├── .gitignore ├── .travis.yml ├── index.js ├── docs ├── fonts │ ├── OpenSans-Bold-webfont.eot │ ├── OpenSans-Bold-webfont.woff │ ├── OpenSans-Italic-webfont.eot │ ├── OpenSans-Light-webfont.eot │ ├── OpenSans-Light-webfont.woff │ ├── OpenSans-Italic-webfont.woff │ ├── OpenSans-Regular-webfont.eot │ ├── OpenSans-Regular-webfont.woff │ ├── OpenSans-BoldItalic-webfont.eot │ ├── OpenSans-BoldItalic-webfont.woff │ ├── OpenSans-LightItalic-webfont.eot │ └── OpenSans-LightItalic-webfont.woff ├── README.hbs ├── scripts │ ├── linenumber.js │ └── prettify │ │ ├── lang-css.js │ │ ├── Apache-License-2.0.txt │ │ └── prettify.js ├── index.html ├── styles │ ├── prettify-jsdoc.css │ ├── prettify-tomorrow.css │ └── jsdoc-default.css ├── quickgo.js.html └── module-bionode-quickgo.html ├── test ├── obo.spec.js └── test.js ├── src ├── cli.js └── quickgo.js ├── package.json ├── CODE_OF_CONDUCT.md └── README.md /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | node_modules 3 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: node_js 2 | node_js: 3 | - "7" 4 | -------------------------------------------------------------------------------- /index.js: -------------------------------------------------------------------------------- 1 | module.exports = require('./src/quickgo.js') 2 | -------------------------------------------------------------------------------- /docs/fonts/OpenSans-Bold-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-quickgo/master/docs/fonts/OpenSans-Bold-webfont.eot -------------------------------------------------------------------------------- /docs/fonts/OpenSans-Bold-webfont.woff: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /test/obo.spec.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | 3 | const chai = require('chai') 4 | const should = chai.should() 5 | 6 | const obo = require('../index.js') 7 | 8 | describe('obo', function() { 9 | describe('#parse()', function() { 10 | 11 | it('should be a function', function() { 12 | obo.parse.should.be.a('function') 13 | }) 14 | 15 | it('should return `foo`', function() { 16 | obo.parse().should.equal('foo') 17 | }) 18 | }) 19 | }) 20 | -------------------------------------------------------------------------------- /test/test.js: -------------------------------------------------------------------------------- 1 | const quickgo = require('../src/quickgo') 2 | 3 | // quickgo.GAnnotationAsync({ 4 | // goid: 'GO:0047497', 5 | // format: 'tsv' 6 | // }) 7 | // .then((body) => console.log(body)) 8 | // .catch((err) => console.error(err)) 9 | 10 | // quickgo.GAnnotation({ 11 | // goid: 'GO:0047497', 12 | // format: 'tsv' 13 | // }) 14 | // .pipe(process.stdout) 15 | 16 | 17 | // quickgo.GTerm({id: 'GO:0003824'}).pipe(process.stdout) 18 | 19 | quickgo.GTermAsync({id: 'GO:0003824'}) 20 | .then((body) => console.log(body)) 21 | .catch((err) => console.error(err)) 22 | -------------------------------------------------------------------------------- /src/cli.js: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env node 2 | 3 | 'use strict'; 4 | 5 | const commandLineArgs = require('command-line-args') 6 | 7 | const quickgo = require('./quickgo') 8 | 9 | let cli = commandLineArgs([ 10 | {name: 'gannotation', alias: 'a', type: Boolean}, 11 | {name: 'gterm', alias: 't', type: Boolean}, 12 | {name: 'goid', type: String}, 13 | {name: 'format', type: String}, 14 | {name: 'col', type: String} 15 | ]) 16 | 17 | const opts = cli.parse() 18 | 19 | if (opts.gannotation) { 20 | quickgo.GAnnotation(opts).pipe(process.stdout) 21 | } else if (opts.gterm) { 22 | opts.id = opts.goid 23 | quickgo.GTerm(opts).pipe(process.stdout) 24 | } 25 | -------------------------------------------------------------------------------- /docs/scripts/linenumber.js: -------------------------------------------------------------------------------- 1 | /*global document */ 2 | (function() { 3 | var source = document.getElementsByClassName('prettyprint source linenums'); 4 | var i = 0; 5 | var lineNumber = 0; 6 | var lineId; 7 | var lines; 8 | var totalLines; 9 | var anchorHash; 10 | 11 | if (source && source[0]) { 12 | anchorHash = document.location.hash.substring(1); 13 | lines = source[0].getElementsByTagName('li'); 14 | totalLines = lines.length; 15 | 16 | for (; i < totalLines; i++) { 17 | lineNumber++; 18 | lineId = 'line' + lineNumber; 19 | lines[i].id = lineId; 20 | if (lineId === anchorHash) { 21 | lines[i].className += ' selected'; 22 | } 23 | } 24 | } 25 | })(); 26 | -------------------------------------------------------------------------------- /docs/scripts/prettify/lang-css.js: -------------------------------------------------------------------------------- 1 | PR.registerLangHandler(PR.createSimpleLexer([["pln",/^[\t\n\f\r ]+/,null," \t\r\n "]],[["str",/^"(?:[^\n\f\r"\\]|\\(?:\r\n?|\n|\f)|\\[\S\s])*"/,null],["str",/^'(?:[^\n\f\r'\\]|\\(?:\r\n?|\n|\f)|\\[\S\s])*'/,null],["lang-css-str",/^url\(([^"')]*)\)/i],["kwd",/^(?:url|rgb|!important|@import|@page|@media|@charset|inherit)(?=[^\w-]|$)/i,null],["lang-css-kw",/^(-?(?:[_a-z]|\\[\da-f]+ ?)(?:[\w-]|\\\\[\da-f]+ ?)*)\s*:/i],["com",/^\/\*[^*]*\*+(?:[^*/][^*]*\*+)*\//],["com", 2 | /^(?:<\!--|--\>)/],["lit",/^(?:\d+|\d*\.\d+)(?:%|[a-z]+)?/i],["lit",/^#[\da-f]{3,6}/i],["pln",/^-?(?:[_a-z]|\\[\da-f]+ ?)(?:[\w-]|\\\\[\da-f]+ ?)*/i],["pun",/^[^\s\w"']+/]]),["css"]);PR.registerLangHandler(PR.createSimpleLexer([],[["kwd",/^-?(?:[_a-z]|\\[\da-f]+ ?)(?:[\w-]|\\\\[\da-f]+ ?)*/i]]),["css-kw"]);PR.registerLangHandler(PR.createSimpleLexer([],[["str",/^[^"')]+/]]),["css-str"]); 3 | -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "bionode-quickgo", 3 | "version": "0.1.0", 4 | "description": "Access EBI QuickGO REST API with promises and streams", 5 | "main": "index.js", 6 | "scripts": { 7 | "test": "mocha test/obo.spec.js", 8 | "docs": "jsdoc2md --template docs/README.hbs src/*.js > README.md && jsdoc src/*.js -d docs" 9 | }, 10 | "bin": { 11 | "bionode-quickgo": "src/cli.js" 12 | }, 13 | "repository": { 14 | "type": "git", 15 | "url": "git+https://github.com/bionode/bionode-quickgo.git" 16 | }, 17 | "author": "Julian Mazzitelli ", 18 | "license": "MIT", 19 | "bugs": { 20 | "url": "https://github.com/bionode/bionode-quickgo/issues" 21 | }, 22 | "homepage": "https://github.com/bionode/bionode-quickgo#readme", 23 | "devDependencies": { 24 | "chai": "^4.0.1", 25 | "mocha": "^3.4.2" 26 | }, 27 | "dependencies": { 28 | "request": "^2.81.0", 29 | "request-promise": "^4.2.1" 30 | } 31 | } 32 | -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Home 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
19 | 20 |

