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Development notes 23 July 2014

  • Reviewing the class definitions - all good so far, so will be updated int he OWL file.
  • Restructuring ontology to support Phi-base query
  1. introduce the subclasses of "Organism" -> "Host_organism" and "Pathogen_organism". Defined as role ("host") that can be fulfilled by an organism. Another option is to define the relationship using a predicate e.g. "has_host", "has_pathogen".
  2. Introduce explicit relationships between strains and their corresponding species. Add "is_strain_of" and inverse "has_strain". Other information is added at appropriate level - e.g. organims or strain.
  3. Add predicates to indicate database source - Larisa will check the established way for doing it.
  • Modifications will be made in the OWL file first and the rest will be updated accordingly
  • Version control options discussed: GitHub (problems with Git not understanding OWL formats and version conflict comments breaking the file). Will try GitHub to verify what the problems are... The ontology will now be stored in a sub-folder "onto" of the GitHub project for the Phi-base RDF website.
  1. Follow-up work - Larisa will start adding definitions and the rest will review and comment. Version with definitions will likely be ready in ~3 weeks.
  • Website discussion - output formats for SPARQL interface. Current default is HTML table, support to be added for simple text formats (tab, csv, etc.)
  • Paper draft - provisionally early September. All currently written material will be shared on GoogleDrive

Development notes 9 July 2014

We (N and LS) went through ontology wiki pages. Comments/ suggestions

- Action Artem: write down how the wiki pages were produced. This will go to the methods section in our paper. - Wiki pages are excellent for our internal use, but we will advertise them for external users. Therefore every page needs to have sufficient information about what it is (definitions) and how it will be used and who can edit. We need to decide about editing privileges. Users should register first.

- the name of the ontology OIP (an ontology for investigations on pathogenicity): it is hard to pronounce the short name. We need to consider other names and abbreviations. For example OntoPath, IPO.

- The term “Reference” is not strictly speaking used correctly. We changed it for ‘notes’ (only for one class ‘Accession ID'), but we are not happy with it either. We need to think of a better term. - We removed [] around the reference number, again only for the class ‘Accession ID'. We hope there is a way to do it consistently everywhere. - Replace everywhere in definitions/ comments ‘is a kind of’ with ‘is a’ - Change the structure of wiki pages for ontology terms. Have an area ‘suggested definition’, ‘external references’

Definitions are required (we cannot make them): e.g. Accession ID

Definitions/ labels needs to be improved, e.g. Condition. Suggestion to use EFO term ‘experimental factor’

Disruption. Of what?