ASPAR_KR– Thesis writing phase

The writing plan

Sibbe Bakker

12/1/23

This week

  • Wrote a new outline for the thesis.

  • Got the ASPAR_KR project working locally.

Improved outline

Introduction

  • Data sharing is an issue in the lifesciences.
    • There is a lack of awareness about the importance of good data management
      • How data management is done;
      • Metadata is an important thing to do well
      • There are a few ways to manage experimental metadata: JERM, ISA, MIxS.
      • When data is not managed well, sharing is more difficult.
      • The use of FAIR guidelines help data management.
    • FAIR data principles may solve the data sharing issues in the lifesciences.
      • What is FAIR?
      • What role do ontologies and taxonomies play?
        Describe that they are.
      • The RDF technology linked data technology is central to FAIR.
  • Due to it simplicity, the FAIR data station may be a helpful FAIR data tool.
    • What is FAIR data and what alternatives are there?
      • What programmes exist to manage research output in a FAIR manner?
      • What makes FAIRDS special?
    • Technologies on which FAIRDS depends
      • RDF
      • SPARQL.
    • Research aim: Applying the FAIRDS to the lifescience domain using the Aspfum example.
      • Why Aspfum makes for a good usecase
        • It is an important topic, fungi in general are more important to human health.
        • Aspfum develops resistance (biology of resistance)
        • Tackling the problems of Aspfum is a data dependent issue.
      • What will be done
        • Requirements of ASPAR_KR
        • Adoption of ASPAR_KR.
        • Uses outside the Aspfum case.

Methods

  • Data standardisation using fairds.
    • Adoption of the FAIRDS.
      • How does fairds work?
      • The rust clone of FAIRDS for experimentation reasons.
    • Ontology of FAIRDS
      • What is the structure.
    • Adding domain specific terms to FAIRDS.
      • How packages can be added and what packages can be added.
    • Promoting the use of FAIRDS
      • How disemination went: Talks, meetings and emails.
  • Creating the ASPAR_KR platform
    • Making the webservice
    • Creating documentation and tutorial materials.
  • Applying the ASPAR_KR platform for a case study.
    • Ctgb example using Mariana her data.

Results

  • Reflection on the development process
    • What went well: Working with other developers.
    • What did not go so well: Promoting the FAIRDS, software design.
  • A brief overview of ASPAR_KR.
    (using the Ctgb usecase)
    • How does the software work?

Discussion

  • What did other platforms do?
    • Analysis of what can make a fair data solution fail or succeed.
  • What can the FAIR ds to be more successful?

ASPAR_KR platform

sibbe@sibbe-ThinkPad-T15-Gen-2i ~/Documents/study/Msc-at-WUR/parts/thesis/ASPER_KS/aspar-networked (main) $ curl http://localhost:8084/endpoint/ds/sparql?query=SELECT%20*%20WHERE%20%7B%3Fs%20%3Fp%20%3Fo%7D%20LIMIT%202
{ "head": {
    "vars": [ "s" , "p" , "o" ]
  } ,
  "results": {
    "bindings": [
      { 
        "s": { "type": "uri" , "value": "http://fairbydesign.nl/ontology/inv_collection_phenotype" } ,
        "p": { "type": "uri" , "value": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" } ,
        "o": { "type": "uri" , "value": "http://jermontology.org/ontology/JERMOntology#Investigation" }
      } ,
      { 
        "s": { "type": "uri" , "value": "http://fairbydesign.nl/ontology/inv_collection_phenotype" } ,
        "p": { "type": "uri" , "value": "http://jermontology.org/ontology/JERMOntology#hasPart" } ,
        "o": { "type": "uri" , "value": "http://fairbydesign.nl/ontology/inv_collection_phenotype/stu_MIC_phenotyping" }
      }
    ]
  }
}

Next weeks

  • Next week
    • Load Mariana her Ctgb data into FAIRDS.
    • Meet with Jasper. Discuss iRODs.
    • Meet with Martin
      • FAIRification of MIC assay data.
      • Automated analysis with R.
    • Email Johanna’s colleagues.
  • The week after that
    • Meet with Hylke about environmental sampling.
      FAIRification using FAIRDS. Explore linked data analysis benefits.

Questions?

If you need more information?

Check out the git page.

Thanks for

  • Jasper Koehorst and Bart Nijsen.
    Helping me contribute to FAIRDS.

  • Mariana and Anna
    Supervision during my stay at the genetics department.