { + "source code": "AGPL" + }, + "note": "work in progress (WIP)", + "see also": "https://genenetwork.org/api/2.0/meta", + "next level": "species", + "next level options": "https://genenetwork.org/api/2.0/index" +} +``` + +https://genenetwork.org/api/2.0/index *Has the advantage that the 'index' keyword works at all levels even if the next level is unknown to the user.* +``` +{ + "API": { + "https://genenetwork.org/api/2.0/species": "Get a list of all species", + "https://genenetwork.org/api/2.0/Arabidopsis_thaliana": "Get information on mouse (Arabidopsis thaliana; Taxonomy ID 3702)", + "https://genenetwork.org/api/2.0/Drosophila_melanogaster": "Get information on fruit fly (Drosophila melanogaster; Taxonomy ID 7227)", + "https://genenetwork.org/api/2.0/Glossophaga_soricina": "Get information on bat (Glossophaga soricina; Taxonomy ID 27638)", + "https://genenetwork.org/api/2.0/Glycine_max": "Get information on soybean (Glycine max; Taxonomy ID 3847)", + "https://genenetwork.org/api/2.0/Homo_sapiens": "Get information on human (Homo sapiens; Taxonomy ID 9606)", + "https://genenetwork.org/api/2.0/Hordeum_vulgare": "Get information on barley (Hordeum_vulgare; Taxonomy ID 4513)", + "https://genenetwork.org/api/2.0/Mus_musculus": "Get information on mouse (Mus musculus; Taxonomy ID 10090)", + "https://genenetwork.org/api/2.0/Oryzias_latipes": "Get information on medaka fish (Oryzias latipes; Taxonomy ID 8090)", + "https://genenetwork.org/api/2.0/Populus_trichocarpa": "Get information on California poplar/black cottonwood (Populus trichocarpa; Taxonomy ID 3694)", + "https://genenetwork.org/api/2.0/Rattus_norvegicus": "Get information on rat (Rattus norvegicus; Taxonomy ID 10116)", + "https://genenetwork.org/api/2.0/Solanum_lycopersicum": "Get information on tomato (Solanum lycopersicum; Taxonomy ID 4081)" + } +} +``` + + +### Species +The next level is 'species'. +A listing of all the species available can be obtained from `$api/2.0/index` as above, but it might also be useful to have an alias like `$api/2.0/species`. + +https://genenetwork.org/api/2.0/species +``` +{ + "API": { + "https://genenetwork.org/api/2.0/species": "Get a list of all species", + "https://genenetwork.org/api/2.0/Arabidopsis_thaliana": "Get information on mouse (Arabidopsis thaliana; Taxonomy ID 3702)", + "https://genenetwork.org/api/2.0/Drosophila_melanogaster": "Get information on fruit fly (Drosophila melanogaster; Taxonomy ID 7227)", + "https://genenetwork.org/api/2.0/Glossophaga_soricina": "Get information on bat (Glossophaga soricina; Taxonomy ID 27638)", + "https://genenetwork.org/api/2.0/Glycine_max": "Get information on soybean (Glycine max; Taxonomy ID 3847)", + "https://genenetwork.org/api/2.0/Homo_sapiens": "Get information on human (Homo sapiens; Taxonomy ID 9606)", + "https://genenetwork.org/api/2.0/Hordeum_vulgare": "Get information on barley (Hordeum_vulgare; Taxonomy ID 4513)", + "https://genenetwork.org/api/2.0/Mus_musculus": "Get information on mouse (Mus musculus; Taxonomy ID 10090)", + "https://genenetwork.org/api/2.0/Oryzias_latipes": "Get information on medaka fish (Oryzias latipes; Taxonomy ID 8090)", + "https://genenetwork.org/api/2.0/Populus_trichocarpa": "Get information on California poplar/black cottonwood (Populus trichocarpa; Taxonomy ID 3694)", + "https://genenetwork.org/api/2.0/Rattus_norvegicus": "Get information on rat (Rattus norvegicus; Taxonomy ID 10116)", + "https://genenetwork.org/api/2.0/Solanum_lycopersicum": "Get information on tomato (Solanum lycopersicum; Taxonomy ID 4081)" + } +} +``` + +To get information on a particular species, use the ID/key given in the listing: + +https://genenetwork.org/api/2.0/Mus_musculus + +``` +{ + "binomial_name": "Mus musculus", + "id": Mus_musculus, + "alias": "mouse", + "taxon_id": "10090", + "wikidata_id": "Q83310", + "tags", ["vertebrate", "mammal", "rodent"] +} +``` + +At the next level are 'populations' and the available mouse populations can be determined using the index endpoint as above: + +https://genenetwork.org/api/2.0/Mus_musculus/index + +``` +{ + "API": { + "https://genenetwork.org/api/2.0/Mus_musculus/populations": "Get a list of all populations available for this species", + "https://genenetwork.org/api/2.0/Mus_musculus/BXD": "Get information on the BXD population", + "https://genenetwork.org/api/2.0/Mus_musculus/MDP": "Get information on the MDP population", + "https://genenetwork.org/api/2.0/Mus_musculus/LXS": "Get information on the LXS population", + "https://genenetwork.org/api/2.0/Mus_musculus/BXH": "Get information on the BXH population", + "https://genenetwork.org/api/2.0/Mus_musculus/AXBXA": "Get information on the AXBXA population", + "https://genenetwork.org/api/2.0/Mus_musculus/B6D2F2": "Get information on the B6D2F2 population", + "https://genenetwork.org/api/2.0/Mus_musculus/AKXD": "Get information on the AKXD population", + "https://genenetwork.org/api/2.0/Mus_musculus/CFW": "Get information on the CFW population", + "https://genenetwork.org/api/2.0/Mus_musculus/HS": "Get information on the HS population", + "https://genenetwork.org/api/2.0/Mus_musculus/LGSM": "Get information on the LGSM population", + "https://genenetwork.org/api/2.0/Mus_musculus/DO": "Get information on the DO population", + "https://genenetwork.org/api/2.0/Mus_musculus/CC": "Get information on the CC population" + } +} +``` + +## Fetch tests (to be updated with real URLs as they are implemented) ### Fetch species listing Species are the highest level of grouping. ```{r echo = FALSE} |