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vsm-dictionary-ensembl-genomes

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Summary

vsm-dictionary-ensembl-genomes is an implementation of the 'VsmDictionary' parent-class/interface (from the package vsm-dictionary), that uses the EBI Search RESTful Web Services to interact with the Ensembl genome database for non-vertebrate species and translate the provided gene information into a VSM-specific format.

Install

Run: npm install

Example use

Node.js

Create a directory test-dir and inside run npm install vsm-dictionary-ensembl-gemones. Then, create a test.js file and include this code for example:

const DictionaryEnsemblGenomes = require('vsm-dictionary-ensembl-genomes');
const dict = new DictionaryEnsemblGenomes({log: true});

dict.getEntryMatchesForString('tp53', { page: 1, perPage: 10 }, 
  (err, res) => {
    if (err) 
      console.log(JSON.stringify(err, null, 4));
    else
      console.log(JSON.stringify(res, null, 4));
  }
);

Then, run node test.js

Browsers

<script src="https://unpkg.com/vsm-dictionary-ensembl-genomes@^1.0.0/dist/vsm-dictionary-ensembl-genomes.min.js"></script>

after which it is accessible as the global variable VsmDictionaryEnsemblGenomes.

Tests

Run npm test, which runs the source code tests with Mocha.
If you want to quickly live test the EBI Search API, go to the test directory and run:

node getEntries.test.js
node getEntryMatchesForString.test.js

'Build' configuration

To use a VsmDictionary in Node.js, one can simply run npm install and then use require(). But it is also convenient to have a version of the code that can just be loaded via a <script>-tag in the browser.

Therefore, we included webpack.config.js, which is a Webpack configuration file for generating such a browser-ready package.

By running npm build, the built file will appear in a 'dist' subfolder. You can use it by including: <script src="../dist/vsm-dictionary-ensembl-genomes.min.js"></script> in the header of an HTML file.

Specification

Like all VsmDictionary subclass implementations, this package follows the parent class specification. In the next sections we will explain the mapping between the data offered by EBI Search's API and the corresponding VSM objects. Find the documentation for the API here: https://www.ebi.ac.uk/ebisearch/documentation.ebi

Note that if we receive an error response from the EBI Search servers (see the URL requests for getEnties and getEntryMatchesForString below) that is not a JSON string that we can parse, we formulate the error as a JSON object ourselves in the following format:

{
  status: <number>,
  error: <response> 
}

where the response from the server is JSON stringified.

Map Ensembl Genomes to DictInfo VSM object

This specification relates to the function:
getDictInfos(options, cb)

If the options.filter.id is not properly defined or the http://www.ensemblgenomes.org dictID is included in the list of ids used for filtering, getDictInfos returns a static object with the following properties:

Otherwise, an empty result is returned.

Map Ensembl Genomes to Entry VSM object

This specification relates to the function:
getEntries(options, cb)

Firstly, if the options.filter.dictID is properly defined and in the list of dictIDs the http://www.ensemblgenomes.org dictID is not included, then an empty array of entry objects is returned.

If the options.filter.id is properly defined (with IDs like http://www.ensemblgenomes.org/id/AT3G52430) then we use a query like this:

https://www.ebi.ac.uk/ebisearch/ws/rest/ensemblGenomes_gene/entry/Z208_01625,EMPG_14124,AT3G52430?fields=id%2Cname%2Cdescription%2Cgene_synonyms%2Cspecies&format=json

For the above URL, we provide a brief description for each sub-part:

  • The first part refers to the EBI Search's main REST endpoint: https://www.ebi.ac.uk/ebisearch/ws/rest/
  • The second part refers to the domain of search (ensemblGenomes_gene)
  • The third part refers to the entry endpoint (which allows us to request for entry information associated with entry identifiers)
  • The fourth part is the entry IDs, comma separated (we extract the last part of the EnsemblGenomes-specific URI for each ID). Note that for VSM the URI ID is something like: http://www.ensemblgenomes.org/id/Z208_01625, while the EnsemblGenomes entry IDs are created based on the IDs imported from external sources (for more info see here).
  • The fifth part is the fields of interest - i.e. the information related to the entries that we will map to VSM-entry properties. For a complete list of the available fields for the ensemblGenomes_gene domain, see: https://www.ebi.ac.uk/ebisearch/metadata.ebi?db=ensemblGenomes_gene
  • The last part defines the format of the returned data (JSON)

Otherwise, we ask for all ids (by default id sorted) with this query:

https://www.ebi.ac.uk/ebisearch/ws/rest/ensemblGenomes_gene?query=domain_source:ensemblGenomes_gene&fields=id%2Cname%2Cdescription%2Cgene_synonyms%2Cspecies&sort=id&size=50&start=0&format=json

Note that depending on the options.page and options.perPage options we adjust the size and start parameters accordingly. The size requested can be between 0 and 100 and if its not in those limits or not properly defined, we set it to the default page size which is 50. The start (offset, zero-based) can be between 0 and 1000000. The default value for start is 0 (if options.page is not properly defined) and if the (page size) * (#page requested - 1) exceeds 1000000, then we set it to 999999, allowing thus the retrieval of the last entry (EBI Search does not allow us to retrieve more than the 1000000th entry of a domain).

Only when requesting for specific IDs, we sort the results depending on the options.sort value: results can be either id-sorted or str-sorted, according to the specification of the parent 'VsmDictionary' class. We then prune these results according to the values options.page (default: 1) and options.perPage (default: 50).

When using the EBI search API, we get back a JSON object with an entries property, which has as a value an array of objects (the entries). Every entry object has a fields property whose value is an object with properties all the fields that we defined in the initial query. We now provide a mapping of these fields to VSM-entry specific properties:

EnsemblGenomes field Type Required VSM entry/match object property Notes
id Array YES id,str,terms[0].str The VSM entry id is the full URI. We use the simple id string for str when name is empty.
name Array NO str,terms[0].str We use the first element only.
description Array NO descr We use the first element only
gene_synonyms Array NO terms[i].str We map the whole array
species Array NO z.species We use the first element only

Note that the above mapping describes what we as developers thought as the most reasonable. There is though a global option optimap that you can pass to the DictionaryEnsemblGenomes object, which optimizes the above mapping for curator clarity and use. The default value is true and what changes in the mapping table above (which is the mapping for optimap: false actually) is that the VSM's descr entry/match object property takes the combined value of the species (first two words), the gene identifier and synonyms (id, gene_synonym) and the description (in that order). The reason behind this is that the description is sometimes the same for different genes or even empty when optimap: false and thus not distinguishable, so we had to provide a more clarified description string for each entry.

Map Ensembl Genomes to Match VSM object

This specification relates to the function:
getEntryMatchesForString(str, options, cb)

Firstly, if the options.filter.dictID is properly defined and in the list of dictIDs the http://www.ensemblgenomes.org dictID is not included, then an empty array of match objects is returned.

Otherwise, an example of a URL string that is being built and send to the EBI Search's REST API when requesting for tp53, is:

https://www.ebi.ac.uk/ebisearch/ws/rest/ensemblGenomes_gene?query=tp53&fields=id%2Cname%2Cdescription%2Cgene_synonyms%2Cspecies&size=20&start=0&format=json

The fields requested are the same as in the getEntries(options, cb) case as well as the mapping shown in the table above. Also for the size and start parameters the same things apply as in the getEntries specification.

No sorting whatsoever is done on the server or client side.

License

This project is licensed under the AGPL license - see LICENSE.md.