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README.md

phenoscaperb

gem version Build Status codecov.io

phenoscaperb is a low level client for the Phenoscape API

Phenoscape is a datastore of computable phenotypes for studies of evolution and genetics.

Changes

For changes see the Changelog

API

Taxa

  • /taxon - Phenoscape::Taxon.taxon
  • /taxon/with_rank - Phenoscape::Taxon.taxon_with_rank
  • /taxon/with_phenotype - Phenoscape::Taxon.with_phenotype
  • /taxon/annotations - Phenoscape::Taxon.annotations

Genes

  • /gene - Phenoscape::Gene.gene
  • /gene/search - Phenoscape::Gene.search
  • /gene/affecting_entity_phenotype - Phenoscape::Gene.affecting_entity_phenotype

Terms

  • /term - Phenoscape::Terms.term
  • /term/search - Phenoscape::Terms.search
  • /term/search_classes - Phenoscape::Terms.search_classes
  • /term/label - Phenoscape::Terms.label
  • /term/labels - Phenoscape::Terms.labels
  • /term/classification - Phenoscape::Terms.classification
  • /term/all_ancestors - Phenoscape::Terms.all_ancestors
  • /term/all_descendants - Phenoscape::Terms.all_descendants
  • /term/least_common_subsumers - Phenoscape::Terms.least_common_subsumers

Ontotrace

  • /ontotrace - Phenoscape::Ontotrace.ontotrace

Studies

  • /studies/query - Phenoscape::Studies.query
  • /studies/taxa - Phenoscape::Studies.taxa
  • /studies/phenotypes - Phenoscape::Studies.phenotypes
  • /studies/matrix - Phenoscape::Studies.matrix

Install

Development version

git clone git@github.com:phenoscape/phenoscaperb.git
cd phenoscaperb
rake install

Release version

gem install phenoscaperb

Setup

This is most likely not needed ...

You can swap out the base URL by passing named options in a block to Phenoscape.configuration.

This will also be the way to set up other user options, if any are needed down the road (though base_url is the only one right now).

Phenoscape.configuration do |config|
  config.base_url = "the new url"
end

in Ruby

A few examples

Phenoscape::Taxa.taxon

require 'phenoscaperb'
tax = Phenoscape::Taxa
tax.taxon(iri: "http://purl.obolibrary.org/obo/VTO_0067193")
#> => {"rank"=>{"@id"=>"http://purl.obolibrary.org/obo/TAXRANK_0000006", "label"=>"species"},
#>  "label"=>"Apterichtus equatorialis",
#>  "extinct"=>false,
#>  "common_name"=>"Finless eel",
#>  "@id"=>"http://purl.obolibrary.org/obo/VTO_0067193"}

Phenoscape::Genes.gene

require 'phenoscaperb'
ge = Phenoscape::Genes
ge.gene(iri: "http://www.informatics.jax.org/marker/MGI:104842")
#> => {"@id"=>"http://www.informatics.jax.org/marker/MGI:104842", "label"=>"Coil", "taxon"=>{"@id"=>"http://purl.obolibrary.org/obo/NCBITaxon_10090", "label"=>"Mus musculus"}}

Phenoscape::Ontotrace.ontotrace

require 'phenoscaperb'
onto = Phenoscape::Ontotrace
onto.ontotrace(taxon: "<http://purl.obolibrary.org/obo/VTO_0058051>", entity: "<http://purl.obolibrary.org/obo/BFO_0000050>", ret: "text")
#> => <?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n<nexml xmlns=\"http://www.nexml.org/2009\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:dwc=\"http://rs.tdwg.org/dwc/terms/\" xmlns:obo=\"http://purl.obolibrary.org/obo/\" xmlns:ps=\"http://vocab.phenoscape.org/\" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" version=\"0.9\" xsi:schemaLocation=\"http://www.nexml.org/2009 http://www.nexml.org/2009/nexml.xsd http://www.bioontologies.org/obd/schema/pheno http://purl.org/phenoscape/phenoxml.xsd\">\r\n  <meta xsi:type=\"LiteralMeta\" property=\"dc:creator\" />\r\n  <meta xsi:type=\"LiteralMeta\" property=\"dc:description\">Generated from the Phenoscape Knowledgebase on 2017-12-19 by Ontotrace query:\r\n* taxa: &lt;http://purl.obolibrary.org/obo/VTO_0058051&gt;\r\n* entities: &lt;http://purl.obolibrary.org/obo/BFO_0000050&gt;</meta>\r\n  <otus id=\"t4813128d-4f2b-417f-bf5a-d568dd584a64\" />\r\n  <characters id=\"c49fb5508-08a8-4252-93eb-50ac042eca46\" xsi:type=\"StandardCells\" otus=\"t4813128d-4f2b-417f-bf5a-d568dd584a64\">\r\n    <format />\r\n    <matrix />\r\n  </characters>\r\n  <trees id=\"t416da46f-0871-4c9a-ae39-43edbe473b6d\" otus=\"t4813128d-4f2b-417f-bf5a-d568dd584a64\" />\r\n</nexml>\r\n

cli

cli options thus far

  • ph version
  • ph taxon
  • ph term

For the jq command line tool see https://stedolan.github.io/jq/

ph taxon http://purl.obolibrary.org/obo/VTO_0067193 | jq .
{
  "rank": {
    "@id": "http://purl.obolibrary.org/obo/TAXRANK_0000006",
    "label": "species"
  },
  "label": "Apterichtus equatorialis",
  "extinct": false,
  "common_name": "Finless eel",
  "@id": "http://purl.obolibrary.org/obo/VTO_0067193"
}

Meta

  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
  • License: MIT

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