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57 | 58 | 61 | 62 | 63 | 64 | 65 | -------------------------------------------------------------------------------- /docs/styles/prettify-jsdoc.css: -------------------------------------------------------------------------------- 1 | /* JSDoc prettify.js theme */ 2 | 3 | /* plain text */ 4 | .pln { 5 | color: #000000; 6 | font-weight: normal; 7 | font-style: normal; 8 | } 9 | 10 | /* string content */ 11 | .str { 12 | color: #006400; 13 | font-weight: normal; 14 | font-style: normal; 15 | } 16 | 17 | /* a keyword */ 18 | .kwd { 19 | color: #000000; 20 | font-weight: bold; 21 | font-style: normal; 22 | } 23 | 24 | /* a comment */ 25 | .com { 26 | font-weight: normal; 27 | font-style: italic; 28 | } 29 | 30 | /* a type name */ 31 | .typ { 32 | color: #000000; 33 | font-weight: normal; 34 | font-style: normal; 35 | } 36 | 37 | /* a literal value */ 38 | .lit { 39 | color: #006400; 40 | font-weight: normal; 41 | font-style: normal; 42 | } 43 | 44 | /* punctuation */ 45 | .pun { 46 | color: #000000; 47 | font-weight: bold; 48 | font-style: normal; 49 | } 50 | 51 | /* lisp open bracket */ 52 | .opn { 53 | color: #000000; 54 | font-weight: bold; 55 | font-style: normal; 56 | } 57 | 58 | /* lisp close bracket */ 59 | .clo { 60 | color: #000000; 61 | font-weight: bold; 62 | font-style: normal; 63 | } 64 | 65 | /* a markup tag name */ 66 | .tag { 67 | color: #006400; 68 | font-weight: normal; 69 | font-style: normal; 70 | } 71 | 72 | /* a markup attribute name */ 73 | .atn { 74 | color: #006400; 75 | font-weight: normal; 76 | font-style: normal; 77 | } 78 | 79 | /* a markup attribute value */ 80 | .atv { 81 | color: #006400; 82 | font-weight: normal; 83 | font-style: normal; 84 | } 85 | 86 | /* a declaration */ 87 | .dec { 88 | color: #000000; 89 | font-weight: bold; 90 | font-style: normal; 91 | } 92 | 93 | /* a variable name */ 94 | .var { 95 | color: #000000; 96 | font-weight: normal; 97 | font-style: normal; 98 | } 99 | 100 | /* a function name */ 101 | .fun { 102 | color: #000000; 103 | font-weight: bold; 104 | font-style: normal; 105 | } 106 | 107 | /* Specify class=linenums on a pre to get line numbering */ 108 | ol.linenums { 109 | margin-top: 0; 110 | margin-bottom: 0; 111 | } 112 | -------------------------------------------------------------------------------- /docs/styles/prettify-tomorrow.css: -------------------------------------------------------------------------------- 1 | /* Tomorrow Theme */ 2 | /* Original theme - https://github.com/chriskempson/tomorrow-theme */ 3 | /* Pretty printing styles. Used with prettify.js. */ 4 | /* SPAN elements with the classes below are added by prettyprint. */ 5 | /* plain text */ 6 | .pln { 7 | color: #4d4d4c; } 8 | 9 | @media screen { 10 | /* string content */ 11 | .str { 12 | color: #718c00; } 13 | 14 | /* a keyword */ 15 | .kwd { 16 | color: #8959a8; } 17 | 18 | /* a comment */ 19 | .com { 20 | color: #8e908c; } 21 | 22 | /* a type name */ 23 | .typ { 24 | color: #4271ae; } 25 | 26 | /* a literal value */ 27 | .lit { 28 | color: #f5871f; } 29 | 30 | /* punctuation */ 31 | .pun { 32 | color: #4d4d4c; } 33 | 34 | /* lisp open bracket */ 35 | .opn { 36 | color: #4d4d4c; } 37 | 38 | /* lisp close bracket */ 39 | .clo { 40 | color: #4d4d4c; } 41 | 42 | /* a markup tag name */ 43 | .tag { 44 | color: #c82829; } 45 | 46 | /* a markup attribute name */ 47 | .atn { 48 | color: #f5871f; } 49 | 50 | /* a markup attribute value */ 51 | .atv { 52 | color: #3e999f; } 53 | 54 | /* a declaration */ 55 | .dec { 56 | color: #f5871f; } 57 | 58 | /* a variable name */ 59 | .var { 60 | color: #c82829; } 61 | 62 | /* a function name */ 63 | .fun { 64 | color: #4271ae; } } 65 | /* Use higher contrast and text-weight for printable form. */ 66 | @media print, projection { 67 | .str { 68 | color: #060; } 69 | 70 | .kwd { 71 | color: #006; 72 | font-weight: bold; } 73 | 74 | .com { 75 | color: #600; 76 | font-style: italic; } 77 | 78 | .typ { 79 | color: #404; 80 | font-weight: bold; } 81 | 82 | .lit { 83 | color: #044; } 84 | 85 | .pun, .opn, .clo { 86 | color: #440; } 87 | 88 | .tag { 89 | color: #006; 90 | font-weight: bold; } 91 | 92 | .atn { 93 | color: #404; } 94 | 95 | .atv { 96 | color: #060; } } 97 | /* Style */ 98 | /* 99 | pre.prettyprint { 100 | background: white; 101 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 102 | font-size: 12px; 103 | line-height: 1.5; 104 | border: 1px solid #ccc; 105 | padding: 10px; } 106 | */ 107 | 108 | /* Specify class=linenums on a pre to get line numbering */ 109 | ol.linenums { 110 | margin-top: 0; 111 | margin-bottom: 0; } 112 | 113 | /* IE indents via margin-left */ 114 | li.L0, 115 | li.L1, 116 | li.L2, 117 | li.L3, 118 | li.L4, 119 | li.L5, 120 | li.L6, 121 | li.L7, 122 | li.L8, 123 | li.L9 { 124 | /* */ } 125 | 126 | /* Alternate shading for lines */ 127 | li.L1, 128 | li.L3, 129 | li.L5, 130 | li.L7, 131 | li.L9 { 132 | /* */ } 133 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open and welcoming environment, we as 6 | contributors and maintainers pledge to making participation in our project and 7 | our community a harassment-free experience for everyone, regardless of age, body 8 | size, disability, ethnicity, gender identity and expression, level of experience, 9 | nationality, personal appearance, race, religion, or sexual identity and 10 | orientation. 11 | 12 | ## Our Standards 13 | 14 | Examples of behavior that contributes to creating a positive environment 15 | include: 16 | 17 | * Using welcoming and inclusive language 18 | * Being respectful of differing viewpoints and experiences 19 | * Gracefully accepting constructive criticism 20 | * Focusing on what is best for the community 21 | * Showing empathy towards other community members 22 | 23 | Examples of unacceptable behavior by participants include: 24 | 25 | * The use of sexualized language or imagery and unwelcome sexual attention or 26 | advances 27 | * Trolling, insulting/derogatory comments, and personal or political attacks 28 | * Public or private harassment 29 | * Publishing others' private information, such as a physical or electronic 30 | address, without explicit permission 31 | * Other conduct which could reasonably be considered inappropriate in a 32 | professional setting 33 | 34 | ## Our Responsibilities 35 | 36 | Project maintainers are responsible for clarifying the standards of acceptable 37 | behavior and are expected to take appropriate and fair corrective action in 38 | response to any instances of unacceptable behavior. 39 | 40 | Project maintainers have the right and responsibility to remove, edit, or 41 | reject comments, commits, code, wiki edits, issues, and other contributions 42 | that are not aligned to this Code of Conduct, or to ban temporarily or 43 | permanently any contributor for other behaviors that they deem inappropriate, 44 | threatening, offensive, or harmful. 45 | 46 | ## Scope 47 | 48 | This Code of Conduct applies both within project spaces and in public spaces 49 | when an individual is representing the project or its community. Examples of 50 | representing a project or community include using an official project e-mail 51 | address, posting via an official social media account, or acting as an appointed 52 | representative at an online or offline event. Representation of a project may be 53 | further defined and clarified by project maintainers. 54 | 55 | ## Enforcement 56 | 57 | Instances of abusive, harassing, or otherwise unacceptable behavior may be 58 | reported by contacting the project team at mail@bionode.io. All 59 | complaints will be reviewed and investigated and will result in a response that 60 | is deemed necessary and appropriate to the circumstances. The project team is 61 | obligated to maintain confidentiality with regard to the reporter of an incident. 62 | Further details of specific enforcement policies may be posted separately. 63 | 64 | Project maintainers who do not follow or enforce the Code of Conduct in good 65 | faith may face temporary or permanent repercussions as determined by other 66 | members of the project's leadership. 67 | 68 | ## Attribution 69 | 70 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, 71 | available at [http://contributor-covenant.org/version/1/4][version] 72 | 73 | [homepage]: http://contributor-covenant.org 74 | [version]: http://contributor-covenant.org/version/1/4/ 75 | -------------------------------------------------------------------------------- /docs/styles/jsdoc-default.css: -------------------------------------------------------------------------------- 1 | @font-face { 2 | font-family: 'Open Sans'; 3 | font-weight: normal; 4 | font-style: normal; 5 | src: url('../fonts/OpenSans-Regular-webfont.eot'); 6 | src: 7 | local('Open Sans'), 8 | local('OpenSans'), 9 | url('../fonts/OpenSans-Regular-webfont.eot?#iefix') format('embedded-opentype'), 10 | url('../fonts/OpenSans-Regular-webfont.woff') format('woff'), 11 | url('../fonts/OpenSans-Regular-webfont.svg#open_sansregular') format('svg'); 12 | } 13 | 14 | @font-face { 15 | font-family: 'Open Sans Light'; 16 | font-weight: normal; 17 | font-style: normal; 18 | src: url('../fonts/OpenSans-Light-webfont.eot'); 19 | src: 20 | local('Open Sans Light'), 21 | local('OpenSans Light'), 22 | url('../fonts/OpenSans-Light-webfont.eot?#iefix') format('embedded-opentype'), 23 | url('../fonts/OpenSans-Light-webfont.woff') format('woff'), 24 | url('../fonts/OpenSans-Light-webfont.svg#open_sanslight') format('svg'); 25 | } 26 | 27 | html 28 | { 29 | overflow: auto; 30 | background-color: #fff; 31 | font-size: 14px; 32 | } 33 | 34 | body 35 | { 36 | font-family: 'Open Sans', sans-serif; 37 | line-height: 1.5; 38 | color: #4d4e53; 39 | background-color: white; 40 | } 41 | 42 | a, a:visited, a:active { 43 | color: #0095dd; 44 | text-decoration: none; 45 | } 46 | 47 | a:hover { 48 | text-decoration: underline; 49 | } 50 | 51 | header 52 | { 53 | display: block; 54 | padding: 0px 4px; 55 | } 56 | 57 | tt, code, kbd, samp { 58 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 59 | } 60 | 61 | .class-description { 62 | font-size: 130%; 63 | line-height: 140%; 64 | margin-bottom: 1em; 65 | margin-top: 1em; 66 | } 67 | 68 | .class-description:empty { 69 | margin: 0; 70 | } 71 | 72 | #main { 73 | float: left; 74 | width: 70%; 75 | } 76 | 77 | article dl { 78 | margin-bottom: 40px; 79 | } 80 | 81 | section 82 | { 83 | display: block; 84 | background-color: #fff; 85 | padding: 12px 24px; 86 | border-bottom: 1px solid #ccc; 87 | margin-right: 30px; 88 | } 89 | 90 | .variation { 91 | display: none; 92 | } 93 | 94 | .signature-attributes { 95 | font-size: 60%; 96 | color: #aaa; 97 | font-style: italic; 98 | font-weight: lighter; 99 | } 100 | 101 | nav 102 | { 103 | display: block; 104 | float: right; 105 | margin-top: 28px; 106 | width: 30%; 107 | box-sizing: border-box; 108 | border-left: 1px solid #ccc; 109 | padding-left: 16px; 110 | } 111 | 112 | nav ul { 113 | font-family: 'Lucida Grande', 'Lucida Sans Unicode', arial, sans-serif; 114 | font-size: 100%; 115 | line-height: 17px; 116 | padding: 0; 117 | margin: 0; 118 | list-style-type: none; 119 | } 120 | 121 | nav ul a, nav ul a:visited, nav ul a:active { 122 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 123 | line-height: 18px; 124 | color: #4D4E53; 125 | } 126 | 127 | nav h3 { 128 | margin-top: 12px; 129 | } 130 | 131 | nav li { 132 | margin-top: 6px; 133 | } 134 | 135 | footer { 136 | display: block; 137 | padding: 6px; 138 | margin-top: 12px; 139 | font-style: italic; 140 | font-size: 90%; 141 | } 142 | 143 | h1, h2, h3, h4 { 144 | font-weight: 200; 145 | margin: 0; 146 | } 147 | 148 | h1 149 | { 150 | font-family: 'Open Sans Light', sans-serif; 151 | font-size: 48px; 152 | letter-spacing: -2px; 153 | margin: 12px 24px 20px; 154 | } 155 | 156 | h2, h3 157 | { 158 | font-size: 30px; 159 | font-weight: 700; 160 | letter-spacing: -1px; 161 | margin-bottom: 12px; 162 | } 163 | 164 | h4 165 | { 166 | font-size: 18px; 167 | letter-spacing: -0.33px; 168 | margin-bottom: 12px; 169 | color: #4d4e53; 170 | } 171 | 172 | h5, .container-overview .subsection-title 173 | { 174 | font-size: 120%; 175 | font-weight: bold; 176 | letter-spacing: -0.01em; 177 | margin: 8px 0 3px 0; 178 | } 179 | 180 | h6 181 | { 182 | font-size: 100%; 183 | letter-spacing: -0.01em; 184 | margin: 6px 0 3px 0; 185 | font-style: italic; 186 | } 187 | 188 | .ancestors { color: #999; } 189 | .ancestors a 190 | { 191 | color: #999 !important; 192 | text-decoration: none; 193 | } 194 | 195 | .clear 196 | { 197 | clear: both; 198 | } 199 | 200 | .important 201 | { 202 | font-weight: bold; 203 | color: #950B02; 204 | } 205 | 206 | .yes-def { 207 | text-indent: -1000px; 208 | } 209 | 210 | .type-signature { 211 | color: #aaa; 212 | } 213 | 214 | .name, .signature { 215 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 216 | } 217 | 218 | .details { margin-top: 14px; border-left: 2px solid #DDD; } 219 | .details dt { width: 120px; float: left; padding-left: 10px; padding-top: 6px; } 220 | .details dd { margin-left: 70px; } 221 | .details ul { margin: 0; } 222 | .details ul { list-style-type: none; } 223 | .details li { margin-left: 30px; padding-top: 6px; } 224 | .details pre.prettyprint { margin: 0 } 225 | .details .object-value { padding-top: 0; } 226 | 227 | .description { 228 | margin-bottom: 1em; 229 | margin-top: 1em; 230 | } 231 | 232 | .code-caption 233 | { 234 | font-style: italic; 235 | font-size: 107%; 236 | margin: 0; 237 | } 238 | 239 | .prettyprint 240 | { 241 | border: 1px solid #ddd; 242 | width: 80%; 243 | overflow: auto; 244 | } 245 | 