{"_id":"5508a8960f146f3500b031cf","title":"Getting Started","project":"5508a8940f146f3500b031c9","sync_unique":"","slug":"getting-started","hidden":false,"createdAt":"2015-03-17T22:20:06.269Z","link_url":"","excerpt":"This page will help you get started with fishbaseapi. You'll be up and running in a jiffy!","githubsync":"","api":{"params":[],"url":"","auth":"required","results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":""},"body":"Welcome to the Fishbase API! You can use our API to access Fishbase data.\n\nWe have examples for Shell (using `curl` and `jq`). You can view code examples in the dark area to the right.\n\n\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"body\": \"We're still in the process of filling out examples...Some routes below have examples, while some do not.\",\n  \"title\": \"\"\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"danger\",\n  \"title\": \"Commerical Users\",\n  \"body\": \"Make sure you read information on licensing in the [license section](https://fishbaseapi.readme.io/docs/license).\"\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Check on the status of the API at our [status page](https://ropensci.github.io/fishbasestatus/)\"\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"danger\",\n  \"title\": \"FishBase Needs Your Help\",\n  \"body\": \"Dear FishBase Users,\\n\\nFishBase needs help and I am writing to you because you either have at one point or another requested data to be extracted from FishBase for your own research purposes or have contributed your own data to FishBase.\\n\\nOne of the FishBase funders has had to reduce its commitment and as a result, there is a US$200,000 gap in the FishBase 2018/2019 budget, which will result in forced unpaid leave of key staff with direct consequences for the constant updating and growth of FishBase, a resource on which many of us rely.\\n\\nMany of us use FishBase regularly in our work given it provides important data on distribution, traits etc. Indeed, these data are so valuable that FishBase receives over 700,000 unique visits per month and underpins key scientific breakthroughs such as the Nature paper on rates of evolution [it’s slower in the tropics!] (see Nature (see https://www.nature.com/articles/d41586-018-05575-2 and https://www.facebook.com/FishBase/posts/1885134558216592).\\n\\nKey about FishBase is that it is free to everyone in the world, regardless of whether their institutions can afford journal subscriptions.\\n\\nFishBase co-founder Daniel Pauly once said “sending a bibliography is like providing cookbooks in a famine” and it has been the underpinning ethos of FishBase to make information available equally, regardless of where one works.\\n\\nSo for nearly 30 years, FishBase (www.fishbase.org), with its team of biologists and programmers has done just that, while constantly improving and expanding this valued resource.\\n\\nBut FishBase needs our help now. So, when you are next online on FishBase and see the donate request pop up, please donate at least $25. That’s one bottle of good VQA wine in Canada or half a carton of decent beer in Australia, 3 packs of organic Hess avocados from Loblaws or 6 latte grandes at Starbucks. If you drink more beer, use more avocado on your toast or are caffeine dependent, please consider a larger donation. IF EVERY MARINE RESEARCHER GETS ON BOARD, we can make a major contribution to FishBase. Imagine if you had to pay to access this type of information.\\n\\nIt’s time to pay it forward!\\n\\nThank you for your consideration and we all look forward to a flood of world-wide support to FishBase.\"\n}\n[/block]","updates":[],"link_external":false,"order":0,"type":"basic","__v":1,"version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","isReference":false,"next":{"description":"","pages":[]},"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e4f72c01242001cac3ec1","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:54:42.277Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"<https://fishbase.ropensci.org/>","excerpt":"","slug":"base-url","type":"basic","title":"Base URL","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e4fba44969800124f50df","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:55:54.698Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":3,"body":"In addition to Fishbase, we also server [Sealifebase](http://www.sealifebase.org/) data from this API.