├── .gitignore
├── package.json
├── README.md
├── go.js
├── lib
    └── go_gene_annotation.js
└── CODE_OF_CONDUCT.md


/.gitignore:
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1 | .DS_Store
2 | node_modules
3 | coverage
4 | *.log
5 | .coveralls.yml
6 | 


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/package.json:
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 1 | {
 2 |   "name": "bionode-go",
 3 |   "version": "1.0.0",
 4 |   "description": "Bionode module for Gene Ontology",
 5 |   "main": "go.js",
 6 |   "scripts": {
 7 |     "test": "echo \"Error: no test specified\" && exit 1"
 8 |   },
 9 |   "repository": {
10 |     "type": "git",
11 |     "url": "https://github.com/bionode/bionode-go.git"
12 |   },
13 |   "keywords": [
14 |     "bio",
15 |     "bioinformatics",
16 |     "biology",
17 |     "bionode",
18 |     "gene",
19 |     "ontology"
20 |   ],
21 |   "author": "Boris Adryan",
22 |   "license": "MIT",
23 |   "bugs": {
24 |     "url": "https://github.com/bionode/bionode-go/issues"
25 |   },
26 |   "homepage": "https://github.com/bionode/bionode-go",
27 |   "dependencies": {
28 |     "mysql": "^2.5.4",
29 |     "through2": "^0.6.3"
30 |   }
31 | }
32 | 


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/README.md:
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 1 | bionode-go
 2 | ==========
 3 | 
 4 | Gene Ontology in Bionode
 5 | 
 6 | Will provide access to the public MySQL services of the Gene Ontology.
 7 | 
 8 | Have a look at go.js how to use go\_gene\_annotation.js to retrieve GO annotations for a particular gene. It's not much, but it's a start for your own explorations. All of GO can be queried via internet access to their MySQL server. Details and sample queries available here: http://amigo.geneontology.org/goose
 9 | <br>
10 | 
11 | <b>Note:</b> Another quick and dirty way to associate GO terms to target genes is the use of InterMine via their npm module. Alex from FlyMine wrote on 11/12/2014: "Sorry about the lack of good doc links on the NPM page - our API docs
12 | are here: http://intermine.github.io/imjs/, and http://alexkalderimis.github.io/imjs/ (mine are sometimes
13 | a little ahead of intermine's). I will make sure that they are more
14 | discoverable in the future.
15 | 
16 | We also have some documentation here:
17 | http://intermine.readthedocs.org/en/latest/web-services/#api-and-client-libraries
18 | 
19 | With some examples here:
20 | http://intermine.readthedocs.org/en/latest/web-services/how-do-i/#howtows
21 | 
22 | If there are some examples you want to see, just let us know, and we
23 | will add them to the how-do-I section."
24 | 
25 | All best,
26 | 
27 | Alex Kalderimis
28 | 


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/go.js:
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 1 | // demoes how GO annotation can be retrieved
 2 | 
 3 | // load the relevant module
 4 | var GOquery = require('./lib/go_gene_annotation.js')
 5 | 
 6 | // initiate contact to GO MySQL server at EBI
 7 | GOquery.start_session();
 8 | 
 9 | // ask for a fly ("FB") gene
10 | GOquery.direct_annotation.write({
11 |   geneID: 'FBgn0262139',
12 |   dbName: 'FB'
13 | })
14 | 
15 | // retrieve annotation
16 | GOquery.direct_annotation
17 | .on('data', console.log)
18 | .on('error', function (err) {
19 |   return console.error('Something went wrong here: ', err)
20 | })
21 | 
22 | // how to efficiently query for many genes
23 | // NOTE: this still needs implementing: collate a few genes before firing up a query with all
24 | // with parameters determined in maxBatchTimeout and maxBatchSize (go_gene_annotation.js)
25 | var seriesOfGenesfromFB = ['FBgn0262139','FBgn0003720','FBgn0001077','FBgn0000166','FBgn0003866','FBgn0011655','FBgn0024250','FBgn0001150','FBgn0004915','FBgn0040765','FBgn0003900','FBgn0000028','FBgn0000099']; // 14 genes
26 | var seriesofGenesDB = 'FB';
27 | 
28 | for (i = 0; i < seriesOfGenesfromFB.length; i++) { 
29 |   GOquery.direct_annotation.write({
30 |   geneID: seriesOfGenesfromFB[i],
31 |   dbName: seriesofGenesDB
32 |   })
33 | }
34 | 
35 | GOquery.direct_annotation
36 | .on('data', console.log)
37 | .on('error', function (err) {
38 |   return console.error('Something went wrong here: ', err)
39 | })
40 | 
41 | // disconnect from the EBI database
42 | GOquery.end_session();


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/lib/go_gene_annotation.js:
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 1 | var through    = require('through2');
 2 | var mysql      = require('mysql');
 3 | var connection = undefined;
 4 | var maxBatchTimeout = 1000;
 5 | var maxBatchSize = 20; 
 6 | 
 7 | var GO = exports
 8 | 
 9 | // call this function to initiate a database connection with the public server at EBI
10 | // set different batch query options where needed.
11 | GO.start_session = function(fastOptions) {
12 | 	connection = mysql.createConnection({
13 | 	    host     : 'mysql.ebi.ac.uk',
14 | 	    user     : 'go_select',
15 | 	    database : 'go_latest',
16 | 	    password : 'amigo',
17 | 	    port     : 4085
18 | 	  });
19 | 	connection.connect();
20 | }
21 | 
22 | // call this function for good practice to formally end the database connection
23 | GO.end_session = function () {
24 | 	connection.end();
25 | } 
26 | 
27 | // call this function with a geneID and source DB for getting all direct gene annotations
28 | // http://amigo.geneontology.org/goose provides some more help until I get around to full doc
29 | GO.direct_annotation = through.obj(function transform(obj, enc, next) {
30 |   var self = this;
31 | 	connection.query("SELECT gene_product.symbol, gene_product.full_name, dbxref.xref_dbname, dbxref.xref_key, species.genus, species.species, association.is_not, evidence.code, term.acc, term.name FROM gene_product INNER JOIN dbxref ON (gene_product.dbxref_id=dbxref.id) INNER JOIN species ON (gene_product.species_id=species.id) INNER JOIN association ON (gene_product.id=association.gene_product_id) INNER JOIN evidence ON (association.id=evidence.association_id) INNER JOIN term ON (association.term_id=term.id) WHERE dbxref.xref_key = '"+obj.geneID+"' AND dbxref.xref_dbname = '"+obj.dbName+"';", function(err, rows, fields) {
32 |     if (err) return self.emit('error', err);
33 |     rows.forEach(function(row) {
34 |       self.push(row);
35 |       //console.log('The solution is: ', rows[0]);
36 |     });
37 |   });
38 |   next();
39 | })


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/CODE_OF_CONDUCT.md:
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 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 | 


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