246 | .prettyprint.source { 247 | width: inherit; 248 | } 249 | 250 | .prettyprint code 251 | { 252 | font-size: 100%; 253 | line-height: 18px; 254 | display: block; 255 | padding: 4px 12px; 256 | margin: 0; 257 | background-color: #fff; 258 | color: #4D4E53; 259 | } 260 | 261 | .prettyprint code span.line 262 | { 263 | display: inline-block; 264 | } 265 | 266 | .prettyprint.linenums 267 | { 268 | padding-left: 70px; 269 | -webkit-user-select: none; 270 | -moz-user-select: none; 271 | -ms-user-select: none; 272 | user-select: none; 273 | } 274 | 275 | .prettyprint.linenums ol 276 | { 277 | padding-left: 0; 278 | } 279 | 280 | .prettyprint.linenums li 281 | { 282 | border-left: 3px #ddd solid; 283 | } 284 | 285 | .prettyprint.linenums li.selected, 286 | .prettyprint.linenums li.selected * 287 | { 288 | background-color: lightyellow; 289 | } 290 | 291 | .prettyprint.linenums li * 292 | { 293 | -webkit-user-select: text; 294 | -moz-user-select: text; 295 | -ms-user-select: text; 296 | user-select: text; 297 | } 298 | 299 | .params, .props 300 | { 301 | border-spacing: 0; 302 | border: 0; 303 | border-collapse: collapse; 304 | } 305 | 306 | .params .name, .props .name, .name code { 307 | color: #4D4E53; 308 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 309 | font-size: 100%; 310 | } 311 | 312 | .params td, .params th, .props td, .props th 313 | { 314 | border: 1px solid #ddd; 315 | margin: 0px; 316 | text-align: left; 317 | vertical-align: top; 318 | padding: 4px 6px; 319 | display: table-cell; 320 | } 321 | 322 | .params thead tr, .props thead tr 323 | { 324 | background-color: #ddd; 325 | font-weight: bold; 326 | } 327 | 328 | .params .params thead tr, .props .props thead tr 329 | { 330 | background-color: #fff; 331 | font-weight: bold; 332 | } 333 | 334 | .params th, .props th { border-right: 1px solid #aaa; } 335 | .params thead .last, .props thead .last { border-right: 1px solid #ddd; } 336 | 337 | .params td.description > p:first-child, 338 | .props td.description > p:first-child 339 | { 340 | margin-top: 0; 341 | padding-top: 0; 342 | } 343 | 344 | .params td.description > p:last-child, 345 | .props td.description > p:last-child 346 | { 347 | margin-bottom: 0; 348 | padding-bottom: 0; 349 | } 350 | 351 | .disabled { 352 | color: #454545; 353 | } 354 | -------------------------------------------------------------------------------- /src/quickgo.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | 3 | const request = require('request') 4 | const requestAsync = require('request-promise') 5 | 6 | /** 7 | * Access EBI QuickGO REST API with promises and streams. 8 | * @module bionode-quickgo 9 | */ 10 | 11 | 12 | const baseUri = 'http://www.ebi.ac.uk/QuickGO/' 13 | const method = 'POST' 14 | 15 | /** 16 | * generate an annotation request object 17 | * @param {Object} fields valid query fields 18 | * @return {Object} {method, uri, form} object for request 19 | */ 20 | function annotationRequest(fields) { 21 | const uri = baseUri + 'GAnnotation' 22 | 23 | /** 24 | * @name format 25 | * @desc Download file format 26 | * @type {String} 27 | * @default gaf 28 | * @example gaf, gpa, gene2go, proteinList, fasta, tsv 29 | */ 30 | const format = fields.format || 'gaf' 31 | 32 | /** 33 | * @name limit 34 | * @desc Download limit (number of lines). Note that the default limit is 35 | * 10,000 rows, which may not be sufficient for the data set that you are 36 | * downloading. To bypass this default, and return the entire data set, 37 | * specify a limit of -1. 38 | * @type {String} 39 | * @default '' 40 | * @example 9001, -1 41 | */ 42 | const limit = fields.limit || '' 43 | 44 | /** 45 | * @name gz 46 | * @desc gzips the downloaded file 47 | * @type {String} 48 | * @default false 49 | * @example false, true 50 | */ 51 | const gz = fields.gz || 'false' 52 | 53 | /** 54 | * @name goid 55 | * @desc GO identifiers either directly or indirectly (descendant GO 56 | * identifiers) applied in annotations 57 | * @type {String} 58 | * @default '' 59 | * @example GO:0002080 60 | */ 61 | const goid = fields.goid || '' 62 | 63 | /** 64 | * @name aspect 65 | * @desc Use this to limit the annotations returned to a specific ontology or 66 | * ontologies (Molecular Function, Biological Process or Cellular Component) 67 | * @type {String} 68 | * @default '' 69 | * @example F, P, C 70 | */ 71 | const aspect = fields.espect || '' 72 | 73 | /** 74 | * @name relType 75 | * @desc By default, QuickGO will display annotations to GO terms that are 76 | * related to that specified in the goid parameter by is_a, part_of and 77 | * occurs_in relations; this parameter allows you to override that behaviour. 78 | * See [Ontology Relations](http://geneontology.org/page/ontology-relations). 79 | * @type {String} 80 | * @default IPO= 81 | * @example 82 | * ? (ancestor) 83 | * = (indentity) 84 | * I (is_a) 85 | * P (part_of) 86 | * O (occurs_in) 87 | * R (regulates) 88 | * + (positively_regulates) 89 | * - (negatively_regulates) 90 | */ 91 | const relType = fields.relType || 'IPO=' 92 | 93 | /** 94 | * @name termUse 95 | * @desc If you set this parameter to slim, then QuickGO will use the 96 | * supplied set of GO identifiers as a slim and will map the annotations up 97 | * to these terms. See [here](http://www.ebi.ac.uk/QuickGO/GMultiTerm) for 98 | * more details. The default behaviour (termUse=ancestor) is to not perform 99 | * this mapping. 100 | * @type {String} 101 | * @default ancestor 102 | * @example ancestor, slim 103 | */ 104 | const termUse = fields.termUse || 'ancestor' 105 | 106 | /** 107 | * @name evidence 108 | * @desc Annotation evidence code (Ev) category 109 | * @type {String} 110 | * @default '' 111 | * @example IDA, IC, ISS, IEA 112 | */ 113 | const evidence = fields.evidence || '' 114 | 115 | /** 116 | * @name source 117 | * @desc Annotation provider 118 | * @type {String} 119 | * @default '' 120 | * @example UniProtKB, HGNC 121 | */ 122 | const source = fields.source || '' 123 | 124 | /** 125 | * @name ref 126 | * @desc PubMed or GO reference supporting annotation. Can refer to a specific 127 | * reference identifier or category (for category level, use * after ref type) 128 | * @type {String} 129 | * @default '' 130 | * @example PUBMED:*, GO_REF:0000002, 16262699 131 | */ 132 | const ref = fields.ref || '' 133 | 134 | /** 135 | * @name with 136 | * @desc Additional supporting information supplied in IEA, ISS, IPI, IC 137 | * evidenced annotations; see: 138 | * [GO documentation](http://www.geneontology.org/GO.evidence.shtml). 139 | * Can refer to a specific identifier or category (for category level, use * 140 | * after with type) 141 | * @type {String} 142 | * @default '' 143 | * @example EC:2.5.1.30, IPR000092, HAMAP:* 144 | */ 145 | // jsdoc3 throws 'unexpected token with' on 'with' 146 | const _with = fields.with || '' 147 | 148 | /** 149 | * @name tax 150 | * @desc NCBI taxonomic identifer of annotated protein 151 | * @type {String} 152 | * @default '' 153 | * @example 9606 154 | */ 155 | const tax = fields.tax || '' 156 | 157 | /** 158 | * @name protein 159 | * @desc Specifies one or more sequence identifiers or accessions from 160 | * available database(s) (see DB filter column) 161 | * @type {String} 162 | * @default '' 163 | * @example Mm.363225, P99999 164 | */ 165 | const protein = fields.protein || '' 166 | 167 | /** 168 | * @name qualifier 169 | * @desc Tags that modify the interpretation of an annotation 170 | * @type {String} 171 | * @default '' 172 | * @example NOT, colocalizes_with, contributes_to 173 | */ 174 | const qualifier = fields.qualifier || '' 175 | 176 | /** 177 | * @name db 178 | * @desc Protein database (identifier type) 179 | * @type {String} 180 | * @default '' 181 | * @example UniProtKB, UniGene, Ensembl 182 | */ 183 | const db = fields.db || '' 184 | 185 | /** 186 | * @name q 187 | * @desc Advanced query. Used to customize GO annotation sets using Boolean 188 | * operators. See [Advanced Annotation Search](http://www.ebi.ac.uk/QuickGO/reference.html#advanced_annotation) 189 | * @type {String} 190 | * @default '' 191 | */ 192 | const q = fields.q || '' 193 | 194 | /** 195 | * @name col 196 | * @desc This parameter, which is currently only applicable to the tsv 197 | * download format, allows you to specify a comma-separated list of columns 198 | * that you want to be included in the returned data set. The list below shows 199 | * the available column names; clicking on the name of a column will take you 200 | * to the description of the column in the QuickGO help file. The default set 201 | * of columns is shown in bold text. 202 | * * [**proteinDB**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinDB) 203 | * * [**proteinID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinID) 204 | * * [**proteinSymbol**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSymbol) 205 | * * [**qualifier**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-qualifier) 206 | * * [**goID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goID) 207 | * * [**goName**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goName) 208 | * * [**aspect**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-aspect) 209 | * * [**evidence**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-evidence) 210 | * * [**ref**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-ref) 211 | * * [**with**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-with) 212 | * * [**proteinTaxon**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxon) 213 | * * [**date**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-date) 214 | * * [**from**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-from) 215 | * * [**splice**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-splice) 216 | * * [proteinName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinName) 217 | * * [proteinSynonym](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSynonym) 218 | * * [proteinType](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinType) 219 | * * [proteinTaxonName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxonName) 220 | * * [orginalTermID](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalTermID) 221 | * * [originalGOName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalGOName) 222 | * @type {String} 223 | * @default 'proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice' 224 | * @example 'proteinDB,proteinID,goID,goName,aspect' 225 | */ 226 | const col = fields.col || 'proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice' 227 | 228 | const form = { 229 | format, 230 | limit, 231 | gz, 232 | goid, 233 | aspect, 234 | relType, 235 | termUse, 236 | evidence, 237 | source, 238 | ref, 239 | with: _with, 240 | tax, 241 | protein, 242 | qualifier, 243 | db, 244 | q, 245 | col 246 | } 247 | 248 | return { 249 | method, 250 | uri, 251 | form 252 | } 253 | } 254 | 255 | /** 256 | * QuickGO Annotation service 257 | * @param {Object} fields valid query fields 258 | * @return {Promise} 259 | */ 260 | exports.GAnnotationAsync = function (fields) { 261 | return requestAsync(annotationRequest(fields)) 262 | } 263 | 264 | /** 265 | * QuickGO Annotation service 266 | * @param {Object} fields valid query fields 267 | * @return {Stream} 268 | */ 269 | exports.GAnnotation = function (fields) { 270 | return request(annotationRequest(fields)) 271 | } 272 | 273 | /** 274 | * generate an term request object 275 | * @param {Object} fields valid query fields 276 | * @return {Object} {method, uri, form} object for request 277 | */ 278 | function termRequest(fields) { 279 | const uri = baseUri + 'GTerm' 280 | 281 | /** 282 | * @name id 283 | * @desc GO identifier 284 | * @type {String} 285 | * @default none 286 | * @example GO:0003824 287 | */ 288 | const id = fields.id 289 | 290 | /** 291 | * @name format 292 | * @type {String} 293 | * @default obo 294 | * @desc 295 | * | Format | Description | 296 | * |:-------------------------------------------------------------------------|:------------------------------------------------------------------| 297 | * | [mini](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=mini) | Mini Mini HTML, suitable for dynamically embedding in popup boxes | 298 | * | [obo](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=obo) | OBO format snippet | 299 | * | [oboxml](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=oboxml) | OBO XML format snippet | 300 | */ 301 | const format = fields.format || 'obo' 302 | 303 | const form = { 304 | id, 305 | format 306 | } 307 | 308 | return { 309 | method, 310 | uri, 311 | form 312 | } 313 | } 314 | 315 | /** 316 | * GO term information 317 | * @param {Object} fields valid query fields, id required 318 | * @returns {Stream} 319 | */ 320 | exports.GTerm = function (fields) { 321 | if (!fields.id) { 322 | return 'Did not specify `id`' 323 | } 324 | 325 | return request(termRequest(fields)) 326 | } 327 | 328 | /** 329 | * GO term information 330 | * @param {Object} fields valid query fields, id required 331 | * @returns {Promise} 332 | */ 333 | exports.GTermAsync = function (fields) { 334 | if (!fields.id) { 335 | return 'Did not specify `id`' 336 | } 337 | 338 | return requestAsync(termRequest(fields)) 339 | } 340 | -------------------------------------------------------------------------------- /docs/scripts/prettify/Apache-License-2.0.txt: -------------------------------------------------------------------------------- 1 | 2 | Apache License 3 | Version 2.0, January 2004 4 | http://www.apache.org/licenses/ 5 | 6 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 7 | 8 | 1. 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19 | 20 |