\n\nTo use Sealifebase API instead of Fishbase, add `/sealifebase` to the base URL, like:\n\n<https://fishbase.ropensci.org/sealifebase>\n\nEverything described below should work the same for both Fishbase and Sealife base APIs.","excerpt":"","slug":"fishbase-vs-sealifebase","type":"basic","title":"Fishbase vs. Sealifebase","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e4fdcc01242001cac3ec2","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:56:28.560Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":4,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"body\": \"Database versions are supported in the Fishbase API only at this time. We may support multiple versions of Sealifebase in the future.\"\n}\n[/block]\nThe Fishbase API supports multiple different versions of the underlying database.\n\nYou can request a different database version with a HTTP header like `Accept: application/vnd.ropensci.v3+json`\n\nWhere `v3` represents \"version 3\" and so on. These versions correspond to specific dates associated with different database versions. The current versions for Fishbase are:\n\n- 201505\n- 201604\n- 201703\n- 201712\n\nThe date format `YYYYMM` is four digits for year, then two digits for month, with no spaces/characters between them.\n\nBy default, we return the latest date version.\n\nSee the [`/versions`](#versions) route for description of the different versions and their names.\n\nIn the R client `rfishbase` the database version will be controlled by a parameter or option/env var, so users won't have to pass headers themselves.","excerpt":"","slug":"database-versions","type":"basic","title":"Database versions","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e5003ff22d5001e9590dc","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:57:07.347Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":5,"body":"This is essentially a `read only` API. That is, we only allow `GET` (and `HEAD`) requests on this API.\n\nRequests of all other types will be rejected with appropriate `405` code, including `POST`, `PUT`, `COPY`, `HEAD`, `DELETE`, etc.","excerpt":"","slug":"http-methods","type":"basic","title":"HTTP Methods","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e5015c96bc7001288e551","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:57:25.272Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":6,"body":"* 200 (OK) - request good!\n* 302 (Found) - the root `/`, redirects to `/heartbeat`, and `/docs` redirects to these documents\n* 400 (Bad request) - When you have a malformed request, fix it and try again\n* 404 (Not found) - When you request a route that does not exist, fix it and try again\n* 405 (Method not allowed) - When you use a prohibited HTTP method (we only allow `GET` and `HEAD`)\n* 500 (Internal server error) - Server got itself in trouble; get in touch with us. (in [Issues](https://github.com/ropensci/fishbaseapi/issues))\n\n## 400 responses will look something like\n\n```\nHTTP/1.1 400 Bad Request\nCache-Control: public, must-revalidate, max-age=60\nConnection: close\nContent-Length: 61\nContent-Type: application/json\nDate: Thu, 26 Feb 2015 23:27:57 GMT\nServer: nginx/1.7.9\nStatus: 400 Bad Request\nX-Content-Type-Options: nosniff\n\n{\n    \"error\": \"invalid request\",\n    \"message\": \"maximum limit is 5000\"\n}\n```\n\n## 404 responses will look something like\n\n```\nHTTP/1.1 404 Not Found\nCache-Control: public, must-revalidate, max-age=60\nConnection: close\nContent-Length: 27\nContent-Type: application/json\nDate: Thu, 26 Feb 2015 23:27:16 GMT\nServer: nginx/1.7.9\nStatus: 404 Not Found\nX-Cascade: pass\nX-Content-Type-Options: nosniff\n\n{\n    \"error\": \"route not found\"\n}\n```\n\n## 405 responses will look something like (with an empty body)\n\n```\nHTTP/1.1 405 Method Not Allowed\nAccess-Control-Allow-Methods: HEAD, GET\nAccess-Control-Allow-Origin: *\nCache-Control: public, must-revalidate, max-age=60\nConnection: close\nContent-Length: 0\nContent-Type: application/json; charset=utf8\nDate: Mon, 27 Jul 2015 20:48:27 GMT\nServer: nginx/1.9.3\nStatus: 405 Method Not Allowed\nX-Content-Type-Options: nosniff\n```\n\n## 500 responses will look something like\n\n```\nHTTP/1.1 500 Internal Server Error\nCache-Control: public, must-revalidate, max-age=60\nConnection: close\nContent-Length: 24\nContent-Type: application/json\nDate: Thu, 26 Feb 2015 23:19:57 GMT\nServer: nginx/1.7.9\nStatus: 500 Internal Server Error\nX-Content-Type-Options: nosniff\n\n{\n    \"error\": \"server error\"\n}\n```\n\nOccassionally you may get a MySQL error message in your `error` slot. Get in touch\nwith us if that