Summary of Plant Markupathon

Hi All

Last Friday we had a hackathon focusing on marking up resources in the ELIXIR Plants Community. While we did not implement any finished markup, we had a very productive day. The full notes for the day can be found in this document, with the outcomes summary repeated below.

Of particular note was our continuing discussion for how to markup pages that present the results of a study/experiment, e.g. a page like PIPPA experiment D4 on platform wiwam2 or Mouse Phenotype Cib2 data chart (links follow), and its relationship with the Phenotype profile.
https://pippa.psb.ugent.be/wiwam/consult_experiment_basic_info/56


https://www.mousephenotype.org/data/charts?accession=MGI:1929293&allele_accession_id=MGI:5548707&parameter_stable_id=IMPC_ACS_006_001&zygosity=homozygote&phenotyping_center=MRC%20Harwell&pipeline_stable_id=HRWL_001


During the hackathon we drafted a proposal for an Experiment profile (and potentially type), which you can see the template for at the following link. The idea is to capture the independent variables of the experiment – the experiment factors and protocols – as well as the dependent variables; note that Schema.org already has a variableMeasured property but not one for indicating the variables that are set as part of the experiment design. It would be useful to get wider community input on this idea.
https://github.com/BioSchemas/specifications/blob/master/ExperimentTemplate.jsonld


Best regards

Alasdair
Wrap Up/Summary

The Hackathon proceeded with two main strands of activity.

We first focused the discussion on mapping MIAPPE properties to Bioschemas types and properties. This is captured MIAPPE/Bioschemas Mapping above<https://docs.google.com/document/d/1EkVy-zQH0zdHbkI8OzzRYjkFmgtup-0DKAVX2hvJf4M/edit#heading=h.7fl3evb33wmf>. This led to a discussion of capturing experiment details in markup which focused on experimental factors (e.g. which Allele has been knocked out) and experiment protocol (e.g. life stage, growth facility used, treatments). An initial template<https://github.com/BioSchemas/specifications/blob/e46e635fd6ef60cc04d57a04f86ff7343177179c/ExperimentTemplate.jsonld> JSON-LD structure for an Experiment type was mocked up (this template involves the creation of two new properties – experimentalFactor and experimentProtocol). This was tested with three independent markups

  *   Experiment profile JSON-LD example for mousephenotype.org data pages.<https://gist.github.com/ficolo/95dd70cae2f9076caeef28963e96dde4>
  *   PIPPA
  *   GnpIS

Feedback was to add name and description to the template<https://github.com/BioSchemas/specifications/blob/0ee885f30f1c9154b85a506fd21e1d2c8bbd776d/ExperimentTemplate.jsonld>.


Based on analytics of Mouse Phenotype search, most people get to pages through Gene name


The second activity focused on mapping CorkOakDB pages to relevant Bioschemas types and discussing how to embed the markup using the Drupal extension used in the website. Identified the following mapping of pages to types:

  *   Home page → DataCatalog (possibly with an embedded Dataset)
  *   http://corkoakdb.org/organism/1 → Taxon
  *   BioProjects: http://corkoakdb.org/bioprojects → Study/Experiment
  *   Gene: http://corkoakdb.org/gene/1424041 (and similar pages) → Gene
  *   PolyPeptide: http://corkoakdb.org/polypeptide/1538989 (and similar pages) → Protein
  *   mRNA: http://corkoakdb.org/mRNA/1472861 → RNA?

Actions

  *   MIAPPE/Bioschemas Mapping
     *   Complete MIAPPE/Bioschemas mapping for deliverable D2.2 (due M18 – June 2021, lead BE)
  *   Experiment Type
     *   Widen discussion of Experiment type to the wider Bioschemas community
     *   Experiment type is missing the ability to capture the start and end times of the experiment which would be important for the plant use case. Possibly with schemas.org.startDate
     *   Decide whether to Use of Emphasis.”INSTALLATION” instead of “growth facility” in experimentProtocol.propertyValue.name
     *   Controlled vocabulary of propertyValues for plant vocabulary ?
  *   CorkOak Markup
     *   Develop markup for each of the types
     *   Embed in website
  *   Tutorial for marking up plant community resources with Bioschemas
     *   Deliverable D2.1 – due M12 (December 2020) lead PT


--
Alasdair J G Gray
Associate Professor in Computer Science,
School of Mathematical and Computer Sciences
Heriot-Watt University, Edinburgh, UK.

Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33

ORCID: http://orcid.org/0000-0002-5711-4872

Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair

To arrange a meeting: https://doodle.com/mm/alasdairgray/book-a-time


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