Source: quickgo.js

21 | 22 | 23 | 24 | 25 | 26 | 27 |
28 |
29 | 
'use strict'
 30 | 
 31 | const request = require('request')
 32 | const requestAsync = require('request-promise')
 33 | 
 34 | /**
 35 |  * Access EBI QuickGO REST API with promises and streams.
 36 |  * @module bionode-quickgo
 37 |  */
 38 | 
 39 | 
 40 | const baseUri = 'http://www.ebi.ac.uk/QuickGO/'
 41 | const method = 'POST'
 42 | 
 43 | /**
 44 |  * generate an annotation request object
 45 |  * @param  {Object} fields valid query fields
 46 |  * @return {Object}        {{method, uri, form} object for request}
 47 |  */
 48 | function annotationRequest(fields) {
 49 |   const uri = baseUri + 'GAnnotation'
 50 | 
 51 |   /**
 52 |    * @name format
 53 |    * @desc Download file format
 54 |    * @type {String}
 55 |    * @default gaf
 56 |    * @example gaf, gpa, gene2go, proteinList, fasta, tsv
 57 |    */
 58 |   const format = fields.format || 'gaf'
 59 | 
 60 |   /**
 61 |    * @name limit
 62 |    * @desc Download limit (number of lines). Note that the default limit is
 63 |    * 10,000 rows, which may not be sufficient for the data set that you are
 64 |    * downloading. To bypass this default, and return the entire data set,
 65 |    * specify a limit of -1.
 66 |    * @type {String}
 67 |    * @default ''
 68 |    * @example 9001, -1
 69 |    */
 70 |   const limit = fields.limit || ''
 71 | 
 72 |   /**
 73 |    * @name gz
 74 |    * @desc gzips the downloaded file
 75 |    * @type {String}
 76 |    * @default false
 77 |    * @example false, true
 78 |    */
 79 |   const gz = fields.gz || 'false'
 80 | 
 81 |   /**
 82 |    * @name goid
 83 |    * @desc GO identifiers either directly or indirectly (descendant GO
 84 |    * identifiers) applied in annotations
 85 |    * @type {String}
 86 |    * @default ''
 87 |    * @example GO:0002080
 88 |    */
 89 |   const goid = fields.goid || ''
 90 | 
 91 |   /**
 92 |    * @name aspect
 93 |    * @desc Use this to limit the annotations returned to a specific ontology or
 94 |    * ontologies (Molecular Function, Biological Process or Cellular Component)
 95 |    * @type {String}
 96 |    * @default ''
 97 |    * @example F, P, C
 98 |    */
 99 |   const aspect = fields.espect || ''
100 | 
101 |   /**
102 |    * @name relType
103 |    * @desc By default, QuickGO will display annotations to GO terms that are
104 |    * related to that specified in the goid parameter by is_a, part_of and
105 |    * occurs_in relations; this parameter allows you to override that behaviour.
106 |    * See [Ontology Relations](http://geneontology.org/page/ontology-relations).
107 |    * @type {String}
108 |    * @default IPO=
109 |    * @example
110 |    * ? (ancestor)
111 |    * = (indentity)
112 |    * I (is_a)
113 |    * P (part_of)
114 |    * O (occurs_in)
115 |    * R (regulates)
116 |    * + (positively_regulates)
117 |    * - (negatively_regulates)
118 |    */
119 |   const relType = fields.relType || 'IPO='
120 | 
121 |   /**
122 |    * @name termUse
123 |    * @desc If you set this parameter to slim, then QuickGO will use the
124 |    * supplied set of GO identifiers as a slim and will map the annotations up
125 |    * to these terms. See [here](http://www.ebi.ac.uk/QuickGO/GMultiTerm) for
126 |    * more details. The default behaviour (termUse=ancestor) is to not perform
127 |    * this mapping.
128 |    * @type {String}
129 |    * @default ancestor
130 |    * @example ancestor, slim
131 |    */
132 |   const termUse = fields.termUse || 'ancestor'
133 | 
134 |   /**
135 |    * @name evidence
136 |    * @desc Annotation evidence code (Ev) category
137 |    * @type {String}
138 |    * @default ''
139 |    * @example IDA, IC, ISS, IEA
140 |    */
141 |   const evidence = fields.evidence || ''
142 | 
143 |   /**
144 |    * @name source
145 |    * @desc Annotation provider
146 |    * @type {String}
147 |    * @default ''
148 |    * @example UniProtKB, HGNC
149 |    */
150 |   const source = fields.source || ''
151 | 
152 |   /**
153 |    * @name ref
154 |    * @desc PubMed or GO reference supporting annotation. Can refer to a specific
155 |    * reference identifier or category (for category level, use * after ref type)
156 |    * @type {String}
157 |    * @default ''
158 |    * @example PUBMED:*, GO_REF:0000002, 16262699
159 |    */
160 |   const ref = fields.ref || ''
161 | 
162 |   /**
163 |    * @name with
164 |    * @desc Additional supporting information supplied in IEA, ISS, IPI, IC
165 |    * evidenced annotations; see:
166 |    * [GO documentation](http://www.geneontology.org/GO.evidence.shtml).
167 |    * Can refer to a specific identifier or category (for category level, use *
168 |    * after with type)
169 |    * @type {String}
170 |    * @default ''
171 |    * @example EC:2.5.1.30, IPR000092, HAMAP:*
172 |    */
173 |   // jsdoc3 throws 'unexpected token with' on 'with'
174 |   const _with = fields.with || ''
175 | 
176 |   /**
177 |    * @name tax
178 |    * @desc NCBI taxonomic identifer of annotated protein
179 |    * @type {String}
180 |    * @default ''
181 |    * @example 9606
182 |    */
183 |   const tax = fields.tax || ''
184 | 
185 |   /**
186 |    * @name protein
187 |    * @desc Specifies one or more sequence identifiers or accessions from
188 |    * available database(s) (see DB filter column)
189 |    * @type {String}
190 |    * @default ''
191 |    * @example Mm.363225, P99999
192 |    */
193 |   const protein = fields.protein || ''
194 | 
195 |   /**
196 |    * @name qualifier
197 |    * @desc Tags that modify the interpretation of an annotation
198 |    * @type {String}
199 |    * @default ''
200 |    * @example NOT, colocalizes_with, contributes_to
201 |    */
202 |   const qualifier = fields.qualifier || ''
203 | 
204 |   /**
205 |    * @name db
206 |    * @desc Protein database (identifier type)
207 |    * @type {String}
208 |    * @default ''
209 |    * @example UniProtKB, UniGene, Ensembl
210 |    */
211 |   const db = fields.db || ''
212 | 
213 |   /**
214 |    * @name q
215 |    * @desc Advanced query. Used to customize GO annotation sets using Boolean
216 |    * operators. See [Advanced Annotation Search](http://www.ebi.ac.uk/QuickGO/reference.html#advanced_annotation)
217 |    * @type {String}
218 |    * @default ''
219 |    */
220 |   const q = fields.q || ''
221 | 
222 |   /**
223 |    * @name col
224 |    * @desc This parameter, which is currently only applicable to the tsv
225 |    * download format, allows you to specify a comma-separated list of columns
226 |    * that you want to be included in the returned data set. The list below shows
227 |    * the available column names; clicking on the name of a column will take you
228 |    * to the description of the column in the QuickGO help file. The default set
229 |    * of columns is shown in bold text.
230 |    * * [**proteinDB**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinDB)
231 |    * * [**proteinID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinID)
232 |    * * [**proteinSymbol**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSymbol)
233 |    * * [**qualifier**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-qualifier)
234 |    * * [**goID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goID)
235 |    * * [**goName**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goName)
236 |    * * [**aspect**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-aspect)
237 |    * * [**evidence**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-evidence)
238 |    * * [**ref**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-ref)
239 |    * * [**with**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-with)
240 |    * * [**proteinTaxon**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxon)
241 |    * * [**date**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-date)
242 |    * * [**from**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-from)
243 |    * * [**splice**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-splice)
244 |    * * [proteinName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinName)
245 |    * * [proteinSynonym](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSynonym)
246 |    * * [proteinType](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinType)
247 |    * * [proteinTaxonName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxonName)
248 |    * * [orginalTermID](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalTermID)
249 |    * * [originalGOName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalGOName)
250 |    * @type {String}
251 |    * @default 'proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice'
252 |    * @example 'proteinDB,proteinID,goID,goName,aspect'
253 |    */
254 |   const col = fields.col || ''
255 | 
256 |   const form = {
257 |     format,
258 |     limit,
259 |     gz,
260 |     goid,
261 |     aspect,
262 |     relType,
263 |     termUse,
264 |     evidence,
265 |     source,
266 |     ref,
267 |     with: _with,
268 |       tax,
269 |       protein,
270 |       qualifier,
271 |       db,
272 |       q,
273 |       col
274 |   }
275 | 
276 |   return {
277 |     method,
278 |     uri,
279 |     form
280 |   }
281 | }
282 | 
283 | /**
284 |  * QuickGO Annotation service
285 |  * @param {Object} fields valid query fields
286 |  * @return {Promise}
287 |  */
288 | exports.GAnnotationAsync = function (fields) {
289 |   return requestAsync(annotationRequest(fields))
290 | }
291 | 
292 | /**
293 |  * QuickGO Annotation service
294 |  * @param {Object} fields valid query fields
295 |  * @return {Stream}
296 |  */
297 | exports.GAnnotation = function (fields) {
298 |   return request(annotationRequest(fields))
299 | }
300 | 
301 | /**
302 |  * generate an term request object
303 |  * @param  {Object} fields valid query fields
304 |  * @return {Object}        {{method, uri, form} object for request}
305 |  */
306 | function termRequest(fields) {
307 |   const uri = baseUri + 'GTerm'
308 | 
309 |   /**
310 |    * @name id
311 |    * @desc GO identifier
312 |    * @type {String}
313 |    * @default none
314 |    * @example GO:0003824
315 |    */
316 |   const id = fields.id
317 | 
318 |   /**
319 |    * @name format
320 |    * @type {String}
321 |    * @default obo
322 |    * @desc
323 |    * | Format                                                                   | Description                                                       |
324 |    * |:-------------------------------------------------------------------------|:------------------------------------------------------------------|
325 |    * | [mini](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=mini)     | Mini Mini HTML, suitable for dynamically embedding in popup boxes |
326 |    * | [obo](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=obo)       | OBO format snippet                                                |
327 |    * | [oboxml](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=oboxml) | OBO XML format snippet                                            |
328 |    */
329 |   const format = fields.format || 'obo'
330 | 
331 |   const form = {
332 |     id,
333 |     format
334 |   }
335 | 
336 |   return {
337 |     method,
338 |     uri,
339 |     form
340 |   }
341 | }
342 | 
343 | /**
344 |  * GO term information
345 |  * @param {Object} fields valid query fields, id required
346 |  * @returns {Stream}
347 |  */
348 | exports.GTerm = function (fields) {
349 |   if (!fields.id) {
350 |     return 'Did not specify `id`'
351 |   }
352 | 
353 |   return request(termRequest(fields))
354 | }
355 | 
356 | /**
357 |  * GO term information
358 |  * @param {Object} fields valid query fields, id required
359 |  * @returns {Promise}
360 |  */
361 | exports.GTermAsync = function (fields) {
362 |   if (!fields.id) {
363 |     return 'Did not specify `id`'
364 |   }
365 | 
366 |   return requestAsync(termRequest(fields))
367 | }
368 |
369 |
370 |
371 | 372 | 373 | 374 | 375 |
376 | 377 | 380 | 381 |