happens as that shouldn't be happening, and we'll need to fix\nsomething on our end.","excerpt":"","slug":"response-codes","type":"basic","title":"Response Codes","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e5022c96bc7001288e552","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:57:38.865Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":7,"body":"Response headers give the following noteable things:\n\n* allowed methods on a route\n* allowed origins\n* cache information\n* body content length\n* content type (JSON)\n* date\n* server info\n* http status code\n\n## 200 response header will look something like\n\n```\nAccess-Control-Allow-Methods: HEAD, GET\nAccess-Control-Allow-Origin: *\nCache-Control: public, must-revalidate, max-age=60\nConnection: close\nContent-Length: 10379\nContent-Type: application/json; charset=utf8\nDate: Mon, 09 Mar 2015 23:01:23 GMT\nServer: nginx/1.7.10\nStatus: 200 OK\nX-Content-Type-Options: nosniff\n```","excerpt":"","slug":"response-headers","type":"basic","title":"Response headers","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e503e3de7c500262d574f","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:58:06.603Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":8,"body":"Response bodies generally look like:\n\n```json\n{\n    \"count\": 1,\n    \"returned\": 1,\n    \"data\": [\n      {\n        \"AnaCat\": \"potamodromous\",\n        \"AquacultureRef\": 12108,\n        \"Aquarium\": \"never/rarely\",\n        \"AquariumFishII\": \" \",\n        \"AquariumRef\": null,\n        \"Author\": \"(Linnaeus, 1758)\"\n      }\n    ],\n    \"error\": null\n}\n```\n\nResponses have 4 slots:\n\n* count: Number records found\n* returned: Number records returned\n* error: If an error did not occur this is `null`, otherwise, an error message.\n* data: The hash of data if any data returned. If no data found, this is an empty hash (hash of length zero)\n\nResponses with errors also have the same 4 slots, but no data returned, and there should be an\ninformative error message.","excerpt":"","slug":"response-bodies","type":"basic","title":"Response bodies","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e5047ff22d5001e9590dd","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:58:15.143Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":9,"body":"We serve up only JSON in this API. All responses will have `Content-Type: application/json; charset=utf8`.","excerpt":"","slug":"media-types","type":"basic","title":"Media Types","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e5055c96bc7001288e553","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:58:29.870Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":10,"body":"The query parameters `limit` (default = 10) and `offset` (default = 0) can be used\nto toggle the number of results you get back and what record you start at. This\ndoesn't apply to some routes, which don't accept any parameters (e.g., [docs](#docs)).\n\nThe response body from the server will include data on records found in `count` and number returned in `returned`:\n\n* `\"count\": 1056`\n* `\"returned\": 10`\n\nIdeally, we'd put in a helpful [links object](http://jsonapi.org/format/#fetching-pagination) - hopefully we'll get that done in the future.","excerpt":"","slug":"pagination","type":"basic","title":"Pagination","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e506144969800124f50e0","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:58:41.237Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":11,"body":"We don't require any. Cheers :)","excerpt":"","slug":"authentication","type":"basic","title":"Authentication","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e5075c96bc7001288e554","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T02:59:01.023Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":12,"body":"## Common parameters\n\n+ limit (integer, optional) `number` of records to return.\n    + Default: `10`\n+ offset (integer, optional) Record `number` to start at.\n    + Default: `0`\n+ fields (string, optional) Comma-separated `string` of fieds to return.\n    + Example: `SpecCode,Vulnerability`\n\nAbove parameters common to all routes except:\n\n* [root](#root)\n* [heartbeat](#heartbeat)\n* [docs](#docs)\n\nIn addition, these routes do not support `limit` or `offset`:\n\n* [listfields](#listfields)\n\n## Additional parameters\n\nRight now, any field that is returned from a route can also be queried on, except for the [/taxa route](#taxa), which only accepts `species` and `genus` in addition to the common parameters. All of the fields from each route are too long to list here - inspect data returned from a small data request, then change your query as desired.