Knowledgeblog ArrayExpress Plugin

The Knowledgeblog ArrayExpress plugin allows authors to extract and embed metadata from the ArrayExpress XML API in WordPress posts

Using the [aexp][/aexp] shortcode, metadata can be extracted for a number of components for an ArrayExpress entry.  Descriptions, citations, links to raw files etc. can all be inserted into a WordPress post.

Currently the following attributes are supported for shortcodes of the format [aexp id=”E-MEXP-NNNN”]metadata_type[/aexp]

The following metadata types can be returned:

  • species : returns species
  • accession : returns linked accession
  • submissiondate : returns submission date
  • lastupdate : returns last update date
  • releasedate : returns release date
  • name : returns short experiment description
  • description : returns long experiment description
  • score : returns MIAME scores (out of 5)
  • contact : returns contact email address and role if supplied
  • citation : returns citation, publication information and link to PubMed if supplied
  • datafiles : returns links to raw and processed data files, sdrf and idf files
  • png : returns and links the experimental design png
  • svg : returns and links the experimental design svg
  • assays : returns the number of assays
  • samples : returns the number of samples
  • arraydesign : returns and links to the array platform
  • experimenttypes : returns the experiment types (time course data, aCGH, dye swapped etc.)
  • experimentalfactors : returns the experiment factors (drug dose, timepoints, genotypes, compounds etc.)
  • sampleattributes : returns the sample attributes (organism part, developmental stage, tissue source, sex, strain etc.)

The following is a short demonstration of the metadata returned for these types for experiment [aexp id=”E-MEXP-1557″]accession[/aexp] in ArrayExpress. This link to the dataset page is generated by the “accession” shortcode in the previous sentence.

The short title of the experiment is “[aexp id=”E-MEXP-1557″]name[/aexp]” and the experiment used [aexp id=”E-MEXP-1557″]species[/aexp]. It was submitted on [aexp id=”E-MEXP-1557″]submissiondate[/aexp], released on [aexp id=”E-MEXP-1557″]releasedate[/aexp] and last updated on [aexp id=”E-MEXP-1557″]lastupdate[/aexp].

The longer experimental description is “[aexp id=”E-MEXP-1557″]description[/aexp]”

ArrayExpress categorises the experiment with a MIAME [aexp id=”E-MEXP-1557″]score[/aexp]. The contact for the experiment is [aexp id=”E-MEXP-1557″]contact[/aexp].

This experiment has no publication associated with it but has the following citation information: “[aexp id=”E-MEXP-1557″]citation[/aexp]”.

To show an example dataset with a citation here is the same information for [aexp id=”E-MEXP-1551″]accession[/aexp]: “[aexp id=”E-MEXP-1551″]citation[/aexp]”

In [aexp id=”E-MEXP-1557″]accession[/aexp] there are [aexp id=”E-MEXP-1557″]samples[/aexp] samples and [aexp id=”E-MEXP-1551″]assays[/aexp] assays. The array design used is [aexp id=”E-MEXP-1557″]arraydesign[/aexp]

These are the links to the dataset files: [aexp id=”E-MEXP-1557″]datafiles[/aexp]

It is possible to interrogate the types of experiment: [aexp id=”E-MEXP-1557″]experimenttypes[/aexp]

It is possible also to retrieve the factors of the experiment: [aexp id=”E-MEXP-1557″]experimentalfactors[/aexp]

And we can pull out information about the sample attributes: [aexp id=”E-MEXP-1557″]sampleattributes[/aexp]

Finally it is possible to link to png and svg versions showing the origin of the biosamples in the experiment:

[aexp id=”E-MEXP-1557″]png[/aexp]

[aexp id=”E-MEXP-1557″]svg[/aexp]

1 Comment

  1. An Exercise in Irrelevance » Blog Archive » Three Steps to Heaven

    May 7, 2012 @ 12:44 pm

    […] the knowledgeblog-arrayexpress plugin (, therefore, we have again used a shortcode representation, but allowed the author to automatically […]

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