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k=k.match(g),f,b;if(b= 26 | !k){b=n;for(var o=void 0,c=b.firstChild;c;c=c.nextSibling)var i=c.nodeType,o=i===1?o?b:c:i===3?N.test(c.nodeValue)?b:o:o;b=(f=o===b?void 0:o)&&"CODE"===f.tagName}b&&(k=f.className.match(g));k&&(k=k[1]);b=!1;for(o=n.parentNode;o;o=o.parentNode)if((o.tagName==="pre"||o.tagName==="code"||o.tagName==="xmp")&&o.className&&o.className.indexOf("prettyprint")>=0){b=!0;break}b||((b=(b=n.className.match(/\blinenums\b(?::(\d+))?/))?b[1]&&b[1].length?+b[1]:!0:!1)&&D(n,b),d={g:k,h:n,i:b},E(d))}}pPromise 13 | * [.GAnnotation(fields)](#module_bionode-quickgo.GAnnotation) ⇒ Stream 14 | * [.GTerm(fields)](#module_bionode-quickgo.GTerm) ⇒ Stream 15 | * [.GTermAsync(fields)](#module_bionode-quickgo.GTermAsync) ⇒ Promise 16 | * _inner_ 17 | * [~format](#module_bionode-quickgo..format) : String 18 | * [~limit](#module_bionode-quickgo..limit) : String 19 | * [~gz](#module_bionode-quickgo..gz) : String 20 | * [~goid](#module_bionode-quickgo..goid) : String 21 | * [~aspect](#module_bionode-quickgo..aspect) : String 22 | * [~relType](#module_bionode-quickgo..relType) : String 23 | * [~termUse](#module_bionode-quickgo..termUse) : String 24 | * [~evidence](#module_bionode-quickgo..evidence) : String 25 | * [~source](#module_bionode-quickgo..source) : String 26 | * [~ref](#module_bionode-quickgo..ref) : String 27 | * [~with](#module_bionode-quickgo..with) : String 28 | * [~tax](#module_bionode-quickgo..tax) : String 29 | * [~protein](#module_bionode-quickgo..protein) : String 30 | * [~qualifier](#module_bionode-quickgo..qualifier) : String 31 | * [~db](#module_bionode-quickgo..db) : String 32 | * [~q](#module_bionode-quickgo..q) : String 33 | * [~col](#module_bionode-quickgo..col) : String 34 | * [~id](#module_bionode-quickgo..id) : String 35 | * [~format](#module_bionode-quickgo..format) : String 36 | * [~annotationRequest(fields)](#module_bionode-quickgo..annotationRequest) ⇒ Object 37 | * [~termRequest(fields)](#module_bionode-quickgo..termRequest) ⇒ Object 38 | 39 | 40 | ### bionode-quickgo.GAnnotationAsync(fields) ⇒ Promise 41 | QuickGO Annotation service 42 | 43 | **Kind**: static method of [bionode-quickgo](#module_bionode-quickgo) 44 | 45 | | Param | Type | Description | 46 | | --- | --- | --- | 47 | | fields | Object | valid query fields | 48 | 49 | 50 | ### bionode-quickgo.GAnnotation(fields) ⇒ Stream 51 | QuickGO Annotation service 52 | 53 | **Kind**: static method of [bionode-quickgo](#module_bionode-quickgo) 54 | 55 | | Param | Type | Description | 56 | | --- | --- | --- | 57 | | fields | Object | valid query fields | 58 | 59 | 60 | ### bionode-quickgo.GTerm(fields) ⇒ Stream 61 | GO term information 62 | 63 | **Kind**: static method of [bionode-quickgo](#module_bionode-quickgo) 64 | 65 | | Param | Type | Description | 66 | | --- | --- | --- | 67 | | fields | Object | valid query fields, id required | 68 | 69 | 70 | ### bionode-quickgo.GTermAsync(fields) ⇒ Promise 71 | GO term information 72 | 73 | **Kind**: static method of [bionode-quickgo](#module_bionode-quickgo) 74 | 75 | | Param | Type | Description | 76 | | --- | --- | --- | 77 | | fields | Object | valid query fields, id required | 78 | 79 | 80 | ### bionode-quickgo~format : String 81 | Download file format 82 | 83 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 84 | **Default**: gaf 85 | **Example** 86 | ```js 87 | gaf, gpa, gene2go, proteinList, fasta, tsv 88 | ``` 89 | 90 | ### bionode-quickgo~limit : String 91 | Download limit (number of lines). Note that the default limit is 92 | 10,000 rows, which may not be sufficient for the data set that you are 93 | downloading. To bypass this default, and return the entire data set, 94 | specify a limit of -1. 95 | 96 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 97 | **Default**: '' 98 | **Example** 99 | ```js 100 | 9001, -1 101 | ``` 102 | 103 | ### bionode-quickgo~gz : String 104 | gzips the downloaded file 105 | 106 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 107 | **Default**: false 108 | **Example** 109 | ```js 110 | false, true 111 | ``` 112 | 113 | ### bionode-quickgo~goid : String 114 | GO identifiers either directly or indirectly (descendant GO 115 | identifiers) applied in annotations 116 | 117 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 118 | **Default**: '' 119 | **Example** 120 | ```js 121 | GO:0002080 122 | ``` 123 | 124 | ### bionode-quickgo~aspect : String 125 | Use this to limit the annotations returned to a specific ontology or 126 | ontologies (Molecular Function, Biological Process or Cellular Component) 127 | 128 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 129 | **Default**: '' 130 | **Example** 131 | ```js 132 | F, P, C 133 | ``` 134 | 135 | ### bionode-quickgo~relType : String 136 | By default, QuickGO will display annotations to GO terms that are 137 | related to that specified in the goid parameter by is_a, part_of and 138 | occurs_in relations; this parameter allows you to override that behaviour. 139 | See [Ontology Relations](http://geneontology.org/page/ontology-relations). 140 | 141 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 142 | **Default**: IPO= 143 | **Example** 144 | ```js 145 | ? (ancestor) 146 | = (indentity) 147 | I (is_a) 148 | P (part_of) 149 | O (occurs_in) 150 | R (regulates) 151 | + (positively_regulates) 152 | - (negatively_regulates) 153 | ``` 154 | 155 | ### bionode-quickgo~termUse : String 156 | If you set this parameter to slim, then QuickGO will use the 157 | supplied set of GO identifiers as a slim and will map the annotations up 158 | to these terms. See [here](http://www.ebi.ac.uk/QuickGO/GMultiTerm) for 159 | more details. The default behaviour (termUse=ancestor) is to not perform 160 | this mapping. 161 | 162 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 163 | **Default**: ancestor 164 | **Example** 165 | ```js 166 | ancestor, slim 167 | ``` 168 | 169 | ### bionode-quickgo~evidence : String 170 | Annotation evidence code (Ev) category 171 | 172 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 173 | **Default**: '' 174 | **Example** 175 | ```js 176 | IDA, IC, ISS, IEA 177 | ``` 178 | 179 | ### bionode-quickgo~source : String 180 | Annotation provider 181 | 182 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 183 | **Default**: '' 184 | **Example** 185 | ```js 186 | UniProtKB, HGNC 187 | ``` 188 | 189 | ### bionode-quickgo~ref : String 190 | PubMed or GO reference supporting annotation. Can refer to a specific 191 | reference identifier or category (for category level, use * after ref type) 192 | 193 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 194 | **Default**: '' 195 | **Example** 196 | ```js 197 | PUBMED:*, GO_REF:0000002, 16262699 198 | ``` 199 | 200 | ### bionode-quickgo~with : String 201 | Additional supporting information supplied in IEA, ISS, IPI, IC 202 | evidenced annotations; see: 203 | [GO documentation](http://www.geneontology.org/GO.evidence.shtml). 204 | Can refer to a specific identifier or category (for category level, use * 205 | after with type) 206 | 207 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 208 | **Default**: '' 209 | **Example** 210 | ```js 211 | EC:2.5.1.30, IPR000092, HAMAP:* 212 | ``` 213 | 214 | ### bionode-quickgo~tax : String 215 | NCBI taxonomic identifer of annotated protein 216 | 217 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 218 | **Default**: '' 219 | **Example** 220 | ```js 221 | 9606 222 | ``` 223 | 224 | ### bionode-quickgo~protein : String 225 | Specifies one or more sequence identifiers or accessions from 226 | available database(s) (see DB filter column) 227 | 228 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 229 | **Default**: '' 230 | **Example** 231 | ```js 232 | Mm.363225, P99999 233 | ``` 234 | 235 | ### bionode-quickgo~qualifier : String 236 | Tags that modify the interpretation of an annotation 237 | 238 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 239 | **Default**: '' 240 | **Example** 241 | ```js 242 | NOT, colocalizes_with, contributes_to 243 | ``` 244 | 245 | ### bionode-quickgo~db : String 246 | Protein database (identifier type) 247 | 248 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 249 | **Default**: '' 250 | **Example** 251 | ```js 252 | UniProtKB, UniGene, Ensembl 253 | ``` 254 | 255 | ### bionode-quickgo~q : String 256 | Advanced query. Used to customize GO annotation sets using Boolean 257 | operators. See [Advanced Annotation Search](http://www.ebi.ac.uk/QuickGO/reference.html#advanced_annotation) 258 | 259 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 260 | **Default**: '' 261 | 262 | ### bionode-quickgo~col : String 263 | This parameter, which is currently only applicable to the tsv 264 | download format, allows you to specify a comma-separated list of columns 265 | that you want to be included in the returned data set. The list below shows 266 | the available column names; clicking on the name of a column will take you 267 | to the description of the column in the QuickGO help file. The default set 268 | of columns is shown in bold text. 269 | * [**proteinDB**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinDB) 270 | * [**proteinID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinID) 271 | * [**proteinSymbol**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSymbol) 272 | * [**qualifier**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-qualifier) 273 | * [**goID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goID) 274 | * [**goName**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goName) 275 | * [**aspect**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-aspect) 276 | * [**evidence**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-evidence) 277 | * [**ref**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-ref) 278 | * [**with**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-with) 279 | * [**proteinTaxon**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxon) 280 | * [**date**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-date) 281 | * [**from**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-from) 282 | * [**splice**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-splice) 283 | * [proteinName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinName) 284 | * [proteinSynonym](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSynonym) 285 | * [proteinType](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinType) 286 | * [proteinTaxonName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxonName) 287 | * [orginalTermID](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalTermID) 288 | * [originalGOName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalGOName) 289 | 290 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 291 | **Default**: 'proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice' 292 | **Example** 293 | ```js 294 | 'proteinDB,proteinID,goID,goName,aspect' 295 | ``` 296 | 297 | ### bionode-quickgo~id : String 298 | GO identifier 299 | 300 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 301 | **Default**: none 302 | **Example** 303 | ```js 304 | GO:0003824 305 | ``` 306 | 307 | ### bionode-quickgo~format : String 308 | | Format | Description | 309 | |:-------------------------------------------------------------------------|:------------------------------------------------------------------| 310 | | [mini](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=mini) | Mini Mini HTML, suitable for dynamically embedding in popup boxes | 311 | | [obo](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=obo) | OBO format snippet | 312 | | [oboxml](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=oboxml) | OBO XML format snippet | 313 | 314 | **Kind**: inner property of [bionode-quickgo](#module_bionode-quickgo) 315 | **Default**: obo 316 | 317 | ### bionode-quickgo~annotationRequest(fields) ⇒ Object 318 | generate an annotation request object 319 | 320 | **Kind**: inner method of [bionode-quickgo](#module_bionode-quickgo) 321 | **Returns**: Object - {{method, uri, form} object for request} 322 | 323 | | Param | Type | Description | 324 | | --- | --- | --- | 325 | | fields | Object | valid query fields | 326 | 327 | 328 | ### bionode-quickgo~termRequest(fields) ⇒ Object 329 | generate an term request object 330 | 331 | **Kind**: inner method of [bionode-quickgo](#module_bionode-quickgo) 332 | **Returns**: Object - {{method, uri, form} object for request} 333 | 334 | | Param | Type | Description | 335 | | --- | --- | --- | 336 | | fields | Object | valid query fields | 337 | 338 | 339 | ## License 340 | 341 | MIT [http://jmazz.mit-license.org](http://jmazz.mit-license.org) 342 | -------------------------------------------------------------------------------- /docs/module-bionode-quickgo.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Module: bionode-quickgo 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
19 | 20 |