\n\nRight now, parameters that are not found are silently dropped. For example, if you query with `/species?foo=bar` in a query, and `foo` is not a field in `species` route, then the `foo=bar` part is ignored. We may in the future error when parameters are not found.","excerpt":"","slug":"parameters","type":"basic","title":"Parameters","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a60e144792a330012d71f55","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5508a8950f146f3500b031cd","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2018-01-18T18:02:44.479Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"settings":"","results":{"codes":[{"status":200,"language":"json","code":"{}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"auth":"required","params":[],"url":""},"isReference":false,"order":999,"body":"<a rel=\"license\" href=\"http://creativecommons.org/licenses/by-nc/3.0/\"><img alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by-nc/3.0/88x31.png\" /></a><br />Fishbase is licensed under a <a rel=\"license\" href=\"http://creativecommons.org/licenses/by-nc/3.0/\">Creative Commons Attribution-NonCommercial 3.0 Unported License</a>.\n\nSee the bottom of <a href=\"http://www.fishbase.us/\">the Fishbase website</a> for details on usage.\n\nThe Fishbase API follows the same license as Fishbase. It is free for non-commercial use with attribution as defined by the terms of the CC-BY-NC license (see above). Commercial users should first contact Fishbase maintainers at <a href=\"http://www.fishbase.us/mail/MailForm.php\">www.fishbase.us/mail/MailForm.php</a>.","excerpt":"","slug":"license","type":"basic","title":"License","__v":0,"parentDoc":null,"childrenPages":[]}

{"_id":"5a0e2ff344969800124f4d3c","project":"5508a8940f146f3500b031c9","version":"5508a8950f146f3500b031cc","category":"5a0e2fdcc96bc7001288e17d","user":"5508a87b99a1832100bf9569","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-11-17T00:40:19.661Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"examples":{"codes":[{"language":"shell","code":"curl -L https://fishbase.ropensci.org/heartbeat/ |  jq ."}]},"results":{"codes":[{"status":200,"language":"json","code":"{\n  \"routes\": [\n    \"/docs/:table?\",\n    \"/heartbeat\",\n    \"/mysqlping\",\n    \"/listfields\",\n    \"/classes/:id?<params>\",\n    \"/comnames?<params>\",\n    \"/country?<params>\",\n    \"/countrysub?<params>\",\n    \"/countrysubref/:id?<params>\",\n    \"/countref/:id?<params>\",\n    \"/ecology/:id?<params>\",\n    \"/ecosystemref/:id?<params>\",\n    \"/fecundity?<params>\",\n    \"/fooditems?<params>\",\n    \"/intrcase?<params>\",\n    \"/larvae?<params>\",\n    \"/listfields/:id?<params>\",\n    \"/matrix/:id?<params>\",\n    \"/maturity?<params>\",\n    \"/morphdat/:id?<params>\",\n    \"/morphmet/:id?<params>\",\n    \"/myersdata?<params>\",\n    \"/myersrecruitmentdatabase/:id?<params>\",\n    \"/orders/:id?<params>\",\n    \"/oxygen/:id?<params>\",\n    \"/popchar?<params>\",\n    \"/popgrowth/:id?<params>\",\n    \"/poplf?<params>\",\n    \"/popll/:id?<params>\",\n    \"/popqb/:id?<params>\",\n    \"/poplw/:id?<params>\",\n    \"/predats?<params>\",\n    \"/ration/:id?<params>\",\n    \"/refrens/:id?<params>\",\n    \"/reproduc/:id?<params>\",\n    \"/spawning?<params>\",\n    \"/speed/:id?<params>\",\n    \"/stocks?<params>\",\n    \"/swimming/:id?<params>\",\n    \"/synonyms?<params>\",\n    \"/faoareas/:id?<params>\",\n    \"/faoarref/:id?<params>\",\n    \"/genera/:id?<params>\",\n    \"/species/:id?<params>\",\n    \"/eggs/:id?<params>\",\n    \"/eggdev/:id?<params>\",\n    \"/estimate/:id?<params>\",\n    \"/families/:id?<params>\",\n    \"/taxa?<params>\",\n    \"/ecosystem?<params>\",\n    \"/diet?<params>\"\n  ]\n}","name":""},{"status":400,"language":"json","code":"{}","name":""}]},"settings":"","auth":"required","params":[],"url":"/heartbeat","method":"get"},"isReference":false,"order":0,"body":"`/` redirects to this route - if using `curl` on the command line make sure to pass the `-L` flag to follow redirects.","excerpt":"Lists all the routes, and gives some indicaion of what can be passed to them.","slug":"heartbeat","type":"get","title":"heartbeat","__v":1,"parentDoc":null,"childrenPages":[]}

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