Module: bionode-quickgo

21 | 22 | 23 | 24 | 25 | 26 | 27 |
28 | 29 |
30 | 31 | 32 | 33 | 34 | 35 |
36 | 37 |
38 |
39 | 40 | 41 |
Access EBI QuickGO REST API with promises and streams.
42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 |
62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 |
Source:
89 |
92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 |
100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 |
119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 |

Members

132 | 133 | 134 | 135 |

(inner) aspect :String

136 | 137 | 138 | 139 | 140 |
141 | Use this to limit the annotations returned to a specific ontology or 142 | ontologies (Molecular Function, Biological Process or Cellular Component) 143 |
144 | 145 | 146 | 147 |
Type:
148 |
    149 |
  • 150 | 151 | String 152 | 153 | 154 |
    • 155 |
156 | 157 | 158 | 159 | 160 | 161 |
162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 |
Default Value:
187 |
    188 |
  • ''
    • 189 |
190 | 191 | 192 | 193 |
Source:
194 |
197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 |
205 | 206 | 207 | 208 | 209 | 210 |
Example
211 | 212 | 
F, P, C
213 | 214 | 215 | 216 | 217 | 218 |

(inner) col :String

219 | 220 | 221 | 222 | 223 |
224 | This parameter, which is currently only applicable to the tsv 225 | download format, allows you to specify a comma-separated list of columns 226 | that you want to be included in the returned data set. The list below shows 227 | the available column names; clicking on the name of a column will take you 228 | to the description of the column in the QuickGO help file. The default set 229 | of columns is shown in bold text. 230 | * [**proteinDB**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinDB) 231 | * [**proteinID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinID) 232 | * [**proteinSymbol**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSymbol) 233 | * [**qualifier**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-qualifier) 234 | * [**goID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goID) 235 | * [**goName**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goName) 236 | * [**aspect**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-aspect) 237 | * [**evidence**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-evidence) 238 | * [**ref**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-ref) 239 | * [**with**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-with) 240 | * [**proteinTaxon**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxon) 241 | * [**date**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-date) 242 | * [**from**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-from) 243 | * [**splice**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-splice) 244 | * [proteinName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinName) 245 | * [proteinSynonym](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSynonym) 246 | * [proteinType](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinType) 247 | * [proteinTaxonName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxonName) 248 | * [orginalTermID](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalTermID) 249 | * [originalGOName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalGOName) 250 |
251 | 252 | 253 | 254 |
Type:
255 |
    256 |
  • 257 | 258 | String 259 | 260 | 261 |
    • 262 |
263 | 264 | 265 | 266 | 267 | 268 |
269 | 270 | 271 | 272 | 273 | 274 | 275 | 276 | 277 | 278 | 279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 | 287 | 288 | 289 | 290 | 291 | 292 | 293 |
Default Value:
294 |
    295 |
  • 'proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice'
    • 296 |
297 | 298 | 299 | 300 |
Source:
301 |
304 | 305 | 306 | 307 | 308 | 309 | 310 | 311 |
312 | 313 | 314 | 315 | 316 | 317 |
Example
318 | 319 | 
'proteinDB,proteinID,goID,goName,aspect'
320 | 321 | 322 | 323 | 324 | 325 |

(inner) db :String

326 | 327 | 328 | 329 | 330 |
331 | Protein database (identifier type) 332 |
333 | 334 | 335 | 336 |
Type:
337 |
    338 |
  • 339 | 340 | String 341 | 342 | 343 |
    • 344 |
345 | 346 | 347 | 348 | 349 | 350 |
351 | 352 | 353 | 354 | 355 | 356 | 357 | 358 | 359 | 360 | 361 | 362 | 363 | 364 | 365 | 366 | 367 | 368 | 369 | 370 | 371 | 372 | 373 | 374 | 375 |
Default Value:
376 |
    377 |
  • ''
    • 378 |
379 | 380 | 381 | 382 |
Source:
383 |
386 | 387 | 388 | 389 | 390 | 391 | 392 | 393 |
394 | 395 | 396 | 397 | 398 | 399 |
Example
400 | 401 | 
UniProtKB, UniGene, Ensembl
402 | 403 | 404 | 405 | 406 | 407 |

(inner) evidence :String

408 | 409 | 410 | 411 | 412 |
413 | Annotation evidence code (Ev) category 414 |
415 | 416 | 417 | 418 |
Type:
419 |
    420 |
  • 421 | 422 | String 423 | 424 | 425 |
    • 426 |
427 | 428 | 429 | 430 | 431 | 432 |
433 | 434 | 435 | 436 | 437 | 438 | 439 | 440 | 441 | 442 | 443 | 444 | 445 | 446 | 447 | 448 | 449 | 450 | 451 | 452 | 453 | 454 | 455 | 456 | 457 |
Default Value:
458 |
    459 |
  • ''
    • 460 |
461 | 462 | 463 | 464 |
Source:
465 |
468 | 469 | 470 | 471 | 472 | 473 | 474 | 475 |
476 | 477 | 478 | 479 | 480 | 481 |
Example
482 | 483 | 
IDA, IC, ISS, IEA
484 | 485 | 486 | 487 | 488 | 489 |

(inner) format :String

490 | 491 | 492 | 493 | 494 |
495 | | Format | Description | 496 | |:-------------------------------------------------------------------------|:------------------------------------------------------------------| 497 | | [mini](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=mini) | Mini Mini HTML, suitable for dynamically embedding in popup boxes | 498 | | [obo](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=obo) | OBO format snippet | 499 | | [oboxml](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824&format=oboxml) | OBO XML format snippet | 500 |
501 | 502 | 503 | 504 |
Type:
505 |
    506 |
  • 507 | 508 | String 509 | 510 | 511 |
    • 512 |
513 | 514 | 515 | 516 | 517 | 518 |
519 | 520 | 521 | 522 | 523 | 524 | 525 | 526 | 527 | 528 | 529 | 530 | 531 | 532 | 533 | 534 | 535 | 536 | 537 | 538 | 539 | 540 | 541 | 542 | 543 |
Default Value:
544 |
    545 |
  • obo
    • 546 |
547 | 548 | 549 | 550 |
Source:
551 |
554 | 555 | 556 | 557 | 558 | 559 | 560 | 561 |
562 | 563 | 564 | 565 | 566 | 567 | 568 | 569 | 570 |

(inner) format :String

571 | 572 | 573 | 574 | 575 |
576 | Download file format 577 |
578 | 579 | 580 | 581 |
Type:
582 |
    583 |
  • 584 | 585 | String 586 | 587 | 588 |
    • 589 |
590 | 591 | 592 | 593 | 594 | 595 |
596 | 597 | 598 | 599 | 600 | 601 | 602 | 603 | 604 | 605 | 606 | 607 | 608 | 609 | 610 | 611 | 612 | 613 | 614 | 615 | 616 | 617 | 618 | 619 | 620 |
Default Value:
621 |
    622 |
  • gaf
    • 623 |
624 | 625 | 626 | 627 |
Source:
628 |
631 | 632 | 633 | 634 | 635 | 636 | 637 | 638 |
639 | 640 | 641 | 642 | 643 | 644 |
Example
645 | 646 | 
gaf, gpa, gene2go, proteinList, fasta, tsv
647 | 648 | 649 | 650 | 651 | 652 |

(inner) goid :String

653 | 654 | 655 | 656 | 657 |
658 | GO identifiers either directly or indirectly (descendant GO 659 | identifiers) applied in annotations 660 |
661 | 662 | 663 | 664 |
Type:
665 |
    666 |
  • 667 | 668 | String 669 | 670 | 671 |
    • 672 |
673 | 674 | 675 | 676 | 677 | 678 |
679 | 680 | 681 | 682 | 683 | 684 | 685 | 686 | 687 | 688 | 689 | 690 | 691 | 692 | 693 | 694 | 695 | 696 | 697 | 698 | 699 | 700 | 701 | 702 | 703 |
Default Value:
704 |
    705 |
  • ''
    • 706 |
707 | 708 | 709 | 710 |
Source:
711 |
714 | 715 | 716 | 717 | 718 | 719 | 720 | 721 |
722 | 723 | 724 | 725 | 726 | 727 |
Example
728 | 729 | 
GO:0002080
730 | 731 | 732 | 733 | 734 | 735 |

(inner) gz :String

736 | 737 | 738 | 739 | 740 |
741 | gzips the downloaded file 742 |
743 | 744 | 745 | 746 |
Type:
747 |
    748 |
  • 749 | 750 | String 751 | 752 | 753 |
    • 754 |
755 | 756 | 757 | 758 | 759 | 760 |
761 | 762 | 763 | 764 | 765 | 766 | 767 | 768 | 769 | 770 | 771 | 772 | 773 | 774 | 775 | 776 | 777 | 778 | 779 | 780 | 781 | 782 | 783 | 784 | 785 |
Default Value:
786 |
    787 |
  • false
    • 788 |
789 | 790 | 791 | 792 |
Source:
793 |
796 | 797 | 798 | 799 | 800 | 801 | 802 | 803 |
804 | 805 | 806 | 807 | 808 | 809 |
Example
810 | 811 | 
false, true
812 | 813 | 814 | 815 | 816 | 817 |

(inner) id :String

818 | 819 | 820 | 821 | 822 |
823 | GO identifier 824 |
825 | 826 | 827 | 828 |
Type:
829 |
    830 |
  • 831 | 832 | String 833 | 834 | 835 |
    • 836 |
837 | 838 | 839 | 840 | 841 | 842 |
843 | 844 | 845 | 846 | 847 | 848 | 849 | 850 | 851 | 852 | 853 | 854 | 855 | 856 | 857 | 858 | 859 | 860 | 861 | 862 | 863 | 864 | 865 | 866 | 867 |
Default Value:
868 |
    869 |
  • none
    • 870 |
871 | 872 | 873 | 874 |
Source:
875 |
878 | 879 | 880 | 881 | 882 | 883 | 884 | 885 |
886 | 887 | 888 | 889 | 890 | 891 |
Example
892 | 893 | 
GO:0003824
894 | 895 | 896 | 897 | 898 | 899 |

(inner) limit :String

900 | 901 | 902 | 903 | 904 |
905 | Download limit (number of lines). Note that the default limit is 906 | 10,000 rows, which may not be sufficient for the data set that you are 907 | downloading. To bypass this default, and return the entire data set, 908 | specify a limit of -1. 909 |
910 | 911 | 912 | 913 |
Type:
914 |
    915 |
  • 916 | 917 | String 918 | 919 | 920 |
    • 921 |
922 | 923 | 924 | 925 | 926 | 927 |
928 | 929 | 930 | 931 | 932 | 933 | 934 | 935 | 936 | 937 | 938 | 939 | 940 | 941 | 942 | 943 | 944 | 945 | 946 | 947 | 948 | 949 | 950 | 951 | 952 |
Default Value:
953 |
    954 |
  • ''
    • 955 |
956 | 957 | 958 | 959 |
Source:
960 |
963 | 964 | 965 | 966 | 967 | 968 | 969 | 970 |
971 | 972 | 973 | 974 | 975 | 976 |
Example
977 | 978 | 
9001, -1
979 | 980 | 981 | 982 | 983 | 984 |

(inner) protein :String

985 | 986 | 987 | 988 | 989 |
990 | Specifies one or more sequence identifiers or accessions from 991 | available database(s) (see DB filter column) 992 |
993 | 994 | 995 | 996 |
Type:
997 |
    998 |
  • 999 | 1000 | String 1001 | 1002 | 1003 |
    • 1004 |
1005 | 1006 | 1007 | 1008 | 1009 | 1010 |
1011 | 1012 | 1013 | 1014 | 1015 | 1016 | 1017 | 1018 | 1019 | 1020 | 1021 | 1022 | 1023 | 1024 | 1025 | 1026 | 1027 | 1028 | 1029 | 1030 | 1031 | 1032 | 1033 | 1034 | 1035 |
Default Value:
1036 |
    1037 |
  • ''
    • 1038 |
1039 | 1040 | 1041 | 1042 |
Source:
1043 |
1046 | 1047 | 1048 | 1049 | 1050 | 1051 | 1052 | 1053 |
1054 | 1055 | 1056 | 1057 | 1058 | 1059 |
Example
1060 | 1061 | 
Mm.363225, P99999
1062 | 1063 | 1064 | 1065 | 1066 | 1067 |

(inner) q :String

1068 | 1069 | 1070 | 1071 | 1072 |
1073 | Advanced query. Used to customize GO annotation sets using Boolean 1074 | operators. See [Advanced Annotation Search](http://www.ebi.ac.uk/QuickGO/reference.html#advanced_annotation) 1075 |
1076 | 1077 | 1078 | 1079 |
Type:
1080 |
    1081 |
  • 1082 | 1083 | String 1084 | 1085 | 1086 |
    • 1087 |
1088 | 1089 | 1090 | 1091 | 1092 | 1093 |
1094 | 1095 | 1096 | 1097 | 1098 | 1099 | 1100 | 1101 | 1102 | 1103 | 1104 | 1105 | 1106 | 1107 | 1108 | 1109 | 1110 | 1111 | 1112 | 1113 | 1114 | 1115 | 1116 | 1117 | 1118 |
Default Value:
1119 |
    1120 |
  • ''
    • 1121 |
1122 | 1123 | 1124 | 1125 |
Source:
1126 |
1129 | 1130 | 1131 | 1132 | 1133 | 1134 | 1135 | 1136 |
1137 | 1138 | 1139 | 1140 | 1141 | 1142 | 1143 | 1144 | 1145 |

(inner) qualifier :String

1146 | 1147 | 1148 | 1149 | 1150 |
1151 | Tags that modify the interpretation of an annotation 1152 |
1153 | 1154 | 1155 | 1156 |
Type:
1157 |
    1158 |
  • 1159 | 1160 | String 1161 | 1162 | 1163 |
    • 1164 |
1165 | 1166 | 1167 | 1168 | 1169 | 1170 |
1171 | 1172 | 1173 | 1174 | 1175 | 1176 | 1177 | 1178 | 1179 | 1180 | 1181 | 1182 | 1183 | 1184 | 1185 | 1186 | 1187 | 1188 | 1189 | 1190 | 1191 | 1192 | 1193 | 1194 | 1195 |
Default Value:
1196 |
    1197 |
  • ''
    • 1198 |
1199 | 1200 | 1201 | 1202 |
Source:
1203 |
1206 | 1207 | 1208 | 1209 | 1210 | 1211 | 1212 | 1213 |
1214 | 1215 | 1216 | 1217 | 1218 | 1219 |
Example
1220 | 1221 | 
NOT, colocalizes_with, contributes_to
1222 | 1223 | 1224 | 1225 | 1226 | 1227 |

(inner) ref :String

1228 | 1229 | 1230 | 1231 | 1232 |
1233 | PubMed or GO reference supporting annotation. Can refer to a specific 1234 | reference identifier or category (for category level, use * after ref type) 1235 |
1236 | 1237 | 1238 | 1239 |
Type:
1240 |
    1241 |
  • 1242 | 1243 | String 1244 | 1245 | 1246 |
    • 1247 |
1248 | 1249 | 1250 | 1251 | 1252 | 1253 |
1254 | 1255 | 1256 | 1257 | 1258 | 1259 | 1260 | 1261 | 1262 | 1263 | 1264 | 1265 | 1266 | 1267 | 1268 | 1269 | 1270 | 1271 | 1272 | 1273 | 1274 | 1275 | 1276 | 1277 | 1278 |
Default Value:
1279 |
    1280 |
  • ''
    • 1281 |
1282 | 1283 | 1284 | 1285 |
Source:
1286 |
1289 | 1290 | 1291 | 1292 | 1293 | 1294 | 1295 | 1296 |
1297 | 1298 | 1299 | 1300 | 1301 | 1302 |
Example
1303 | 1304 | 
PUBMED:*, GO_REF:0000002, 16262699
1305 | 1306 | 1307 | 1308 | 1309 | 1310 |

(inner) relType :String

1311 | 1312 | 1313 | 1314 | 1315 |
1316 | By default, QuickGO will display annotations to GO terms that are 1317 | related to that specified in the goid parameter by is_a, part_of and 1318 | occurs_in relations; this parameter allows you to override that behaviour. 1319 | See [Ontology Relations](http://geneontology.org/page/ontology-relations). 1320 |
1321 | 1322 | 1323 | 1324 |
Type:
1325 |
    1326 |
  • 1327 | 1328 | String 1329 | 1330 | 1331 |
    • 1332 |
1333 | 1334 | 1335 | 1336 | 1337 | 1338 |
1339 | 1340 | 1341 | 1342 | 1343 | 1344 | 1345 | 1346 | 1347 | 1348 | 1349 | 1350 | 1351 | 1352 | 1353 | 1354 | 1355 | 1356 | 1357 | 1358 | 1359 | 1360 | 1361 | 1362 | 1363 |
Default Value:
1364 |
    1365 |
  • IPO=
    • 1366 |
1367 | 1368 | 1369 | 1370 |
Source:
1371 |
1374 | 1375 | 1376 | 1377 | 1378 | 1379 | 1380 | 1381 |
1382 | 1383 | 1384 | 1385 | 1386 | 1387 |
Example
1388 | 1389 | 
? (ancestor)
1390 | = (indentity)
1391 | I (is_a)
1392 | P (part_of)
1393 | O (occurs_in)
1394 | R (regulates)
1395 | + (positively_regulates)
1396 | - (negatively_regulates)
1397 | 1398 | 1399 | 1400 | 1401 | 1402 |

(inner) source :String

1403 | 1404 | 1405 | 1406 | 1407 |
1408 | Annotation provider 1409 |
1410 | 1411 | 1412 | 1413 |
Type:
1414 |
    1415 |
  • 1416 | 1417 | String 1418 | 1419 | 1420 |
    • 1421 |
1422 | 1423 | 1424 | 1425 | 1426 | 1427 |
1428 | 1429 | 1430 | 1431 | 1432 | 1433 | 1434 | 1435 | 1436 | 1437 | 1438 | 1439 | 1440 | 1441 | 1442 | 1443 | 1444 | 1445 | 1446 | 1447 | 1448 | 1449 | 1450 | 1451 | 1452 |
Default Value:
1453 |
    1454 |
  • ''
    • 1455 |
1456 | 1457 | 1458 | 1459 |
Source:
1460 |
1463 | 1464 | 1465 | 1466 | 1467 | 1468 | 1469 | 1470 |
1471 | 1472 | 1473 | 1474 | 1475 | 1476 |
Example
1477 | 1478 | 
UniProtKB, HGNC
1479 | 1480 | 1481 | 1482 | 1483 | 1484 |

(inner) tax :String

1485 | 1486 | 1487 | 1488 | 1489 |
1490 | NCBI taxonomic identifer of annotated protein 1491 |
1492 | 1493 | 1494 | 1495 |
Type:
1496 |
    1497 |
  • 1498 | 1499 | String 1500 | 1501 | 1502 |
    • 1503 |
1504 | 1505 | 1506 | 1507 | 1508 | 1509 |
1510 | 1511 | 1512 | 1513 | 1514 | 1515 | 1516 | 1517 | 1518 | 1519 | 1520 | 1521 | 1522 | 1523 | 1524 | 1525 | 1526 | 1527 | 1528 | 1529 | 1530 | 1531 | 1532 | 1533 | 1534 |
Default Value:
1535 |
    1536 |
  • ''
    • 1537 |
1538 | 1539 | 1540 | 1541 |
Source:
1542 |
1545 | 1546 | 1547 | 1548 | 1549 | 1550 | 1551 | 1552 |
1553 | 1554 | 1555 | 1556 | 1557 | 1558 |
Example
1559 | 1560 | 
9606
1561 | 1562 | 1563 | 1564 | 1565 | 1566 |

(inner) termUse :String

1567 | 1568 | 1569 | 1570 | 1571 |
1572 | If you set this parameter to slim, then QuickGO will use the 1573 | supplied set of GO identifiers as a slim and will map the annotations up 1574 | to these terms. See [here](http://www.ebi.ac.uk/QuickGO/GMultiTerm) for 1575 | more details. The default behaviour (termUse=ancestor) is to not perform 1576 | this mapping. 1577 |
1578 | 1579 | 1580 | 1581 |
Type:
1582 |
    1583 |
  • 1584 | 1585 | String 1586 | 1587 | 1588 |
    • 1589 |
1590 | 1591 | 1592 | 1593 | 1594 | 1595 |
1596 | 1597 | 1598 | 1599 | 1600 | 1601 | 1602 | 1603 | 1604 | 1605 | 1606 | 1607 | 1608 | 1609 | 1610 | 1611 | 1612 | 1613 | 1614 | 1615 | 1616 | 1617 | 1618 | 1619 | 1620 |
Default Value:
1621 |
    1622 |
  • ancestor
    • 1623 |
1624 | 1625 | 1626 | 1627 |
Source:
1628 |
1631 | 1632 | 1633 | 1634 | 1635 | 1636 | 1637 | 1638 |
1639 | 1640 | 1641 | 1642 | 1643 | 1644 |
Example
1645 | 1646 | 
ancestor, slim
1647 | 1648 | 1649 | 1650 | 1651 | 1652 |

(inner) with :String

1653 | 1654 | 1655 | 1656 | 1657 |
1658 | Additional supporting information supplied in IEA, ISS, IPI, IC 1659 | evidenced annotations; see: 1660 | [GO documentation](http://www.geneontology.org/GO.evidence.shtml). 1661 | Can refer to a specific identifier or category (for category level, use * 1662 | after with type) 1663 |
1664 | 1665 | 1666 | 1667 |
Type:
1668 |
    1669 |
  • 1670 | 1671 | String 1672 | 1673 | 1674 |
    • 1675 |
1676 | 1677 | 1678 | 1679 | 1680 | 1681 |
1682 | 1683 | 1684 | 1685 | 1686 | 1687 | 1688 | 1689 | 1690 | 1691 | 1692 | 1693 | 1694 | 1695 | 1696 | 1697 | 1698 | 1699 | 1700 | 1701 | 1702 | 1703 | 1704 | 1705 | 1706 |
Default Value:
1707 |
    1708 |
  • ''
    • 1709 |
1710 | 1711 | 1712 | 1713 |
Source:
1714 |
1717 | 1718 | 1719 | 1720 | 1721 | 1722 | 1723 | 1724 |
1725 | 1726 | 1727 | 1728 | 1729 | 1730 |
Example
1731 | 1732 | 
EC:2.5.1.30, IPR000092, HAMAP:*
1733 | 1734 | 1735 | 1736 | 1737 | 1738 | 1739 | 1740 |

Methods

1741 | 1742 | 1743 | 1744 | 1745 | 1746 | 1747 |

(static) GAnnotation(fields) → {Stream}

1748 | 1749 | 1750 | 1751 | 1752 | 1753 |
1754 | QuickGO Annotation service 1755 |
1756 | 1757 | 1758 | 1759 | 1760 | 1761 | 1762 | 1763 | 1764 | 1765 |
Parameters:
1766 | 1767 | 1768 | 1769 | 1770 | 1771 | 1772 | 1773 | 1774 | 1775 | 1776 | 1777 | 1778 | 1779 | 1780 | 1781 | 1782 | 1783 | 1784 | 1785 | 1786 | 1787 | 1788 | 1789 | 1790 | 1791 | 1792 | 1793 | 1801 | 1802 | 1803 | 1804 | 1805 | 1806 | 1807 | 1808 | 1809 | 1810 | 1811 |
NameTypeDescription
fields 1794 | 1795 | 1796 | Object 1797 | 1798 | 1799 | 1800 | valid query fields
1812 | 1813 | 1814 | 1815 | 1816 | 1817 | 1818 |
1819 | 1820 | 1821 | 1822 | 1823 | 1824 | 1825 | 1826 | 1827 | 1828 | 1829 | 1830 | 1831 | 1832 | 1833 | 1834 | 1835 | 1836 | 1837 | 1838 | 1839 | 1840 | 1841 | 1842 | 1843 | 1844 | 1845 |
Source:
1846 |
1849 | 1850 | 1851 | 1852 | 1853 | 1854 | 1855 | 1856 |
1857 | 1858 | 1859 | 1860 | 1861 | 1862 | 1863 | 1864 | 1865 | 1866 | 1867 | 1868 | 1869 | 1870 |
Returns:
1871 | 1872 | 1873 | 1874 | 1875 |
1876 |
1877 | Type 1878 |
1879 |
1880 | 1881 | Stream 1882 | 1883 | 1884 |
1885 |
1886 | 1887 | 1888 | 1889 | 1890 | 1891 | 1892 | 1893 | 1894 | 1895 | 1896 |

(static) GAnnotationAsync(fields) → {Promise}

1897 | 1898 | 1899 | 1900 | 1901 | 1902 |
1903 | QuickGO Annotation service 1904 |
1905 | 1906 | 1907 | 1908 | 1909 | 1910 | 1911 | 1912 | 1913 | 1914 |
Parameters:
1915 | 1916 | 1917 | 1918 | 1919 | 1920 | 1921 | 1922 | 1923 | 1924 | 1925 | 1926 | 1927 | 1928 | 1929 | 1930 | 1931 | 1932 | 1933 | 1934 | 1935 | 1936 | 1937 | 1938 | 1939 | 1940 | 1941 | 1942 | 1950 | 1951 | 1952 | 1953 | 1954 | 1955 | 1956 | 1957 | 1958 | 1959 | 1960 |
NameTypeDescription
fields 1943 | 1944 | 1945 | Object 1946 | 1947 | 1948 | 1949 | valid query fields
1961 | 1962 | 1963 | 1964 | 1965 | 1966 | 1967 |
1968 | 1969 | 1970 | 1971 | 1972 | 1973 | 1974 | 1975 | 1976 | 1977 | 1978 | 1979 | 1980 | 1981 | 1982 | 1983 | 1984 | 1985 | 1986 | 1987 | 1988 | 1989 | 1990 | 1991 | 1992 | 1993 | 1994 |
Source:
1995 |
1998 | 1999 | 2000 | 2001 | 2002 | 2003 | 2004 | 2005 |
2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | 2018 | 2019 |
Returns:
2020 | 2021 | 2022 | 2023 | 2024 |
2025 |
2026 | Type 2027 |
2028 |
2029 | 2030 | Promise 2031 | 2032 | 2033 |
2034 |
2035 | 2036 | 2037 | 2038 | 2039 | 2040 | 2041 | 2042 | 2043 | 2044 | 2045 |

(static) GTerm(fields) → {Stream}

2046 | 2047 | 2048 | 2049 | 2050 | 2051 |
2052 | GO term information 2053 |
2054 | 2055 | 2056 | 2057 | 2058 | 2059 | 2060 | 2061 | 2062 | 2063 |
Parameters:
2064 | 2065 | 2066 | 2067 | 2068 | 2069 | 2070 | 2071 | 2072 | 2073 | 2074 | 2075 | 2076 | 2077 | 2078 | 2079 | 2080 | 2081 | 2082 | 2083 | 2084 | 2085 | 2086 | 2087 | 2088 | 2089 | 2090 | 2091 | 2099 | 2100 | 2101 | 2102 | 2103 | 2104 | 2105 | 2106 | 2107 | 2108 | 2109 |
NameTypeDescription
fields 2092 | 2093 | 2094 | Object 2095 | 2096 | 2097 | 2098 | valid query fields, id required
2110 | 2111 | 2112 | 2113 | 2114 | 2115 | 2116 |
2117 | 2118 | 2119 | 2120 | 2121 | 2122 | 2123 | 2124 | 2125 | 2126 | 2127 | 2128 | 2129 | 2130 | 2131 | 2132 | 2133 | 2134 | 2135 | 2136 | 2137 | 2138 | 2139 | 2140 | 2141 | 2142 | 2143 |
Source:
2144 |
2147 | 2148 | 2149 | 2150 | 2151 | 2152 | 2153 | 2154 |
2155 | 2156 | 2157 | 2158 | 2159 | 2160 | 2161 | 2162 | 2163 | 2164 | 2165 | 2166 | 2167 | 2168 |
Returns:
2169 | 2170 | 2171 | 2172 | 2173 |
2174 |
2175 | Type 2176 |
2177 |
2178 | 2179 | Stream 2180 | 2181 | 2182 |
2183 |
2184 | 2185 | 2186 | 2187 | 2188 | 2189 | 2190 | 2191 | 2192 | 2193 | 2194 |

(static) GTermAsync(fields) → {Promise}

2195 | 2196 | 2197 | 2198 | 2199 | 2200 |
2201 | GO term information 2202 |
2203 | 2204 | 2205 | 2206 | 2207 | 2208 | 2209 | 2210 | 2211 | 2212 |
Parameters:
2213 | 2214 | 2215 | 2216 | 2217 | 2218 | 2219 | 2220 | 2221 | 2222 | 2223 | 2224 | 2225 | 2226 | 2227 | 2228 | 2229 | 2230 | 2231 | 2232 | 2233 | 2234 | 2235 | 2236 | 2237 | 2238 | 2239 | 2240 | 2248 | 2249 | 2250 | 2251 | 2252 | 2253 | 2254 | 2255 | 2256 | 2257 | 2258 |
NameTypeDescription
fields 2241 | 2242 | 2243 | Object 2244 | 2245 | 2246 | 2247 | valid query fields, id required
2259 | 2260 | 2261 | 2262 | 2263 | 2264 | 2265 |
2266 | 2267 | 2268 | 2269 | 2270 | 2271 | 2272 | 2273 | 2274 | 2275 | 2276 | 2277 | 2278 | 2279 | 2280 | 2281 | 2282 | 2283 | 2284 | 2285 | 2286 | 2287 | 2288 | 2289 | 2290 | 2291 | 2292 |
Source:
2293 |
2296 | 2297 | 2298 | 2299 | 2300 | 2301 | 2302 | 2303 |
2304 | 2305 | 2306 | 2307 | 2308 | 2309 | 2310 | 2311 | 2312 | 2313 | 2314 | 2315 | 2316 | 2317 |
Returns:
2318 | 2319 | 2320 | 2321 | 2322 |
2323 |
2324 | Type 2325 |
2326 |
2327 | 2328 | Promise 2329 | 2330 | 2331 |
2332 |
2333 | 2334 | 2335 | 2336 | 2337 | 2338 | 2339 | 2340 | 2341 | 2342 | 2343 |

(inner) annotationRequest(fields) → {Object}

2344 | 2345 | 2346 | 2347 | 2348 | 2349 |
2350 | generate an annotation request object 2351 |
2352 | 2353 | 2354 | 2355 | 2356 | 2357 | 2358 | 2359 | 2360 | 2361 |
Parameters:
2362 | 2363 | 2364 | 2365 | 2366 | 2367 | 2368 | 2369 | 2370 | 2371 | 2372 | 2373 | 2374 | 2375 | 2376 | 2377 | 2378 | 2379 | 2380 | 2381 | 2382 | 2383 | 2384 | 2385 | 2386 | 2387 | 2388 | 2389 | 2397 | 2398 | 2399 | 2400 | 2401 | 2402 | 2403 | 2404 | 2405 | 2406 | 2407 |
NameTypeDescription
fields 2390 | 2391 | 2392 | Object 2393 | 2394 | 2395 | 2396 | valid query fields
2408 | 2409 | 2410 | 2411 | 2412 | 2413 | 2414 |
2415 | 2416 | 2417 | 2418 | 2419 | 2420 | 2421 | 2422 | 2423 | 2424 | 2425 | 2426 | 2427 | 2428 | 2429 | 2430 | 2431 | 2432 | 2433 | 2434 | 2435 | 2436 | 2437 | 2438 | 2439 | 2440 | 2441 |
Source:
2442 |
2445 | 2446 | 2447 | 2448 | 2449 | 2450 | 2451 | 2452 |
2453 | 2454 | 2455 | 2456 | 2457 | 2458 | 2459 | 2460 | 2461 | 2462 | 2463 | 2464 | 2465 | 2466 |
Returns:
2467 | 2468 | 2469 |
2470 | {{method, uri, form} object for request} 2471 |
2472 | 2473 | 2474 | 2475 |
2476 |
2477 | Type 2478 |
2479 |
2480 | 2481 | Object 2482 | 2483 | 2484 |
2485 |
2486 | 2487 | 2488 | 2489 | 2490 | 2491 | 2492 | 2493 | 2494 | 2495 | 2496 |

(inner) termRequest(fields) → {Object}

2497 | 2498 | 2499 | 2500 | 2501 | 2502 |
2503 | generate an term request object 2504 |
2505 | 2506 | 2507 | 2508 | 2509 | 2510 | 2511 | 2512 | 2513 | 2514 |
Parameters:
2515 | 2516 | 2517 | 2518 | 2519 | 2520 | 2521 | 2522 | 2523 | 2524 | 2525 | 2526 | 2527 | 2528 | 2529 | 2530 | 2531 | 2532 | 2533 | 2534 | 2535 | 2536 | 2537 | 2538 | 2539 | 2540 | 2541 | 2542 | 2550 | 2551 | 2552 | 2553 | 2554 | 2555 | 2556 | 2557 | 2558 | 2559 | 2560 |
NameTypeDescription
fields 2543 | 2544 | 2545 | Object 2546 | 2547 | 2548 | 2549 | valid query fields
2561 | 2562 | 2563 | 2564 | 2565 | 2566 | 2567 |
2568 | 2569 | 2570 | 2571 | 2572 | 2573 | 2574 | 2575 | 2576 | 2577 | 2578 | 2579 | 2580 | 2581 | 2582 | 2583 | 2584 | 2585 | 2586 | 2587 | 2588 | 2589 | 2590 | 2591 | 2592 | 2593 | 2594 |
Source:
2595 |
2598 | 2599 | 2600 | 2601 | 2602 | 2603 | 2604 | 2605 |
2606 | 2607 | 2608 | 2609 | 2610 | 2611 | 2612 | 2613 | 2614 | 2615 | 2616 | 2617 | 2618 | 2619 |
Returns:
2620 | 2621 | 2622 |
2623 | {{method, uri, form} object for request} 2624 |
2625 | 2626 | 2627 | 2628 |
2629 |
2630 | Type 2631 |
2632 |
2633 | 2634 | Object 2635 | 2636 | 2637 |
2638 |
2639 | 2640 | 2641 | 2642 | 2643 | 2644 | 2645 | 2646 | 2647 | 2648 | 2649 | 2650 |
2651 | 2652 |
2653 | 2654 | 2655 | 2656 | 2657 |
2658 | 2659 | 2662 | 2663 |
2664 | 2665 |
2666 | Documentation generated by JSDoc 3.4.0 on Tue Dec 22 2015 21:10:42 GMT-0500 (EST) 2667 |
2668 | 2669 | 2670 | 2671 | 2672 | --------------------------------------------------------------------------------